title: G1E-ER4 LDB1-AID RCMC, Auxin 4 hr, Biological Replicate 2

city: Cambridge

first: Viraat

middle: Yogi

last: Goel

state: Massachusetts

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

description: Processed data file merges biological replicates 1 & 2. Raw data files from the NovaSeq 6000 contain "NovaS1" in their filename while raw data files from the NovaSeq X contain "NovaX" in their filename.

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm9 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Loops were identified using cooltools (v0.5.3)
Assembly: mm9
Supplementary files format and content: mcool:multi-resolution contact map
Library strategy: Region Capture Micro-C

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified using a DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size-selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 5-7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. 80-mer biotinylated probes were designed end-to-end to tile across regioins of interest with Twist Bioscience. Capture was performed using the custom target enrichment panels using Twist Bioscience's Standard Hybridization Target Enrichment Protocol (Twist Bioscience, 104178) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution. The library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 4 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

value: proerythroblast

value: Auxin, 4hr


title: DNP07_2_T0

status: Public on Nov 27 2024

type: SRA

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description: T0 of kinetics  biol rep 2

library_source: transcriptomic

data_processing:
Reads were then mapped onto the Escherichia coli genome (version NC_000913.3, GenBank) with Bowtie2.
Counting was performed with featureCounts.
To measure genome-wide RNA half-lives, 12 RNA-sequencing data ( 2 T0 samples and 10 time points after addition of rifampicin) were used. Normalization between sequencing data was performed using the first three invariant genes for the 12 sequencing data of each condition (genes with the lowest variance in rank between sequencing data, namely b2621 (ssrA), b3123 (rnpB) and b2092 (gatC)).
Assembly: NC_000913.3
Supplementary files format and content: csv file includes raw counts of each gene in each SAMPLE

molecule: total RNA

organism: Escherichia coli

source_name: cells

growth_protocol: After overnight growth in M9-glucose (16.7 mM glucose), cells were washed with M9-succinate (85 mM of succinate), and used to inoculate Erlenmeyer flasks with M9-succinate at OD600nm= 0.1. At OD600nm= 0.8, rifampicin (0.5 g/L) was added, and cell samples were taken over time and rapidly frozen in liquid nitrogen.

extract_protocol:
After mechanical lysis with glass beads, total RNA was extracted using the RNeasy Mini Kit (Qiagen) at times T0, 0.4, 1, 2, 4 and 7 min for the two biological replicates. DNA contamination was removed by DNase I treatment.
Total RNA was ribodepeleted using the riboPOOLs kit (Illumina). A paired-end 150 bp sequencing strategy was performed on Illumina PE150 platform (Novogene).

treatment_protocol: Cells were treated with either 0.7 or 2 mM 2,4-dinitrophenol (DNP). Rifampicin and DNP were added simultaneously.

tag: tissue

value: cells

tag: genotype

tag: treatment

value: 0.7mM DNP


title: mRNA CRC-3

city: Shanghai

first: Hanchen

last: Xu

address: No.725, South Wanping Rd

country: China

institute: Institute of Digestive, Longhua Hospital, Shanghai University of Traditional Chinese Medicine

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. hisat2 software (v2.7.9a) was used to align the high-quality clean reads to the reference genome (hg19). cufflinks software (v2.2.4) was used to calculate the FPKM values of each gene.
Assembly: hg19
Supplementary files format and content: Excel format files with FPKM

organism: Homo sapiens

source_name: Colorectal cancer

extract_protocol:
mRNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026).  The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer's instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument with paired end mode.

value: Colorectal cancer


title: mRNA CRC-2


title: E20-4

city: Rehovot

first: Jonathan

last: Dayan

address: Herzel 229

country: Israel

institute: Faculty of Agriculture Hebrew University of Jerusalem

description: Library name: 340_E20-4

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cut-adapt, resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome according to Refseq annotations, using STAR 2.7.10a  with End-to-end option and out Filter Mismatch Nover Lmax was set to 0.05. Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Counts for each gene were quantified using HTSeq-count 2.0.2 , using the gene transfer format (GTF) above. UMI counts were corrected for saturation by considering the expected number of unique elements when sampling without replacement. Differentially expressed genes were identified using DESeq2 with the beta Prior, cooks Cutoff and independent Filtering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snake-make.
Assembly: Gallus genome
Supplementary files format and content: CSV, name: DEoutput_all, raw counts and DE comparisons
Library strategy: MARS-Seq

organism: Gallus gallus

source_name: Broiler Chicken

extract_protocol:
Total RNA was isolated from 100 mg of frozen muscle tissue using  TRI-Reagent (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol
Sequencing Libraries were prepared using LIB_PREP_PROTOCOL. READ_TYPE, 75bp single reads were sequenced on NUM_LANES lane(s) of an Illumina ILLUMINA_INSTRUMENT. The output was ~16 million reads per sample.

value: Complexus Muscle

value: Embryonic day 20

tag: batch

value: single


title: DNP07_2_T2

description: T2 of kinetics  biol rep 2


title: DNP07_2_T1

description: T1 of kinetics  biol rep 2


title: DNP07_1_T7

description: T7 of kinetics  biol  rep 1


title: mRNA CRC-1


title: G1E-ER4 LDB1-AID RCMC, Untreated, Biological Replicate 2

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type


title: DNP07_1_T4

description: T4 of kinetics   biol rep 1


title: E20-2

description: Library name: 338_E20-2


title: Infancy3

city: Chengdu

first: Li

last: Chen

state: Sichuann

address: No.17, South Renmin Road

institute: Sichuan University West China Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Tree shrew genome sequence (https://useast.ensembl.org/Tupaia_belangeri/Info/Index?db=core)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Tupaia belangeri

source_name: Retina

extract_protocol:
The retina was carefully dissected out from TS with strict compliance to the ethical guidelines. In detail, the dissected tissues were washed with cold phosphate buffered saline (PBS; Invitrogen, Carlsbad, USA), quickly frozen and then stored in liquid nitrogen before use. Preceding the library construction process, the tissues were first thawed, cut into small pieces, and then transferred to 1.5 mL tube contained with 1× homogenization buffer containing 30 mmol/L CaCl2, 18 mmol/L Mg(Ac)2, 60 mmol/L Tris-HCl (pH 7.8), 320 mmol/L sucrose, 0.1% nonidet P-40, and 0.1 mmol/L ethylene diamine tetraacetic acid (Invitrogen). The tissue pieces werethen transferred to a 2 mL Dounce homogenizer and stroke on the ice with loose pestles and then with tight pestles for 15 times. The nucleus extraction was filtered with 40 mm strainer and spanned down at the speed of 500 g for 10 min at 4 ℃ to carefully discard the supernatant. The pellets were resuspended with PBS containing 0.1% bovine serum albumin (Invitrogen) and 20 U/mL RNase Inhibitor for later 10x Genomics 30 library construction (10x Genomics, Pleasanton, USA).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Retina

tag: developmental stage

value: Infancy


title: mRNA CRA-5

source_name: Colorectal adenoma

value: Colorectal adenoma


title: Wastewater COVIDseq WAS 240218 PIR

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: Library name: COVIDseq_WAS_240218_zymo_S23

library_source: other

data_processing:
Sequencing on target reads and coverage are available in the processed data file. Additionally PCR results for SARS-CoV-2 are provided.
Assembly: Reads were mapped to SARS-CoV-2 via a bowtie2-samtools pipeline. Mapping only no assembly was performed.
Supplementary files format and content: CSV: Wastewater_COVIDseq_inhibitor_removal_processed_data.csv; Columns: "title","organism","sampling site","date","location type","treatment","inhibitor removal","on_target_alignment_rate","coverage","log10 SARS-CoV-2 copies per liter (PIR+D)"

molecule: other

organism: wastewater metagenome

source_name: wastewater

extract_protocol:
Using the Wizard® Enviro TNA Kit (Promega Corp., Madison, USA) as a direct capture method, total nucleic acids (TNAs) were extracted and concentrated from 40 ml of 24 h composite samples, resulting in a final volume of 50-100 µl following the manufacturer’s instructions
Sequencing were prepared using the COVIDseq kit (Illumina) according to manufacturer's instructions, and sequenced on a NextSeq 2000 device using P1 300 cycles flowcells with 2x151 bp.
Targeted/amplicons

treatment_protocol: Following the operating instructions, the OneStepTM PCR inhibitor removal (PIR) kit (D6030, Zymo Research, Irvine, CA, USA) was used to remove inhibitors of molecular enzymatic reactions. The kit encompasses one cleaning step over a column, which efficiently retains inhibitors, including long and short chain humic acids, tannins or polyphenols. After column preparation, 100 µl aqueous TNA solution was transferred to the column and centrifuged for 3 min at 16,000 x g.

