title: BL3POS

description: CD44+CD62L-PD1+CD8 T cells from mouse 3

data_processing:
Illumina RTA2 software was used for base calling
Reads were aligned to the Mus Musculus GRCm39 reference genome using STAR (v2.6.0a)
Counts were summarized using the featureCount command from Subread (v2.0.3) run in paired-end mode using the GRCm39.104 genome annotation file
Assembly: Mus Musculus GRCm39
Supplementary files format and content: Summarized reads (.txt) as generated by the featureCount command from the Subread package (v2.0.3)

source_name: blood

extract_protocol:
Mice were euthanized by intraperitoneal injection of sodium pentobarbital and then intracardiacally perfused with 30 ml of Phosphate Buffer Saline (Corning). Blood were collected in PBS with 0.5 mM of Ethylenediaminetetraacetic acid (EDTA, Boston BioProducts, Inc.). Red blood cells were lysed in 5 ml of RBC Lysis Buffer (Affymetrix eBioscience). 500 CD44+ CD62L- PD-1+ and PD-1- CD8 T cells from the blood were sorted directly into nuclease free water (final volume = 9.5 l) and processed by the NGS Platform of the Center for Advanced Genomics Technology at ISMMS.
Cell samples were passed to whole-transcriptome library preparation using the Takara Bio SMART-Seq v4 PLUS Kit following the manufacturer’s instructions. Briefly, cDNA synthesis from low amounts of RNA was enabled through Takara Bio's SMART technology. 3’ ends of cDNA were then adenylated prior to ligation with adapters utilizing unique dual indices (96 UDIs) to barcode samples to allow for efficient pooling and high throughput sequencing. Libraries were enriched with PCR, with all samples undergoing 16 cycles of amplification prior to purification and pooling for sequencing. Completed libraries were quantified using Quant-iT reagents and equimolar pools were generated and sequenced on the NextSeq 550 using a high output 150 cycle flow cell generating paired end 75 bp reads and approximately 30 million reads per sample.

tag: strain


title: BL3NEG

status: Public on Apr 22 2022

type: SRA

city: New York

first: Laura

last: Campisi

state: NY

address: 1468 Madison Avenue

department: Microbiology

country: USA

institute: Icahn School Of Medicine at Mount Sinai

description: CD44+CD62L-PD1-CD8 T cells from mouse 3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

value: CD8 T cells

tag: genotype

value: Setx L389S +/-


title: TW2.6 CMV-LOXL2-2

type: RNA

city: Taipei

first: YI-JIE

last: LU

address: 1, Chang-Te street

country: Taiwan

institute: National Taiwan University

description: buccal

hyb_protocol: Procedures are available from http://www.phalanxbiotech.com/tech_support/general.php are available from http://www.phalanxbiotech.com/tech_support/general.php

scan_protocol: Phalanx HOA 7.1 arrays were scanned by Agilent Microarray Scanner (G2505C) and quantify the fluoresence intensity.

data_processing: The gene expression microarray analyses were conducted by the Phalanx Biotech Group (Hsinchu, Taiwan), which included RNA amplification, labeling of probe, hybridization, and data extraction.

organism: Homo sapiens

source_name: TW2.6 CMV-LOXL2-2

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit (Phalanx) , and using Amersham Cy5 NHS Ester (GE) for labeling

growth_protocol: TW2.6 (buccal SCC) and FaDu (hypopharyngeal SCC)  were cultured in Dulbecco’s modified Eagle’s medium (DMEM) and supplemented with 10% fetal bovine serum (FBS), penicillin (100 units/mL), and streptomycin (100 μg/mL) at 37 °C in a humidified atmosphere containing 5% CO2 as previously described . All the tissue culture agents were obtained from Invitrogen (Waltham, MA, USA).

extract_protocol: Total RNA was prepared from transfected TW2.6/FaDU cells and extracted by Trizol (Invitrogen). RNA purity was checked by optical density  by NanoDrop Spectrophotometer ND100(Thermo SCIENTIFIC).

treatment_protocol: Transfection of HNSCC cells TW2.6 (buccalSCC)/FaDu (hypopharyngeal SCC) with plasmids [pCMV-LOXL2, pCMV vector (OriGene Technologies, Rockville, MD, USA).For stable clone selection, the plasmid DNA was mixed with7Lipofectamine 3000 for 20 min before being adding to the cells. After 24 h of transfection, the cells were plated in fresh DMEM with 10% FBS and G418 sulfate (500 µg/mL, Invitrogen, for pCMV)

value: oral squamous carcinoma cells

tag: cell line

tag: transfection

value: LOXL2 overexpression


title: KI 3

description:
RNA from bulk spinal cord samples
A3SS.MATS.JC.txt
A5SS.MATS.JC.txt
MXE.MATS.JC.txt
RI.MATS.JC.txt

data_processing:
RTA 2.11.3 software was used for base calling. Bcl to Fastq conversion was performed using FASTQ generation pipeline in Illumina Basespace.
For analysis, adaptor removal was performed with cutadapt and base-quality trimming to remove 3′read sequences if more than 20 bases with Q < 20 were present. Paired-end reads were mapped to the mus musculus (mm10) reference genomes with STAR. Alternative splicing analysis was perfomed using rMATS 4.1.081. Downstream splicing predictions was carried out using SPLINTER.
Assembly: mm10
Supplementary files format and content: rMATS output file (Junction Counts only)

source_name: Spinal Cord

extract_protocol:
After intracardiac perfusion, spinal cords from 10-12 month old KI and WT mice were dissociated in Hank’s Balanced Salt Solution (HBSS) medium (Gibco), 1 mg/ml of DNAse I and 2 mg/ml of papain (Worhington) at 37°C for 30 min with mild shaking. Tissue suspensions were then filtered through a 70-mm cell strainer. Cell debris were eliminated after resuspension in HBSS 3.5% Bovine Serum Albumin (BSA, Sigma) and centrifuged at 120 g for 10 min. WT1, WT2, WT3, KI1, KI2 and KI3 were isolated as a single batch, while WT4 was isolated on a separate date. Cell pellets were resuspended in HBSS, layered over a 1.06 g/ml solution of Optiprep (Sigma). After centrifugation at 900g for 20 min, cells were collected in the upper layer, washed and resuspended in 1 ml of TRIzol.
RNA from bulk spinal cord samples were isolated using Trizol, following manusfacturer's recomendations. RNA was DNAse-treated using the TURBO DNA-free Kit (Thermofisher scientific). 300ng RNA from the spinal cord samples was used for downstream library preparation.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations. Final libraries were quantified and sizing was determined using the High Sensitivity DNA Assay reagents and chip in the Agilent 2100 Bioanalyzer System and the Qubit 1X dsDNA HS Assay Kit respectively. Individual libraries were then pooled and sequenced using 75bp paired end on the NextSeq 500 using the NextSeq 500/550 High Output Kit.

tag: tissue

value: bulk spinal cord

tag: isolation day

tag: Sex

value: F


title: RNA-seq_∆WAPL_0h_batch2-rep2

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Homozygous cell line with endogenous WAPL loci tagged with an auxin-inducible degron

data_processing: no processed data provided

source_name: Embryonic stem cells

growth_protocol: JM8.N4 mESCs were grown on gelatin-coated plates in knock-out DMEM supplemented with 15% FBS, non-essential amino acids, glutamax, Penicillin-streptomycin, 2-mercapoethanol and LIF. mES cells were fed daily and passaged every 2-3 days by trypsinization.

extract_protocol:
RNAs were extracted using the standard TRIzol RNA extraction protocol and then depleted rRNA with NEBNext rRNA Depletion Kit (NEB, #E6310).
The rRNA-depleted RNAs were then subjected to the RNA-seq library construction using the protocol of NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB, #E7765).

treatment_protocol: Degron cell lines were treated for 3 hours with either ethanol only (control, untreated) or with 500 uM, ethanol-dissolved auxin.

value: Embryonic stem cells

value: FLAG-Halo-CTCF / RAD21-SNAPf-V5 / HA-BFP-mAID-WAPL / osTir

tag: treatment

value: Ethanol, 3 hrs

tag: chip antibody


title: TW2.6 CMV-LOXL2-1

description: buccal

source_name: TW2.6 CMV-LOXL2-1


title: RNA-seq_∆WAPL_12h_batch2-rep1

value: 500 mM auxin in ethanol, 3 hrs


title: RNA-seq_∆WAPL_24h_batch2-rep2


title: FaDu CMV-LOXL2-2

description: Pharynx

source_name: FaDu CMV-LOXL2-2

value: head and neck squamous cell carcinoma

value: FaDu


title: FaDu CMV-LOXL2-1

description: Pharynx

source_name: FaDu CMV-LOXL2-1


title: TW2.6 CMV PCDNA-1

description: buccal

source_name: TW2.6 CMV PCDNA-1

value: Vector control


title: FaDu CMV PCDNA-2

description: Pharynx

source_name: FaDu CMV PCDNA-2


title: RNA-seq_∆WAPL_0h_batch2-rep1


title: TW2.6 CMV PCDNA-2

description: buccal

source_name: TW2.6 CMV PCDNA-2


title: miRNA_MoyamoyaDisease#78_rep1

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

country: Japan

institute: Nagoya University Hospital

data_processing:
MiRNA sequencing using 75bp single-read protocol by NextSeq next-generation sequencer (Illumina, USA) was performed at Macrogen Japan Corp. (Tokyo, Japan).
The obtained FASTQ data was uploaded to the geneglobe.qiagen.com website (https://geneglobe.qiagen.com/us/analyze, QIAGEN, USA) for primary data analysis.
The obtained read data was subjected to data normalization and differential expression analysis using the DESeq2 (version 1.28.1) package in the R software (version 4.0.2; http://www.r-project.org/).

source_name: Intracranial cerebrospinal fluid

extract_protocol:
Total RNA extraction from the isolated EVs was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacture's protocol.
One nanogram of miRNA from each sample was used for small RNA library creation using QIAseq miRNA Library Kit (QIAGEN, Germany) according to the manufacturefs protocol.

value: cerebrospinal fluid

tag: age

tag: gender

value: Female

tag: disease

value: moyamoya disease


title: PT3_24: Xenograft of primary tumor

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center

data_processing:
Sequenced reads were checked by FastQC.
Mapping was performed using MiSeq.
The expression matrix was constructed and normlized by Seurat.
Genome_build: GRCh38/hg38

source_name: Xenograft of primary tumor

growth_protocol: MDA-MB-231 cells were seeded in culture dishes in RPMI1640 medium (gibco)with 10% fetal bovine serum (gibco) with streptomycin and penicillin-G at 37 °C in 5% CO2. Cells were orthotopically transplanted into murine mammary fatpad.

extract_protocol:
Total RNA was extracted  from punched micro-tissue, previously reported (Yoda et al., Sci Rep, 2017).
cDNA libraries for RNA sequencing were

value: Micro-tissue of Primary tumor


title: FaDu CMV PCDNA-1

description: Pharynx

source_name: FaDu CMV PCDNA-1


title: miRNA_AtheroscleroticBrainIschemia#102_rep1

value: Male

value: atherosclerotic brain ischemia


title: PT3_23: Xenograft of primary tumor


title: PT3_21: Xenograft of primary tumor


title: RNA-seq_∆RAD21_24h_batch2-rep2

description: Homozygous cell line with endogenous RAD21 loci tagged with an auxin-inducible degron

value: FLAG-Halo-CTCF / RAD21-BFP-mAID-V5 / osTir


title: RNA-seq_∆RAD21_24h_batch2-rep1


title: RNA-seq_∆RAD21_12h_batch2-rep2


title: BL2POS

description: CD44+CD62L-PD1+CD8 T cells from mouse 2

value: CD8 T cells

value: Setx L389S +/-


title: miRNA_MoyamoyaDisease#9_rep1


title: PT3_18: Xenograft of primary tumor


title: miRNA_MoyamoyaDisease#69_rep1


title: miRNA_MoyamoyaDisease#64_rep1


title: RNA-seq_∆RAD21_12h_batch2-rep1


title: aCDC10

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Reads Processing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and Cutadapt 1.7.1 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type)  were filtered using using FastX 0.0.13 and ShortRead 1.24.0 (Morgan et al, 2009). With Bowtie2 2.2.4 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: Preprocessed reads were aligned with Tophat v2.0.13 to the reference genome of Homo Sapiens (GRCh37.73).  Default Tophat parameter settings were used, except for ‘min-intron-length=50’, ‘max-intron-length=500,000’, ‘no-coverage-search’ and ‘read-realign-edit-dist=3’. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009).
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.4.6 (Liao et al, 2014). Following parameters were chosen: -Q 0 –s 2 –t exon –g gene_id. We removed genes for which all samples had less than 1 count-per-million. The merge of sequencing data from different runs was done at the raw counts level. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor
Differential Expression Analysis: With the EdgeR 3.8.6 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts. Differential expression was calculated with a GLM likelihood ratio test in EdgeR. The resulting P-values were corrected for multiple testing with Benjamini-Hochberg (FDR, False Discovery Rate).
Genome_build: Homo Sapiens (GRCh37.73)
Supplementary_files_format_and_content: Raw counts are in text file.

