title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_1_060121]

description: BSSE_QGF_161795_HLWHKBGXH_1_BR16_WBC_2200_1_060121_GATTCTGAAT_AGCGGTGGAC_S149

tag: number of wbcs attached

tag: timepoint


title: WA1 1μg-3 (ST) [scVDJ-seq]

status: Public on Apr 25 2022

type: SRA

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

country: USA

institute: Yale University

description:
ST-WA1-1-3
10x Genomics
LNP-mRNA vaccine

library_source: transcriptomic

data_processing:
Single-cell sequencing data was processed using the Cellranger v5.0.1 (10x Genomics) pipeline and aligned to the mm10 VDJ reference.
Assembly: mm10 mouse reference transcriptome
Supplementary files format and content: Cell Ranger AIRR-formated output.
Library strategy: scVDJ-seq

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Spleens were collected from mice that were treated with either LNP-mRNA or PBS, and spleens were homogenized gently and filtered with a 100 μm cell strainer (BD Falcon, Heidelberg, Germany). The cell suspension was centrifuged for 5 min with 400 g at 4 °C. Erythrocytes were lysed briefly using ACK lysis buffer (Lonza) with 1mL per spleen for 1~2 mins before adding 10 mL PBS containing 2% FBS to restore iso-osmolarity. The single-cell suspensions were filtered through a 40 μm cell strainer (BD Falcon, Heidelberg, Germany).
Cell suspension were normalized to 1000 cells/ml and loaded to achieve targeted cell recovery to 10000 cells. The samples were subjected to 14 cycles of cDNA amplification. Following this, gene expression (GEX), TCR-enriched and BCR-enriched libraries were prepared according to the manufacturer’s protocol (10x Genomics). All libraries were sequenced using a NovaSeq 6000 (Illumina) with 2*150 read length.

tag: tissue

value: Spleen

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: WA1 1ug


title: genomic DNA from whole blood - 202128330165_R05C01

type: genomic

city: London

first: Stephan

last: Beck

address: 72 Huntley Street

department: Department of Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

description: Whole Blood sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC array using standard Illumina protocol

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

data_processing:
Raw IDAT files were processed using R package minfi with SWAN normalisation. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating lack of methylation and “1” full methylation. We excluded measurements from non-CG probes (i.e. SNP targetting probes).
The processed_data.tsv contains SWAN normalized Average Beta
The signal_intensities.tsv contains Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: For each sample, 500ng high-quality DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research), using alternative incubation conditions recommended for Illumina methylation arrays.

extract_protocol: Genomic DNA was extracted from whole blood samples using the QIAamp DNA Blood Mini Kit (Qiagen)

tag: Sex

value: Male

tag: age

value: whole blood

tag: batch


title: genomic DNA from whole blood - 202128330165_R06C01

description: Whole Blood sample

value: Female


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_11_060121]

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: BSSE_QGF_161877_HLWHKBGXH_1_LM2_Clusters_1000_11_060121_TACAAGACTT_CAGGTGTTCA_S230

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.6.5; parameters : –q 20 –length 20).
Trimmed reads were aligned to human (GRCh38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) with splice junctions from the human GENCODE annotation (release 35). To eliminate residual contamination from mouse RNA, reads derived from xenograft models were also aligned to mouse (GRCm38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) , with splice junctions from the mouse GENCODE annotation (release M25), and assigned to either human or mouse using Disambiguate (v1.0.0).
The gene-level expression counts were computed with featureCounts (v.2.0.1; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 35).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing per sample raw counts as obtained from featureCounts.

molecule: polyA RNA

source_name: LM2 CTC cluster at 10h

extract_protocol:
Using the CellCelector, an automated single-cell picking system (ALS), single CTCs, CTC clusters and CTC-WBC clusters were collected and immediately transferred into individual tubes (Axygen, 321-032-501) containing 2.5 μl RLT Plus lysis buffer and 1U SUPERase IN RNA inhibitor (Invitrogen, AM2694). Samples were immediately frozen and kept at 800C until further processing.
cDNA was amplifiead and libraries prepared according to the Smart-seq2 protocol.

tag: cancer type

value: breast

tag: origin

value: xenograft

tag: donor

tag: sample type

tag: number of ctcs

value: resting


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_9_060121]

description: BSSE_QGF_161714_HLWHKBGXH_1_BR16_WBC_1000_9_060121_TGGAGTACTT_TCTGTGTGGA_S69

source_name: BR16 CTC-WBC cluster at 10h


title: 1.7Gy_5491551_D3.txt

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Porcine (v2) Gene Expression Microarrays 4x44K Design ID 026440 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

label: Alexa 555

organism: Sus scrofa

source_name: Blood

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: Total RNA was isolated from the whole blood samples using the RNAeasy Protect Animal Blood Kit (Cat # 73224, Qiagen) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a Denovix DS-11 nanodrop spectrophotometer (Denovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Five to six-month-old male Gottingen minipigs (Sus scrofa) were used in this study. Animals were exposed to total-body irradiation using a Cobalt-60 source in the AFFRI Cobalt facility, to a total dose of 1.7, 1.9, 2.1 or 2.3 Gy (n=6/dose) selected to bracket the anticipated LD50/45  (Lethal dose for 50% of the animals). animals were unilaterally sequentially exposed to total midline body doses at a dose rate of 0.5-0.6Gy/minute. Animals were anesthetized with an IM injection of TelazolVR (100 mg/mL, 2 mg/kg) and Xylazine (50 mg/mL, 1 mg/kg) before placing in a sling for the duration of irradiation. The two sources were raised sequentially with a lateral geometry of exposure. The unilateral sequential exposure is derived from the set-up of the AFRRI Cobalt-60 Radiation Facility which contains two sets of Cobalt-60 rods that are lifted sequentially to generate a field. Dose rates were determined using an alanine/ESR (electron spin resonance) dosimetry system (American Society for Testing and Material Standard E 1607) contained in water-filled cylindrical pig phantoms. Dose rates in phantoms were converted to the dose rate for the animals by accounting for the decay of the 60Co source, the small difference in mass energy-absorption coefficients for water and soft tissue, and size of the animal. The radiation field was uniform within ±2%. Additionally, real time dosimetry of the output dose was measured using an ion chamber system.  Day of exposure was considered as day 0. Blood was collected one day prior to exposure (day -1) and on days 1, 3 and 7 post-exposure directly into RNAeasy Protect Animal Blood Tubes (Cat #76544, Qiagen). These animals were followed up for 45 days. During the 45-day study period, pigs were assessed at least twice daily for signs of pre-established criteria that necessitated unscheduled euthanasia. Prior to euthanasia, anesthesia was induced with 5-2% isoflurane and animals received an IM injection of Xylazine and Telazol (as described above). Euthasol® (sodium pentobarbital) was injected IV for euthanasia. Unscheduled euthanasia was necessitated if one absolute criteria (non-responsiveness, dyspnea, loss of ≥20% body weight, hypothermia) or four non-absolute criteria (hyperthermia, anorexia, anemia, vomiting/diarrhea, lethargy, seizures/vestibular signs, prolonged hemorrhage) were observed.

value: Blood

tag: breed

value: Gottingen minipigs

tag: gender

value: male

tag: animal id

tag: dose

tag: time point


title: MtWOX9-1 overexpressing callus, 35th day of cell culture, biol rep 1

city: St Petersburg

first: Varvara

last: Tvorogova

address: 7/9 Universitetskaya emb

department: Genetics and Biotechnology

country: Russia

institute: St Petersburg State University

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (Bolger et al., Bioinformatics. 2014;30(15):2114-2120) with paramenters HEADCROP:0 CROP:50 MINLEN:30 SLIDINGWINDOW:10:28.
Filtration of ribosomal RNA was performed with SortMeRNA (Kopylova  et al., Bioinformatics. 2012;28(24):3211-3217) with rRNA sequences from M. truncatula taken from NCBI Nucleotide database used as reference database.
Alignment on reference genome (MtrunA17r5.0-ANR, Pecrix et al.,  Nat. Plants. 2018;4(12)) was performed with HISAT2 (Kim et al., Nat. Methods. 2015;12(4):357-360.).
Reads were counted with Stringtie (Pertea  et al., Nat. Biotechnol. 2015;33(3):290-295) with the usage of reference genome mentioned above and without de novo assembled transcripts.
Assembly: MtrunA17r5.0-ANR
Supplementary files format and content: wt_vs_w9o_calli.csv - comma delimited .csv files including raw count values for each Sample
Supplementary files format and content: annotresUNfiltered_2_wt_vs_2_w9oe.csv - comma delimited .csv files including output from DESeq with DESeq normalized count values for each Sample, results of differential expression analysis with comparison of wildtype and MtWOX9-1 overexpressing samples, as well as short annotation of genes dowloaded from https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/ (Gene Acronyms & IDs [20211025])

organism: Medicago truncatula

source_name: Callus from leaf explant

growth_protocol: Control and MtWOX9-1 overexpressing plants were grown in soil for 35 days. Their leaves were sterilized with 1% hypochlorite and, after several scalpel cuts, put on the modified PCI-4 medium (Hoffmann et al., Mol. Plant–Microbe Interact., 1997, V. 10, pp. 307–315.), containing 18 μM 2,4-dichlorophenoxyacetic acid (2,4-D), 2.22 μM BAP, and 8% agar. Calli were transferred to fresh medium every 10 days. After 30 days of cultivation on such medium, obtained calli were transferred to the medium identical to the above-described modified PCI-4 but containing no plant hormones to the medium identical to the above-described modified PCI-4 but containing no plant hormones and cultured for additional 5 days

extract_protocol:
Total RNA was extracted from calli with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacturer instruction. Quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). PolyA RNA was purified with Dynabeads mRNA Purification Kit (Ambion).
Illumina library was made from polyA RNA with NEBNext ® UltraTMII RNA Library Prep Kit for Illumina ® (NEB) according to manual.

tag: tissue

value: Callus from leaf explant

value: callus cells

value: R108 with transgenic insertion from pMDC32 plasmid containing cds of MtWOX9-1 (MtrunA17_Chr2g0283141 / Medtr2g015000) gene

tag: culture method

value: 35 days of in vitro cultivation


title: 1.7Gy_5501815_Ctrl.txt

value: Control

value: day -1


title: WA1 1μg-1 (ST) [scVDJ-seq]

description:
ST-WA1-1-1
10x Genomics
LNP-mRNA vaccine

value: Spleen

tag: cell type

value: T cell

tag: genotype

value: WT


title: WA1 10μg-3 (ST) [scVDJ-seq]

description:
ST-WA1-10-3
10x Genomics
LNP-mRNA vaccine

tag: treatment

value: WA1 10ug


title: genomic DNA from whole blood - 202128330165_R03C01

description: Whole Blood sample

tag: Sex

value: Male

tag: age

value: whole blood


title: 1.7Gy_5491551_D7.txt

tag: batch


title: genomic DNA from whole blood - 202128330165_R04C01

description: Whole Blood sample

value: Female


title: 1.7Gy_5491551_Ctrl.txt


title: 1.7Gy_5491062_D7.txt


title: genomic DNA from whole blood - 202128330165_R02C01

description: Whole Blood sample


title: WA1 10μg-2 (ST) [scVDJ-seq]

description:
ST-WA1-10-2
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_7_060121]

description: BSSE_QGF_161712_HLWHKBGXH_1_BR16_WBC_1000_7_060121_AGGATGTGCT_TTACAATTCC_S67

tag: cancer type

value: breast

tag: origin

value: xenograft

tag: number of wbcs attached

tag: timepoint

value: resting


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_6_060121]

description: BSSE_QGF_161711_HLWHKBGXH_1_BR16_WBC_1000_6_060121_ATACCAACGC_AATTGCTGCG_S66

tag: donor

tag: sample type

tag: number of ctcs


title: WA1 1μg-2 (ST) [scVDJ-seq]

description:
ST-WA1-1-2
10x Genomics
LNP-mRNA vaccine

value: WA1 1ug


title: genomic DNA from whole blood - 202128330165_R01C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_8_060121]

description: BSSE_QGF_161713_HLWHKBGXH_1_BR16_WBC_1000_8_060121_CACGGAACAA_AACCTAGCAC_S68