value: wastewater

tag: sampling site

value: WAS

tag: location type

value: WWTP

tag: date

tag: tna extraction_method

value: Promega Enviro TNA

tag: inhibitor removal

value: yes

tag: library preparation

value: Illumina COVIDseq


title: Wastewater COVIDseq WAS 240218

description: Library name: COVIDseq_WAS_240218_S27

value: no


title: DNP07_1_T2

description: T2 of kinetics   biol rep 1


title: Wastewater COVIDseq WAS 240211 PIR

description: Library name: COVIDseq_WAS_240211_zymo_S21


title: mRNA CRA-4


title: E19-6

description: Library name: 330_E19-6

value: Embryonic day 19


title: E20-1

description: Library name: 337_E20-1


title: DNP07_1_T1

description: T1 of kinetics   biol rep 1

value: cells


title: Wastewater COVIDseq WAS 240211

description: Library name: COVIDseq_WAS_240211_S25


title: mRNA CRA-3


title: E19-5

description: Library name: 329_E19-5


title: DNP07_1_T25

description: T 25 sec of kinetics  biol  rep 1

value: 0.7mM DNP


title: mRNA CRA-2


title: Wastewater COVIDseq RUH 240218 PIR

description: Library name: COVIDseq_RUH_240218_zymo_S22

value: RUH


title: DNP07_1_T0

description: T0 of kinetics biol rep 1


title: E19-3

description: Library name: 327_E19-3

value: Complexus Muscle


title: E20-3

description: Library name: 339_E20-3

value: Embryonic day 20


title: mRNA CRA-1


title: Wastewater COVIDseq RUH 240218

description: Library name: COVIDseq_RUH_240218_S26


title: Wastewater COVIDseq WAS 240908

description: Library name: COVIDseq_WAS_240908_ohne_S21


title: mRNA HC-5

source_name: Normal colorectal epithelium

value: Normal colorectal epithelium


title: Sox2CreER

city: Rochester

first: Stijn

last: De Langhe

state: Minnesota

address: 200 First street SW

department: Medicine

institute: Mayo Clinic Rochester Minnesota

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression levels of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg - aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue.jpg - image of tissue and spots
Supplementary files format and content: scalefactors_json.json - scalefactors in json format
Supplementary files format and content: tissue_hires_image.png - high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png - low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv - list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5 - processed spatial transcritomics data in h5 format
Library strategy: Spatial transcriptomics

source_name: Lung

extract_protocol:
Lungs were fixed with 4%PFA and paraffin embedded, and 5um FFPE sections were cut on a microtome and placed on 10x Genomics Visium Spataial slides. Following manufacturer's instructions, samples were immunostained and imaged.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Spatial Gene Expression slides and Reagent kit according to manufacurer's instructions

treatment_protocol: Lungs of mice were injured with intratracheal administration of bleomycin in which we inactivated Myc, Yap1/Wwtr1, Stk3/4 or overexpressed Myc. At 6 weeks after injury lungs were analyzed using sptaial transcritpomics.

value: Lung

value: Bleomycin


title: Scgb1a1CreER_LSL rtTA_TetMyc

value: Scgb1a1CreER+;LSL rtTAFF;TetMyc+


title: mRNA HC-4


title: E19-2

description: Library name: 326_E19-2

value: single


title: E17-6

description: Library name: 306_E17-6

value: Embryonic day 17


title: Sox2CreER_Yap1FF_Wwtr1FF


title: mRNA HC-3


title: Wastewater COVIDseq WAS 240901 PIR

description: Library name: COVIDseq_WAS_240901_mit_S20

value: wastewater

value: WAS

value: WWTP


title: Wastewater COVIDseq WAS 240901

description: Library name: COVIDseq_WAS_240901_ohne_S19

value: Promega Enviro TNA

value: Illumina COVIDseq


title: mRNA HC-2


title: E17-4

description: Library name: 304_E17-4


title: Wastewater COVIDseq WAS 240327

description: Library name: COVIDseq_WAS_240327_ohne_S15

value: no


title: Sox2CreER_MycFF


title: Sox2CreER_Stk3FF_Stk41FF


title: mRNA HC-1


title: E17-5

description: Library name: 305_E17-5


title: E17-3

description: Library name: 303_E17-3


title: eccDNA CRC-5

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.1), the high quality clean reads were aligned to the reference genome (UCSC hg19) with bwa software v(v0.7.12).
Then, circle-map software (v1.1.4) was used to detect eccDNA within all samples, and samtools (v0.2) software was used to get raw soft-clipped read counts of the break point. Then edgeR (v0.6.9) software was used to perform normalization and differentially expressed eccDNA filter by p-value and fold change. bedtools (v2.27.1) software was used to annotate the eccDNAs.
Assembly: hg19
Supplementary files format and content: excel format file contains eccDNA counts of each sample

extract_protocol:
eccDNA high throughput sequencing was performed by NewCore Biotech. (Shanghai, China). Briefly, tissues were suspended in L1 solution (Plasmid Mini AX; A&A Biotechnology) and supplemented with Proteinase K (ThermoFisher) before incubation overnight at 50 °C with agitation. After Lysis, samples were alkaline treated,followed by precipitation of proteins and separation of chromosomal DNA from circular DNA through an ion exchange membrane column (Plasmid Mini AX; A&A Biotechnology). Column-purified DNA was treated with FastDigest MssI (Thermo Scientifific) to remove mitochondrial circular DNA and incubated at 37 °C for 16 h. Remaining linear DNA was removed by exonuclease (Plasmid-Safe ATP-dependent DNase, Epicentre) at 37 °C in a heating block and enzyme reaction was carried out continuously for 1 week, adding additional ATP and DNase every 24 h (30 units per day) according to the manufacturer’s protocol (Plasmid-Safe ATP-dependent DNase, Epicentre). eccDNA-enriched samples was used as template for phi29 polymerase amplification reactions (REPLI-g Midi Kit) amplifying eccDNA at 30 °C for 2 days (46–48 h).
Phi29-amplifified DNA was sheared by sonication (Bioruptor), and the fragmented DNA was subjected to library preparation with NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was carried out on Illumina NovaSeq 6000 with 150bp paired end mode according to the manufacturer’s instructions.
eccDNA-seq

value: Colorectal cancer


title: Wastewater COVIDseq WAS 240327 PIR

description: Library name: COVIDseq_WAS_240327_mit_S16

value: yes


title: E17-2

description: Library name: 302_E17-2


title: CG1603PBac mutant larvae, biol rep 2

city: Bethesda

first: Fan

last: Zhang

address: 10 Center Dr.

institute: NHLBI

description: Library name: CG1603PBac2

data_processing:
Bioinformatics Pipeline of mRNA Analysis, NCI, NIH.
Quality assessment of FASTQ files using FastQC
Aligned against Drosophila Melanogaster reference genome using a two-pass method with STAR
Gene level read counts were produced by HTseq
Assembly: dm6
Supplementary files format and content: Output text files generated by HTseq containing raw counts for each sample

organism: Drosophila melanogaster

source_name: larva

extract_protocol:
Total RNA was extracted by Trizol (Thermo Fisher Scientific) following standard protocol. Contaminating DNA was removed by DNA-free™ DNA Removal Kit (Thermo Fisher Scientific). 1µg total RNA used for library construction.
Poly (A) capture libraries were generated at the DNA Sequencing and Genomics Core, NHLBI, NIH following standard protocol.

value: larva

value: CG1603PBac mutant


title: CG1603PBac mutant larvae, biol rep 3

description: Library name: CG1603PBac3


title: E19-1

description: Library name: 325_E19-1

value: Complexus Muscle

value: Embryonic day 19


title: CG1603PBac mutant larvae, biol rep 1

description: Library name: CG1603PBac1


title: Wastewater COVIDseq WAS 240317

description: Library name: COVIDseq_WAS_240317_ohne_S13


title: Wastewater COVIDseq WAS 240317 PIR

description: Library name: COVIDseq_WAS_240317_mit_S14


title: E17-1

description: Library name: 301_E17-1


title: Wastewater COVIDseq WAS 240908 PIR

description: Library name: COVIDseq_WAS_240908_mit_S22


title: eccDNA CRC-3


title: wt larvae, biol rep3

description: Library name: wt3

value: WT


title: E15-6

description: Library name: 294_E15-6

value: Embryonic day 15


title: Wastewater COVIDseq WAS 240307

description: Library name: COVIDseq_WAS_240307_ohne_S11


title: wt larvae, biol rep2

description: Library name: wt2


title: eccDNA CRC-2


title: E15-4

description: Library name: 292_E15-4


title: Wastewater COVIDseq WAS 240305

description: Library name: COVIDseq_WAS_240305_ohne_S9


title: eccDNA CRA-5

value: Colorectal adenoma


title: eccDNA CRC-1


title: wt larvae, biol rep1

description: Library name: wt1


title: Wastewater COVIDseq WAS 240307 PIR

description: Library name: COVIDseq_WAS_240307_mit_S12


title: eccDNA CRA-4


title: Wastewater COVIDseq WAS 240305 PIR

description: Library name: COVIDseq_WAS_240305_mit_S10


title: E15-3

description: Library name: 291_E15-3

value: single


title: E15-2

description: Library name: 290_E15-2


title: K8_GFP-4

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

data_processing:
nf-core/cutandrun for alignment and deduplication
MACS3 for peak calling and pileup
bdgToBigWig for convert pileuped file into bigwig file
Assembly: dm6
Supplementary files format and content: bigwig; pileuped, averaged and normalized target binding signal
Library strategy: CUT&RUN

source_name: 3rd instar wing imaginal disc

extract_protocol: We utilized the CUT&RUN assay kit purchased from Cell Signaling Technology (#86652), using IgG from the kit as the negative control, along with the anti-GFP antibody obtained from Abcam (ab290).