source_name: Adult donor_cardiac progenitor

growth_protocol: CDCs were cultured on fibronectin-coated (25 µg/mL) culture plates in CGM medium (35% IMDM and 65% D-MEM-F12 supplemented with 10% iFBS, 1% penicillin/streptomycin (5,000 units/mL penicillin, 5,000 µg/mL streptomycin), 2 mM L-glutamine (200 mM), 0.1 mM 2-mercaptoethanol (50 mM) and 1X B-27 supplement (50X)). c-kitpos CPCs were on bare cell culture-treated plates in growth medium (Ham’s F12 medium supplemented with 10% FBS, 1% penicillin/streptomycin (5,000 units/mL penicillin, 5,000 µg/mL streptomycin), 5 mU/mL human erythropoietin (EPO)). Both cell types were passaged when 80-90% confluency was reached.

extract_protocol:
Progenitors were harvested at passage 5-7, and Total RNA was extracted using the Qiagen RNeasy micro kit with DNase treatment, followed by a clean-up step (Qiagen RNeasy minElute columns). The RNA quality and quantity were verified with a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA sequencing and processing was performed by VIB Nucleomics Core (www.nucleomics.be).
Illumina TruSeq® Stranded mRNA Sample Prep Kit was used with 250 ng total RNA per sample. RNA libraries were prepared for sequencing using standard Illumina protocols (protocol 15031047Rev E,October 2013 ). Sequence-libraries of each sample were equimolarly pooled and sequenced on the Illumina NextSeq 500 (75 cycles High output kit, Single Reads) at the VIB Nucleomics core (www.nucleomics.be).

tag: donor age group

value: Adult donor

value: Heart-derived cardiac progenitor

tag: passages

tag: progenitor type

value: Cardiosphere-derived cell


title: PT3_20: Xenograft of primary tumor


title: RNA-seq_∆CTCF_24h_batch2-rep2

description: Homozygous cell line with endogenous CTCF loci tagged with an auxin-inducible degron

value: Embryonic stem cells

value: FLAG-BFP-mAID-CTCF / RAD21-SNAPf-V5 / osTir


title: Amplicon negative control library 2 [CBS1_49]

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
protocol: Total RNA was extracted from HEK293T cells with Qiazol (Qiagen, 79306). 500 ng total RNA was primed with 125 ng random hexamers (Thermo Fisher Scientific, N8080127) and 100 nM final custom oligodT primer (dT30VN) at 65 ˚C for 5 min. Primed RNA was included in a 20 uL RT reaction with 200 U SuperScript III (Thermo Fisher Scientific, 18080051) and incubated at 42˚C for 30 min, 50˚C for 30 min, and 70˚C for 15 min. Reactions were treated with 2.5 U RNaseH (NEB, M0297) at 37 ˚C for 20 min. Each of fifteen CBS tiled amplicons were amplified from 1st strand cDNA with a 25 µL NEB Q5 PCR (NEB, M0491) including 500 nM primers, high GC enhancer, and the following cycling: 98˚C for 30 s; 98 ˚C for 10 s, 62 ˚C for 20 s, 72 ˚C for 30s (18 cycles); final extension at 72 ˚C for 2 min. 22 µL PCR1 product from each tile were pooled and purified by Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 15 µL buffer. 40 ng pooled PCR1 product was input to each of two 50 µL NEB Q5 PCRs with high GC enhancer and NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S), with the following cycling conditions: 98˚C for 30 s; 98 ˚C for 10 s, 65 ˚C for 20 s, 72 ˚C for 30 s (4 and 6 cycles); final extension at 72 ˚C for 2 min. Product from the 4 and 6 cycle reactions were pooled and size selected with the Sage Bioscience BluePippin 2% gel (marker M1) with 260-340 bp range. Eluate was concentrated with 1.8x AMPure XP beads (Beckman Coulter, A63881) and eluted in 15 µL water.

satmut_utils parameters: -r CBS_pEZY3.fa -p CBS_pEZY3_primers_coding.bed call -1 CBS1_49_R1.fastq.gz -2 CBS1_49_R2.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT,CAAGTTTGTACAAAAAAGTTGGC --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT,CCAACTTTCTTGTACAAAGTGGT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT,ACCACTTTGTACAAGAAAGTTGG --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA,GCCAACTTTTTTGTACAAACTTG -g CBS_pEZY3.gff -k CBS_pEZY3.fa -m 1 -s NNK

Illumina HiSeq 2500 at Psomagen

data_processing:
Data was analyzed with satmut_utils version 1.0.0. Source code and documentation are available at https://github.com/CenikLab/satmut_utils. A brief description of the satmut_utils data processing steps is outlined below. Analysis parameters are indicated in the 'description: satmut_utils parameters' field.
For RACE-like libraries, 8 bp unique molecular index sequences were extracted with UMItools extract using the following parameters: --extract-method=regex -p (?P<umi_1>[ATCG]{%8}) (?P<discard_1>%AACCGCCAGGAGT){e<=%2}. The regular expression is passed to the satmut_utils call --umi_regex argument.
cutadapt was used for adapter and 3' base quality trimming with the following parameters -q 15 -m 16 -O 8. Adapter sequences differed by sequencing library and are noted in the 'description: satmut_utils parameters' field.
Reads were aligned with bowtie2 in paired-end mode with the following parameters: --maxins=1000 --no-discordant --fr --mp 4 --rdg 6,4 --rfg 6,4
satmut_utils base quality masking: base qualities for read segments originating from synthetic primer sequences were masked by setting them to 0. For amplicon libraries, the 5' and 3' termini of both R1 and R2 may be masked. For RACE-like libraries, only the 3' end of R1 and the 5' end of R2 may be masked.
For RACE-like libraries, reads were grouped with UMItools directional adjacency method and the following parameters: --edit-distance-threshold=1 --paired --ignore-tlen --unpaired-reads=discard --unmapped-reads=discard --multimapping-detection-method=X0 --umi-separator=_. satmut_utils consensus deduplication: group IDs from R1 alignment tags were copied to R2s and paired alignments were sorted by tag. R1s and R2s were consensus deduplicated individually using a majority vote (among duplicates) for the base call at each aligned position. Insertions are not retained in generation of consensus reads. Deletions were retained and deletion gaps longer than 10 bases were converted to the unknown base N.
satmut_utils variant calling: Read pairs are iterated over and pairs were filtered if either read had an edit distance <= 10. Variants were only called if mismatches were found in both mates (concordant base calls) and had base qualities >= 30.
Assembly: Data were aligned to custom reference FASTA files depending on the input source and library preparation chemistry (see description: satmut_utils parameters). Reference files and primer sequences are available at https://github.com/ijhoskins/satmut_utils_supplementary/tree/main/reference_files. Reads may be aligned to the CBS transcript ENST00000398165.7 but some reads may not align as they contain vector sequence.
Supplementary files format and content: Text files containing VCF fields with each INFO tag value in a unique column. See https://github.com/CenikLab/satmut_utils/blob/master/docs/satmut_utils_manual.md for details on each field.
Library strategy: amplicon

source_name: HEK293T cells

growth_protocol: HEK293T LLP iCasp9 Blast cells were obtained from Doug Fowler's lab and cultured in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific, 11995065) with 10% fetal bovine serum (Gibco, and 1% penicillin-streptomycin (Gibco, 15140122) at 37°C in 5% CO2 atmosphere. Prior to recombination at passage 16, cells were selected for one week with 2 µg/mL Doxycycline (Sigma-Aldrich, D3072) and 10 µM Blasticidin (Gibco, A1113903) to maintain cells with the integrated landing pad. Cell lines were tested for mycoplasma contamination and were consistently found negative.

extract_protocol:
Negative control libraries were generated by methods detailed in the "description: protocol" field. For samples CBS1_68 through CBS1_82, extraction was as follows. gDNA was extracted from approximately 3-5 million cells with the Cell and Tissue DNA Isolation Kit (Norgen Biotek Corp, 24700), including RNaseA treatment and eluting in 200 µL warm elution buffer. For RNA extraction, 15 million cells were solubilized with 1 mL QIAzol (Qiagen, 79306) and 0.2 mL chloroform in 5PRIME Phase-Lock Gel heavy tubes (QuantaBio, 2302830). RNA was precipitated at -20 ˚C following the addition of 2 µL GlycoBlue (Thermo Fisher, AM9515) and 2.5 volumes of cold absolute ethanol. RNA was washed once with cold 70% ethanol then resuspended in 30 µL water. 10 µg total RNA was treated with DNaseI (NEB, M0303), then re-purified by the RNA Clean and Concentrator kit (Zymo Research, R1015) and eluted in 15 µL water. RNA quality was assessed with the Bioanalyzer Eukaryotic RNA Pico kit (Agilent, 5067-1513).
See library input source- and chemistry-specific preparation details in the "description: protocol" field. For samples CBS1_68 through CBS1_70 and CBS1_79 through CBS1_81, 1st strand cDNA was synthesized as follows: for each of six 20 µL reverse transcription reactions, 2.5 µg DNaseI-treated total RNA was denatured at 65 ˚C for 5 min followed by RT primer annealing at 4 ˚C for 2 min, using 2 pmol RT primer specific for the landing pad (pDEST_HC_Rec_Bxb_v2_R: GGCAGTCTCTCTGATTCCACAGTCAT).  Primed total RNA was included in six 20 µL SuperScript IV cDNA synthesis reactions (Thermo Fisher, 18090010) with SUPERase-In RNase inhibitor (Thermo Fisher, AM2696), and first-strand cDNA was synthesized by incubating at 55 ˚C for 1 h, followed by RT inactivation at 80 ˚C for 10 min. RNA was digested with addition of 5 U RNaseH (NEB, M0297) to the first strand cDNA synthesis reaction and incubation at 37 ˚C for 20 min. One reaction was saved for amplicon library preparation, while the other five were pooled for RACE-like (Anchored Multiplex PCR) library preparation. See library-specific preparation methods in the "description: protocol" field. Unless otherwise noted, NEB Q5 polymerase with high GC enhancer was used in 50 µL PCR reactions with 500 nM primers and the following cycling conditions: initial denaturation at 98 ˚C for 30 s; 3-step cycling with denaturation at 98 ˚C for 10 s, anneal at 65 ˚C for 30 s, extension at 72 ˚C for 1 min; final extension at 72 ˚C for 2 min. Final libraries were quantified using the KAPA Library Quantification Kit for Illumina (Roche, KK4873) according to the manufacturer’s recommendation, using 1:10,000 dilution of libraries and size-correction using an average fragment size of 300 nt. qPCR was performed on the Applied Biosystems ViiA 7 instrument. The final pool was size-selected using Sage Bioscience BluePippin 2% gel (marker V1 and/or V2) to select fragments from 200-400 nt. Following size-selection, the final pool was quantified by both the High Sensitivity DNA Kit (Agilent, 5067-4626), integrating between the 200-600 nt range.