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_4_060121]

description: BSSE_QGF_161709_HLWHKBGXH_1_BR16_WBC_1000_4_060121_TGGCGCGAAC_AACTGATACT_S64


title: WA1 10μg-1 (ST) [scVDJ-seq]

description:
ST-WA1-10-1
10x Genomics
LNP-mRNA vaccine


title: 1.7Gy_5491062_D1.txt

value: Blood

tag: breed

value: Gottingen minipigs

tag: gender

value: male

tag: animal id

tag: dose


title: 1.7Gy_5491062_Ctrl.txt

tag: tissue

tag: time point


title: B.1.351 1μg-3 (ST) [scVDJ-seq]

description:
ST-SA-1-3
10x Genomics
LNP-mRNA vaccine

tag: cell type

tag: genotype

tag: treatment


title: 1.7Gy_5491551_D1.txt

tag: batch


title: spike-in_pool1

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

description: in vitro synthesized RNA

data_processing:
RNA-seq and Rend-seq data processing and mapping was done as described in (Lalanne et al., Cell 2018; Parker et al., Cell Systems 2020). For 3’ end-seq in analogy to Rend-seq, 3’ end linker sequences were trimmed. To deal with non-template addition during reverse transcription, all reads were further trimmed with the fastx_trimmer of the fastxtoolkit/0.0.13 by 1nt at their 5’end and only reads of 15nt length or longer were kept for mapping with bowtie/1.2 using the options -v 0 -k 1. For further data analysis mapped data were transformed into bam-format and bedgraph-format using samtools/1.5 and bedtools/2.25.0. Coverage data include 3’ terminal single nucleotide counts per read. To identify 3’adenylated transcript ends, the unmapped reads were trimmed using cutadapt/1.16. First, 3’terminal CCAs were removed with the following settings: -a "CCA$" --minimum-length 15 -O 3 --trimmed-only. Second, A-tails of any length were trimmed (-a "A{38}" --minimum-length 15 -O 1 --trimmed-only). These trimmed reads were mapped and further converted with the same settings and code as untrimmed reads above. For total RNA 3’ end analysis mapped trimmed (i.e. A-tailed) and untrimmed 3’ end coverage profiles were summed.
Genome_build: E. coli NC_000913.2, B. subtilis NC_000964.3
Supplementary_files_format_and_content: bedgraph-files

organism: synthetic construct

growth_protocol: E. coli cells were grown in LB, MOPS Complete or MOPS Minimal media supplemented with 0.2% Glucose. B. subtilis cells were grown in MCCG media (Parker et al., Cell Systems 2020). To harvest cells in exponential growth, cells were backdiluted from overnight cultures into the respective growth media to enable ~10 doublings at 37°C prior to harvest at an OD600 smaller or equal to 0.3 (Sezonov et al. J Bac 2007). To harvest cells in early stationary growth, cells were harvested shortly after growth had plateaued (harvest at OD600 2.8 for MOPS Complete and at OD600 2.26 for MOPS Minimal). For Kasugamycin treatment, Kasugamycin was added at a final concentration of 1mg/ml to cells at OD600 0.22 grown in MOPS Complete media. After 15 min treated and untreated cells were harvested for total RNA analysis.

extract_protocol:
Samples have been either extracted by RNAsnap (Stead et al., NAR 2012), Hot Phenol, RiboPure (ThermoFisher/Ambion), RNeasy (Qiagen) or Trizol, precipitated, Dnase treated and cleaned uo with RNA clean & concentrator columns (Zymo research).
RNA-seq for E. coli Δpnp, Δrnb, ΔpcnB and MG1655 wildtype was executed as described in (Parker et al., Cell Systems 2020). Rend-seq libraries were prepared as described in (Lalanne et al., Cell 2018) with 25s RNA fragmentation. For 3’ end sequencing the Rend-seq protocol was modified in a way that 3’ end ligation (5'_App/CTGTAGGCACCATCAAT/3ddC_3') was done preceding fragmentation for 2min. Final libraries were sequenced on Illumina HiSeq 2000 or NextSeq500 machines.

treatment_protocol: For total RNA analysis, 5ml of cells were transferred into 0.55ml of ice-cold stop solution (95:5 Ethanol:Phenol) in a 15ml conical tube, quickly inverted and spun at 3220g at 4°C for 5-10min. The supernatant was discarded and cell pellets flash-frozen in liquid nitrogen and stored at -80C until lysis and RNA extraction. For nascent RNA and polysome analysis, 250ml of cells were filter harvested at 37°C and scraped into liquid nitrogen (Johnson and Li, 2018). The cell paste was kept at -80°C until lysis and RNA extraction.

tag: spike-in


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_5_060121]

description: BSSE_QGF_161710_HLWHKBGXH_1_BR16_WBC_1000_5_060121_TAATGTGTCT_GTAAGGCATA_S65

tag: cancer type

tag: origin


title: genomic DNA from whole blood - 202128330145_R08C01

description: Whole Blood sample

tag: Sex

tag: age


title: 1.7Gy_5491062_D3.txt


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_3_060121]

description: BSSE_QGF_161708_HLWHKBGXH_1_BR16_WBC_1000_3_060121_ATTGCGCGGT_TTGGCTCCGC_S63

tag: donor

tag: sample type

tag: number of wbcs attached

tag: timepoint


title: genomic DNA from whole blood - 202128330145_R07C01

description: Whole Blood sample


title: B.1.351 1μg-2 (ST) [scVDJ-seq]

description:
ST-SA-1-2
10x Genomics
LNP-mRNA vaccine


title: 19wks

city: Philadelphia

first: Xiaodun

last: Yang

state: PA

address: 3451 Walnut St

institute: University of Pennsylvenia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Secondary bioinformatic analysis was performed using the Seurat (v.2.3.4) packages in R. Briefly, sequenced 10x libraries were individually evaluated on multiple criteria to determine cells of interest including low expression of Hemoglobin (average log2 UMI of HBA1, HBA2, HBB < 8) and number of UMI (0 – 65536).
Assembly: GRCh38
Supplementary files format and content: cloupe files and excel files

source_name: whole pancreas

extract_protocol:
Single islet cells were dissociated with TrypLe, and loaded on the 10x Genomics (Pleasanton, CA) platform in the Center for Applied Genomics at The Children’s Hospital of Philadelphia.
Single-cell transcriptome libraries were sequenced on the HiSeq platform (Illumina, San Diego, CA). The cellranger (v.2.1,10x genomics) pipeline was used for barcode filtering, alignment (to GRCh38), and UMI counting.

value: pancreatic cells

value: whole pancreas

value: 19 weeks gestation


title: B.1.351 1μg-1 (ST) [scVDJ-seq]

description:
ST-SA-1-1
10x Genomics
LNP-mRNA vaccine

value: Spleen


title: 20wks

description: 10x Genomics

value: 20 weeks gestation


title: 1.7Gy_5501815_D1.txt

tag: breed

tag: gender

tag: animal id


title: genomic DNA from whole blood - 202128330145_R06C01

description: Whole Blood sample

tag: tissue


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_26_060121]

description: BSSE_QGF_161731_HLWHKBGXH_1_BR16_WBC_1000_26_060121_TTGGAATTCC_ACGTCAATAC_S86

tag: number of ctcs


title: 18wks

description: 10x Genomics

tag: cell type

value: 18 weeks gestation


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_27_060121]

description: BSSE_QGF_161732_HLWHKBGXH_1_BR16_WBC_1000_27_060121_CCTCTACATG_GATACCTCCT_S87


title: B.1.351 10μg-3 (ST) [scVDJ-seq]

description:
ST-SA-10-3
10x Genomics
LNP-mRNA vaccine

value: T cell

tag: genotype

value: WT

tag: treatment


title: genomic DNA from whole blood - 202128330145_R05C01

description: Whole Blood sample

value: whole blood

tag: batch


title: 15wks

description: 10x Genomics

value: 15 weeks gestation


title: B.1.351 10μg-2 (ST) [scVDJ-seq]

description:
ST-SA-10-2
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_25_060121]

description: BSSE_QGF_161730_HLWHKBGXH_1_BR16_WBC_1000_25_060121_TGGTACCTAA_CATGAGTACT_S85

tag: cancer type

value: breast


title: Parenchyma heifer 5

city: Bet Dagan

first: Itamar

last: Barash

state: israel

address: P.O. Box 6

country: Israel

institute: ARO, The Volcani Center

description: Untreated

data_processing:
Poly(A/T) stretches and Illumina adapters were trimmed from the reads using Cutadapt, and reads shorter than 30 bp were discarded.
Reads were mapped to the Bos taurus reference genome ARS-UCD1.2 using STAR, supplied with gene annotations downloaded from Ensembl (with end-to-end option).
Expression levels for each gene were quantified with htseq-count, using the above gene transfer format. Differentially expressed genes were identified using DESeq2  with the betaPrior, cooksCutoff and independent filtering parameters set to False.
Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: DESeq2 normalized counts

organism: Bos taurus

source_name: Heifer

extract_protocol:
Mammary tissues were removed into RNA-save solution and kept at -380C. RNA was extracted with Trisol reagent.
Total RNA was fragmented, followed by reverse transcription and second-strand cDNA synthesis. The double-stranded cDNA was subjected to end repair, a base addition, adapter ligation and PCR amplification to create libraries. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing.
RNA-Seq; poly A selection

value: Mammary sample

tag: strain

value: Holstein

value: 10-12 month old


title: genomic DNA from whole blood - 202128330145_R03C01

description: Whole Blood sample

tag: Sex

value: Female


title: Parenchyma heifer 4

description: Untreated


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_23_060121]

description: BSSE_QGF_161728_HLWHKBGXH_1_BR16_WBC_1000_23_060121_TATGCCTTAC_AGACACATTA_S83

tag: origin

value: xenograft

value: resting


title: Parenchyma heifer 3

description: Untreated


title: 1.9Gy_5490775_D1.txt

value: Blood

value: Gottingen minipigs

value: male

tag: dose

tag: time point


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_22_060121]

description: BSSE_QGF_161727_HLWHKBGXH_1_BR16_WBC_1000_22_060121_ACCGTTACAA_CTCATAGCGA_S82

tag: donor

tag: sample type

tag: number of wbcs attached


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_14_060121]

description: BSSE_QGF_161880_HLWHKBGXH_1_LM2_Clusters_1000_14_060121_ATAGTTAGCA_CTCTAAGTAG_S233

tag: timepoint


title: genomic DNA from whole blood - 202128330145_R02C01

description: Whole Blood sample

tag: age


title: PBS-6 (ST) [scVDJ-seq]

description:
ST-PBS-6
10x Genomics
LNP-mRNA vaccine

tag: tissue

value: Spleen

value: PBS


title: PBS-5 (ST) [scVDJ-seq]

description:
ST-PBS-5
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202128330145_R04C01