value: 3rd instar wing imaginal disc


title: K8_GFP-2


title: K8_GFP-3


title: eccDNA CRA-3


title: E15-1

description: Library name: 289_E15-1


title: Wastewater COVIDseq SCH 240908 PIR

description: Library name: COVIDseq_SCH_240908_mit_S30

value: wastewater

value: SCH


title: K8_IgG-4


title: Wastewater COVIDseq SCH 240901

description: Library name: COVIDseq_SCH_240901_ohne_S27

value: WWTP


title: K8_IgG-3


title: eccDNA CRA-1


title: Wastewater COVIDseq SCH 240901 PIR

description: Library name: COVIDseq_SCH_240901_mit_S28

value: Promega Enviro TNA


title: eccDNA HC-5

value: Normal colorectal epithelium


title: E15-5

description: Library name: 293_E15-5


title: somite HH15, scRNAseq

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

country: Switzerland

institute: University of Basel

data_processing:
Cell Ranger software (10X Genomics)
Assembly: Gallus gallus GRCg6a
Supplementary files format and content: Tab-separated values and matrix files

source_name: somite

extract_protocol:
Samples were dissected in cold PBS, and chopped coarsely with a razorblade. Dissociation into single cells was done using 0.25% trypsin in DMEM and incubation for 15 min at 37°. Occasional mechanical shearing by careful pipetting was applied during the incubation time.
Following instructions from 10X Genomics Chromium Next GEM  Gene Expression 3'.

value: somite


title: K8_IgG-2


title: eccDNA HC-4


title: somite HH12, scRNAseq


title: Wastewater COVIDseq RUH 240901

description: Library name: COVIDseq_RUH_240901_ohne_S17

value: RUH

value: no

value: Illumina COVIDseq


title: SD_GFP-4


title: somite HH20, scRNAseq


title: eccDNA HC-3


title: Wastewater COVIDseq RUH 240901 PIR

description: Library name: COVIDseq_RUH_240901_mit_S18

value: yes


title: frontonasal prominence HH22, scRNAseq

source_name: frontonasal prominence

value: frontonasal prominence


title: SD_GFP-3


title: frontonasal prominence HH18, scRNAseq


title: Wastewater COVIDseq RUH 240327

description: Library name: COVIDseq_RUH_240327_ohne_S7


title: Wastewater COVIDseq SCH 240908

description: Library name: COVIDseq_SCH_240908_ohne_S29


title: eccDNA CRA-2


title: eccDNA HC-2


title: SD_GFP-1


title: Wastewater COVIDseq RUH 240327 PIR

description: Library name: COVIDseq_RUH_240327_mit_S8


title: SD_GFP-2


title: eccDNA HC-1


title: frontonasal prominence HH15, scRNAseq


title: Wastewater COVIDseq RUH 240317

description: Library name: COVIDseq_RUH_240317_ohne_S5


title: frontonasal prominence HH18, scATACseq

library_source: genomic single cell

extract_protocol:
Samples were dissected in cold PBS, and chopped coarsely with a razorblade. Dissociation into single cells was done using 0.25% trypsin in DMEM and incubation for 15 min at 37°. Occasional mechanical shearing by careful pipetting was applied during the incubation time.
Following instructions from 10X Genomics Chromium Next GEM Single Cell ATAC.


title: eccDNA CRC-4

value: Colorectal cancer


title: limb HH24, scATACseq

source_name: limb

value: limb


title: SD_IgG-3


title: Wastewater COVIDseq RUH 240317 PIR

description: Library name: COVIDseq_RUH_240317_mit_S6


title: Wastewater COVIDseq RUH 240307

description: Library name: COVIDseq_RUH_240307_ohne_S3


title: SD_IgG-2


title: Wastewater COVIDseq RUH 240307 PIR

description: Library name: COVIDseq_RUH_240307_mit_S4


title: SD_IgG-1


title: DP_GFP-3


title: Wastewater COVIDseq RUH 240305

description: Library name: COVIDseq_RUH_240305_ohne_S1


title: somite HH15, scATACseq


title: DP_GFP-2


title: MDA-MB-231 cells treated with compound 28, rep2

first: Jingya

last: Sun

state: Shanghai

address: No.501 Haike Road

institute: Shanghai Institute of Materia Medica CAS: Shanghai Institute of Materia Medica Chinese Academy of Sciences

description: Library name: D35_2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default. parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based. approach.
Assembly: Raw RNA sequences data were mapped to the GRCh37 (hg19) genome by hisat2, then sorted by samtools and counted by htseq-count in linux system.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: MDA-MB-231 cells werecultured in Leibovitz’s (L-15) media supplemented with 10% FBS and1% penicillin−streptomycin antibiotics in an incubator without CO2 at 37 °C.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Ambion, 15596 026).
RNA purification,reverse transcription,library construction and sequencig were performed at ShanghalMajorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer's instructions . The RNA-seq transcriptome librariy was prepared following llumina® Stranded mRNA Prep, Ligation (San Diego,CA) using 1μg of total RNA.

treatment_protocol: MDA-MB-231 cell line were incubated with 500 nM of 28 for 4 h, then the RNA of the cell line is extracted.

value: Triple-negative breast cancer

value: WT

value: Compound 28


title: MDA-MB-231 cells treated with compound 28, rep3

description: Library name: D35_3


title: Wastewater COVIDseq RUH 240305 PIR

description: Library name: COVIDseq_RUH_240305_mit_S2


title: somite HH12, scATACseq


title: Wastewater COVIDseq BER 240908

description: Library name: COVIDseq_BER_240908_ohne_S25

value: BER

value: airport


title: DP_GFP-1

value: 3rd instar wing imaginal disc


title: MDA-MB-231 cells treated with compound 28, rep1

description: Library name: D35_1


title: Wastewater COVIDseq BER 240908 PIR

description: Library name: COVIDseq_BER_240908_mit_S26

value: wastewater


title: frontonasal prominence HH15, scATACseq


title: MDA-MB-231 cells treated with DMSO, rep2

description: Library name: DMSO_2

value: DMSO


title: MDA-MB-231 cells treated with DMSO, rep3

description: Library name: DMSO_3


title: DP_IgG-3


title: Wastewater COVIDseq BER 240901 PIR

description: Library name: COVIDseq_BER_240901_mit_S24

value: Promega Enviro TNA


title: DP_IgG-2


title: DP_IgG-1


title: BALBc mice, 8 weeks, female, 3 days after CP, normal diet, biol rep 3

status: Public on Nov 26 2024

city: Ljubljana

first: Brina

last: Dragar

address: Vrazov trg 2

department: Institute of Cell Biology

country: Slovenia

institute: University of Ljubljana, Faculty of Medicine

description: Library name: I5

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including Hisat2, FeatureCounts and Novogene's wrapped scripts.
High quality reads were aligned to mouse (Ensembl GRCm39) reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. The fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups (CP1dvsCP1d+VitA, FR1dvsFR1d+VitA, CP3dvs>CP3d+VItA; three replicates per group) was performed using DESeq2 R package (1.20.0). P value was calculated using the negative binomial distribution and the resulting p values were adjusted using the Benjamini-Hochberg’s approach for controlling the false discovery rate.
The clusterProfiler (v. 3.8.1) software was used for enrichment analysis of differentially expressed genes, including Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome database
Assembly: GRCm39
Supplementary files format and content: excel file includes counts for each gene for each sample (gene_count.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample (gene_fpkm.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of CP1d group vs CP1d+VitA group (CP1dvsCP1d_VitA_deg_all.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of FR1d group vs FR1d+VitA group (FR1dvsFR1d_VitA_deg_all.xls_deg_all.xls)
Supplementary files format and content: excel text file includes FPKM values for each gene for each sample and diferential analysis of CP3d group vs CP3d+VitA group (CP3dvsCP3d_VitA_deg_all.xls)

source_name: urinary bladder

growth_protocol: Animales were housed in groups of 3 animals in polyacrylamide cages at constant humidity (55%) and temperature (22°C) with water and food ad libitum and 12h/12h light-dark cycle.