treatment_protocol: See additional details in the "description: protocol" field. For samples CBS1_68 through CBS1_82, treatment was as follows. A CBS variant entry library (Sun and Weile, et al. 2020) was transferred into pDEST_HC_rec_bxb_v2, a vector containing recombination sites for the HEK293T LLP iCasp9 Blast landing pad line, by a Gateway LR II reaction (Thermo Fisher Scientific, 11-791-020) following manufacturer’s recommendations. 1.5 µL of LR reaction was transformed into 25 µL Endura Electrocompetent cells (Lucigen, 60242), plated on Nunc Square Bioassay dishes, scraped in 6 mL LB Miller broth, and 3 mL resuspension was processed with the ZymoPURE II Plasmid Maxiprep kit (Zymo Research, D4203). Library size was estimated at ~540,000 species, or ~30-fold coverage of each possible SNP or MNP variant in the CBS coding sequence. 20 µg of the CBS variant library (in pDEST_HC_Rec_Bxb_V2), along with an equal mass of Bxb1 recombinase (pCAG-NLS-HA-Bxb1) was transfected into three 15 cm dishes of HEK293T LLP iCasp9 Blast cells (passage 18, 65% confluency) using Lipofectamine 3000 (Thermo Fisher Scientific, L3000008), with volumes scaled based on 3.75 µL reagent per 6-well. 24 h later, cells were split 1:2 into 15 cm dishes. 48 h after transfection, 2 µg/mL Doxycycline (Sigma-Aldrich, D3072) and 10 nM AP1903 (MedChemExpress, HY-16046) in DMSO were added for negative selection of non-recombined cells. The next day, dead cells were removed and recombined cells were grown out for an additional two days with addition of fresh media containing Doxycycline and AP1903. Cells were recovered for one day by growth in  media without Doxycycline and AP1903. Transcription was induced with 2 µg/mL Doxycycline for 24 h, cells were stimulated with fresh media for 3 h, and then harvested at 95% confluency.

value: Wild type

tag: molecule

value: Total RNA


title: BL1NEG

description: CD44+CD62L-PD1-CD8 T cells from mouse 1

tag: strain


title: PT3_17: Xenograft of primary tumor


title: RACE-like (Anchored Multiplex PCR) negative control library 1 [CBS1_50]

description:
protocol: Total RNA was extracted from HEK293T cells with Qiazol (Qiagen, 79306). 500 ng total RNA was primed with 2 pmol primer for endogenous CBS (AGGAGAAGTGGGCAAGGGTG). Primed RNA was included in a 20 uL RT reaction with 200 U SuperScript IV (Thermo Fisher, 18090010) with SUPERase-In RNase inhibitor (Thermo Fisher, AM2696) and incubated at 55 ˚C for 1 h, and 80˚C for 10 min. Reactions were treated with 5 U RNaseH (NEB, M0297) at 37 ˚C for 20 min. Second strand cDNA was synthesized by linear primer extension with 2 pmol endogenous CBS forward primer (ATCTGTCCGGTCCCAGCATG) and 1 µL Q5 polymerase (NEB, M0491) as follows: 65 ˚C for 30 s, 55 ˚C anneal for 30 s, 72 ˚C extension for 3 min. Double strand cDNA purified by the Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 50 µL buffer. cDNA was fragmented to 300 bp with the Covaris S2 and the following parameters: microTUBE AFA Fiber Snap-Cap, 10% duty cycle, 5 intensity, 200 cycles per burst, 1 min treatment. Sheared ds cDNA was brought up to 50 µL with ultrapure water and libraries were prepared using the ArcherDX (now Invitae) High Sensitivity Reveal ctDNA Kit according to the manufacturer recommendations (ArcherDX, PRO027.4) and with the following modifications: Ligation step 1 was carried out at 37 ˚C for 30 min; Ligation step 2 was carried out at 22 ˚C for 10 min; only PCR2 was carried out for 32 cycles, with supplementation of 1 µL NEB Q5 polymerase diluted 1:10 in 10 mM Tris pH 8.0. The library was size selected by a dual size selection protocol (NEB protocol for E6040). The large small fragment eluate was further size selected by extracting library between 300-700 bp from a 0.8% agarose/TAE gel stained with 1x SYBR Gold, and library was purified with the Zymoclean Gel DNA Recovery kit (Zymo Research, D4007) and eluted in 7 µL. The library was sequenced at Psomagen.

satmut_utils parameters: -z -r CBS.fa -p CBS_primers_coding_GSP2.bed call -1 CBS1_50_R1.fastq.gz -2 CBS1_50_R2.fastq.gz --r1_fiveprime_adapters AACCGCCAGGAGT --r1_threeprime_adapters AGATCGGAAGAGCACACGTCTGAAC --r2_fiveprime_adapters GTTCAGACGTGTGCTCTTCCGATCT --r2_threeprime_adapters ACTCCTGGCGGTT -g CBS.gff -k GRCh38.fa -m 1 -s NNK -d

Illumina HiSeq 2500 at Psomagen

data_processing:
Data was analyzed with satmut_utils version 1.0.0. Source code and documentation are available at https://github.com/CenikLab/satmut_utils. A brief description of the satmut_utils data processing steps is outlined below. Analysis parameters are indicated in the 'description: satmut_utils parameters' field.
For RACE-like libraries, 8 bp unique molecular index sequences were extracted with UMItools extract using the following parameters: --extract-method=regex -p (?P<umi_1>[ATCG]{%8}) (?P<discard_1>%AACCGCCAGGAGT){e<=%2}. The regular expression is passed to the satmut_utils call --umi_regex argument.
cutadapt was used for adapter and 3' base quality trimming with the following parameters -q 15 -m 16 -O 8. Adapter sequences differed by sequencing library and are noted in the 'description: satmut_utils parameters' field.
Reads were aligned with bowtie2 in paired-end mode with the following parameters: --maxins=1000 --no-discordant --fr --mp 4 --rdg 6,4 --rfg 6,4
satmut_utils base quality masking: base qualities for read segments originating from synthetic primer sequences were masked by setting them to 0. For amplicon libraries, the 5' and 3' termini of both R1 and R2 may be masked. For RACE-like libraries, only the 3' end of R1 and the 5' end of R2 may be masked.
For RACE-like libraries, reads were grouped with UMItools directional adjacency method and the following parameters: --edit-distance-threshold=1 --paired --ignore-tlen --unpaired-reads=discard --unmapped-reads=discard --multimapping-detection-method=X0 --umi-separator=_. satmut_utils consensus deduplication: group IDs from R1 alignment tags were copied to R2s and paired alignments were sorted by tag. R1s and R2s were consensus deduplicated individually using a majority vote (among duplicates) for the base call at each aligned position. Insertions are not retained in generation of consensus reads. Deletions were retained and deletion gaps longer than 10 bases were converted to the unknown base N.
satmut_utils variant calling: Read pairs are iterated over and pairs were filtered if either read had an edit distance <= 10. Variants were only called if mismatches were found in both mates (concordant base calls) and had base qualities >= 30.
Assembly: Data were aligned to custom reference FASTA files depending on the input source and library preparation chemistry (see description: satmut_utils parameters). Reference files and primer sequences are available at https://github.com/ijhoskins/satmut_utils_supplementary/tree/main/reference_files. Reads may be aligned to the CBS transcript ENST00000398165.7 but some reads may not align as they contain vector sequence.
Supplementary files format and content: Text files containing VCF fields with each INFO tag value in a unique column. See https://github.com/CenikLab/satmut_utils/blob/master/docs/satmut_utils_manual.md for details on each field.
Library strategy: RACE-like

tag: cell type


title: BL1POS

description: CD44+CD62L-PD1+CD8 T cells from mouse 1

tag: genotype


title: aCDC9


title: PT3_16: Xenograft of primary tumor


title: PT3_13: Xenograft of primary tumor


title: shARAF+R362H_rep2

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Homo_sapiens.GRCh38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v82) was used.
Exploratory data analysis was performed with the pcaExplorer package (version version 2.12.0, Marini et al., 2019)
Differential expression analysis was performed with DESeq2 (version 1.26.0), setting the False Discovery Rate to 0.05
Accurate estimation of the effect sizes (in terms of log fold change) is performed using the apeglm shrinkage estimator (version 1.8.0)
Further analyses included Gene Ontology pathway enrichment of DEG using topGO (v2.38.0) and goseq (v1.38.0) (with all expressed genes set as background) were performed using the ideal package (version 1.10.0) [Marini et al. 2020].
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: A549 lung adenocarcinoma cell line

growth_protocol: RPMI 1640 medium (Gibco BRL) supplemented with 10% heat inactivated FBS and 2 mM L-glutamine.

extract_protocol:
After PBS-wash, cells were either detached with EDTA or directly lysed on plate using High Pure RNA Isolation kit (Cat#11828665001, Roche) according to maufacturer´s instructions.
Total RNA was quantified by a Qubit 2.0 fluorometer (Invitrogen) and RNA quality and integrity was determined using a RNA6000 Nano chip on Bioanalyzer 2100 (Agilent). Samples with RNA integrity number (RIN) > 8 were further subjected for RNA library preparation.
Barcoded cDNA libraries were prepared from 500 ng of total RNA using the NEBnext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). Average size of final cDNA libraries was determined using a HS DNA chip on a Bioanalyzer 2100 and quantity was assesed by Qubit 2.0.

treatment_protocol: Two biological replicates of A549 cells (ARAF depleted -/+ ARAF WT/+ARAFR362H) were seeded in adhesive cell culture dishes at initial density of 2x105 cells/well and 48h later washed with cold PBS and subjected to RNA isolation (High Pure RNA Isolation kit, Cat#11828665001, Roche) according to manufacturer’s instructions.

tag: condition

tag: selection

value: 2.5microg/ml Puromycin (selection knock down), 200microg/ml Zeocin (selection reconstitution)


title: RNA-seq_∆RAD21_0h_batch2-rep1

tag: cell line

value: Ethanol, 3 hrs


title: shARAF+R362H_rep1


title: PT3_15: Xenograft of primary tumor

tag: tissue


title: shARAF+EV_rep2

value: shARAF+EV


title: PT3_22: Xenograft of primary tumor


title: shARAF+EV_rep1


title: BL2NEG

description: CD44+CD62L-PD1-CD8 T cells from mouse 2


title: aCDC8


title: PT3_28: Xenograft of primary tumor


title: aCDC6


title: PT3_10: Xenograft of primary tumor


title: RNA-seq_∆RAD21_0h_batch2-rep2


title: shARAF+ARAF_rep2

value: shARAF+ARAF


title: aCDC5


title: RNA-seq_∆CTCF_12h_batch2-rep2

value: 500 mM auxin in ethanol, 3 hrs


title: RNA-seq_∆CTCF_12h_batch2-rep1


title: yCDC7

source_name: Young donor_cardiac progenitor

value: Young donor


title: PT3_11: Xenograft of primary tumor

value: Micro-tissue of Primary tumor


title: yCDC3


title: PT3_14: Xenograft of primary tumor


title: RNA-seq_∆CTCF_0h_batch2-rep2


title: yCDC4


title: yCDC2


title: RNA-seq_∆CTCF_24h_batch2-rep1


title: aCPC17

value: c-kitpos


title: shARAF+ARAF_rep1


title: yCDC6


title: PT3_09: Xenograft of primary tumor


title: PT3_12: Xenograft of primary tumor


title: RTP_organoid2

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

country: China

institute: University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg19,GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: kidney tubular progenitor organoid

extract_protocol:
Follow the manufacturer's protocol of RNeasy® Mini Kit(REF# 74104). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: 3D differentiated renal progenitor organoid

tag: diagnosis

value: Chronic kidney disease (CKD)