description: Whole Blood sample

value: Male


title: Far stroma heifer 5

description: Untreated


title: Parenchyma heifer 1

description: Untreated


title: genomic DNA from whole blood - 202128330145_R01C01

description: Whole Blood sample


title: PBS-4 (ST) [scVDJ-seq]

description:
ST-PBS-4
10x Genomics
LNP-mRNA vaccine

value: T cell


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_2_060121]

description: BSSE_QGF_161707_HLWHKBGXH_1_BR16_WBC_1000_2_060121_AACACTGTTA_GCAAGTCTCA_S62

tag: number of ctcs


title: genomic DNA from whole blood - 202128330270_R08C01

description: Whole Blood sample


title: PBS-3 (ST) [scVDJ-seq]

description:
ST-PBS-3
10x Genomics
LNP-mRNA vaccine

tag: cell type

value: WT


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_19_060121]

description: BSSE_QGF_161724_HLWHKBGXH_1_BR16_WBC_1000_19_060121_ACGGTCAGGA_CGGCCTCGTT_S79


title: genomic DNA from whole blood - 202128330270_R07C01

description: Whole Blood sample

value: whole blood


title: B.1.351 10μg-1 (ST) [scVDJ-seq]

description:
ST-SA-10-1
10x Genomics
LNP-mRNA vaccine

tag: genotype


title: Far stroma heifer 4

description: Untreated

tag: treatment


title: PBS-2 (ST) [scVDJ-seq]

description:
ST-PBS-2
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_18_060121]

description: BSSE_QGF_161723_HLWHKBGXH_1_BR16_WBC_1000_18_060121_CATTAGTGCG_TGACTACATA_S78


title: Far stroma heifer 3

description: Untreated


title: genomic DNA from whole blood - 202128330270_R06C01

description: Whole Blood sample

tag: batch


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_17_060121]

description: BSSE_QGF_161722_HLWHKBGXH_1_BR16_WBC_1000_17_060121_TCTGGTATCC_CGTTGCTTAC_S77

tag: cancer type


title: PBS-1 (ST) [scVDJ-seq]

description:
ST-PBS-1
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_21_060121]

description: BSSE_QGF_161726_HLWHKBGXH_1_BR16_WBC_1000_21_060121_TGTCGCTGGT_TCGTCTGACT_S81


title: genomic DNA from whole blood - 202128330270_R05C01

description: Whole Blood sample


title: Close stroma heifer 5

description: Untreated

tag: strain


title: Mock_2_B

city: Seattle

first: Joseph

last: Mougous

state: WA

address: 1959 NE Pacific St Box 357710

institute: University of Washington /HHMI

description:
Sample 1 B
Immunoprecipitated DNA was not size-selected during library construction

library_source: genomic

data_processing:
Paired ChIP-Seq reads corresponding to fragment sizes of 200 bp (see SAMPLES section) were aligned to the PAO1 genome using bowtie2 (version 2.3.5.1) allowing 1 mismatch in a 28 bp seed region with no discordant or unpaired alignments.
The program samtools (version 1.9) was used to extract read 1 from each mapped read pair.
For GcsR and FleQ experiments (samples 2, 5): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from wild-type PAO1 cells (sample 1) with the following settings: KDE = 45,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.0, positive region size = 300.
For GacA ChIP experiments (sample 4): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from a parental strains lacking the retS gene (PAO1 ∆retS, sample 3). The following settings were used for peak identification during QuEST analysis: KDE = 45,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.0, positive region size = 300.
Bed files for each experimental replicate were created by QuEST and the final processed bed files were generated by identifying the largest overlapping peak region which statisfy the following conditions: (1) peak regions must have a positive peak shift, (2) peak regions must have a positive strand correlation, (3) peak regions must have a q-value of less than 0.01, and (4) peak regions must be shared by two or more experimental replicates.
Assembly: NC_002516.2
Supplementary files format and content: wig files were generated using QuEST; Scores represent normalized smoothed read density
Supplementary files format and content: bed intervals reflect regions with signicant (as defined above in data processing steps) enrichment of reads in the experimental condition in comparision to the mock control condition.

organism: Pseudomonas aeruginosa PAO1

source_name: wild-type

growth_protocol: Bacterial cultures were started from single colonies, grown overnight to saturation, and back-diluted in LB media to an OD600~0.01  and subsequently cultured to an OD600 of 2.0 before harvesting.

extract_protocol:
DNA associated with proteins of interest were immunoprecipitated from lysates with anti-VSVG monocolonal antibody
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions. Size selection of DNA fragments was not used.

treatment_protocol: At the time of harvest, 80 mL of culture was treated with formaldehyde (1% final concentration) for 30 minutes with gentle agitation to form cross-links between DNA and protein. Following this, Glycine was added to a final concentration of 250mM and incubated for 15 minutes at room temperature with gentle agitation to quench the crosslinking reaction. The cells were washed thrice with PBS and stored at -80C until further processing.

value: wild-type

tag: growth phase

value: Bacterial cells grown to OD 2.0

tag: chip antibody

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: genomic DNA from whole blood - 202128330270_R04C01

description: Whole Blood sample

tag: Sex


title: B.1.617 1μg-3 (ST) [scVDJ-seq]

description:
ST-In-1-3
10x Genomics
LNP-mRNA vaccine


title: Far stroma heifer 1

description: Untreated

value: Mammary sample

value: Holstein


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_16_060121]

description: BSSE_QGF_161721_HLWHKBGXH_1_BR16_WBC_1000_16_060121_CTGACTCTAC_ACGGCCGTCA_S76

value: breast

tag: origin


title: genomic DNA from whole blood - 202128330270_R03C01

description: Whole Blood sample


title: Close stroma heifer 4

description: Untreated

value: 10-12 month old


title: genomic DNA from whole blood - 202128330270_R02C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_15_060121]

description: BSSE_QGF_161720_HLWHKBGXH_1_BR16_WBC_1000_15_060121_CTCTGCAGCG_GATGGATGTA_S75

value: xenograft

tag: donor

value: resting


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_14_060121]

description: BSSE_QGF_161719_HLWHKBGXH_1_BR16_WBC_1000_14_060121_TTCATAAGGT_TGTTAGAAGG_S74

tag: sample type


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_13_060121]

description: BSSE_QGF_161718_HLWHKBGXH_1_BR16_WBC_1000_13_060121_CCTGCGGAAC_ATCATAGGCT_S73

tag: number of wbcs attached


title: spike-in_pool4

description: in vitro synthesized RNA

tag: spike-in


title: spike-in_pool3

description: in vitro synthesized RNA


title: genomic DNA from whole blood - 202128330270_R01C01

description: Whole Blood sample

tag: age


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_11_060121]

description: BSSE_QGF_161716_HLWHKBGXH_1_BR16_WBC_1000_11_060121_CTTGTACACC_AAGCGCGCTT_S71

tag: timepoint


title: B.1.617 10μg-2 (ST) [scVDJ-seq]

description:
ST-In-10-2
10x Genomics
LNP-mRNA vaccine

tag: tissue


title: genomic DNA from whole blood - 202066270059_R08C01

description: Whole Blood sample


title: B.1.617 10μg-1 (ST) [scVDJ-seq]

description:
ST-In-10-1
10x Genomics
LNP-mRNA vaccine

tag: cell type


title: B.1.617 1μg-2 (ST) [scVDJ-seq]

description:
ST-In-1-2
10x Genomics
LNP-mRNA vaccine

tag: genotype


title: spike-in_pool2

description: in vitro synthesized RNA


title: WA1 1μg-3 (SB) [scVDJ-seq]

description:
SB-WA1-1-3
10x Genomics
LNP-mRNA vaccine

value: B cell

tag: treatment

value: WA1 1ug


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_1_060121]

description: BSSE_QGF_161706_HLWHKBGXH_1_BR16_WBC_1000_1_060121_TGGCTAATCA_AGGCATGTAG_S61

tag: number of ctcs


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_10_060121]

description: BSSE_QGF_161715_HLWHKBGXH_1_BR16_WBC_1000_10_060121_GTATTGACGT_GGAATTCCAA_S70

tag: cancer type


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_19_060121]

description: BSSE_QGF_161813_HLWHKBGXH_1_BR16_WBC_2200_19_060121_AGCCTATGAT_CACCACCTAC_S167

source_name: BR16 CTC-WBC cluster at 22h

value: active


title: Removed_2

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

description: Removed: no genotype match found

data_processing:
Reads were aligned to the Rnor_6.0 genome using STAR in two-pass mode.
Samples were tested for mismatches with their genotypes by counting coding SNP alleles in the RNA sequences using GATK ASEReadCounter and comparing to the coding SNP genotypes of each rat.
Gene expression was quantified using RSEM.
Assembly: Rnor_6.0
Supplementary files format and content: Eye.expr.log2.bed is a table of log2(read count + 1) expression in BED format. The start and end columns refer only to the gene's TSS.

organism: Rattus norvegicus

source_name: eye

extract_protocol:
Whole eyes from 53 rats (one eye per rat) were frozen immediately after the rat was killed and stored at -80°C until RNA could be extracted. During RNA extraction, eyes were first thawed to room temperature and extraocular muscles were carefully removed. RNA was extracted using the Qiagen RNeasy Midi kit following the manufacturer's instructions.
Libraries were constructed for sequencing using Illumina NovaSeq instrument by Novogen, Inc using standard protocols for generating 150 bp paired-end reads.

treatment_protocol: As part of another study, some of the rats were exposed to a battery of behavioral tests and were allowed to self administer nicotine for 2.5 hours per day over the course of 12 days.

value: eye

tag: population

value: Heterogeneous Stock


title: WA1 1μg-2 (SB) [scVDJ-seq]

description:
SB-WA1-1-2
10x Genomics
LNP-mRNA vaccine

value: Spleen


title: Removed_1

description: Removed: no genotype match found


title: genomic DNA from whole blood - 202066270059_R05C01

description: Whole Blood sample

value: Male

tag: batch


title: Close stroma  heifer 3

description: Untreated

tag: strain


title: BR16 single CTC at 22h [BR16_Singles_2200_9_060121]

description: BSSE_QGF_161743_HLWHKBGXH_1_BR16_Singles_2200_9_060121_TGCCGGTCAG_CCTGATACAA_S97

source_name: BR16 single CTC at 22h


title: 0007D3C437

description: Original label before genotype mismatch fix: 00077E9D1B


title: BR16 CTC-WBC cluster at 10h [BR16_WBC_1000_12_060121]

description: BSSE_QGF_161717_HLWHKBGXH_1_BR16_WBC_1000_12_060121_ACACAGGTGG_TGAGCGTTGT_S72


title: genomic DNA from whole blood - 202066270059_R04C01

description: Whole Blood sample

tag: Sex

value: whole blood


title: BR16 single CTC at 22h [BR16_Singles_2200_5_060121]

description: BSSE_QGF_161738_HLWHKBGXH_1_BR16_Singles_2200_5_060121_ACATATCCAG_TATGTGCAAT_S93

tag: origin


title: WA1 10μg-3 (SB) [scVDJ-seq]

description:
SB-WA1-10-3
10x Genomics
LNP-mRNA vaccine

value: WT

value: WA1 10ug


title: B.1.617 1μg-1 (ST) [scVDJ-seq]

description:
ST-In-1-1
10x Genomics
LNP-mRNA vaccine

value: T cell


title: 000792A2B8


title: genomic DNA from whole blood - 202066270059_R03C01

description: Whole Blood sample

value: Female


title: genomic DNA from whole blood - 202066270059_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270059_R07C01