extract_protocol:
Total RNA was isolated using TRI Reagent (VWR) and PeqGOLD Total RNA Kit (VWR). Library preparation was performed by Novogene Co., Ltd, using at least 0.5 ug high-quality total RNA input per sample.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: Half of the mice's diet was changed to Vitamin A-enriched diet (566081UI retinyl-acetate per kilogram) one week before application (i.p. injection) of cyclophosphamide (CP;150 mg/kg b.w.) or saline (S). Mice injected with saline served as controls. Eutanisations were executed one and three days after CP or S application.

value: urinary bladder

value: wild type

value: cyclophosphamide  (150 mg/kg b.w.)


title: SD_IgG-4


title: Murine Splenic NK cells; sample 2

city: New York

first: William

last: Coetzee

state: United States

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

description:
Library name: WtMouse_S9
10x Genomics

data_processing:
Sequencing was performed by NYU Langone’s Genome Technology Center using an Illumina NovaSeq 6000 instrument. Demultiplexing raw base call (BCL) files into FASTQ format was performed using Cell Ranger software (10X Genomics). The latter software was also used for alignment, filtering, barcode counting, and UMI counting to generate feature-barcode matrices. Further analysis including quality filtering, the identification of highly variable genes, dimensionality reduction, standard unsupervised clustering algorithms, and the discovery of differentially expressed genes was performed using the Seurat R package. We filtered out cells with unique feature counts (genes) over 5,000 or less than 200. We also filtered out cells with more than 15% mitochondrial gene counts. Global-scaling normalization (“LogNormalize”) was performed that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000) and log-transforms the result. Linear transformation (scaling) was performed, followed by dimensional reduction using a principal component analysis (PCA). Nearest-neighbor analysis, constrained to a maximum of 20 dimensions, was performed, followed by a graph-based approach to cluster cells at a resolution value of 0.5. Clusters were displayed after non-linear dimensional reduction with t-distributed stochastic neighbor embedding (tSNE) and uniform manifold approximation and projection (UMAP) methods. Differentially overexpressed features (cluster biomarkers) were determined using the ‘FindAllMarkers’ function at a minimum fold difference (log-scale) of 0.25.
Assembly: mm10 mouse genome
Supplementary files format and content: Seurat barcodes, features and matrix files

source_name: Spleen

extract_protocol:
All animal handling procedures were in accordance with National Institutes of Health guidelines and were approved by the Institutional Animal Care and Use Committees of New York University School of Medicine. Isolated splenocytes were washed 2x with media and passed again through 70 µm cell strainer. In other experiments, spleens were dissociated with the gentleMACS spleen disassociation kit (Miltenyi Biotec). Cells were then filtered, erythrocytes were depleted via isotonic hemolysis, and NK cells were isolated using a negative selection method (NK Cell Isolation Kit, Miltenyi Biotec) following the manufacture’s guidelines. In this negative selection method, non-NK cells, i.e. T cells, dendritic cells, B cells, granulocytes, macrophages, and erythroid cells are magnetically labelled with a cocktail of biotin-conjugated antibodies and anti-biotin MicroBeads, and then removed from isolated splenic cells using magnetic columns.
We used the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics) to perform gel beads-in-emulsion (GEM) generation and barcoding, Post GEM-reverse transcriptase (RT) cleanup and cDNA amplification, and 3’ gene expression library construction.

value: Spleen

value: NK cells (isolated by negative selection)

value: Wild-type


title: MDA-MB-231 cells treated with DMSO, rep1

description: Library name: DMSO_1


title: limb HH21, scATACseq


title: Murine Splenic NK cells; sample 1

description:
Library name: WtMouse_S8
10x Genomics


title: BALBc mice, 8 weeks, female, 3 days after CP, normal diet, biol rep 2

description: Library name: I2


title: BALBc mice, 8 weeks, female, 1 day after saline, normal diet, biol rep 3

description: Library name: G3

value: saline


title: BALBc mice, 8 weeks, female, 3 days after CP, VitA-enriched diet, biol rep 3

description: Library name: H3

value: cyclophosphamide (150 mg/kg b.w.), Vitamin A-enriched diet (566081UI retinyl-acetate per kilogram)


title: BALBc mice, 8 weeks, female, 3 days after CP, VitA-enriched diet, biol rep 1

description: Library name: H1


title: BALBc mice, 8 weeks, female, 3 days after CP, VitA-enriched diet, biol rep 2

description: Library name: H2


title: BALBc mice, 8 weeks, female, 3 days after CP, normal diet, biol rep 1

description: Library name: I1


title: BALBc mice, 8 weeks, female, 1 day after saline, VitA-enriched diet, biol rep 2

description: Library name: F2

value: saline, Vitamin A-enriched diet (566081UI retinyl-acetate per kilogram)


title: BALBc mice, 8 weeks, female, 1 day after saline, normal diet, biol rep 2

description: Library name: G2


title: BALBc mice, 8 weeks, female, 1 day after saline, VitA-enriched diet, biol rep 3

description: Library name: F3


title: BALBc mice, 8 weeks, female, 1 day after CP, normal diet, biol rep 3

description: Library name: E3


title: Wastewater COVIDseq BER 240901

description: Library name: COVIDseq_BER_240901_ohne_S23

value: no

value: Illumina COVIDseq


title: BALBc mice, 8 weeks, female, 1 day after CP, normal diet, biol rep 1

description: Library name: E1


title: BALBc mice, 8 weeks, female, 1 day after saline, VitA-enriched diet, biol rep 1

description: Library name: F1


title: BALBc mice, 8 weeks, female, 1 day after CP, normal diet, biol rep 2

description: Library name: E2


title: BALBc mice, 8 weeks, female, 1 day after CP, VitA-enriched diet, biol rep 3

description: Library name: D4


title: BALBc mice, 8 weeks, female, 1 day after CP, VitA-enriched diet, biol rep 2

description: Library name: D3


title: BALBc mice, 8 weeks, female, 1 day after CP, VitA-enriched diet, biol rep 1

description: Library name: D1


title: D21_rep3

city: Palo Alto

first: Ishita

last: Jain

address: 3801 Miranda Avenue

institute: Stanford University

data_processing:
Raw data (raw reads) of fastq format were filtered  based on quality metrics relating to adapter content, ploy-N reads and low-quality reads. All the downstream analyses were based on clean data with high quality. The reads were then aligned to a reference genome using Hisat v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. The FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: not provided
Supplementary files format and content: The FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: tibialis anterior muscle

extract_protocol:
Explanted muscle samples were stabilized in RNAlater (Invitrogen) at -80°C prior to RNA extraction. Tissues were mechanically homogenized in Trizol, followed routine Trizol-based RNA isolation.  In brief, the lysed tissues were treated with chloroform, allowing for a biphasic separation of the RNA content, followed by RNA precipitation in isopropyl alcohol. The purified RNA was then resuspended in RNAase-free water.
Bulk RNA sequencing was performed by Novogene Corporation, in which messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.  cDNA was synthesized followed by non-directional library preparation for sequencing on a Novaseq 6000 instrument.

value: tibialis anterior muscle

tag: strain

value: D21 after injury


title: D14_rep4

value: D14 after injury


title: D14_rep6


title: D21_rep2


title: D14_rep1


title: BALBc mice, 8 weeks, female, 1 day after saline, normal diet, biol rep 1

description: Library name: G1


title: D21_rep5


title: D7_rep5

value: D7 after injury


title: D14_rep5


title: D7_rep4


title: D14_rep3


title: D21_rep4


title: D7_rep1


title: D3_rep5

value: D3 after injury


title: D3_rep3


title: D7_rep2


title: D14_rep2


title: D3_rep2


title: C_rep5

value: Control


title: D3_rep1


title: D21_rep1


title: C_rep1


title: C_rep3


title: C_rep4


title: C_rep2


title: Low allele burden Jak2VF, 4D9

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Fastq files were processed by cellranger multi pipeline from Cell Ranger 6.1.2. Pre-built mouse reference mm10-2020-A from 10x Genomics was used for quantification. TotalSeq-B hashtags B301, B302, B303, B304 were used to for demultiplexing. Samples from hashtag B302 and B303 were included in this study.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
Following termination of WD, aortas were isolated, digested with 2.5 mg/ml liberase (Millipore Sigma, LIBTM-RO), 120 U/ml hyaluronidase (Millipore Sigma, H3506), and 160 U/ml DNase I (Millipore Sigma, DN25) for 45 min at 37°C.
Library was constructed using 10x Genomics Single Cell 3' v3.1 protocol with multiplexing. Hashtag antibodies from BioLegend TotalSeq-B were added to label each mouse.

treatment_protocol: In the TREM2 activating antibody (4D9) treated cohort, isotype control IgG (DC1887) and 4D9 (DC1847) mouse antibodies were injected intraperitoneal to the mice at 10 mg/kg per week for 14 weeks.