title: RTP_organoid1


title: Kidney2

source_name: kidney tissue

value: adult kidney tissue


title: PT3_07: Xenograft of primary tumor


title: aCPC15

value: Adult donor

value: Heart-derived cardiac progenitor


title: PT3_06: Xenograft of primary tumor


title: RNA-seq_∆YY1_0h_batch2-rep2

description: Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron

value: Embryonic stem cells

value: mIAA7-mScarletI-YY1 / osTir

tag: treatment


title: RNA-seq_∆YY1_12h_batch2-rep1

tag: chip antibody


title: RNA-seq_∆YY1_24h_batch2-rep1


title: RTP1

source_name: kidney tubular progenitor cell

value: renal progenitor


title: RNA-seq_∆CTCF_0h_batch2-rep1

source_name: Embryonic stem cells

value: FLAG-BFP-mAID-CTCF / RAD21-SNAPf-V5 / osTir


title: PT3_05: Xenograft of primary tumor


title: RTP2


title: PT3_08: Xenograft of primary tumor


title: DYY1_IAA_YY1_bethyl_ChIP_spikeIn

library_source: genomic

data_processing:
ChIP-Seq quality check: FastQC
ChIP-Seq read alignment: Bowtie (-n 2, -m 1)
ChIP-Seq peak calling: MACS2 (--nomodel --extsize 300); merged inputs used as controls
ChIP-Seq heatmaps: deepTools (version 2.4.1) bamCoverage (--binSize 50 --scaleFactor [scale factor determined by the number of unique, deduplicated reads aligning to the yeast genome]  --extendReads 300 --ignoreDuplicates -of bigwig) to scale read numbers according to the yeast spike-in control, obtaining read coverage per 50-bp bins across the whole genome (bigWig files). We then used the bigWig files to compute read numbers across 6 kb centered on  ChIP-Seq MACS2 peak summits (computeMatrix reference-point --referencePoint=TSS --upstream 3000 --downstream 3000 --missingDataAsZero --sortRegions=no). We sorted the output matrices by decreasing UT enrichment, calculated as the total number of reads within a MACS2 called ChIP-seq peak. Finally, heatmaps were created with the plotHeatmap tool (--averageTypeSummaryPlot=mean --colorMap='Blues' --sortRegions=no).
mm10, sacCer3
processed data files format and content: ChIP-Seq bigWig files: read coverage per 50-bp bins across the whole genome (read numbers normalized to yeast spike-in controls)

molecule: genomic DNA

extract_protocol:
Cells were cross-linked 7’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10’ and pellets were flash-frozen. Cell pellets were thawed and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) w/ protease inhibitors and incubated for 10’ on ice. Lysates were centrifuged for 10’ at 4000 rpm and nuclear pellets resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS) w/ protease inhibitors, incubated on ice for 10’, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 10-20 cycles 50” on and 30" off). Sonicated lysates were cleared by centrifugation and chromatin (400 ug per antibody) was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) w/ protease inhibitors to a final concentration of 0.8 ug/ul, precleared with Protein G sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 4 ug of specific antibodies. About 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 36 ul of 0.1X TE (1 mM Tris-HCl pH 8.0, 0.01 mM EDTA) and analyzed by qPCR together with 2% of the input chromatin prior to ChIP-seq library preparation.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. 20 ng of ChIP input DNA (as measured by Nanodrop) and 20 ul of the immunoprecipitated DNA were added of 50 pg of MNase-digested yeast genomic DNA and used as a starting material. The recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:10 in Tris/NaCl, pH 8.0 (10 mM Tris-HCl pH 8.0, 10 mM NaCl) and the ligation step extended to 30’. After ligation, a single purification step with 0.9X volumes of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed, eluting DNA in 22 ul of 10 mM Tris-HCl pH 8.0. 20 l of the eluted DNA were used for the library enrichment step, performed with the KAPA HotStart PCR kit (Roche Diagnostics KK2502) in 50 ul of total reaction volume (10 ul 5X KAPA buffer, 1.5 ul 10 mM dNTPs, 0.5 ul 10 uM NEB Universal PCR primer, 0.5 ul 10 uM NEB index primer, 1 ul KAPA polymerase, 16.5 ul nuclease-free water and 20 ul sample). Samples were enriched with 9 PCR cycles (98 'C, 45”; [98 'C, 15”; 60 'C, 10”] x 9; 72 'C, 1’; 4 'C, hold), purified with 0.9 volumes of AMPure XP PCR purification beads and eluted with 33 ul of 10 mM Tris-HCl pH 8.0. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 12 multiplexed libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (50-bp, single end-reads)

value: 500 uM auxin in ethanol, 3 hrs

value: YY1 (Bethyl Laboratories Inc. A302-778A and A302-779A)


title: PT3_04: Xenograft of primary tumor


title: RNA-seq_∆YY1_0h_batch2-rep1

value: Ethanol, 3 hrs


title: PT3_03: Xenograft of primary tumor


title: aCPC13


title: RNA-seq_∆YY1_24h_batch2-rep2


title: PT3_02: Xenograft of primary tumor


title: RNA-seq_∆YY1_12h_batch2-rep2


title: DYY1_IAA_YY1_abcam_ChIP_spikeIn

value: YY1 (Abcam ab109237)


title: Kidney1


title: aCPC16


title: yCPC15


title: RNA-seq_JM8.N4_24h_batch2-rep2

description: wildtype

value: wildtype

value: 500 mM auxin in ethanol, 3 hrs


title: PT3_01: Xenograft of primary tumor

value: Micro-tissue of Primary tumor


title: DYY1_IAA_RFP_ChIP_spikeIn


title: RNA-seq_JM8.N4_24h_batch2-rep1

description: wildtype


title: RNA-seq_JM8.N4_12h_batch2-rep2

description: wildtype


title: RNA-seq_JM8.N4_12h_batch2-rep1

description: wildtype


title: DYY1_IAA_input_spikeIn


title: yCPC13

value: Young donor

value: c-kitpos


title: RACE-like (Anchored Multiplex PCR) negative control library 2 [CBS1_82]

description:
protocol: 10 ng plasmid DNA (pDest.HC.Rec.Bxb.v2-CBS-WT) was fragmented using the Covaris S2 with the following parameters: microTUBE AFA Fiber Snap-Cap, 10% duty cycle, 5 intensity, 200 cycles per burst, 1 min treatment. Sheared plasmid DNA was brought up to 50 µL with ultrapure water. A library was prepared with the ArcherDX (now Invitae) High Sensitivity ctDNA Kit according to the manufacturer recommendations (ArcherDX, PRO027.4), using 15 cycles for both PCR1 and PCR2 with custom CBS primers.

satmut_utils parameters: -z -r pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -p pDEST_HC_Rec_Bxb_v2_CBS_WT_primers_coding_GSP2_noendo.bed call -1 CBS1_76_R1.fastq.gz -2 CBS1_76_R2.fastq.gz --r1_fiveprime_adapters AACCGCCAGGAGT --r1_threeprime_adapters AGATCGGAAGAGCACACGTCTGAAC --r2_fiveprime_adapters GTTCAGACGTGTGCTCTTCCGATCT --r2_threeprime_adapters ACTCCTGGCGGTT -g pDEST_HC_Rec_Bxb_v2_CBS_WT.gff -k pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -n 2 -m 1 -s NNK -d

Illumina HiSeq X, NovaSeq 6000 at MedGenome, Inc.

library_source: other

molecule: other

organism: unidentified plasmid

source_name: Plasmid

value: Wild type

value: Plasmid DNA


title: yCPC8


title: yCPC11


title: Amplicon negative control library 3 [CBS1_75]

description:
protocol: 20 ng of plasmid DNA (pDest.HC.Rec.Bxb.v2-CBS-WT) was amplified with Q5 polymerase (NEB, M0491) for 14 cycles in a 50 µL PCR reactions with 500 nM landing-pad-specific primers (CAACTACACGAGCTCACAAGTTTGTACAA, GGCAGTCTCTCTGATTCCACAGTCAT) flanking the entire CBS insert (~1.7 kb), and including the high GC enhancer reagent. The cycling parameters were: initial denaturation at 98 ˚C for 30 s; 3-step cycling with denaturation at 98 ˚C for 10 s, anneal at 65 ˚C for 30 s, extension at 72 ˚C for 1 min; final extension at 72 ˚C for 2 min. Products were pooled, resolved on a 0.8% agarose/TAE gel, visualized with 1x SYBR Gold, and extracted from the gel using the Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) with 25 µL 70 ˚C elution buffer. 500 pg of the PCR1 product was amplified for each of two CBS tiles (2, 4) in a 50 µL NEB Q5 reaction (NEB, M0491) with high GC enhancer for 8 cycles, following the same cycling parameters as for PCR1. CBS tile 2 primers were TACACGACGCTCTTCCGATCTGAAGGGGTCCCCAGAGGATAAG and AGACGTGTGCTCTTCCGATCTTCTGGCAAGATTTTTGGAGATTTTGC. CBS tile 4 primers were TACACGACGCTCTTCCGATCTGAAGTGTGAGCTCTTGGCCAAG  and AGACGTGTGCTCTTCCGATCTCGATCCCGGTGTTCCCGG. Products for tile 2 and 4 amplicons were cleaned up with the Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 30 µL 70 ˚C elution buffer. PCR2 products were mixed together at equal volumes (5 µL each) and input into a final NEB Q5 reaction for 8 cycles with the same conditions using NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S) according to manufacturer’s recommendations (65 ˚C annealing). Final library was purified with the Nucleospin Gel and PCR Cleanup kit and eluted in 30 µL 70 ˚C buffer.

satmut_utils parameters: -r pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -p pDEST_HC_Rec_Bxb_v2_CBS_WT_primers_coding_tiles_2_4.bed call -1 CBS1_68_R1.fastq.gz -2 CBS1_68_R2.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA -g pDEST_HC_Rec_Bxb_v2_CBS_WT.gff -k pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -n 2 -m 1 -s NNK

Illumina HiSeq X at MedGenome, Inc.


title: DYY1_UT_YY1_bethyl_ChIP_spikeIn


title: yCPC6


title: RNA-seq_JM8.N4_0h_batch2-rep2

description: wildtype


title: DYY1_UT_RFP_ChIP_spikeIn


title: aCPC14

value: Adult donor


title: smeb-2 4°C rep2

city: Hefei

first: Zhen

last: Wang

state: Anhui

address: 130 Changjiangxilu

institute: Anhui Agricultural University

description: smeb-2 Cd-rep2

data_processing:
RNA-seq raw reads were processed with the Trimmomatic v0.32 and PRINSEQ v0.20.4 programs
Trimmomatic was used to remove the potential Illumina adapter contamination and conduct read trimming and clipping the low-quality bases.
PRINSEQ was subsequently employed to mainly remove low-complexity reads. The remaining reads were aligned to the Col-0 reference genome (version TAIR10) using the TopHat v2.0.13 program (D. Kim et al., 2013) with customized parameters.
A series of python scripts from juncBASE v0.6 were employed to deﬁne alternative 5' splice site, alternative 3' splice site, exon skipping, mutually exclusive exon, and intron retention events, qualify the events and generate signiﬁcantly differentially splicing events (P value < 0.05 and abs (delta_val) > 5) between pairwise samples.
The genes with alternative splicing patterns in all biological replicates of both smeb-1 and smeb-2 mutant plants are enrolled as differentially alternatively spliced genes.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample. Matrix table with raw gene counts for every gene and every sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Twelve-day-old smeb-1, smeb-2, and Col-0 seedlings grown on 0.5× MS medium.

extract_protocol:
Total RNA was isolated with the Total RNA Extraction Kit (Hua Yue Yang) and disposed with TURBO DNA-free Kit (Ambion) to remove any potential genomic DNA.
The libraries were constructed following the standard Illumina protocols.

treatment_protocol: Treatment at 4°C for 0 or 24 h.