description: Whole Blood sample


title: 00077E9ACA


title: BR16 single CTC at 22h [BR16_Singles_2200_4_060121]

description: BSSE_QGF_161737_HLWHKBGXH_1_BR16_Singles_2200_4_060121_GCGTTGGTAT_ACATACTTCC_S92

tag: donor


title: B.1.617 10μg-3 (ST) [scVDJ-seq]

description:
ST-In-10-3
10x Genomics
LNP-mRNA vaccine


title: WA1 10μg-2 (SB) [scVDJ-seq]

description:
SB-WA1-10-2
10x Genomics
LNP-mRNA vaccine


title: WA1 10μg-1 (SB) [scVDJ-seq]

description:
SB-WA1-10-1
10x Genomics
LNP-mRNA vaccine


title: 00077E9F3A


title: genomic DNA from whole blood - 202066270059_R06C01

description: Whole Blood sample


title: WA1 1μg-1 (SB) [scVDJ-seq]

description:
SB-WA1-1-1
10x Genomics
LNP-mRNA vaccine


title: 00077E8AE2


title: genomic DNA from whole blood - 202066270059_R01C01

description: Whole Blood sample


title: 00077E9C26

description: Original label before genotype mismatch fix: 00077E94A0


title: B.1.351 1μg-2 (SB) [scVDJ-seq]

description:
SB-SA-1-2
10x Genomics
LNP-mRNA vaccine


title: B.1.351 1μg-1 (SB) [scVDJ-seq]

description:
SB-SA-1-1
10x Genomics
LNP-mRNA vaccine


title: B.1.351 1μg-3 (SB) [scVDJ-seq]

description:
SB-SA-1-3
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_30_060121]

description: BSSE_QGF_161764_HLWHKBGXH_1_BR16_Singles_2200_30_060121_ATACTTGTTC_TAACCGCCGA_S118

tag: sample type


title: genomic DNA from whole blood - 202066270060_R06C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_3_060121]

description: BSSE_QGF_161736_HLWHKBGXH_1_BR16_Singles_2200_3_060121_TCAGAAGGCG_GGCCATCATA_S91

tag: number of wbcs attached


title: genomic DNA from whole blood - 202066270060_R07C01

description: Whole Blood sample


title: 00077E9BD9


title: genomic DNA from whole blood - 202066270060_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270060_R08C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_28_060121]

description: BSSE_QGF_161762_HLWHKBGXH_1_BR16_Singles_2200_28_060121_ATCGGCGAAG_TCCAAGAATT_S116


title: 00077E7CBE


title: BR16 single CTC at 22h [BR16_Singles_2200_26_060121]

description: BSSE_QGF_161760_HLWHKBGXH_1_BR16_Singles_2200_26_060121_TAGAATTGGA_GTTAATCTGA_S114


title: B.1.351 10μg-3 (SB) [scVDJ-seq]

description:
SB-SA-10-3
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_29_060121]

description: BSSE_QGF_161763_HLWHKBGXH_1_BR16_Singles_2200_29_060121_CCGTGACCGA_CCGAACGTTG_S117


title: genomic DNA from whole blood - 202066270060_R04C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_23_060121]

description: BSSE_QGF_161757_HLWHKBGXH_1_BR16_Singles_2200_23_060121_ATTAACAAGG_TGTTGTTCGT_S111


title: BR16 single CTC at 22h [BR16_Singles_2200_25_060121]

description: BSSE_QGF_161759_HLWHKBGXH_1_BR16_Singles_2200_25_060121_GAATTACAAG_ACCGGCTCAG_S113


title: 00077E9995


title: genomic DNA from whole blood - 202066270060_R02C01

description: Whole Blood sample


title: B.1.351 10μg-2 (SB) [scVDJ-seq]

description:
SB-SA-10-2
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_24_060121]

description: BSSE_QGF_161758_HLWHKBGXH_1_BR16_Singles_2200_24_060121_TGATGGCTAC_CCAACAACAT_S112


title: PBS-6 (SB) [scVDJ-seq]

description:
SB-PBS-6
10x Genomics
LNP-mRNA vaccine

value: PBS


title: 0007D2C474


title: genomic DNA from whole blood - 202053820168_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270060_R01C01

description: Whole Blood sample


title: 000792A1F9

description: Original label before genotype mismatch fix: 00077E9010


title: B.1.351 10μg-1 (SB) [scVDJ-seq]

description:
SB-SA-10-1
10x Genomics
LNP-mRNA vaccine


title: 00077E8BF4


title: BR16 single CTC at 22h [BR16_Singles_2200_20_060121]

description: BSSE_QGF_161754_HLWHKBGXH_1_BR16_Singles_2200_20_060121_AGTACTCATG_ATGTCGTGGT_S108

value: breast


title: BR16 single CTC at 22h [BR16_Singles_2200_22_060121]

description: BSSE_QGF_161756_HLWHKBGXH_1_BR16_Singles_2200_22_060121_TAATTAGCGT_TGGTTAAGAA_S110


title: 00077E9C1F


title: PBS-5 (SB) [scVDJ-seq]

description:
SB-PBS-5
10x Genomics
LNP-mRNA vaccine


title: PBS-4 (SB) [scVDJ-seq]

description:
SB-PBS-4
10x Genomics
LNP-mRNA vaccine


title: 00077E8FAD

description: Original label before genotype mismatch fix: 00077E8FA0


title: BR16 single CTC at 22h [BR16_Singles_2200_21_060121]

description: BSSE_QGF_161755_HLWHKBGXH_1_BR16_Singles_2200_21_060121_GGTAGAATTA_GTAGCCATCA_S109


title: genomic DNA from whole blood - 202053820168_R07C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_2_060121]

description: BSSE_QGF_161735_HLWHKBGXH_1_BR16_Singles_2200_2_060121_ACTTCAAGCG_GAACCATGAA_S90


title: genomic DNA from whole blood - 202066270060_R03C01

description: Whole Blood sample


title: 0007D2CBB5


title: BR16 single CTC at 22h [BR16_Singles_2200_17_060121]

description: BSSE_QGF_161751_HLWHKBGXH_1_BR16_Singles_2200_17_060121_CAGCAATCGT_TGTGATGTAT_S105


title: PBS-2 (SB) [scVDJ-seq]

description:
SB-PBS-2
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202053820168_R06C01

description: Whole Blood sample


title: 00077E957E


title: 0007D2B45D


title: genomic DNA from whole blood - 202053820168_R05C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_16_060121]

description: BSSE_QGF_161750_HLWHKBGXH_1_BR16_Singles_2200_16_060121_GGTCTATTAA_CCACGACACG_S104


title: genomic DNA from whole blood - 202053820168_R03C01

description: Whole Blood sample


title: PBS-3 (SB) [scVDJ-seq]

description:
SB-PBS-3
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_15_060121]

description: BSSE_QGF_161749_HLWHKBGXH_1_BR16_Singles_2200_15_060121_TCCGTTATGT_TTGTAGTGTA_S103


title: PBS-1 (SB) [scVDJ-seq]

description:
SB-PBS-1
10x Genomics
LNP-mRNA vaccine


title: 00077E9E77


title: B.1.617 1μg-2 (SB) [scVDJ-seq]

description:
SB-In-1-2
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_18_060121]

description: BSSE_QGF_161752_HLWHKBGXH_1_BR16_Singles_2200_18_060121_TTCTGTAGAA_GAGCGCAATA_S106


title: B.1.617 1μg-3 (SB) [scVDJ-seq]

description:
SB-In-1-3
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202053820168_R01C01

description: Whole Blood sample


title: 00077E7AC5


title: genomic DNA from whole blood - 202053820167_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202053820167_R06C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_12_060121]

description: BSSE_QGF_161746_HLWHKBGXH_1_BR16_Singles_2200_12_060121_TCAATGGAGA_GCACTACAAC_S100


title: 00077E8F69


title: B.1.617 1μg-1 (SB) [scVDJ-seq]

description:
SB-In-1-1
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202053820167_R07C01

description: Whole Blood sample


title: B.1.617 10μg-3 (SB) [scVDJ-seq]

description:
SB-In-10-3
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_19_060121]

description: BSSE_QGF_161753_HLWHKBGXH_1_BR16_Singles_2200_19_060121_GAACGCAATA_ATCTTACTGT_S107


title: genomic DNA from whole blood - 202053820168_R02C01

description: Whole Blood sample


title: B.1.617 10μg-2 (SB) [scVDJ-seq]

description:
SB-In-10-2
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 22h [BR16_Singles_2200_14_060121]

description: BSSE_QGF_161748_HLWHKBGXH_1_BR16_Singles_2200_14_060121_ATGGCGCCTG_TCCACGGCCT_S102


title: 00077E9288


title: 00077E9968


title: B.1.617 10μg-1 (SB) [scVDJ-seq]

description:
SB-In-10-1
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202053820168_R04C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_11_060121]

description: BSSE_QGF_161745_HLWHKBGXH_1_BR16_Singles_2200_11_060121_TCTCACACGC_CGGACAGTGA_S99


title: WA1 1μg-3

description:
SG-WA1-1-3
10x Genomics
LNP-mRNA vaccine

data_processing:
Single cell gene expression data were pre-processed with a standard Cell Ranger v6.0.1 (10x Genomics) pipeline, aligning reads to the mm10 mouse reference transcriptome.
Assembly: mm10 mouse reference transcriptome
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

value: Heterogeneous splenocyte


title: WA1 10μg-3

description:
SG-WA1-10-3
10x Genomics
LNP-mRNA vaccine


title: WA1 1μg-1

description:
SG-WA1-1-1
10x Genomics
LNP-mRNA vaccine


title: 00077E995B


title: genomic DNA from whole blood - 202053820167_R05C01

description: Whole Blood sample


title: BR16 single CTC at 22h [BR16_Singles_2200_10_060121]

description: BSSE_QGF_161744_HLWHKBGXH_1_BR16_Singles_2200_10_060121_CACTCAATTC_TTAAGTTGTG_S98

value: xenograft


title: BR16 single CTC at 10h [BR16_Singles_1000_9_060121]

description: BSSE_QGF_161654_HLWHKBGXH_1_BR16_Singles_1000_9_060121_GACTGAGTAG_GTTGATAGTG_S9

source_name: BR16 single CTC at 10h

value: resting


title: 00077E96CF

description: Original label before genotype mismatch fix: 000789990A


title: genomic DNA from whole blood - 202053820167_R04C01

description: Whole Blood sample


title: BR16 single CTC at 10h [BR16_Singles_1000_7_060121]

description: BSSE_QGF_161652_HLWHKBGXH_1_BR16_Singles_1000_7_060121_CTAGTGCTCT_TGGAACAGTA_S7


title: 00077E94CF


title: genomic DNA from whole blood - 202053820167_R01C01

description: Whole Blood sample


title: BR16 single CTC at 10h [BR16_Singles_1000_6_060121]

description: BSSE_QGF_161651_HLWHKBGXH_1_BR16_Singles_1000_6_060121_AACATCGCGC_GTCCACTTGT_S6


title: B.1.351 1μg-3

description:
SG-SA-1-3
10x Genomics
LNP-mRNA vaccine


title: 00077E9391


title: WA1 10μg-2

description:
SG-WA1-10-2
10x Genomics
LNP-mRNA vaccine


title: genomic DNA from whole blood - 202053820167_R02C01

description: Whole Blood sample


title: 00077E993E

description: Original label before genotype mismatch fix: 000792A14D


title: 0007D2C6E2


title: 0007D48378


title: WA1 1μg-2

description:
SG-WA1-1-2
10x Genomics
LNP-mRNA vaccine


title: B.1.351 1μg-1

description:
SG-SA-1-1
10x Genomics
LNP-mRNA vaccine


title: B.1.351 10μg-2

description:
SG-SA-10-2
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 10h [BR16_Singles_1000_3_060121]