value: Aorta

value: Jak2VF, Ldlr(-/-)

value: 4D9 (TREM2 antibody)

tag: library type

value: mRNA


title: Low allele burden Jak2VF, IgG

value: IgG


title: D7_rep6


title: CT26, ARID1AknockoutPD1_2

city: Harbin

first: Yanqiao

address: No.150 Haping Road, Nangang District, Harbin, Heilongjiang, 150081, China

institute: Third Affiliated Hospital of Harbin Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include gene count for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: mouse colorectal cancer cells

value: PD1 therapy


title: CT26, ARID1AknockoutPD1_1


title: CT26, ARID1AknockoutPD1_5


title: D7_rep3


title: D3_rep4


title: CT26, ARID1AknockoutPD1_4


title: CT26, ARID1AknockoutIgG5

value: IgG therapy


title: CT26, ARID1AknockoutIgG3


title: CT26, ARID1AknockoutPD1_3


title: CT26, ARID1Aknockout1

value: ARID1A knockout


title: CT26, ARID1Awildtype2

value: not treated


title: CT26, ARID1Aknockout3


title: CT26, ARID1AknockoutIgG1


title: CT26, ARID1Aknockout2


title: CT26, WT_input

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks.
Called peaks were then annotated using R package ChIPseeker.
HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif.
Differential peaks analysis was performed using R package  Diffbind for experimental design with replication.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

extract_protocol:
Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. Extract chromatin from cross-linked cells by adding Lysis Buffer
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min.  And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads.

tag: antibody

value: input


title: CT26, ARID1Awildtype1


title: CT26, ARID1AknockoutIgG4


title: CT26, ARID1AknockoutIgG2


title: CT26, ARID1Awildtype3


title: CT26, KO_H3K4me3

value: H3K4me3（CST, #9751）


title: CT26, KO_H3K27ac

value: H3K27ac（CST, #8173）


title: CT26, WT_H3K4me1

value: H3K4me1（CST, #5326）


title: CT26, KO_input


title: CT26, ARID1Aknockout

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (v 0.20.0). In this step, clean data (cleanreads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads (reads with a mass value of less than 15 bases more than 40% of the number of bases of the reads and pruned reads shorter than 18bp) from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyseswere based on the clean data.
Index of the reference genome was built using BWA(v 0.7.12) and clean reads were aligned to the reference genome using BWA mem.
All peak calling was performed with MACS2 (v 2.2.7.1) using ‘macs2 -q 0.05 --call-summits -- nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all data sets.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequenceswere performed using findMotifsGenome.pl program in HOMER (v 4.11) checksoftware with ‘-len 8,10,12,14 -gc -size given -p 2 -S 25 -homer2 -dumpFasta’.
ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

extract_protocol:
Take out the cryovial and shake it in 37°C water to quickly thaw it within 1-2 min.Cells were centrifuged at 4 °C 500×g for 5 min. Cell activity was detected with LUNA-FL and counted. 50000 live cells were centrifuged with 500 g for 5 minutes, supernatant was discarded, The precipitation was resuspended with 50 ul lysis buffer,and placed on ice for 5 minutes, then 1ml wash buffer was added, mixed, 500 g centrifuged for 5 minutes, supernatant was discarded, and nucleus was collected.
Briefly, nucleus was extracted from samples, and the nucleus pellet was resuspended in the Tn5 transposase reaction mix.The transposition reaction was incubated at 37 °C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.


title: CT26, ARID1Awildtype


title: CT26, WT_H3K4me3


title: CT26, KO_H3K4me1


title: EXP_ 9.11_D_Tumor_only_timepoint 0_3_R2

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

data_processing:
The analysis workflow took place in R v.4.0.3. Reads were loaded into R environment as DNAStringSet object and barocodes were located with the aid of vmatchPattern()  from Biostrings v.2.58.0. Differentiall abundance was carried out using DESeq2  v.1.30.0.
Assembly: n/a
Supplementary files format and content: Excel worksheet file containing barcode counts tables per cell line and experiment.
Library strategy: DNA amplicon sequencing

source_name: D

growth_protocol: Cells were cultured in RPMI medium (Gibco) supplemented with 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10% fetal bovine serum (FBS) (Capricorn Scientific),  50 µM β-mercaptoethanol (Sigma-Aldrich) and 2500 U/ml Interleukin-2 (Miltenyi Biotec)

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen)
DNA barcodes were amplified with a three nested PCR step protocol

value: D


title: EXP_ 9.11_D_Tumor_only_timepoint 0_3_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 0_2_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_3_R1

value: Tumor+NK cells


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_2_R1


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_3_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_1_R1


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_2_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 2_1_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_3_R1

value: Tumor+IFNg KO NK cells


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_1_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_2_R1


title: CT26, WT_H3K27ac


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_1_R1


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_3_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 2_2_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 2_3_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 0_1_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 2_2_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 2_2_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 2_1_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_3_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_1_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_1_R1


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_2_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 0_2_R1


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_3_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_3_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 2_3_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_1_R2


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_1_R1


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_2_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 1_1_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 1_3_R2

source_name: A

value: A


title: EXP_ 9.11_D_Tumor+IFNg KO NK cells_timepoint 1_2_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 1_3_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 2_1_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 0_1_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 1_3_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 1_1_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 1_2_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_3_R1


title: EXP_ 9.11_D_Tumor_only_timepoint 1_2_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 1_2_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_3_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 1_1_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 1_1_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_3_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_1_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_2_R2


title: EXP_ 9.11_D_Tumor+NK cells_timepoint 1_2_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_1_R2


title: EXP_ 9.11_D_Tumor_only_timepoint 1_3_R1


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_3_R1


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_3_R2


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_2_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 1_2_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 2_3_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 2_2_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 2_1_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 0_3_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 0_3_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 2_1_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 2_2_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_2_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 2_2_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 0_2_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_3_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 0_2_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_1_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 0_1_R1


title: EXP_ 9.11_A_Tumor_only_timepoint 0_1_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_3_R2


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_3_R1

value: Tumor+Perforin KO NK cells


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_1_R1


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_3_R2


title: EXP_ 9.11_A_Tumor_only_timepoint 2_3_R1


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_1_R1


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_3_R2


title: EXP_ 9.11_A_Tumor+IFNg KO NK cells_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_3_R1


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_1_R2


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_1_R1


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_3_R2


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_1_R1


title: EXP_ 9.11_A_Tumor+NK cells_timepoint 1_2_R1


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_1_R1


title: 3.15_EXP_ 9.8_A_Tumor+Perforin KO NK cells_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_D_Tumor+Perforin KO NK cells_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_D_Tumor+NK cells_timepoint 2_3_R1


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_1_R1


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_3_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_3_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_3_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 2_1_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_3_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_3_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_2_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_1_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 2_1_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_3_R1


title: 3.15_EXP_ 9.8_A_Tumor+NK cells_timepoint 2_3_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_3_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_2_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_2_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_1_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_2_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_3_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 1_1_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_1_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_3_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_2_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_3_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_1_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_2_R2


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_1_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 1_1_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_2_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_3_R1


title: 3.15_EXP_ 9.8_D_Tumor_only_timepoint 0_3_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_3_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_2_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_2_R2


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_1_R2


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 2_1_R2


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 2_1_R1


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 2_1_R2

source_name: C

value: C


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 2_1_R1


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 2_1_R2

source_name: B

value: B


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 2_1_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 2_1_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_3_R1

value: Tumor+NK


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_2_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_1_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 2_1_R1


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_3_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_2_R1


title: 3.15_EXP_ 9.8_A_Tumor_only_timepoint 0_1_R1


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 2_1_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_2_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_3_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_2_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_1_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_2_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_3_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_3_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_2_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_1_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 2_1_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_1_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_1_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_2_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_3_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_3_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_3_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_2_R2


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_2_R2


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_1_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_1_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_3_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_3_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 2_3_R2


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_3_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_2_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 2_2_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_1_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_3_R1


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_1_R1


title: 3.14_EXP_9.7_C_Tumor+NK_timepoint 1_2_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_1_R2


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_1_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_2_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_3_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_2_R1


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_1_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_1_R1


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_3_R2


title: 3.14_EXP_9.7_A_Tumor+NK_timepoint 1_2_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_3_R2


title: 3.14_EXP_9.7_D_Tumor+NK_timepoint 1_1_R2


title: 3.14_EXP_9.7_B_Tumor+NK_timepoint 1_2_R2


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_3_R2


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_2_R2


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_3_R1


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_2_R2


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_1_R1


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_3_R1


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_2_R1


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_1_R2


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_2_R2


title: 3.14_EXP_9.7_D_Tumor_only_timepoint 1_1_R1


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_1_R2


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_2_R1


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_3_R2


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_3_R2


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_1_R2


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_3_R1


title: 3.14_EXP_9.7_B_Tumor_only_timepoint 1_1_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_3_R2


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_1_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_2_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_3_R1


title: 3.14_EXP_9.6_C_Tumor_only_timepoint 2_1_R2


title: 3.14_EXP_9.6_C_Tumor_only_timepoint 2_1_R1


title: 3.14_EXP_9.7_C_Tumor_only_timepoint 1_2_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_2_R1