value: seedlings

value: 12-day old seedlings

tag: time

value: 4 C for 24 h


title: DYY1_UT_input_spikeIn

value: Embryonic stem cells

value: mIAA7-mScarletI-YY1 / osTir


title: smeb-2 4°C rep1

description: smeb-2 Cd-rep1


title: Amplicon negative control library 2 [CBS1_31]

description:
protocol: Total RNA was extracted from HEK293T cells with Qiazol (Qiagen, 79306). 500 ng total RNA was primed with 125 ng random hexamers (Thermo Fisher Scientific, N8080127) and 100 nM final custom oligodT primer (dT30VN) at 65 ˚C for 5 min. Primed RNA was included in a 20 uL RT reaction with 200 U SuperScript III (Thermo Fisher Scientific, 18080051) and incubated at 42˚C for 30 min, 50˚C for 30 min, and 70˚C for 15 min. Reactions were treated with 2.5 U RNaseH (NEB, M0297) at 37 ˚C for 20 min. Each of fifteen CBS tiled amplicons were amplified from 1st strand cDNA with a 25 µL NEB Q5 PCR (NEB, M0491) including 500 nM primers, high GC enhancer, and the following cycling: 98˚C for 30 s; 98 ˚C for 10 s, 62 ˚C for 20 s, 72 ˚C for 30s (18 cycles); final extension at 72 ˚C for 2 min. 22 µL PCR1 product from each tile were pooled and purified by Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 15 µL buffer. 40 ng pooled PCR1 product was input to each of two 50 µL NEB Q5 PCRs with high GC enhancer and NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S), with the following cycling conditions: 98˚C for 30 s; 98 ˚C for 10 s, 65 ˚C for 20 s, 72 ˚C for 30 s (4 and 6 cycles); final extension at 72 ˚C for 2 min. Product from the 4 and 6 cycle reactions were pooled and size selected with the Sage Bioscience BluePippin 2% gel (marker M1) with 260-340 bp range. Eluate was concentrated with 1.8x AMPure XP beads (Beckman Coulter, A63881) and eluted in 15 µL water.

satmut_utils parameters: -r CBS_pEZY3.fa -p CBS_pEZY3_primers_coding.bed call -1 CBS1_31_S10_L006_R1_001.fastq.gz -2 CBS1_31_S10_L006_R2_001.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT,CAAGTTTGTACAAAAAAGTTGGC --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT,CCAACTTTCTTGTACAAAGTGGT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT,ACCACTTTGTACAAGAAAGTTGG --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA,GCCAACTTTTTTGTACAAACTTG -g CBS_pEZY3.gff -k CBS_pEZY3.fa -m 1 -s NNK

Illumina HiSeq 4000 at the Stanford Center for Genomics and Personalized Medicine

value: Total RNA


title: mNET-seq_JM8.N4_dBET6-2hr_batch2-rep2

description: wildtype

extract_protocol:
Nascent RNAs were extracted as the following steps: 1) Chromatin isolation; 2) Chromatin and RNA digestion; 3) Immunoprecipitation of Pol II complex; 4) RNA phosphorylation with T4 PNK; 5) RNA purification; 6) Size-selection for small RNAs.
mNET-seq RNA libraries were prepared according to protocol of NEBNext small RNA library prep kit (NEB, #E7330).

value: 100nM dBET6, 2 hrs


title: RNA-seq_JM8.N4_0h_batch2-rep1

description: wildtype

value: Ethanol, 3 hrs


title: mNET-seq_JM8.N4_dBET6-2hr_batch2-rep1

description: wildtype


title: Cold_24_Rep1

city: 福州市

first: Qiang

last: Zhu

state: 福建省

address: 福建农林大学海峡联合研究院

institute: 福建农林大学

data_processing:
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
These clean reads were then mapped to the reference genome sequence.
Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
FPKM was derived from RNA seq

organism: Phyllostachys edulis

growth_protocol: green house

extract_protocol:
RNeasy Mini Kit (QIAGEN, China)
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: seedlings at the three-leaf stage were subjected to −2 °C in a freezing chamber (LGX-400B-LED) under the same light and photoperiodic conditions as the control for the indicated time periods.

tag: age

value: 3 week old

value: Cold for 24 h


title: Cold_24_Rep2

address: 福建农林大学海峡联合研究院


title: smeb-1 4°C rep2

description: smeb-1 Cd-rep2


title: Amplicon input plasmid variant library [CBS1_74]

description:
protocol: 10 ng of plasmid DNA (pDest.HC.Rec.Bxb.v2-CBS-library) was amplified with Q5 polymerase (NEB, M0491) for 14 cycles in a 50 µL PCR reactions with 500 nM landing-pad-specific primers (CAACTACACGAGCTCACAAGTTTGTACAA, GGCAGTCTCTCTGATTCCACAGTCAT) flanking the entire CBS insert (~1.7 kb), and including the high GC enhancer reagent. The cycling parameters were: initial denaturation at 98 ˚C for 30 s; 3-step cycling with denaturation at 98 ˚C for 10 s, anneal at 65 ˚C for 30 s, extension at 72 ˚C for 1 min; final extension at 72 ˚C for 2 min. Products were pooled, resolved on a 0.8% agarose/TAE gel, visualized with 1x SYBR Gold, and extracted from the gel using the Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) with 25 µL 70 ˚C elution buffer. 500 pg of the PCR1 product was amplified for each of two CBS tiles (2, 4) in a 50 µL NEB Q5 reaction (NEB, M0491) with high GC enhancer for 8 cycles, following the same cycling parameters as for PCR1. CBS tile 2 primers were TACACGACGCTCTTCCGATCTGAAGGGGTCCCCAGAGGATAAG and AGACGTGTGCTCTTCCGATCTTCTGGCAAGATTTTTGGAGATTTTGC. CBS tile 4 primers were TACACGACGCTCTTCCGATCTGAAGTGTGAGCTCTTGGCCAAG  and AGACGTGTGCTCTTCCGATCTCGATCCCGGTGTTCCCGG. Products for tile 2 and 4 amplicons were cleaned up with the Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 30 µL 70 ˚C elution buffer. PCR2 products were mixed together at equal volumes (5 µL each) and input into a final NEB Q5 reaction for 8 cycles with the same conditions using NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S) according to manufacturer’s recommendations (65 ˚C annealing). Final library was purified with the Nucleospin Gel and PCR Cleanup kit and eluted in 30 µL 70 ˚C buffer.

satmut_utils parameters: -r pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -p pDEST_HC_Rec_Bxb_v2_CBS_WT_primers_coding_tiles_2_4.bed call -1 CBS1_68_R1.fastq.gz -2 CBS1_68_R2.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA -g pDEST_HC_Rec_Bxb_v2_CBS_WT.gff -k pDEST_HC_Rec_Bxb_v2_CBS_WT.fa -n 2 -m 1 -s NNK

Illumina HiSeq X at MedGenome, Inc.


title: smeb-1 4°C rep1

description: smeb-1 Cd-rep1


title: Amplicon positive control library 1; cytoplasmic RNA fractions of 20-50% sucrose gradient [CBS1_22]

description:
protocol: A CBS variant entry library (Sun and Weile, et al. 2020) was transferred into pEZY3 by a Gateway LR II reaction (Thermo Fisher Scientific, 11-791-020) with overnight incubation at 25 ˚C. For each of four replicate transformations, 2 µL of LR reaction was electroporated into 50 µL 10-beta electrocompetent cells (NEB, 3020) with 2 mm cuvettes, grown on 24.5 x 24.5 cm plates, collected in 10 mL LB, and processed with the ZymoPURE II Plasmid Midiprep Kit (Zymo Research, D4200) with endotoxin removal. Plasmids from each transformation replicate were pooled and concentrated, for an estimated library size of 860,625 to 975,440. 50 µg of CBS-pEZY3 variant library was transfected into a HEK293T cells at 85% confluency in a T-175 with 75 µL Lipofectamine 3000 (Thermo Fisher Scientific, L3000008) and 100 µL P3000 reagent in 3.5 mL OPTI-MEM. After 12 h the cells were split 1:4. At 48 h post-transfection, cells were stimulated with fresh media for 5 h, then incubated with 100 µg/mL cycloheximide at 37 ˚C for 10 minutes and washed with PBS including cycloheximide. Approximately 21 million cells were trypsinized and flash frozen. Cell pellets were lysed for 10 minutes with 350 µL lysis buffer (20 mM Tris-HCl pH 7.5; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 25 U/mL Turbo DNaseI (Thermo Fisher Scientific, AM2238); 20 mM ribonucleoside vanadyl complex (NEB, 50812650), 1X protease inhibitor cocktail EDTA-free (Sigma-Aldrich, 539131), and 100 μg/ml Cycloheximide (Sigma Aldrich). 20-50% sucrose gradients were made with the BioComp Gradient Maker in 20 mM Tris-HCl pH 7.5; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide using Beckman Coulter UC tubes 9/16 x 3 1/2. 300 µL lysate was loaded on the gradient and centrifuged at 38,000 rpm for 2.5 h at 4 ˚C in a Beckman Coulter SW-41Ti rotor. 500 uL polysome fractions were collected using the Biocomp Piston Gradient Fractionator and Gilson Fraction Collector. RNA was precipitated at -20 ˚C after addition of sodium acetate to 0.3 M pH 5.2, 2.5 µL Glycoblue (Thermo Fisher, AM9515), and 2.5x volumes cold ethanol. RNA was resuspended in 30 µL ultrapure water, RNA from the first four fractions (ribosome- and subunit-free RNA) was pooled and then purified by phenol-chloroform extraction and ethanol precipitation as before. Final polysome fraction RNA was resuspended in 50 µL ultrapure water. cDNA was synthesized by priming 500 ng total RNA with 100 nM final reverse primer capturing pEZY3 vector-expressed mRNA (GAGGCTGATCAGCGAGCTCTAG) at 65 ˚C for 5 min. Total RNA was included in a 40 uL RT reaction with 200 U SuperScript III (Thermo Fisher Scientific, 18080051) and 20 U SUPERase-In RNase inhibitor (Thermo Fisher, AM2696) and incubated at 55 ˚C for 1 h, then 70 ˚C for 15 min. Then, RNA was degraded by addition of 5 U RNaseH (NEB, M0297) and incubation at 37 ˚C for 20 min. Fifteen CBS tiled amplicons (using 250 nM primers) were amplified from cDNA with a 50 µL Q5 polymerase (NEB, M0491) reaction including high GC enhancer reagent and the following cycling: 98˚C for 30 s; 98 ˚C for 5 s, 62 ˚C for 10 s, 72 ˚C for 20s (20 cycles); final extension at 72 ˚C for 2 min. Pooled PCR1 products from each tile were purified by Agencourt AMPure XP beads with 1.8x ratio (Beckman Coulter, A63881) and elution in 20 µL. Purified PCR1 products from each tile were combined and quantified by Bioanalyzer High Sensitivity DNA Kit (Agilent, 5067-4626). 10 ng pooled PCR1 product was input to a second NEB Q5 PCR with high GC enhancer and NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S), with the following cycling conditions: 98˚C for 30 s; 98 ˚C for 10 s, 65 ˚C for 20 s, 72 ˚C for 30 s (6 cycles); final extension at 72 ˚C for 2 min. Libraries were size selected with the Sage Bioscience BluePippin 2% gel (marker V1) and eluate was concentrated with the Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 30 µL buffer. The final library pool was quantified by Bioanalyzer High Sensitivity DNA Kit.

satmut_utils parameters: -r CBS_pEZY3.fa -p CBS_pEZY3_primers_coding.bed call -1 CBS1_22_S1_L006_R1_001.fastq.gz -2 CBS1_22_S1_L006_R2_001.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT,CAAGTTTGTACAAAAAAGTTGGC --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT,CCAACTTTCTTGTACAAAGTGGT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT,ACCACTTTGTACAAGAAAGTTGG --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA,GCCAACTTTTTTGTACAAACTTG -g CBS_pEZY3.gff -k CBS_pEZY3.fa -m 2 -s NNK