description: BSSE_QGF_161648_HLWHKBGXH_1_BR16_Singles_1000_3_060121_CGTCTCATAT_TATAGTAGCT_S3


title: B.1.351 1μg-2

description:
SG-SA-1-2
10x Genomics
LNP-mRNA vaccine


title: 00077E94A0

description: Original label before genotype mismatch fix: 00077E993E


title: BR16 single CTC at 22h [BR16_Singles_2200_13_060121]

description: BSSE_QGF_161747_HLWHKBGXH_1_BR16_Singles_2200_13_060121_ATATGCATGT_TGGTGCCTGG_S101


title: WA1 10μg-1

description:
SG-WA1-10-1
10x Genomics
LNP-mRNA vaccine


title: B.1.351 10μg-1

description:
SG-SA-10-1
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 10h [BR16_Singles_1000_5_060121]

description: BSSE_QGF_161650_HLWHKBGXH_1_BR16_Singles_1000_5_060121_GACGAGATTA_ACATTATCCT_S5


title: 00077E96C6


title: genomic DNA from whole blood - 202053820167_R03C01

description: Whole Blood sample


title: BR16 single CTC at 10h [BR16_Singles_1000_12_060121]

description: BSSE_QGF_161657_HLWHKBGXH_1_BR16_Singles_1000_12_060121_GAGTCATAGG_GTGTGGCGCT_S12


title: BR16 single CTC at 10h [BR16_Singles_1000_2_060121]

description: BSSE_QGF_161647_HLWHKBGXH_1_BR16_Singles_1000_2_060121_AGGTCAGATA_CTACAAGATA_S2


title: BR16 single CTC at 10h [BR16_Singles_1000_13_060121]

description: BSSE_QGF_161658_HLWHKBGXH_1_BR16_Singles_1000_13_060121_CTTGCCATTA_ATCACGAAGG_S13


title: PBS-5

description:
SG-PBS-5
10x Genomics
LNP-mRNA vaccine


title: B.1.351 10μg-3

description:
SG-SA-10-3
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 10h [BR16_Singles_1000_4_060121]

description: BSSE_QGF_161649_HLWHKBGXH_1_BR16_Singles_1000_4_060121_ATTCCATAAG_TGCCTGGTGG_S4


title: 000792A3E7


title: 00077E8A23


title: PBS-4

description:
SG-PBS-4
10x Genomics
LNP-mRNA vaccine


title: 00077E9421


title: 00077E988C


title: BR16 single CTC at 10h [BR16_Singles_1000_14_060121]

description: BSSE_QGF_161659_HLWHKBGXH_1_BR16_Singles_1000_14_060121_GAAGCGGCAC_CGGCTCTACT_S14


title: PBS-3

description:
SG-PBS-3
10x Genomics
LNP-mRNA vaccine


title: 00077E9434


title: PBS-6

description:
SG-PBS-6
10x Genomics
LNP-mRNA vaccine


title: 00077E9BB7


title: PBS-2

description:
SG-PBS-2
10x Genomics
LNP-mRNA vaccine


title: 00077E8985


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_9_060121]

description: BSSE_QGF_161773_HLWHKBGXH_1_BR16_Clusters_2200_9_060121_GCTGACGTTG_TGTTCGCATT_S127

source_name: BR16 CTC cluster at 22h


title: BR16 single CTC at 10h [BR16_Singles_1000_1_060121]

description: BSSE_QGF_161646_HLWHKBGXH_1_BR16_Singles_1000_1_060121_GAACTGAGCG_TCGTGGAGCG_S1


title: PBS-1

description:
SG-PBS-1
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_8_060121]

description: BSSE_QGF_161772_HLWHKBGXH_1_BR16_Clusters_2200_8_060121_AGGAGGTATC_CCAGTTGGCA_S126


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_7_060121]

description: BSSE_QGF_161771_HLWHKBGXH_1_BR16_Clusters_2200_7_060121_AGGCCGTGGA_CTCGTGCGTT_S125


title: BR16 single CTC at 10h [BR16_Singles_1000_10_060121]

description: BSSE_QGF_161655_HLWHKBGXH_1_BR16_Singles_1000_10_060121_AGTCAGACGA_ACCAGCGACA_S10


title: 00077E9010

description: Original label before genotype mismatch fix: 0007D3C437


title: B.1.617 1μg-2

description:
SG-In-1-2
10x Genomics
LNP-mRNA vaccine


title: 00077E7B8A


title: 00077E7C6D


title: 000792A14D

description: Original label before genotype mismatch fix: 000792A1F9


title: B.1.617 1μg-3

description:
SG-In-1-3
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_5_060121]

description: BSSE_QGF_161769_HLWHKBGXH_1_BR16_Clusters_2200_5_060121_CGTACAGGAA_TAGGTTCTCT_S123


title: 0007A027D6


title: 00077E7BF8


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_30_060121]

description: BSSE_QGF_161794_HLWHKBGXH_1_BR16_Clusters_2200_30_060121_CCGCGTATAG_TAGGAACCGG_S148


title: B.1.617 10μg-2

description:
SG-In10-2
10x Genomics
LNP-mRNA vaccine


title: B.1.617 10μg-3

description:
SG-In10-3
10x Genomics
LNP-mRNA vaccine


title: B.1.617 1μg-1

description:
SG-In-1-1
10x Genomics
LNP-mRNA vaccine


title: BR16 single CTC at 10h [BR16_Singles_1000_11_060121]

description: BSSE_QGF_161656_HLWHKBGXH_1_BR16_Singles_1000_11_060121_CCGTATGTTC_CATACACTGT_S11


title: 000789990A

description: Original label before genotype mismatch fix: 00077E9C26


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_29_060121]

description: BSSE_QGF_161793_HLWHKBGXH_1_BR16_Clusters_2200_29_060121_ACGTTCCTTA_GACCGCTGTG_S147


title: 00077E8FAC


title: 00077E9963


title: B.1.617 10μg-1

description:
SG-In10-1
10x Genomics
LNP-mRNA vaccine


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_6_060121]

description: BSSE_QGF_161770_HLWHKBGXH_1_BR16_Clusters_2200_6_060121_CTGCGTTACC_TATGGCTCGA_S124


title: 00077E83F8


title: 00077E8978


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_25_060121]

description: BSSE_QGF_161789_HLWHKBGXH_1_BR16_Clusters_2200_25_060121_GTTGGATGAA_TTCCAGGTAA_S143


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_3_060121]

description: BSSE_QGF_161767_HLWHKBGXH_1_BR16_Clusters_2200_3_060121_AGAGAACCTA_GGTTATGCTA_S121


title: PRR-βE1-2

city: Vellore

first: Saravanabhavan

last: Thangavel

state: Tamil Nadu

address: Lab-7, Centre for Stem Cell Research, Christian Medical College campus,Bagayam.

department: Centre for Stem Cell Research (an unit of InStem-Bengaluru)

country: India

institute: Christian Medical College

data_processing:
All the raw data in .FASTq format was analyzed using DESEQ2.
Assembly: GrCH38
Supplementary files format and content: log2FoldChange

source_name: G-CSF mobilised Healthy donor HSPCs

growth_protocol: G-CSF mobilised HSPCs were pre-stimulated for 48hrs in StemSpan SFEM II media containing SCF, Flt3-L, TPO, and IL6. The HSPCs were electroporated with Cas9 RNP with sgRNA against PRR and βE1 using Lonza 4D nucleofector. For erythroid differentiation, IMDM GlutaMAX Supplement media containing 5% AB serum, Insulin (20µg/ml), Heparin (2U/ml), EPO (3U/ml), Holotransferrin (330 µg/ml), SCF (100ng/ml), IL3 (50ng/ml) and Hydrocortisone (1µg/ml). The cells were collected for RNA Seq analysis on Day 12 of erythroid differentiation.

extract_protocol:
RNA was extracted with Qiagen RNA isolation kit.
RNA libraries were prepared for sequencing using NEB Ultra II Directional RNA-Seq Library Prep kit protocol

treatment_protocol: Nucleofection: For electroporation of CD34+ve HSPCs for PRR-βE1 deletion, 50pmol of Cas9 RNP with sgRNA against PRR and 50pmol of Cas9 RNP with sgRNA against βE1 were used. For electroporation of CD34+ve HSPCs for βE1 editing, 100pmol of Cas9 RNP against βE1 were used. 2x105 cells were electroporated using P3 primary cell solution and supplement and were electroporated using Lonza 4D nucleofector with DZ100 pulse code. For control, CD34+ve HSPCs were electroporated with 100pmol of tracrRNA-Cas9 RNP.

value: HSPCs derived Erythroblats

value: treated with gRNA PRR-BetaE1

tag: day

value: Erythrioid differentiation day 12


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_26_060121]

description: BSSE_QGF_161790_HLWHKBGXH_1_BR16_Clusters_2200_26_060121_AATCCAATTG_CATGTAGAGG_S144

value: active


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_24_060121]

description: BSSE_QGF_161788_HLWHKBGXH_1_BR16_Clusters_2200_24_060121_ACAACTACTG_AGTTATCACA_S142


title: Bap1 cKO H3K4-me3 rep2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
The adapter sequences were trimmed using cutadapt v.1.18. Remaining reads were then aligned to the mouse genome (GRCm38) using Bowtie2 v.2.4.5 with the default parameters. PCR or optical duplicate reads, multi-mapped reads, and the reads aligned with mapping quality (MAPQ) < 5 were filtered out using Picard v.2.25.5 and Samtools v.1.9.
The genomic region between TSS-5kb and TSS+5kb was binned into 50-bp bins, and the number of reads in each bin was counted using the coverage tool from bedtools v.2.30.0 with the default parameters.
The read counts were then converted to counts per million (CPM) based on the library size.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including read counts in individual bins parsed from genomic regions of differentially expressed genes for each sample

source_name: endosteal mesenchymal stromal cells

extract_protocol:
To cross-link DNA to histones, 10^6 endosteal MSCs were harvested and incubated with a 1% formaldehyde solution for 10 min at 37°C on a rocker. After fixation, the cells were lysed with EzRIPA lysis buffer (150mM NaCl, 0.1% SDS, 1% NP-40, 0.5% Deoxycholic acid, 20mM HEPES pH7.5, ATTO) supplemented with a protease inhibitor and sonicated using a Bioruptor to make an average of 300~500 bp length. For pre-clearing, the sonicated cell supernatants were diluted with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.1, 167 mM NaCl) and incubated with Protein A Agarose/Salmon Sperm DNA (Millipore) for 30 min at 4°C on a rocker. Then, the samples were incubated with anti-ubiquityl-H2AK119 (Cell signaling), anti-trimethyl-H3K27 (Upstate), anti-acetyl-H3K27 (Upstate), and anti-trimethyl-H3K4 (Abcam) antibodies overnight at 4°C on a rocker. The beads were consecutively washed twice with a low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), a high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), and TE buffer (10 mM Tris pH 8, 1 mM EDTA). After washing of the beads, DNA-histone complexes were eluted with elution buffer (1% SDS, 0.1M NaHCO3) and were incubated with 5M NaCl for 4h at 65°C to reverse DNA-histone cross-linking. Then, DNA was purified using QIAquick Spin Kit (Qiagen). Purified DNA was analyzed by real-time quantitative PCR using Step One Plus (Applied Biosystems).
The ChIP-seq libraries were prepared using TruSeq DNA Sample prep Kit (Illumina).