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_1_R2


title: 3.14_EXP_9.7_A_Tumor_only_timepoint 1_2_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_1_R1


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_3_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_3_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_3_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_2_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_2_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 2_1_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_3_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_3_R1


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_2_R1


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_1_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_2_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 2_1_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_2_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_1_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_1_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_3_R2


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_1_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_3_R1


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_3_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 1_2_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_2_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_3_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_2_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 1_1_R2


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_2_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_1_R1


title: 3.13_EXP_9.6_B_Tumor+NK_timepoint 1_1_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_3_R1


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_1_R2


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_1_R1


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_2_R1


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor+NK_timepoint 1_2_R2


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_1_R1


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_3_R1


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_2_R2


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_3_R1


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_2_R2


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_2_R1


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 1_1_R2


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_1_R2


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_2_R2


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_1_R1


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_1_R2


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_2_R1


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_1_R1


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_2_R2


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_3_R1


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_2_R1


title: 3.13_EXP_9.6_C_Tumor_only_timepoint 1_2_R1


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_3_R1


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 1_3_R2


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_1_R1


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 1_1_R2


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 2_1_R2


title: 3.13_EXP_9.6_A_Tumor_only_timepoint 2_1_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_3_R1


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 2_1_R2


title: 3.13_EXP_9.6_D_Tumor_only_timepoint 2_1_R1


title: GEX, PBMC, healthy, donor2

city: Bunkyo

first: Yoko

last: Tabe

state: Tokyo

address: 2 Chome-1-1 Hongo

department: Department of Clinical Laboratory Medicine

country: Japan

institute: Juntendo University

data_processing:
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Tab-delimited compressed text file includes barcode data for each Sample
Supplementary files format and content: Tab-delimited compressed text file includes feature data for each Sample
Supplementary files format and content: Tab-delimited compressed text file includes raw counts for each Sample
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
PBMCs were isolated from blood samples from six COVID-19 inpatients admitted to Juntendo University Hospital in Tokyo, Japan, using BD Vacutainer CPT mononuclear cell preparation tubes containing sodium heparin. The isolated cells were washed with Dalbeccos' phosphate buffered saline (PBS), resuspended in 1 mL of CELLBANKER 1 Plus, and stored at -80°C until further use.
scRNA libraries were constructed with library-associated unique indexes, using the library construction kit (1000196), the Single Index Kit T Set A (1000213), and SI primer (2000095)

value: PBMC

tag: Sex

value: Male


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_2_R2


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 2_1_R1


title: GEX, PBMC, healthy, donor3


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_3_R2


title: GEX, PBMC, critical, Patient6, Day29


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_1_R2


title: GEX, PBMC, healthy, donor1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_1_R1


title: 3.13_EXP_9.6_D_Tumor+NK_timepoint 2_2_R1


title: GEX, PBMC, moderate, Patient6, Day14


title: GEX, PBMC, moderate, Patient5, Day12


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_3_R1


title: GEX, PBMC, critical, Patient3, Day21


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_1_R2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_3_R2


title: 3.13_EXP_9.6_B_Tumor_only_timepoint 2_1_R2


title: GEX, PBMC, critical, Patient2, Day11


title: GEX, PBMC, moderate, Patient4, Day5


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_2_R2


title: BCR, PBMC, healthy, donor3

data_processing:
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Comma-delimited text files include clonotype information for each Sample
Supplementary files format and content: Comma-delimited text files include VDJ sequences and annotation for each barcode
Supplementary files format and content: Tab-delimited text files include CDR sequences with start and end sites for each VDJ gene
Library strategy: BCR


title: GEX, PBMC, moderate, Patient3, Day4


title: GEX, PBMC, critical, Patient5, Day30


title: GEX, PBMC, critical, Patient4, Day13


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_3

data_processing:
Raw data was processed with nf-core/atacseq pipeline
Mapping reads to the reference genome with STAR alligner (v2.7.10a)
Duplicates identification with Picard (v2.27.4)
Peak calling with MACS2 (v2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: broadPeak files, containting coordinates of called peaks and counts assigned to them
Supplementary files format and content: Consensus peaks with coordinates and counts assigned to them

extract_protocol:
Cells were processed with the Illumina Tagmentation kit
Library preparation was conducted as in Buenrostro et al, 2015. PCR products were purified with Agencourt AMPure XP beads.

tag: time

value: Day 16

tag: timepoint


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_1

tag: treatment


title: GEX, PBMC, moderate, Patient2, Day2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_1_R1


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.7, rep_2


title: 3.13_EXP_9.6_C_Tumor+NK_timepoint 2_2_R1


title: BCR, PBMC, moderate, Patient5, Day12


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_2


title: BCR, PBMC, moderate, Patient6, Day14


title: BCR, PBMC, critical, Patient6, Day29


title: BCR, PBMC, healthy, donor2


title: BCR, PBMC, moderate, Patient4, Day5


title: BCR, PBMC, critical, Patient5, Day30


title: BCR, PBMC, critical, Patient3, Day21


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_3


title: BCR, PBMC, moderate, Patient3, Day4


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.7, rep_3


title: BCR, PBMC, healthy, donor1


title: BCR, PBMC, critical, Patient4, Day13


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_2


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_3


title: BCR, PBMC, critical, Patient2, Day11


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.7, rep_1


title: BCR, PBMC, moderate, Patient2, Day2


title: BCR, PBMC, critical, Patient1, Day13

value: Female


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_2

value: Day 6


title: BCR, PBMC, moderate, Patient1, Day3


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_3


title: PBMC, healthy, donor2

data_processing:
Cell Ranger v 6.1.2 (multi)
Quality control, mapping to human genome reference, and read count exctraction were performed using Cell Ranger multi
Assembly: hg38
Supplementary files format and content: Comma-delimited text files include clonotype information for each Sample
Supplementary files format and content: Comma-delimited text files include VDJ sequences and annotation for each barcode
Library strategy: TCR-Seq


title: PBMC, healthy, donor3


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_2


title: PBMC, critical, Patient6, Day29


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.7, rep_1


title: PBMC, moderate, Patient6, Day14


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_3


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_2


title: PBMC, critical, Patient5, Day30


title: PBMC, moderate, Patient5, Day12


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.7, rep_3


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_2


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.7, rep_1


title: PBMC, critical, Patient4, Day13


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.7, rep_3


title: PBMC, moderate, Patient4, Day5


title: PBMC, critical, Patient3, Day21


title: PBMC, moderate, Patient3, Day4


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_1


title: PBMC, critical, Patient2, Day11


title: PBMC, healthy, donor1


title: PBMC, moderate, Patient2, Day2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_1


title: Mouse cortical astrocyte 52hrs post sync replicate 2 [MCA.R2-11]

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

data_processing:
The raw reads were aligned to the mm10 mouse genome using STAR aligner (v.2.5.2b). For the gene annotations, Ensemble gene (release 82) was used.
Assembly: mm10
Supplementary files format and content: a tab-delimited text file including raw read count of each gene as a matrix format for all samples

source_name: Mouse cortical astrocyte

growth_protocol: The primary astrocytes were first cultured from a 1-day-old C57BL6/N mouse. 1-day-old pups were anesthetized by hypothermia and their cerebral cortices were dissected out and triturated in Modified Eagle’s medium (MEM) containing 10% fetal bovine serum (FBS), penicillin/streptomycin, 10 µM HEPES  and GlutaMAX  yielding a single-cell suspension. Cells were plated into 75 cm2 T-flasks (1pup/flask) and incubated at 37°C in a humidified 5% CO2 incubator for 2 weeks. Primary astrocytes were then incubated in serum-free MEM for 7 days, after which astrocytes were detached from the T-flask with 0.25% trypsin and plated on culture dishes (1.0X106cells/60 mm dish) for further experiments. Astrocytes were grown in dishes (1.0 X 106cells/60 mm dish) until reaching complete confluence and then incubated in serum-free MEM for 72 hours.

extract_protocol:
Total RNA was extracted and purified from harvested astrocytes utilizing the RNeasy Plus Micro Kit (Qiagen, Germany, 74034), following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Preparation V2 kit following manufacturer’s protocols.

treatment_protocol: After a 72-hour incubation in serum-free MEM (SF MEM), the cells were synchronized by exposure to 50% horse serum in SF MEM for 2 hours. Subsequently, they were washed twice with SF MEM and replenished with fresh SF MEM

value: Mouse cortical astrocyte

value: After synchronizing the circadian clock of cultured astrocytes by serum shock

tag: time point


title: Mouse cortical astrocyte 56hrs post sync replicate 2 [MCA.R2-12]


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_3

tag: cell line


title: Mouse cortical astrocyte 44hrs post sync replicate 2 [MCA.R2-9]

tag: cell type


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_2


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_1


title: Mouse cortical astrocyte 32hrs post sync replicate 2 [MCA.R2-6]


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_2


title: Mouse cortical astrocyte 28hrs post sync replicate 2 [MCA.R2-5]


title: Mouse cortical astrocyte 36hrs post sync replicate 2 [MCA.R2-7]