Illumina HiSeq 4000 at the Stanford Center for Genomics and Personalized Medicine

value: Ribosome-free cytoplasmic fraction total RNA


title: Cold_24_Rep3

address: 福建农林大学海峡联合研究院


title: mNET-seq_JM8.N4_DMSO_batch2-rep2

description: wildtype

value: wildtype

value: DMSO, 2 hrs


title: mNET-seq_∆WAPL_24h_batch2-rep2

value: FLAG-Halo-CTCF / RAD21-SNAPf-V5 / HA-BFP-mAID-WAPL / osTir

value: 500 mM auxin in ethanol, 3 hrs


title: Cold_1_Rep3

address: 福建农林大学海峡联合研究院

value: Cold for 1 h


title: mNET-seq_JM8.N4_DMSO_batch2-rep1

description: wildtype


title: Cold_1_Rep2

address: 福建农林大学海峡联合研究院


title: Col-0 4°C rep2

description: Col-0 Cd-rep2

value: wild-type


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180613_K00134_IL100104211_GTCCGCA-1383_L003]

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

description: TPM_XGEOR_20180613_K00134_IL100104211_GTCCGCA-1383_L003_rsem

data_processing:
Sequencing quality was checked using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminated adaptor and/or row quality portions of sequenced reads were trimmed using Trim Galore (version 0.6.5; https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the genome, concatenating the human (hg38) and mouse (mm10) genome sequences, using STAR (version 2.7.9a) (Dobin et al. Bioinformatics 2013).
Batch effect was normalized using RUVSeq (version 1.26.0) with the RUVg method (Risso et al. Nat Biotech. 2014).
Normalized expression levels were estimated by means of transcripts per million (TPM) using RSEM (version 1.3.1) (Li and Dewey, BMC Bioinformatics 2011): TPM_gene_expression_hg38_matrix.txt
Normalized expression levels of mouse genes due to contamination were also estimated by means of TPM using RSEM: TPM_gene_expression_mm10contam_matrix.txt
Genome_build: hg38 + mm10
Supplementary_files_format_and_content: Text file that includes TPM values for each sample

extract_protocol:
Primary cells cultured in CRC were pelleted and total RNA extracted (Rneasy Mini Kit, Qiagen) and quality analyzed (Nanodrop, Bioanalyzer 2100, Agilent Technologies
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA Library Preparation Kit (polyA cDNA synthesis

tag: cancer vs. non-cancer derived

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell

tag: brca mutation reported

value: Tested negative


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180613_K00134_IL100104211_ATGTCAG-1219_L003]

description: TPM_XGEOR_20180613_K00134_IL100104211_ATGTCAG-1219_L003_rsem

value: BRCA1 mutation


title: mNET-seq_∆WAPL_24h_batch2-rep1

value: Embryonic stem cells


title: Cold_0.5_Rep3

address: 福建农林大学海峡联合研究院

value: Cold for 0.5 h


title: DYY1_UT_YY1_abcam_ChIP_spikeIn

value: mIAA7-mScarletI-YY1 / osTir

value: YY1 (Abcam ab109237)


title: mNET-seq_∆WAPL_12h_batch2-rep2


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180613_K00134_IL100104211_CCGTCCC-1300_L003]

description: TPM_XGEOR_20180613_K00134_IL100104211_CCGTCCC-1300_L003_rsem


title: Col-0 4°C rep1

description: Col-0 Cd-rep1

value: seedlings

value: 12-day old seedlings

value: 4 C for 24 h


title: Non-cancer derived breast cell contralateral [XGEOR_20180613_K00134_IL100104211_AGTTCCG-1218_L003]

description: TPM_XGEOR_20180613_K00134_IL100104211_AGTTCCG-1218_L003_rsem


title: Cold_0.5_Rep2

address: 福建农林大学海峡联合研究院

value: 3 week old


title: mNET-seq_∆WAPL_0h_batch2-rep2

value: Ethanol, 3 hrs


title: smeb-1 22°C rep1

description: smeb-1- rep1

value: 22 C for 24 h


title: Cold_0.5_Rep1

address: 福建农林大学海峡联合研究院


title: mNET-seq_∆WAPL_0h_batch2-rep1

value: FLAG-Halo-CTCF / RAD21-SNAPf-V5 / HA-BFP-mAID-WAPL / osTir


title: mNET-seq_∆WAPL_12h_batch2-rep1

value: 500 mM auxin in ethanol, 3 hrs


title: smeb-2 22°C rep2


title: smeb-2 22°C rep1


title: smeb-1 22°C rep2


title: mNET-seq_∆RAD21_24h_batch2-rep2

value: FLAG-Halo-CTCF / RAD21-BFP-mAID-V5 / osTir


title: Cancer breast cell  [XGEOR_20180613_K00134_IL100104210_AGTTCCG-1068_L002]

description: TPM_XGEOR_20180613_K00134_IL100104210_AGTTCCG-1068_L002_rsem

source_name: Cancer breast cell

value: Cancer derived

value: Not tested


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180613_K00134_IL100104211_AGTCAAC-1167_L003]

description: TPM_XGEOR_20180613_K00134_IL100104211_AGTCAAC-1167_L003_rsem

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell


title: Col-0 22°C rep2

value: wild-type


title: CK_Rep2

address: 福建农林大学海峡联合研究院

value: without cold treatment


title: CK_Rep3

address: 福建农林大学海峡联合研究院


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180613_K00134_IL100104210_GTGAAAC-1164_L002]

description: TPM_XGEOR_20180613_K00134_IL100104210_GTGAAAC-1164_L002_rsem


title: mNET-seq_∆RAD21_12h_batch2-rep2

description: Homozygous cell line with endogenous RAD21 loci tagged with an auxin-inducible degron

value: Embryonic stem cells


title: Liver_NKT_NODc3c4_Treated_rep3

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

description: Liver iNKT cells from treated NOD.c3c4 mice

data_processing:
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Alignment with STAR 2.5.3a to the GENCODE  release 16 of the Mus musculus genome (mm10 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
mm10
Excel sheets (xlsx) containing normalized counts

source_name: Liver

extract_protocol:
RNA purification using Rneasy Mini kit (QIAGEN)
TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)

treatment_protocol: Treated samples are obtained from NOD.c3c4 mice that have received intravenously 10 doses of aGalCer/CD1d-NPs.

value: iNKT cells

value: Treated


title: mNET-seq_∆RAD21_12h_batch2-rep1


title: Liver_NKT_NODc3c4_Treated_rep2


title: Liver_NKT_NODc3c4_Treated_rep1


title: Cancer breast cell  [XGEOR_20180613_K00134_IL100104210_ATGTCAG-1078_L002]

description: TPM_XGEOR_20180613_K00134_IL100104210_ATGTCAG-1078_L002_rsem

value: BRCA2 mutation


title: Cancer breast cell  [XGEOR_20180510_K00134_IL100101891_GCCAATA-1016_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_GCCAATA-1016_L006_rsem


title: mNET-seq_∆RAD21_24h_batch2-rep1


title: DNAseq_Brahman_bull_599_semen

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
Library strategy: DNA-Seq
For genomic sequencing data analyses, we followed the pipeline for 1000 bull genome project (PMID: 30508490). Briefly, raw sequencing reads were trimmed for adapter sequences and low quality bases using trimmomatic (version 0.39) with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 SLIDINGWINDOW:3:15’. Trimmed reads were aligned to the bovine genome using bwa-mem2 (version 2.2.1) with default parameters. Samtools (version 1.13) was used to convert, sort, filter, and index bam files. Aligned reads with mapping quality (MAPQ) less than 20 were excluded from downstream analyses. Read groups were added using AddOrReplaceReadGroups function of picard (version 2.25.5). The dataset of known variants in bovine was acquired from the 1000 bull genome project, namely ARS1.2PlusY_BQSR_v3.vcf.gz. GATK (version 4.2.1.0) was used to recalibrate base quality and identify variants in the genomic sequencing data with the known variant dataset as reference. Parameters used for BaseRecalibrator and HaplotypeCaller were ‘--bqsr-baq-gap-open-penalty 45’ and ‘--pcr-indel-model NONE’, respectively. Raw variants were scored using 2D model of CNNScoreVariants function of GATK with parameter ‘-tensor-type read_tensor’. Scored variants were filtered using FilterVariantTranches function of GATK with parameter ‘--info-key CNN_2D --invalidate-previous-filters --snp-tranche 99.95 --indel-tranche 99.4’.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Genomic variants in VCF format.

organism: Bos indicus

source_name: Brahman bull semen

extract_protocol:
One 0.5ml straw of semen was lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours. Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer (Thermo Fisher Scientific) and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
This DNA-seq was conducted by University of Missouri Genomics Technology Core. Information on library preparation and sequencing obtained from the Core is as follows: The library was constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq DNA PCR-Free sample preparation kit (#FC-121-3001).  Briefly, DNA was sheared using standard Covaris methods to generate average fragmented sizes of 350 bp.  The resulting 3’ and 5’ overhangs were converted to blunt ends by an end repair reaction which uses a 3’ to 5’ exonuclease activity and polymerase activity.  A single adenosine nucleotide was added to the 3’ ends of the blunt fragment followed by the ligation of Illumina indexed paired-end adapters.   The adaptor ligated library was purified twice with AxyPrep Mag purification beads.  The purified library was quantified using KAPA library quantification kit (KK4824) and library fragment size confirmed by Fragment Analyzer (Agilent Technologies, Inc.).  Libraries were diluted and sequenced according to Illumina’s standard sequencing protocol for the NovaSeq 6000.

value: Sperm

tag: breed

value: Brahman


title: CK_Rep1

address: 福建农林大学海峡联合研究院

value: 3 week old


title: mNET-seq_∆RAD21_0h_batch2-rep2

value: Ethanol, 3 hrs


title: Liver_NKT_NODc3c4_Untreated_rep2

description: Liver iNKT cells from untreated NOD.c3c4 mice

value: Untreated


title: Cold_1_Rep1

address: 福建农林大学海峡联合研究院

value: Cold for 1 h


title: mNET-seq_∆RAD21_0h_batch2-rep1

value: FLAG-Halo-CTCF / RAD21-BFP-mAID-V5 / osTir


title: Non-cancer derived breast cell contralateral [XGEOR_20180510_K00134_IL100101891_TGACCAA-996_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_TGACCAA-996_L006_rsem


title: Cancer breast cell  [XGEOR_20180510_K00134_IL100101891_CGATGTA-988_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_CGATGTA-988_L006_rsem

value: Cancer derived


title: Amplicon negative control library 2 [CBS1_34]

description:
protocol: Total RNA was extracted from HEK293T cells with Qiazol (Qiagen, 79306). 500 ng total RNA was primed with 125 ng random hexamers (Thermo Fisher Scientific, N8080127) and 100 nM final custom oligodT primer (dT30VN) at 65 ˚C for 5 min. Primed RNA was included in a 20 uL RT reaction with 200 U SuperScript III (Thermo Fisher Scientific, 18080051) and incubated at 42˚C for 30 min, 50˚C for 30 min, and 70˚C for 15 min. Reactions were treated with 2.5 U RNaseH (NEB, M0297) at 37 ˚C for 20 min. Each of fifteen CBS tiled amplicons were amplified from 1st strand cDNA with a 25 µL NEB Q5 PCR (NEB, M0491) including 500 nM primers, high GC enhancer, and the following cycling: 98˚C for 30 s; 98 ˚C for 10 s, 62 ˚C for 20 s, 72 ˚C for 30s (18 cycles); final extension at 72 ˚C for 2 min. 22 µL PCR1 product from each tile were pooled and purified by Macherey-Nagel Nucleospin Gel and PCR Cleanup Kit (Takara, 740609) and eluted in 15 µL buffer. 40 ng pooled PCR1 product was input to each of two 50 µL NEB Q5 PCRs with high GC enhancer and NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 1 (NEB, E7600S), with the following cycling conditions: 98˚C for 30 s; 98 ˚C for 10 s, 65 ˚C for 20 s, 72 ˚C for 30 s (4 and 6 cycles); final extension at 72 ˚C for 2 min. Product from the 4 and 6 cycle reactions were pooled and size selected with the Sage Bioscience BluePippin 2% gel (marker M1) with 260-340 bp range. Eluate was concentrated with 1.8x AMPure XP beads (Beckman Coulter, A63881) and eluted in 15 µL water.