value: Bap1 cKO (Prx1-cre;Bap1fl/fl)

tag: antibody

value: anti-acetyl-H3K27 (Upstate)


title: PRR-βE1-1


title: 00077E7BAA

description: Original label before genotype mismatch fix: 00077E7B99

value: eye

value: Heterogeneous Stock


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_21_060121]

description: BSSE_QGF_161785_HLWHKBGXH_1_BR16_Clusters_2200_21_060121_GAATACCTAT_ACAATAGAGT_S139

tag: timepoint


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_22_060121]

description: BSSE_QGF_161786_HLWHKBGXH_1_BR16_Clusters_2200_22_060121_TACGTGAAGG_CGGTTATTAG_S140


title: 00077E9993

tag: tissue


title: Bap1 cKO H3K27-ac rep1

value: anti-trimethyl-H3K4 (Abcam)


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_27_060121]

description: BSSE_QGF_161791_HLWHKBGXH_1_BR16_Clusters_2200_27_060121_TATGATGGCC_GATTGTCATA_S145


title: Bap1 cKO H3K27-me3 rep1

value: anti-trimethyl-H3K27 (Upstate)


title: Control

tag: cell type

value: Control


title: Bap1 cKO H2AK119-ub1 rep2

tag: genotype

value: anti-ubiquityl-H2AK119 (Cell signaling)


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_28_060121]

description: BSSE_QGF_161792_HLWHKBGXH_1_BR16_Clusters_2200_28_060121_CGCAGCAATT_ATTCCGCTAT_S146


title: Bap1 cKO H3K4-me3 rep1


title: Bap1 cKO H3K27-me3 rep2


title: βE1-2

tag: treatment

value: treated with gRNA BetaE1


title: Bap1 cKO H3K27-ac rep2


title: hEnSCs_H3K27me3_D0 input

first: Maria

last: Vila de Mucha

data_processing:
ChIP-Seq for FLAG tagged proteins data was aligned to a concatenated genome sequence of mouse (mm10) and spike-in of human (hg19) using bowtie2 [1] with --very-sensitive option. Uniquely mapped reads were extracted using samtools [2] and were used for the downstream analysis. Endogenous (mouse) and exogenous (human) reads were segregated into two bam files per sample using samtools. Spike-in calibration was performed according to the methodology suggested by Fursova et. al [3]. The two replicates for the endogenous and exogenous data were merged separately and peaks were called on the merged bams using MACS2[4] --broad option and --broad-cutoff = 0.001. A combined peak-set was created from the merged peaks from all the factors at the three time-points using DiffBind [5] in R with default parameters. Read counts were obtained for individual replicates for the combined peak-set using dba.count function in DiffBind. For the spike-in calibration, peaks present in all 12 samples were used and the normalisation was performed utilizing the methods described in Fursova et. Al. ChIP-Seq for H3K27me3 and H4ac data was aligned to a concatenated genome sequence of mouse (mm10) and spike-in of drosophila (BDGP5.25) using bowtie2 with --very-sensitive option. Uniquely mapped reads were extracted and separated in to exogenous (drosophila) and endogenous (mouse) reads using samtools.
RNA-seq data were processed using the Nextflow core RNA-seq pipeline with default settings (Ewels et al., 2020). In brief, reads were filtered to remove adaptors and low-quality bases using Trim Galore, aligned to GRCh38 using the STAR aligner (Dobin et al., 2013), and read counts generated using featureCounts (Liao et al., 2014).
Genome_build: mm10, hg19 and BDGP5.25
Supplementary_files_format_and_content: bigwigs

source_name: hEnSC

growth_protocol: Mouse embryonic stem cells Suz12GT/GT were cultured in 0.1% gelatin coated dishes using KO-DMEM (Thermofisher, 10829018) supplemented with 10% FBS validated for mouse embryonic stem cell culture (Thermofisher, 16141079), 5% knockout serum replacement (Thermofisher, 10828028), non-essential amino acids (Thermofisher, 11140035), L-glutamine 2 mM (Thermofisher, 25030-024), 2-mercaptoethanol 50uM (Thermofisher, 31350010), penicillin-streptomycin 100 U/mL (Thermofisher, 15140-122), sodium pyruvate 1 mM (Thermofisher, 11360039) and 1000 U/ml leukemia inhibitory factor (03-0011-100, Stemgent). mESCs were differentiated to form embryoid bodies as described previously (Brien et al., 2012). Briefly, mESCs were cultured and reseeded twice prior to forming EBs. Before seeding, cells were filtered using a 70 um cell strainer, and washed twice with LIF-free mESCs media. Afterwards, cells were seeded in ultra low attachment T75 flasks (Corning, 3814) in a single cell suspension of 2x106 cells per flask. LIF-free media was changed every second day and EBs were harvested at days 4 and 8. The collection of endometrial biopsies was approved by the NHS National Research Ethics - Hammersmith and Queen Charlotte's & Chelsea Research Ethics Committee (REC reference: 1997/5065) and Tommy’s National Reproductive Health Biobank (REC reference: 18/WA/0356). Samples were obtained using a Wallach Endocell sampler 5 to 10 days after the pre-ovulatory luteinizing hormone (LH) surge. hEnSC were harvested as previously described (Barros et al., 2016). Briefly, endometrial biopsies were subjected to enzymatic digestion using 500 µg/ml collagenase type Ia (Sigma-Aldrich,) and 100 µg/mL DNase I (Lorne Laboratories Ltd) for 1 hr at 37°C. Digested tissue was filtered through a 40 µm cell strainer to remove glandular cell clumps, and the flow-through collected and cultured in DMEM/F12 (Thermo Scientific, 31330038) containing 10% dextran-coated charcoal-treated foetal bovine serum (DCC-FBS), 1 × antibiotic-antimycotic mix (ThermoFisher, 15240062), 10 µM L-glutamine, 1 nM estradiol (Sigma, E2758) and 2 μg/mL insulin (Santa Cruz, sc-360248) .   Cells were reseeded at a 1:2 or 1:3 ratio when confluence was reached. All experiments were carried out before reaching the 10th passage. hEnSC were seeded at a confluency of 105 cells/well in 6 well plates and 1.5 ml of concentrated retrovirus added to each well in the presence of 8 μg/ml polybrene (Merck, TR-1003-G). Cells were then spinoculated at 500 x g for 1 hr at RT and incubated for 12 hrs. Cells were washed with fresh media and, after 3 days, selected with 5 g/ml blasticidin until they reached near confluency and no cells were found in the non-transduced control plate. Cells were reseeded and, at confluency two days later, decidualised for up to 8 days in DCC media with 2% DCC FBS supplemented with antibiotic antimycotic solution, l-glutamine, 50 M 8-Bromoadenosine 3’, 5’ cyclic mono-phosphate (8-Br-cAMP, Merck B5386) and 1 M medroxyprogesterone acetate (MPA, Sigma M1629), with the media changed every second day. Samples were taken at 0 and 8 days during decidualisation.

extract_protocol:
ChIP was performed as described, with minor modifications (Kanhere et al., 2012). Briefly, cells were trypsinised, resuspended in PBS and then crosslinked by adding 1/10 of cross-linking solution (11% formaldehyde, 0.1 M NaCl, 1mM EDTA pH 8, 0.5 mM EGTA pH 8, 50 mM HEPES pH 8) for 15 min in suspension. Formaldehyde was quenched by adding glycine to a final concentration of 1.25 mM. Cells were then washed twice with ice-cold PBS, centrifuging at 290G at 4 C for 10 min. After last wash, cells were flash-frozen and stored at -80 C. To carry out ChIP, cells were thawed in 5 ml per 3x107 lysis buffer 1 (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % IGEPAL CA-630, 0.25 % Triton X-100). Then cells were incubated at 4°C for 10 min with rocking. Cells were recovered by centrifuging at 290 C for 10 min at 4 C. Supernatant was discarded, and nuclei were resuspended in the same volume of lysis buffer 2 (10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, supplemented with 0.1 DTT and complete protease inhibitor) and incubated at 4°C for 10 min with rocking. Nuclei were pelleted again at 290 G for 10 min at 4°C, and resuspended in 100 ml of lysis buffer 3 (10mM Tris pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauryl sarcosine, 0.2 % SDS, supplemented with 0.1 DTT and complete protease inhibitor) per 5x106 cells. Cells were incubated for 30 min on ice, to allow lysis. Afterwards, lysates were sonicated for 15 cycles of 30s on and 30s off, using a Diagenode Bioruptor Pico. For EB processing, the same protocol was followed, except using the resulting EB formed by 2 plates per timepoint.  DNA was then quantified using Qubit dsDNA HS Assay kit (Thermofisher) and ChIP was performed using 45 mg of mouse chromatin, with 5 mg of human chromatin extracted from human immortalised fibroblasts (hTERT) cells stably expressing FLAG-tagged SUZ12 for factor, or 5 ug of Drosophila chromatin for histone modifications were added as calibration control for downstream analysis (Furzova et al 2019). The resulting mix of mouse and human chromatin was topped up to 900ul per IP. Then, 100 ml of Triton X-100 10% solution was added, and insoluble material was span down at 17,000 G for 20 mins at 4oC. 2% of the lysate was stored at -20oC to be used as input and whole cell extract and the remaining lysate was incubated overnight at 4oC with 50 ml Protein G Dynabeads preincubated for at least 4 hr with 2.5 mg of FLAG antibody (Sigma, A8592), H3K27me3 (Abcam, ) or H4 pan acetyl (Thermofisher, PA5-40083). Beads were washed and bound complexes were incubated in elution buffer () to reverse crosslinks by heating at 65oC for 1 h. IP and input DNA were then treated with 0.5 mg/ml RNAseA and  mg/ml of proteinase K (Ambion, ), and immunoprecipitated DNA was purified using Kapa Pure beads (Roche, KK8000) using manufacturers recommendations. DNA was resuspended in 60 ml of 10 mM Tris pH 8 and quantified using ds DNA HS Qubit kit (Thermofisher, Q32851). Total RNA was purified from hEnSC using TRIsure (Bioline, BIO-38033), treated with DNaseTurbo (Ambion, AM2238),  quantified with a Qubit RNA High Sensitivity assay kit (Invitrogen, Q32855) and its quality assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513).
DNA libraries were generated using NEBNext Ultra II DNA library prep (NEB) using 1.2 ng of DNA and 9 cycles of PCR. Quality and distribution of all libraries was assessed using 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent, 5067-4626) followed by qPCR quantification with Kapa Library Quant Kit (Roche, KK4824).  Sequencing was performed as 75 bp single end reads on Illumina NEXTseq 550 platform for FLAG immunoprecipitation and 138 bp single single end reads on  Novaseq plataform for histones modifications immunoprecipitation, using biological duplicates. For primary hEnSCs, RNA-seq libraries were prepared with 100 ng of total RNA using the KAPA Stranded RNA-Seq Kit with RiboErase (Roche, KR1151) following the manufacturer’s instructions and were sequenced on Illumina Nextseq 2000 to generate 2x50 bp paired-end reads.