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6.1, rep_3

value: Day 10


title: Mouse cortical astrocyte 40hrs post sync replicate 2 [MCA.R2-8]


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.7, rep_2


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_1


title: Mouse cortical astrocyte 24hrs post sync replicate 2 [MCA.R2-4]


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.7, rep_3


title: Mouse cortical astrocyte 16hrs post sync replicate 2 [MCA.R2-2]


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6.1, rep_1


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6.1, rep_2


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6.1, rep_3

value: Day 4


title: Mouse cortical astrocyte 12hrs post sync replicate 2 [MCA.R2-1]


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6.1, rep_2

value: D


title: Mouse cortical astrocyte 56hrs post sync replicate 1 [MCA.R1-12]


title: Mouse cortical astrocyte 52hrs post sync replicate 1 [MCA.R1-11]


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6.1, rep_2


title: Mouse cortical astrocyte 48hrs post sync replicate 2 [MCA.R2-10]


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6.1, rep_1


title: Mouse cortical astrocyte 48hrs post sync replicate 1 [MCA.R1-10]


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6.1, rep_1


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6, rep_3


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.7, rep_3


title: Mouse cortical astrocyte 20hrs post sync replicate 2 [MCA.R2-3]


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6, rep_2


title: Mouse cortical astrocyte 32hrs post sync replicate 1 [MCA.R1-6]


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_3


title: Mouse cortical astrocyte 24hrs post sync replicate 1 [MCA.R1-4]


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_2


title: Mouse cortical astrocyte 16hrs post sync replicate 1 [MCA.R1-2]


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.6, rep_1


title: Mouse cortical astrocyte 12hrs post sync replicate 1 [MCA.R1-1]


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_3


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_2


title: Mouse cortical astrocyte 44hrs post sync replicate 1 [MCA.R1-9]


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_3


title: GBM6

type: genomic

city: Tampa

first: Anders

last: Berglund

state: Florida

address: 12902 Magnolia Drive

department: Department of Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

description:
GBM
205689130094_R06C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Minfi was used for normalization using Noob and FunNorm functions
Beta value and detection p-value

label: Cy3 and Cy18

source_name: Brain

label_protocol: Standard Illumina protocol

extract_protocol: Total genomic DNA was extracted using the Quick-DNA Miniprep kit (Zymo, Irvine, CA, USA) and followed by RNase A digestion.

tag: tissue

value: Brain

tag: sample type

value: Tumor

value: Surgery


title: GBM5

description:
GBM
205689130094_R05C01

label: Cy3 and Cy17


title: GBM8

description:
GBM
205689130094_R08C01

label: Cy3 and Cy20


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.6, rep_1

value: A


title: GBM7

description:
GBM
205689130094_R07C01

label: Cy3 and Cy19


title: GBM3

description:
GBM
205689130094_R03C01

label: Cy3 and Cy15


title: GBM4

description:
GBM
205689130094_R04C01

label: Cy3 and Cy16


title: Mouse cortical astrocyte 36hrs post sync replicate 1 [MCA.R1-7]


title: Mouse cortical astrocyte 40hrs post sync replicate 1 [MCA.R1-8]


title: Mouse cortical astrocyte 28hrs post sync replicate 1 [MCA.R1-5]


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_2


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.6, rep_1


title: GBM2

description:
GBM
205689130094_R02C01

label: Cy3 and Cy14


title: Mouse cortical astrocyte 20hrs post sync replicate 1 [MCA.R1-3]


title: GBM1

description:
GBM
205689130094_R01C01

label: Cy3 and Cy13


title: GBM16

description:
GBM
205689130022_R08C01

label: Cy3 and Cy12


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_2

value: C


title: GBM15

description:
GBM
205689130022_R07C01

label: Cy3 and Cy11


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.6, rep_2

value: B


title: GBM14

description:
GBM
205689130022_R06C01

label: Cy3 and Cy10


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_1


title: GBM12

description:
GBM
205689130022_R04C01

label: Cy3 and Cy8


title: GBM9

description:
GBM
205689130022_R01C01

label: Cy3 and Cy5


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_3


title: GBM11

description:
GBM
205689130022_R03C01

label: Cy3 and Cy7


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_2


title: GBM10

description:
GBM
205689130022_R02C01

label: Cy3 and Cy6


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_3


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.6, rep_3


title: PNUTSdTAG_5minTTseq_dTAG_rep4

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: calibrated TT-seq

data_processing:
*library strategy: calibrated TT-seq
Reads that aligned to the mm10 and dm6 rDNA genomic sequences (GenBank: BK000964.3 and M21017.1) were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the concatenated mm10 and dm6 genomes using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
To internally calibrate TT-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological triplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated TT-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of TT-seq. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: mm10, dm6
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.

organism:
Drosophila melanogaster
Mus musculus

source_name: E14 PNUTS-dTAG

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
cTT-seq was performed largely as described previously (Gregersen et al., 2020). In brief, 1x10^8 ESCs and 30x10^6 Drosophila SG4 cells were labelled with 500 µM 4-thiouridine (4sU, Glentham Life Sciences) for 5 min and harvested into TRIzol reagent. 4sU-labelled mouse and Drosophila cells were mixed and RNA was isolated by phenol:chloroform exctraction using MaXtract High Density tubes (Quagene). The purified RNA was depleted from any gDNA carry-over using the Turbo DNase-free kit as per the manufacturer’s protocol. 300 µg of RNA was taken into 300 µl nuclease free water and fragmented on ice with 60 µl 1 M NaOH for 20 min. Fragmentation was stopped with 240 μl 1 M Tris, pH 6.8 and the RNA was cleaned up with Micro Bio-Spin P-30 gel columns (Biorad). RNA was biotin-labelled with 150 μl 0.1 mg/ml MTSEA biotin-XX linker (Biotium) with 9 μl biotin buffer (833 mM Tris HCl, pH 7.4, 83.3 mM EDTA) for 30 min at RT. Biotin-labelled RNA was purified with a 1:1 ratio of phenol/chloroform/isoamyl alcohol (Thermo Fisher Scientific). Streptavidin pull-down was performed with the μMACS Streptavidin Kit (Miltenyi Biotec), washing the columns three times with 55 °C pull-down wash buffer (100 mM Tris HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween 20) and 3x RT pull down wash buffer. Biotin-labelled RNA was eluted with 100 μl elution buffer (100 mM DTT in nuclease-free water) and cleaned up with the RNeasy MinElute Cleanup kit (QIAGEN), adjusting the amount of ethanol to capture RNA < 200 nucleotides in length.
RNA was quantified using the Qubit RNA HS assay kit and RNA libraries were prepared from 20 ng RNA with the Ultra II Directional RNA library prep kit, as per the manufacturer’s guidelines for rRNA depleted and FFPE RNA (NEB).

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG13 to induce depletion of PNUTS.

value: E14 PNUTS-dTAG

value: embryonic stem cell line

tag: tag

tag: spike-in cell_line

tag: treatment time

tag: additional treatment_time

tag: labelling

value: 500 µM 4-thiouridine

tag: labelling time

value: 5 min


title: PNUTSdTAG_5minTTseq_dTAG_rep3

description: calibrated TT-seq


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_3


title: PNUTSdTAG_5minTTseq_dTAG_rep1

description: calibrated TT-seq


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.6, rep_2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_3


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_2


title: PNUTSdTAG_5minTTseq_dTAG_rep2

description: calibrated TT-seq


title: PNUTSdTAG_5minTTseq_UNT_rep4

description: calibrated TT-seq

value: Untreated


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.6, rep_1


title: PNUTSdTAG_5minTTseq_UNT_rep3

description: calibrated TT-seq


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_3


title: PNUTSdTAG_5minTTseq_UNT_rep1

description: calibrated TT-seq


title: GBM13

description:
GBM
205689130022_R05C01

label: Cy3 and Cy9


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_2


title: PNUTSdTAG_5minTTseq_UNT_rep2

description: calibrated TT-seq


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.6, rep_1


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_3


title: E14-T3G-TND-DOX-dTAG-rep3

description: calibrated TT-seq

data_processing:
Reads that aligned to the mm10 and dm6 rDNA genomic sequences (GenBank: BK000964.3 and M21017.1) were first identified using Bowtie2 with ‘-very-fast’, ‘-no-mixed’ and ‘-no-discordant’ options) and discarded. Unmapped reads were then aligned to the concatenated mm10 and dm6 genomes using STAR. To improve mapping of intronic sequences, reads that failed to map using STAR were aligned using Bowtie2 with ‘-sensitive-local’, ‘-no-mixed’ and ‘-no-discordant’ options. Uniquely aligned reads from the last two steps were combined for further analysis and PCR duplicates were removed using Sambamba.
To internally calibrate TT-seq, we spiked-in a fixed number of Drosophila SG4 to each experimental sample. For data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 reads in each sample.
Read counts from biological triplicates were determined using custom scripts utilising SAMTools for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered to remove very short genes with poor sequence mappability and highly similar transcripts which resulted in the final set of 20,633 genes. Raw mm10 reads prior to spike-in normalisation were used for read counts quantitation for differential expression analysis.
The final set of 20,633 genes were used for differential analysis using a custom R script adapting DESeq2 (Love et al., 2014) for spike-in calibrated TT-seq data. To incorporate spike-in calibration into this analysis, read counts for the spike-in genome at a control set of intervals were supplied to calculate DESeq2 size factors which were then used for DESeq2 normalisation of raw mm10 read counts. A set of unique dm6 refGene genes was used for spike-in normalisation of TT-seq. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5.
Assembly: mm10, dm6
Supplementary files format and content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary files format and content: DESeq2 results tables for differential gene expression analysis containing normalised read counts, raw and shrunk log2-fold changes (LFC), and statistical significance levels for a non-redundant set of mm10 refGene genes.
Library strategy: cTT-seq