satmut_utils parameters: -r CBS_pEZY3.fa -p CBS_pEZY3_primers_coding.bed call -1 CBS1_34_R1.fastq.gz -2 CBS1_34_R2.fastq.gz --r1_fiveprime_adapters TACACGACGCTCTTCCGATCT,CAAGTTTGTACAAAAAAGTTGGC --r1_threeprime_adapters AGATCGGAAGAGCACACGTCT,CCAACTTTCTTGTACAAAGTGGT --r2_fiveprime_adapters AGACGTGTGCTCTTCCGATCT,ACCACTTTGTACAAGAAAGTTGG --r2_threeprime_adapters AGATCGGAAGAGCGTCGTGTA,GCCAACTTTTTTGTACAAACTTG -g CBS_pEZY3.gff -k CBS_pEZY3.fa -m 1 -s NNK

Illumina NovaSeq 6000 at UT Austin Genome Sequencing and Analysis Facility

value: Wild type

value: Total RNA


title: mNET-seq_∆CTCF_24h_batch2-rep2

description: Homozygous cell line with endogenous CTCF loci tagged with an auxin-inducible degron

value: FLAG-BFP-mAID-CTCF / RAD21-SNAPf-V5 / osTir

value: 500 mM auxin in ethanol, 3 hrs


title: Liver_NKT_NODc3c4_Untreated_rep3


title: Liver_NKT_NODc3c4_Untreated_rep1


title: Col-0 22°C rep1

value: seedlings

value: wild-type

value: 12-day old seedlings

value: 22 C for 24 h


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180510_K00134_IL100101891_CTTGTAA-1037_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_CTTGTAA-1037_L006_rsem

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell

value: Not tested


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180510_K00134_IL100101891_ACAGTGA-998_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_ACAGTGA-998_L006_rsem

value: BRCA2 mutation


title: Liver_NKT_B6_Untreated_rep3

description: Liver iNKT cells from untreated B6 mice

value: iNKT cells


title: mNET-seq_∆CTCF_12h_batch2-rep1

value: Embryonic stem cells


title: scRNA-Seq ALS4 1 to 3 and Controls 1 to 3 (Antibody derived tags)

description:
Antibody derived tags/Hash tag sequencing (scRNA seq)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
meta_fastq_submission.csv
meta_features_submission.csv
meta_sample.csv

data_processing:
Illumina RTA3 and RTA2 software were used for base calling scRNA seq and scTCR seq, respectively.
Base call files were demultiplexed using cellranger mkfastq v3.1.0.
scRNA reads were aligned to the GRCh38-3.0.0 genome assembly. scTCR reads were aligned to GRCh38-alts-ensembl-2.0.0.
scRNA gene expression matrices were generated using cellranger count v3.1.0.
V(D)J sequences and annotations were generated using cellranger vdj v3.1.0.
Gene expression matrices were loaded into a single Seurat object using Seurat v4.0.1.
V(D)J sequences and annotations were integrated with the scRNA Seurat object using scRepertoire v1.1.4.
Genome_build: GRCh38-3.0.0 and GRCh38-alts-ensembl-2.0.0
Supplementary_files_format_and_content: For scRNA seq: Cell barcodes, genes, and expression matrices (tar.gz). For scTCR seq: High-level annotations for high-confident cellular contigs (csv) and high-level description of each clonotype (csv).

source_name: PBMC

extract_protocol:
From each patient, blood was drawn into a Cell Preparation Tube with sodium heparin (BD Vacutainer). Peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation using Ficoll (Ficoll Hystopaque; Sigma) according to the manufacturer’s protocol. PBMCs were aliquoted and frozen at -80°C in FBS (Gibco) containing 10% DMSO (sodium dodecyl sulfate, Sigma). Frozen vials of PBMCs were thawed and washed with culture medium (i.e. RPMI supplemented with 10% FBS, 100 μg/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 10 mM HEPES, and 1 nM sodium pyruvate) containing 2 mg/ml of DNAse I (Roche) (45). Cells were resuspended at the density of 2×106/ml in medium containing 0.1 mg/ml of DNAse I and left in culture for 18 hours in an incubator at 37ºC and 5% CO2 before analysis. PBMCs were incubated on ice for 20 min with 100 ul of the hash mixture in PBS 2% Bovine Serum Albumin (BSA, SIGMA) and then washed three time before CD8 T cell negative selection. human CD8 T cells were purified by negative selection  using a Dynabeads Untouched Human CD8 T Cells Kit (Invitrogen), according to the manufacturer’s protocol.Hashed cells were counted on a Nexcelom Autocounter 2000 using AO/PI dye and pooled based on live cell counts. Pooled samples were centrifuged then subsequently resuspended in 100 l of BioLegend’s Total Seq C CITE-Seq antibody panel and incubated on ice for 30 minutes. Antibodies were used at a concentration of 1:100 and diluted in wash buffer (PBS, 0.5% BSA, 1mM EDTA). After 3 washes, cells were resuspended in loading buffer (PBS, 0.5% BSA) and counted. Cells were loaded on one lane of the 10x 5’v1.1 assay with a targeted cell recovery of 20,000 cells.The following antibodies were used for CITE-seq and purchased from Biolegend:  TotalSeq-C0046 anti-human CD8   TotalSeq-C0049 anti-human CD3   TotalSeq-C0063 anti-human CD45RA   TotalSeq-C0148 anti-human CD197 (CCR7)   TotalSeq-C0390 anti-human CD127 (IL-7Rα)   TotalSeq-C0088 anti-human CD279 (PD-1)   TotalSeq-C0154 anti-human CD27   TotalSeq-C0386 anti-human CD28   TotalSeq-C0140 anti-human CD183 (CXCR3)   TotalSeq-C0071 anti-human CD194 (CCR4)   TotalSeq-C0141 anti-human CD195 (CCR5)   TotalSeq-C0143 anti-human CD196 (CCR6)   TotalSeq-C0160 anti-human CD1c   TotalSeq-C0085 anti-human CD25   TotalSeq-C0171 anti-human/mouse/rat CD278 (ICOS)   TotalSeq-C0410 anti-human CD38   TotalSeq-C0087 anti-human CD45RO   TotalSeq-C0168 anti-human CD57   TotalSeq-C0159 anti-human HLA-DR   TotalSeq-C0089 anti-human TIGIT (VSTM3)   TotalSeq-C0250 anti-mouse/human KLRG1 (MAFA
For scRNA seq and scTCR seq, base call files from a NovaSeq6000 Sequencer (Illumina) and a NextSeq550 Sequencer (Illumina), respectively, were generated by the Human Immune Monitoring Center and the Genomic CoRE at the ISMMS.  BCL files were base-called and demultiplexed using cellranger mkfastq v3.1.0. Alignment of gene expression libraries to human reference GRCh38 as well as the counting of unique features of CITESeq libraries were performed using cellranger count v3.1.0.

value: CD8 T cells

tag: library type

value: Antibody Derived Tags & Hashtag Oligos


title: mNET-seq_∆CTCF_24h_batch2-rep1


title: Non-cancer derived breast cell contralateral [XGEOR_20180510_K00134_IL100101890_CGATGTA-951_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_CGATGTA-951_L005_rsem

value: Tested negative


title: Cancer breast cell  [XGEOR_20180510_K00134_IL100101890_TGACCAA-958_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_TGACCAA-958_L005_rsem

value: Cancer derived


title: mNET-seq_∆CTCF_12h_batch2-rep2


title: Liver_NKT_NOD_Untreated_rep3

description: Liver iNKT cells from untreated NOD mice

value: NOD

value: Untreated


title: mNET-seq_∆CTCF_0h_batch2-rep2

value: FLAG-BFP-mAID-CTCF / RAD21-SNAPf-V5 / osTir

value: Ethanol, 3 hrs


title: scRNA-Seq ALS4 1 to 3 and Controls 1 to 3 (Hashtag)

description:
Hash tag oligo sequencing (scRNA seq)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
meta_fastq_submission.csv
meta_features_submission.csv
meta_sample.csv

value: Hashtag Oligos


title: mNET-seq_∆YY1_24h_batch2-rep2

description: Homozygous cell line with endogenous YY1 loci tagged with an auxin-inducible degron

value: mIAA7-mScarletI-YY1 / osTir

value: 500 mM auxin in ethanol, 3 hrs


title: scRNA-Seq ALS4 1 to 3 and Controls 1 to 3 (Gene expression)

description:
Gene expression sequencing (scRNA-seq)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
meta_fastq_submission.csv
meta_features_submission.csv
meta_sample.csv

value: Gene Expression


title: Liver_NKT_B6_Untreated_rep1

description: Liver iNKT cells from untreated B6 mice


title: Liver_NKT_B6_Untreated_rep2

description: Liver iNKT cells from untreated B6 mice


title: Liver_NKT_NOD_Untreated_rep2


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_TGACCAA-1120_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_TGACCAA-1120_L004_rsem

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell


title: mNET-seq_∆YY1_24h_batch2-rep1


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180510_K00134_IL100101890_CTTGTAA-987_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_CTTGTAA-987_L005_rsem

value: Not tested


title: mNET-seq_∆CTCF_0h_batch2-rep1


title: 293T-ISChIP-DdCBE-WT-rep1

city: Beijing

first: Howard

last: MENG

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: in situ ChIP-seq

data_processing:
The lower steps belong to in situ ChIP-seq
alignment: Bowtie2
remove PCR duplication: Picard
filtering: Samtools view, MAPQ > 20
peak-calling: MACS2
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: Peak-callingl format text by MACS2

extract_protocol: Transfected HEK293T cells were harvested and cross-linked with 0.25% formaldehyde on ice for 5 min. After fixation, cells were quenched via adding 2.5 M glycine and incubating on ice for 5 min. The fixed cells were washed twice with 1% BSA/PBS and conjugated with adequate prepared Con-A beads. Next, the cell-bead mixture was incubated with the primary antibody (anti-FLAG, sigma, F1804), the secondary antibody (donkey anti-mouse-Alexa 488, A21202), and purified PAT-MEA/B, step by step. After washing out free PAT-MEA/B, tagmentation was performed at 30°C for 1 h in a thermal cycler and stopped by adding 10 μL 40 mM EDTA. Cells were then lysed at 55°C for at least 3 h in Lysis Buffer. For library preparation, DNA fragments in the same tube were enriched via 10-18 cycles of PCR amplification with Nextera i5 index primer (5’-AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3’), and Nextera i7 index primer (5’-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3’). After PCR, the library was purified and selected for 200-1,000 bp fragments for sequencing.

value: HEK293T cells

value: treated with DdCBE(ND6 wild type)


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_GCCAATA-1020_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_GCCAATA-1020_L004_rsem


title: Fig4-de_ATACSeq_WildType_rep2

description: ATAC-seq

data_processing:
alignment: Bowtie2
mpileup: samtools mpileup
bmat: parse-mpileup-V04.py
SNV calling: VarScan2
Genome_build: hg38
Supplementary_files_format_and_content: vcf files: Variant Call Format text by VarScan2

extract_protocol: 10,000 viable cells were pelleted, lysed and the genomic DNA was tagmented with 2.5μl self-assembled Tn5 transposase. The tagmented DNA was purified using the DNA Clean and Concentrator-5 Kit (Vistech) and eluted in 20μl ultrapure water. All 20μl eluate was amplified by 12 cycles in a total volume of 50μl and the final library was purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter).