value: Endometrial biopsy

tag: treatment/genotype

value: Day 0 decidualisation (cAMP/MPA)

tag: ip antibody


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_2_060121]

description: BSSE_QGF_161766_HLWHKBGXH_1_BR16_Clusters_2200_2_060121_AGGACAGGCC_CATTCCAGCT_S120

tag: cancer type

value: breast

value: xenograft

tag: number of ctcs


title: Bap1 WT H3K27-ac rep2

tag: strain

value: Wild Type (Bap1fl/fl)


title: Bap1 WT H3K27-ac rep1


title: βE1-1

value: HSPCs derived Erythroblats


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_23_060121]

description: BSSE_QGF_161787_HLWHKBGXH_1_BR16_Clusters_2200_23_060121_CTTATTGGCC_GATAACAAGT_S141


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_18_060121]

description: BSSE_QGF_161782_HLWHKBGXH_1_BR16_Clusters_2200_18_060121_CCAGGCACCA_ACGCTAATTA_S136


title: BR16 single CTC at 22h [BR16_Singles_2200_1_060121]

description: BSSE_QGF_161734_HLWHKBGXH_1_BR16_Singles_2200_1_060121_GTCCGTAAGC_CGTGTATCTT_S89


title: Bap1 WT H3K4-me3 rep2


title: Bap1 WT H3K27-me3 rep2


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_17_060121]

description: BSSE_QGF_161781_HLWHKBGXH_1_BR16_Clusters_2200_17_060121_TGGCCTCTGT_TGAGACAGCG_S135


title: Bap1 cKO H2AK119-ub1 rep1


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_14_060121]

description: BSSE_QGF_161778_HLWHKBGXH_1_BR16_Clusters_2200_14_060121_ATGTAACGTT_ACGATTGCTG_S132


title: Bap1 WT H3K4-me3 rep1


title: Bap1 WT H3K27-me3 rep1


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_13_060121]

description: BSSE_QGF_161777_HLWHKBGXH_1_BR16_Clusters_2200_13_060121_TTCGGTGTGA_GAACAAGTAT_S131


title: hEnSCs_H3K27me3_D0


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_12_060121]

description: BSSE_QGF_161776_HLWHKBGXH_1_BR16_Clusters_2200_12_060121_ATAGCCAAGA_AGTGCCACTG_S130


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_4_060121]

description: BSSE_QGF_161768_HLWHKBGXH_1_BR16_Clusters_2200_4_060121_GATATTGTGT_ACCACACGGT_S122


title: Bap1 WT H2AK119-ub1 rep2


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_20_060121]

description: BSSE_QGF_161784_HLWHKBGXH_1_BR16_Clusters_2200_20_060121_GGCCAATATT_CGGTCCGATA_S138


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_1_060121]

description: BSSE_QGF_161765_HLWHKBGXH_1_BR16_Clusters_2200_1_060121_TCCGCCAATT_CTCCGTGCTG_S119


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_16_060121]

description: BSSE_QGF_161780_HLWHKBGXH_1_BR16_Clusters_2200_16_060121_TGGTGTTATG_TCCAATTCTA_S134


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_19_060121]

description: BSSE_QGF_161783_HLWHKBGXH_1_BR16_Clusters_2200_19_060121_CCGGTTCCTA_TATATTCGAG_S137


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_11_060121]

description: BSSE_QGF_161775_HLWHKBGXH_1_BR16_Clusters_2200_11_060121_TCTAGGCGCG_CGAAGGTTAA_S129


title: H4ac_n2_JAZF1-SUZ12_D0

source_name: mESC

value: mESC

value: Day 0 embryoid body formation

value: H4 pan acetyl PA5-40083


title: H4ac_n2_SUZ12D93_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_4_060121]

description: BSSE_QGF_161679_HLWHKBGXH_1_BR16_Clusters_1000_4_060121_CAGCCGCGTA_ACTAGCCGTG_S34

source_name: BR16 CTC cluster at 10h

value: resting


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_30_060121]

description: BSSE_QGF_161705_HLWHKBGXH_1_BR16_Clusters_1000_30_060121_TTACCTGGAA_ACAGTTCCAG_S60


title: H4ac_n2_SUZ12_D0


title: H4ac_n2_SUZ12D93_D8

value: Day 8 embryoid body formation


title: H4ac_n2_SUZ12_D8


title: Bap1 WT H2AK119-ub1 rep1


title: H3K27me3_n2_SUZ12D93_D0


title: H3K27me3_n2_JAZF1-SUZ12_D0


title: H3K27me3_n2_JAZF1-SUZ12_D8


title: H4ac_n2_JAZF1-SUZ12_D8


title: H3K27me3_n2_SUZ12D93_D8


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_24_060121]

description: BSSE_QGF_161699_HLWHKBGXH_1_BR16_Clusters_1000_24_060121_GCATAAGCTT_TTCCGTCGCA_S54


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_28_060121]

description: BSSE_QGF_161703_HLWHKBGXH_1_BR16_Clusters_1000_28_060121_CTCGCTTCGG_TACTAGTCAA_S58


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_29_060121]

description: BSSE_QGF_161704_HLWHKBGXH_1_BR16_Clusters_1000_29_060121_CTGTTGGTCC_ATAGACCGTT_S59


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_22_060121]

description: BSSE_QGF_161697_HLWHKBGXH_1_BR16_Clusters_1000_22_060121_TGATGTAAGA_GTGCGTCCTT_S52


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_5_060121]

description: BSSE_QGF_161680_HLWHKBGXH_1_BR16_Clusters_1000_5_060121_GGTAACTCGC_AAGTTGGTGA_S35


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_23_060121]

description: BSSE_QGF_161698_HLWHKBGXH_1_BR16_Clusters_1000_23_060121_GGAATTGTAA_AGCACATCCT_S53


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_9_060121]

description: BSSE_QGF_161684_HLWHKBGXH_1_BR16_Clusters_1000_9_060121_CAATCGGCTG_GCTGTAGGAA_S39


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_27_060121]

description: BSSE_QGF_161702_HLWHKBGXH_1_BR16_Clusters_1000_27_060121_TCTATCCTAA_CGTCGACTGG_S57


title: H3K27me3_n2_SUZ12_D8


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_6_060121]

description: BSSE_QGF_161681_HLWHKBGXH_1_BR16_Clusters_1000_6_060121_ACCGGCCGTA_TGGCAATATT_S36


title: H3K27me3_n2_SUZ12_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_21_060121]

description: BSSE_QGF_161696_HLWHKBGXH_1_BR16_Clusters_1000_21_060121_CCTGTCTGTC_ACTGTTGTGA_S51


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_8_060121]

description: BSSE_QGF_161683_HLWHKBGXH_1_BR16_Clusters_1000_8_060121_GTGCAGACAG_TACCATCCGT_S38


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_25_060121]

description: BSSE_QGF_161700_HLWHKBGXH_1_BR16_Clusters_1000_25_060121_CTGAGGAATA_CTTAACCACT_S55


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_26_060121]

description: BSSE_QGF_161701_HLWHKBGXH_1_BR16_Clusters_1000_26_060121_AACGCACGAG_GCCTCGGATA_S56


title: H4ac_n1_JAZF1-SUZ12_D8


title: H4ac_n1_JAZF1-SUZ12_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_20_060121]

description: BSSE_QGF_161695_HLWHKBGXH_1_BR16_Clusters_1000_20_060121_GACACCATGT_TCAACGTGTA_S50


title: H4ac_n1_SUZ12D93_D8


title: H4ac_n1_SUZ12_D8


title: H4ac_n1_SUZ12D93_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_19_060121]

description: BSSE_QGF_161694_HLWHKBGXH_1_BR16_Clusters_1000_19_060121_AGTGTTGCAC_CTGGTACACG_S49


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_18_060121]

description: BSSE_QGF_161693_HLWHKBGXH_1_BR16_Clusters_1000_18_060121_CAGTGGCACT_TAACAATAGG_S48


title: H4ac_n1_SUZ12_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_17_060121]

description: BSSE_QGF_161692_HLWHKBGXH_1_BR16_Clusters_1000_17_060121_GTCCTGGATA_CGGTGGCGAA_S47


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_16_060121]

description: BSSE_QGF_161691_HLWHKBGXH_1_BR16_Clusters_1000_16_060121_AGATCCATTA_ATCTCTACCA_S46


title: H3K27me3_n1_JAZF1-SUZ12_D0


title: H3K27me3_n1_JAZF1-SUZ12_D8


title: RNA_h9coD5_ZNF468_WT-3

city: Amsterdam

first: Frank

last: Jacobs

address: Science Park 904

department: Sammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

data_processing:
Trimming of reads: trimmomatic version 0.36, SLIDINGWINDOW:4:20 MINLEN:30.  Mapping of reads: HISAT2 default settings  Generating count files: featureCounts, GTF.featureType="exon", GTF.attrType="transcript_id", countMultiMappingReads=TRUE,  DESeq2 analysis: DESeq2 default settings
featureCounts output for RNA-seq data.
Supplementary files format and content:tab delimited file containing featureCounts output for RNA-seq data.
Assembly: hg19

source_name: cortical organoids day 5

growth_protocol: For cortical organoid formation, hESC colonies were grown on mouse embryonic fibroblasts in daily refreshed hESC medium (DMEM-F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM Non-Essential Amino Acids solution (Gibco), 100 µM 2-mercaptoethanol (Gibco)) and fresh 8 ng/ml bFGF (Sigma)). Colonies of 1-2 mm were transfered to 60 mm ultra low attachment dishes (corning) in 99% hESC medium supplemented with 1 mM sodium pyruvate (Gibco). The next day, media was replaced for differentiation media with fresh 3 µM IWR-1-Endo, 1 µM Dorsomorphin, 10 µM SB-431542 hydrate, and 1 µM Cyclopamine hydrate and changed every other day. On day 3, the dish was placed on a rocker. From day 18 onwards, organoids were cultured in Neurobasal/N2 media (Neurobasal (Gibco) supplemented with 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x N-2 supplement (Gibco)) with 1 µM Cyclopamine hydrate, and from day 24 onwards, no inhibitors were added anymore.

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol with DNAse I treatment and cleaned-up using the RNA Clean & Concentration kit (ZYMO).
TruSeq Stranded Total RNA Library Prep kit (Illumina)
RNA-seq 75bp paired end reads on a NextSeq 550 device.