source_name: E14 TETON-3G PNUTS-dTAG PNUTS-TND-M rescue

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
cTT-seq was performed largely as described previously (Gregersen et al., 2020). In brief, 9 million ESCs and 3 million Drosophila SG4 cells were labelled with 500 µM 4-thiouridine (4sU, Glentham Life Sciences) for 15 min and harvested into TRIzol reagent. 4sU-labelled mouse and Drosophila cells were mixed and RNA was extracted and depleted from any gDNA carry-over using the Direct-zol RNA Miniprep Plus kit (R2072 Zymo Research) as per the manufacturer’s protocol. An equal quantity of RNA (80-100 µg) was taken into 100 µl nuclease free water and fragmented on ice with 20 µl 1 M NaOH for 20 min. Fragmentation was stopped with 80 μl 1 M Tris, pH 6.8 and the RNA was cleaned up with Micro Bio-Spin P-30 gel columns (Biorad). RNA was biotin-labelled with 50 μl 0.1 mg/ml MTSEA biotin-XX linker (Biotium) with 3 μl biotin buffer (833 mM Tris HCl, pH 7.4, 83.3 mM EDTA) for 30 min at RT. Biotin-labelled RNA was purified with a 1:1 ratio of phenol/chloroform/isoamyl alcohol (Thermo Fisher Scientific). Streptavidin pull-down was performed with the μMACS Streptavidin Kit (Miltenyi Biotec), washing the columns three times with 55 °C pull-down wash buffer (100 mM Tris HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween 20) and 3x RT pull down wash buffer. Biotin-labelled RNA was eluted with 100 μl elution buffer (100 mM DTT in nuclease-free water) and cleaned up with the RNeasy MinElute Cleanup kit (QIAGEN), adjusting the amount of ethanol to capture RNA < 200 nucleotides in length.
RNA was quantified using the Qubit RNA HS assay kit and RNA libraries were prepared from 20 ng RNA with the Ultra II Directional RNA library prep kit, as per the manufacturer’s guidelines for rRNA depleted and FFPE RNA (NEB).

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG13 to induce depletion of PNUTS. For rescue experiments, cells were treated with 1ug/ml DOX to induce the expression of PNUTS WT, PNUTS W401A or PNUTS TND-M and with 100 nM dTAG13 to deplete endogenous PNUTS protein.

value: dTAG

tag: rescue

value: PNUTS-T7 TND-M

tag: additional treatment

value: DOX

value: 15 min


title: E14-T3G-TND-DOX-dTAG-rep4

description: calibrated TT-seq

value: E14 TETON-3G PNUTS-dTAG PNUTS-TND-M rescue


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_2

value: Day 4


title: Tumor_only, Cell_line_A, timepoint_1, EXP_9.6, rep_1


title: E14-T3G-TND-dTAG-rep4

description: calibrated TT-seq


title: E14-T3G-TND-DOX-dTAG-rep1

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5.1, rep_2

value: Day 10


title: E14-T3G-TND-dTAG-rep1

description: calibrated TT-seq


title: E14-T3G-TND-dTAG-rep3

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5.1, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5.1, rep_3


title: E14-T3G-TND-UNT-rep3

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5.1, rep_3


title: E14-T3G-TND-UNT-rep4

description: calibrated TT-seq


title: E14-T3G-W401A-DOX-dTAG-rep2

description: calibrated TT-seq

source_name: E14 TETON-3G PNUTS-dTAG PNUTS-W401A rescue

value: PNUTS-T7 W401A


title: E14-T3G-TND-UNT-rep1

description: calibrated TT-seq


title: E14-T3G-W401A-DOX-dTAG-rep4

description: calibrated TT-seq

value: E14 TETON-3G PNUTS-dTAG PNUTS-W401A rescue


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5.1, rep_3


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5.1, rep_2


title: E14-T3G-W401A-DOX-dTAG-rep3

description: calibrated TT-seq


title: E14-T3G-W401A-DOX-dTAG-rep1

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5.1, rep_1


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_3

value: D


title: E14-T3G-W401A-dTAG-rep4

description: calibrated TT-seq


title: E14-T3G-W401A-dTAG-rep3

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5.1, rep_1

value: C


title: E14-T3G-W401A-UNT-rep4

description: calibrated TT-seq


title: E14-T3G-W401A-UNT-rep3

description: calibrated TT-seq


title: E14-T3G-W401A-dTAG-rep1

description: calibrated TT-seq


title: E14-T3G-W401A-dTAG-rep2

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5.1, rep_2


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_1


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_1

value: B


title: E14-T3G-W401A-UNT-rep1

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_B, timepoint_2, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.6, rep_1


title: E14-T3G-WT-DOX-dTAG-rep4

description: calibrated TT-seq

source_name: E14 TETON-3G PNUTS-dTAG PNUTS-WT rescue

value: E14 TETON-3G PNUTS-dTAG PNUTS-WT rescue

value: PNUTS-T7 WT


title: Tumor_plus_NK, Cell_line_C, timepoint_2, EXP_9.5, rep_2


title: E14-T3G-WT-DOX-dTAG-rep3

description: calibrated TT-seq

value: embryonic stem cell line

value: 500 µM 4-thiouridine


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_2

value: A


title: Tumor_plus_NK, Cell_line_D, timepoint_2, EXP_9.5, rep_1


title: E14-T3G-WT-DOX-dTAG-rep1

description: calibrated TT-seq

value: dTAG


title: E14-T3G-WT-DOX-dTAG-rep2

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_A, timepoint_2, EXP_9.5, rep_1


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_2


title: E14-T3G-WT-dTAG-rep4

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_D, timepoint_1, EXP_9.5, rep_1


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_3


title: E14-T3G-WT-dTAG-rep3

description: calibrated TT-seq


title: E14-T3G-WT-dTAG-rep2

description: calibrated TT-seq


title: E14-T3G-W401A-UNT-rep2

description: calibrated TT-seq

value: Untreated


title: E14-T3G-WT-UNT-rep4

description: calibrated TT-seq


title: E14-T3G-WT-UNT-rep3

description: calibrated TT-seq


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_1


title: PNUTSdTAG_TTseq_dTAG_rep3

description: calibrated TT-seq

value: E14 PNUTS-dTAG


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_2


title: Tumor_plus_NK, Cell_line_C, timepoint_1, EXP_9.5, rep_1


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_1


title: Tumor_only, Cell_line_D, timepoint_1, EXP_9.5, rep_2


title: Tumor_only, Cell_line_C, timepoint_1, EXP_9.5, rep_2


title: PNUTSdTAG_TTseq_UNT_rep2

description: calibrated TT-seq

value: 15 min


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_3


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_3


title: Tumor_plus_NK, Cell_line_A, timepoint_1, EXP_9.5, rep_1


title: Control rep 1

city: Davis

first: Siobhan

last: Brady

state: CA

address: One Shields Avenue, GBSF Room 4409

department: Genome center

institute: UC Davis

data_processing:
Assembly: ITAG4.1 transcriptome (cDNA)
Column based data frame containing estimated raw pseudo-counts by Kallisto (v0.46.2)

organism: Solanum lycopersicum

source_name: 3 cm roots tips from hairy root plates

growth_protocol: Hairy roots grown in MS+vitamins media with 3% sucrose

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (ZYMO).
RNAseq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).
Barcoded libraries were then pooled together, and single 100-bp reads were sequenced on the HiSeq4000 SR100 instrument (Illumina) at the UC Davis DNA Technologies Core.

treatment_protocol: 3 cm from root tips was collected from all genotypes. 6-7 root tips from each genotype were pooled.

value: 3 cm roots tips from hairy root plates

tag: cultivar

value: cv M82

tag: genotype

value: Wild-type


title: Tumor_only, Cell_line_B, timepoint_1, EXP_9.5, rep_2

tag: time

value: Day 4

tag: timepoint


title: E14-T3G-WT-UNT-rep2

description: calibrated TT-seq

tag: treatment


title: Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_3

tag: cell line