value: treated with DdCBE(WildType)


title: Cancer breast cell  [XGEOR_20180510_K00134_IL100101891_CAGATCA-1029_L006]

description: TPM_XGEOR_20180510_K00134_IL100101891_CAGATCA-1029_L006_rsem


title: Liver_NKT_NOD_Untreated_rep1

value: iNKT cells


title: mNET-seq_∆YY1_12h_batch2-rep2

data_processing: no processed data provided

value: Embryonic stem cells


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180510_K00134_IL100101890_GCCAATA-973_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_GCCAATA-973_L005_rsem


title: 293T-ISChIP-DdCBE-WT-rep2

description: in situ ChIP-seq


title: Cancer breast cell  [XGEOR_20180510_K00134_IL100101890_CAGATCA-980_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_CAGATCA-980_L005_rsem

value: Cancer derived

value: Tested negative


title: mNET-seq_∆YY1_12h_batch2-rep1


title: mNET-seq_∆YY1_0h_batch2-rep2


title: Fig4-de_ATACSeq_WildType_rep1

description: ATAC-seq


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_CGATGTA-1092_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_CGATGTA-1092_L004_rsem


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_CAGATCA-1018_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_CAGATCA-1018_L004_rsem


title: Fig4-de_ATACSeq_Untreated_rep3

description: ATAC-seq

value: untreated


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_CTTGTAA-1191_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_CTTGTAA-1191_L004_rsem


title: mNET-seq_JM8.N4_24h_batch2-rep2

description: wildtype

value: wildtype


title: mNET-seq_JM8.N4_12h_batch2-rep2

description: wildtype


title: Non-cancer derived breast cell ipsilateral [XGEOR_20180510_K00134_IL100101890_ACAGTGA-971_L005]

description: TPM_XGEOR_20180510_K00134_IL100101890_ACAGTGA-971_L005_rsem


title: mNET-seq_JM8.N4_12h_batch2-rep1

description: wildtype


title: mNET-seq_∆YY1_0h_batch2-rep1

value: Ethanol, 3 hrs


title: mNET-seq_JM8.N4_24h_batch2-rep1

description: wildtype


title: Fig4-de_ATACSeq_Untreated_rep4

description: ATAC-seq


title: cell organoid cortex-derived, biological rep2

description: Gene expression data from cell organoid cortex-derived

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: renal progenitor cell organoid

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Renal progenitors derived from mouse cortex and medulla tissue were isolated and cultured on a fibroblast feeder system Organoid samples were prepared using a 3D matrigel differentiation system.

extract_protocol: Follow the manufacturer's protocol of RNeasy® Mini Kit(REF# 74104).

tag: region

value: kidney cortex


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_GTCCGCA-1136_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_GTCCGCA-1136_L003_rsem


title: cell organoid cortex-derived, biological rep1


title: cell organoid medulla-derived, biological rep1

description: Gene expression data from cell organoid medulla-derived

value: kidney medulla


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_CCGTCCC-1074_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_CCGTCCC-1074_L003_rsem


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_GTGAAAC-978_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_GTGAAAC-978_L003_rsem


title: Fig4-de_ATACSeq_UGI-NES-ND6_rep1

description: ATAC-seq

value: treated with DdCBE(UGI-NES-ND6)


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_AGTTCCG-1077_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_AGTTCCG-1077_L003_rsem

value: BRCA2 mutation


title: mNET-seq_JM8.N4_0h_batch2-rep1

description: wildtype


title: Fig4-de_ATACSeq_Q1310A-ND6_rep1

description: ATAC-seq

value: treated with DdCBE(Q1310A-ND6)


title: Fig4-de_ATACSeq_Untreated_rep2

description: ATAC-seq


title: mNET-seq_JM8.N4_0h_batch2-rep2

description: wildtype


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_ATGTCAG-1015_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_ATGTCAG-1015_L003_rsem

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell


title: Fig4-de_ATACSeq_DddIA-ND6_rep2

description: ATAC-seq

value: HEK293T cells

value: treated with DdCBE(DddIA-ND6)


title: progenitor cell cortex-derived, biological rep2

description: Gene expression data from progenitor cell cortex-derived

source_name: renal progenitor cell


title: Cancer breast cell  [XGEOR_20170420_K00134_IL100086165_TGACCAA-1013_L002]

description: TPM_XGEOR_20170420_K00134_IL100086165_TGACCAA-1013_L002_rsem

value: Not tested


title: Fig4-de_ATACSeq_Untreated_rep1

description: ATAC-seq


title: pxb_uninf5

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences

description: Human liver-chimeric uPA/SCID mice

data_processing:
fastpv0.19.4 was used to removed low quality reads, homopolymers, and adaapter sequences
trimmed reads were aligned to a combined reference sequence of hg38 and mm10 major contigs using STAR version 2.7.3a
read counts were generated using featureCounts with option --primary only for annotations related to human genome/transcript alignments
Assembly: hg38 and mm10
Supplementary files format and content: gene count matrix

source_name: liver

extract_protocol:
Qiagen RNeasy
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).

value: liver

tag: model

value: uPA/SCID

tag: cohort

value: HBV-


title: pxb_uninf3

description: Human liver-chimeric uPA/SCID mice


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086166_AGTCAAA-1067_L003]

description: TPM_XGEOR_20170420_K00134_IL100086166_AGTCAAA-1067_L003_rsem

tag: cell type


title: Fig4-de_ATACSeq_UGI-NES-ND6_rep2

description: ATAC-seq


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086167_ACAGTGA-1000_L004]

description: TPM_XGEOR_20170420_K00134_IL100086167_ACAGTGA-1000_L004_rsem

value: Tested negative


title: 10x_Human_Liver_iNKT_IHL-486

description:
Liver iNKT cells from liver explant of a patient undergoing liver transplantation
10x library
4-486_S13_L001

data_processing:
CellRanger counts
CellRanger aggr
Downstream analysis in  Seurat (normalization, scaling and differential expression analysis)
GRCh38
One folder containing the aggregated files from CellRanger aggr (3 files: matrix, features and barcodes)

extract_protocol:
Partition of cell suspensions into Gel-Bead-In-Emulsions
10X Single-cell mRNA kit

value: iNKT cells


title: progenitor cell cortex-derived, biological rep1


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086165_GCCAATA-1112_L002]

description: TPM_XGEOR_20170420_K00134_IL100086165_GCCAATA-1112_L002_rsem


title: pxb_uninf2

description: Human liver-chimeric uPA/SCID mice


title: progenitor cell medulla-derived, biological rep1

description: Gene expression data from progenitor cell medulla-derived


title: progenitor cell medulla-derived, biological rep2


title: intestines - SHP-KO input DNA

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq data was analyzed using the AQUAS TF and histone ChIP-seq pipeline and mapped to the mouse reference genome (UCSC mm10) using bwa.
ChIP-seq peaks were identified by MACS followed by IDR (Irreproducible Discovery Rate). Optimal peaks with an IDR value <0.05 were kept.
Genome_build: mm10
Supplementary_files_format_and_content: peak file in narrowPeak format with suffix narrowPeak
Supplementary_files_format_and_content: fold-change and p-value signal tracks in bigWig format with suffix bw

source_name: jejunum and ileum of intestines

growth_protocol: SHP-KO mice and C57BL/6 mice as WT controls were grown to eight to 12 weeks

extract_protocol:
The jejunum and ileum of intestines were collected for ChIP assay using SHP anybody. Three independent sets of input and immunoprecipitated samples were analyzed and each set contained samples pooled from 3 mice.
Eighteen ng of DNA was used for genomic sequencing using the Illumina/Solexa Genome Analyzer II (Biotechnology Center, UIUC).

treatment_protocol: Mice were fasted overnight for 12 h and then, re-fed for 4 h with normal chow (Teklad, 8664, Madison, WI)

value: intestines

tag: strain background

tag: genotype/variation

value: SHP knockout


title: intestines - SHP-KO SHP pulldown

value: SHP (Santa Cruz Biotech, sc-30169)


title: kidney cortex tissue, biological rep2

description: Gene expression data from kidney cortex tissue

value: kidney cortex


title: pxb_uninf4

description: Human liver-chimeric uPA/SCID mice


title: kidney medulla tissue, biological rep2

description: Gene expression data from kidney medulla tissue

value: kidney medulla


title: 10x_Human_Liver_iNKT_IHL-484

description:
Liver iNKT cells from liver explant of a patient undergoing liver transplantation
10x library
3-484_S9_L001


title: cell organoid medulla-derived, biological rep2


title: intestines - WT input DNA

value: WT


title: pxb_uninf1

description: Human liver-chimeric uPA/SCID mice


title: kidney medulla tissue, biological rep1


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086165_CGATGTA-957_L002]

description: TPM_XGEOR_20170420_K00134_IL100086165_CGATGTA-957_L002_rsem


title: Fig4-de_ATACSeq_Q1310A-ND6_rep2

description: ATAC-seq

source_name: HEK293T cells

tag: cell line

value: treated with DdCBE(Q1310A-ND6)


title: C4

first: Yingmei

last: Feng

address: No. 8 Xi-Tou-Tiao

institute: Beijing Youan Hospital, Capital Medical University

description: Raw file not provided due to patient privacy concerns

data_processing:
Raw data of sequencing result of all patients were processed using Cell Ranger (v3.1.0), taking Human GRCh38 annotation file provided by 10X Genomics as reference.
To reduce chemistry associated batch effect, data was then processed using ‘cellranger aggr’.
Cell quality control and gene quality control was subsequently performed in Seurat R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containes single-cell expression matrix of each sample. Each column represents one single cell, each row represents a gene symbol, value in matrix is corresponding raw count.

extract_protocol:
PBMCs were isolated from EDTA venous blood samples (20 ml per patients) by Ficoll-Hypaque density solution following a standard density gradient centrifugation.
Cells were proceeded GEMs preparation and reverse transcription to barcoded scRNA-seq libraries according to the instruction provided by 10X Genomics.

tag: tissue

value: blood

value: PBMC

tag: disease state

value: COVID-19 infection

tag: disease stage

value: critical

tag: disease outcome

value: death


title: intestines - WT SHP pulldown

tag: chip antibody


title: kidney cortex tissue, biological rep1


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086165_CTTGTAA-1028_L002]

description: TPM_XGEOR_20170420_K00134_IL100086165_CTTGTAA-1028_L002_rsem

value: Non-cancer derived

value: CRC-isolated Breast epithelial cell


title: pxb_inf3

description: Human liver-chimeric uPA/SCID mice

value: liver

value: uPA/SCID

value: HBV+


title: 11_16h_SKMEL28_siDUSP4_Tram_2

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

country: Switzerland

institute: F. Hoffmann - La Roche Ltd

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq:2.19 from Illumina
Paired-end RNASeq reads were mapped to the human genome (hg38) with STAR aligner (v2.5.2a) using default mapping parameters
Numbers of mapped reads for all RefSeq transcript variants of a gene (counts) were combined into a single value by using SAMTOOLS software
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: melanoma cells

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s instructions except that lysates were loaded on a QIAshredder column before loading on a spin column. Sequencing libraries were generated from 100ng input RNA using the Illumina TruSeq Stranded mRNA LT Sample Preparation Kit as per manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3x105 cells were seeded in a 6 well plate. In parallel, either 0.25nM Trametinib or vehicle (DMSO) were added in both siDUSP4 and siNT transfected cells. After 16 hours, cells were harvested and frozen at -80 oC.

tag: tissue source

value: melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: siDUSP4+ Trametinib


title: Fig4-de_ATACSeq_DddIA-ND6_rep1

description: ATAC-seq

value: HEK293T cells

value: treated with DdCBE(DddIA-ND6)


title: pxb_inf1

description: Human liver-chimeric uPA/SCID mice


title: 10x_Human_Liver_iNKT_IHL-465

description:
Liver iNKT cells from liver explant of a patient undergoing liver transplantation
10x library
2-465_S5_L001

value: iNKT cells


title: 9_16h_SKMEL28_siDUSP4_3

value: siDUSP4+ DMSO


title: Non-cancer derived breast cell ipsilateral [XGEOR_20170420_K00134_IL100086165_ACAGTGA-1111_L002]

description: TPM_XGEOR_20170420_K00134_IL100086165_ACAGTGA-1111_L002_rsem

tag: cancer vs. non-cancer derived

tag: brca mutation reported

value: BRCA mutation (non-specified)