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the first exon of ZNF441, before cortical organoid formation

value: h9ESC derived cortical organoids

tag: chip antibody

value: WT


title: ADAR1 KD cell line

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: ADAR1 KD cell line

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information to estimate raw counts and FPKM values
DESeq2 was used for normalization
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts and FPKM for each gene

source_name: IMR90 cell llines

extract_protocol:
Total RNA was isolated from cells using RNeasy mini kit (Qiagen, 74106) and digested with DNase I (Qiagen, 79254).
The libraries were prepared using a KAPA RNA HyperPrep kit (cat. no. Roche, Cat. no: 07962312001)

tag: adar1 status

value: KD

tag: cell line


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_14_060121]

description: BSSE_QGF_161689_HLWHKBGXH_1_BR16_Clusters_1000_14_060121_CTGCGAGCCA_AATCCGGCCA_S44

tag: origin

tag: donor

tag: sample type


title: ADAR1 Ctrl cell line

description: ADAR1 Ctrl cell line

value: Ctrl


title: H3K27me3_n1_SUZ12_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_12_060121]

description: BSSE_QGF_161687_HLWHKBGXH_1_BR16_Clusters_1000_12_060121_GTCTAATGGC_AGTGGTCAGG_S42

tag: number of wbcs attached


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_13_060121]

description: BSSE_QGF_161688_HLWHKBGXH_1_BR16_Clusters_1000_13_060121_CCATCTCGCC_TTCTATGGTT_S43

tag: timepoint


title: H3K27me3_n1_SUZ12D93_D0


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_1_060121]

description: BSSE_QGF_161676_HLWHKBGXH_1_BR16_Clusters_1000_1_060121_GTGACACGCA_GCTTACGGAC_S31


title: H3K27me3_n1_SUZ12_D8


title: RNA_h9coD5_ZNF468_KO-3


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_11_060121]

description: BSSE_QGF_161686_HLWHKBGXH_1_BR16_Clusters_1000_11_060121_ACTCGGCAAT_GACAACTGAA_S41


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_10_060121]

description: BSSE_QGF_161685_HLWHKBGXH_1_BR16_Clusters_1000_10_060121_TATGTAGTCA_CGCACTAATG_S40


title: RNA_h9coD5_ZNF468_KO-4


title: RNA_h9coD5_ZNF468_WT-1


title: RNA_h9coD5_ZNF468_KO-2


title: Genomic DNA from myxopapillary ependymoma 48

city: Hamburg

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing: Statistical analysis was performed using the minfi package version 1.30.0 with the statistical programming language R version 3.6.0

source_name: myxopapillary ependymoma 48

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: Sex

value: female

tag: age

tag: mpe subtype

value: A

tag: material

value: FFPE

tag: pfs [years]

tag: pfs status

value: relapsed

tag: localization

value: lumbar

tag: histology

value: myxoid


title: RNA_h9coD5_ZNF468_KO-1

tag: cell type

tag: genotype


title: RNA_h9coD35_ZNF441_WT-3

source_name: cortical organoids day 35

tag: chip antibody


title: RNA_h9coD35_ZNF441_WT-2


title: BR16 CTC cluster at 10h [BR16_Clusters_1000_15_060121]

description: BSSE_QGF_161690_HLWHKBGXH_1_BR16_Clusters_1000_15_060121_CGTTATTCTA_CCATAAGGTT_S45

tag: cancer type

value: breast

value: xenograft

tag: number of ctcs


title: H3K27me3_n1_SUZ12D93_D8

value: mESC

tag: treatment/genotype

tag: ip antibody


title: Genomic DNA from myxopapillary ependymoma 28

source_name: myxopapillary ependymoma 28

value: male

tag: resection

value: STR


title: RNA_h9coD5_ZNF468_WT-4


title: Genomic DNA from myxopapillary ependymoma 32

source_name: myxopapillary ependymoma 32

value: papillary


title: Genomic DNA from myxopapillary ependymoma 34

source_name: myxopapillary ependymoma 34

value: B


title: RNA_h9coD5_ZNF468_WT-2

value: h9ESC derived cortical organoids


title: RNA_h9coD35_ZNF441_KO-3


title: RNA_h9coD35_ZNF441_KO-1

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol with DNAse I treatment and cleaned-up using the RNA Clean & Concentration kit (ZYMO).
RNA-seq 75bp paired end reads on a NextSeq 550 device.


title: RNA_HEK293_EV-control_2

treatment_protocol: transfection + FACS

value: WT


title: RNA_HEK293_ZNF519-OE_2

value: ZNF519 overexpression


title: RNA_HEK293_ZNF519-OE_3


title: RNA_HEK293_EV-control_3


title: RNA_h9coD35_ZNF441_KO-2


title: H3K4me3_h9coD35_ZNF519_KO31-1

data_processing:
Trimming of reads: trimmomatic version 0.36, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40.  Mapping of reads: Bowtie2, --end-to-end --very-sensitive on hg19, followed by samtools view -b, samtools sort and samtools rmdup.  Generation of bigwig coverage tracks: bedtools genomecov -bga, followed by conversion of bedgraph to bigwig format using the bedGraphToBigWig script of UCSC.  Peakcalling: MACS2 version 2.1.1.20160309 callpeak -f BAM -g 2.7e9 --keep-dup all --call-summits.
MACS2 output of ChIP-seq data.
Supplementary files format and content: narrowPeak:MACS2 output of ChIP-seq data.
Assembly: hg19

extract_protocol:
Organoids were rinsed in medium, homogonized in a 2ml Kontes Glass Co. dounce and immediately crosslinked after. Cells were lysed, chromatin was sheared to ~400bp fragments and chromatin was extracted using antibody-coated beads. DNA was purified using RNase cocktail enzyme mix, proteinase K, two phenol:chloroform (1:1) and one chloroform extractions followed by DNA precipitation in ethanol and a Zymo DNA Clean & Concentrator clean-up.
TruSeq ChIP Library Preparation Kit (Illumina) with the following modifications: DNA clean & concentrator-5 kit (Zymo research) was used instead of beads for DNA purification. Size selections were performed before and after amplification on an E-gel Safe Imager (Invitrogen) using 2% E-gel SizeSelect gels (Invitrogen). The ChIP-DNA fraction of 300-400 bp in size (including adapters) was isolated and purified.
ChIP-seq 75bp paired end reads on a NextSeq 550 device.

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the first exon of ZNF519, before cortical organoid formation

value: 6 microgram H3K4me3 (millipore 07-473, lot 2930138)


title: RNA_HEK293_ZNF519-OE_1


title: H3K4me3_h9coD35_ZNF519_EV7-3

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid, before cortical organoid formation


title: H3K4me3_h9coD35_ZNF519_KO31-2


title: H3K4me3_h9coD35_ZNF519_EV7-2


title: RNA_HEK293_EV-control_1


title: H3K4me3_h9coD35_ZNF519_EV7-1


title: RNA_h9coD35_ZNF441_KO-4


title: RNA_h9coD35_ZNF441_WT-4


title: RNA_h9coD35_ZNF441_WT-1


title: RNA_h9coD35_ZNF519_KO31-2


title: RNA_h9coD35_ZNF519_KO31-3


title: Genomic DNA from myxopapillary ependymoma 57

source_name: myxopapillary ependymoma 57

value: NED


title: RNA_h9coD35_ZNF519_KO31-1


title: RNA_h9coD35_ZNF519_EV7-3


title: RNA_h9coD35_ZNF519_EV7-2


title: RNA_h9coD35_ZNF519_EV7-1


title: NRVM_THZ1_3

city: South San Francisco

first: Saptarsi

last: Haldar

address: 1120 Veterans Blvd

institute: Amgen

data_processing:
Each RNA-seq sample was aligned independently with the following procedure. The raw RNA-seq reads from each sample were aligned with TopHat v2.1.1 with options “-p 8 -r 300 --library-type fr-firststrand --no-coverage-search”. Each sample was aligned either against the mm9 or rn5 reference genome as appropriate for the sample.
After alignment, we quantified the number of mapped reads per gene per sample using htseq-counts. Each application of htseq-counts was run with the following options: ”-s reverse –f bam”. Each sample was quantified against the GENCODE mm9 transcript reference or the UCSC rn5 transcript reference, depending on the source of the sample.
We identified differentially expressed genes using DeSeq2. We imported the quantifications from htseq-count into DeSeq2, and we analyzed all samples from the same organism together in one analytical run. Replicate samples were grouped by their type (e.g., baseline, THZ1-treated) in order to better estimate the sample-level variance for comparison across samples. We ran the standard DeSeq2 workflow without modifications, and we used an adjusted p-value of 0.1 (10% FDR) as the cutoff threshold for identifying our differentially expressed genes throughout the paper (with the specific comparison between samples noted in the paper).
Genome_build: rn5
Supplementary_files_format_and_content: Table of normalized RNA-seq expression values by gene and by sample

source_name: NRVM

growth_protocol: Neonatal rat ventricular myocyte (NRVM) were isolated from the hearts of 2-3 day old Sprague-Dawley rat pups from Charles River and maintained under standard conditions as described previously3. After overnight digestion with 0.25% trypsin at 4°C, cells were dissociated from tissue through series of digestion with 300 U/mL collagenase II (Worthington Biochemical Corporation, Lakewood, NJ). The dissociated cells were then preplated for 1.5 hours in cell culture dishes followed by 24 hours exposure to BrdU in culture medium to remove contaminating nonmyocytes and inhibit cardiomyocyte proliferation. Unless otherwise stated, NRVM were plated at a density of 105 cells/mL. Cells were initially plated in growth medium (DMEM supplemented with 5% FBS, 100 U/ml penicillin-streptomycin and 2 mM L-glutamine) for 48 hours. Prior to stimulation with agonists, NRVM were maintained in serum-free medium ((DMEM supplemented with 0.1% BSA, 1% insulin-transferrin-selenium supplement (Sigma I3146), 100 U/ml penicillin-streptomycin, and 2 mM L-glutamine) for additional 48 hours.

extract_protocol:
Total RNA was isolated from NRVM with High Pure RNA isolation kit (Roche 11828665001) with on-column DNAase treatment according to manufacturer’s directions according to manufacturer’s instruction.
RNA libraries were prepared by using KAPA mRNA HyperPrep Kit (Roche)

treatment_protocol: 48 hours of treatment: 1. Vehicle ; 2. PE (100 μM); 3. PE (100 μM)+THZ1(10 nM); 4. THZ1 (10 nM);

tag: strain

value: Sprague Dawley

tag: tissue

value: heart ventricles

value: post natal day 2-3


title: RNA_h9coD14_ZNF519_KO31-3

source_name: cortical organoids day 14


title: H3K4me3_h9coD35_ZNF519_KO31-3


title: NRVM_THZ1_2

tag: age


title: RNA_h9coD14_ZNF519_KO31-2


title: RNA_h9coD14_ZNF519_KO31-1


title: NRVM_THZ1_1


title: WT naive CD8, IgG ChIP-seq

city: washington dc

first: Shaoqi

last: Zhu

state: District of Columbia

address: 725 21st st nw

institute: The George Washington University

data_processing:
The sequencing quality of ChIP-seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9

source_name: CD8 T cells

extract_protocol:
Sort-purified naïve CD8+ T cells were incubated with 2 mM disuccinimidyl glutarate (Millipore Sigma) for 45 min at room temperature and then cross-linked with 1% formaldehyde for 10 min at room temperature. The chromatin was extracted and sonicated with a Q125 sonicator equipped with an 1/8-inch diameter probe (QSonica) at 20% input amplitude, at a 20-second duration for eight times. The resulting chromatin fragments were immunoprecipitated with 3 µl of the anti-CTCF antibody, properly washed and then genomic DNA fragments were extracted with Qiagen minelute reaction cleanup kit.
The DNA segments from CTCF ChIP-seq were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.

value: wild type

value: splenocytes

tag: cell phenotype

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+

value: Antibody name:Normal Rabbit IgG; Vendor:Cell Signaling Technology; Catalog#:2729s; Lot#:9


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq CellSignaling Ab, rep2

value: Antibody name:Anti-CTCF antibody; Vendor:Cell Signaling Technology; Catalog#:3418s; Lot#:4


title: RNA_h9coD14_ZNF519_EV7-2


title: NRVM_THZ1_PE_2


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq Milipore Ab, rep1

value: Antibody name:Anti-CTCF Antibody; Vendor:Millpore Sigma; Catalog#:07-729 Lot#:3388643


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq CellSignaling Ab, rep1


title: RNA_h9ESC_ZNF519_KO93

source_name: hESCs

growth_protocol: hESC colonies were grown on mouse embryonic fibroblasts in daily refreshed hESC medium (DMEM-F12 (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 100 U/ml penicillin/100 µg/ml streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1x MEM Non-Essential Amino Acids solution (Gibco), 100 µM 2-mercaptoethanol (Gibco)) and fresh 8 ng/ml bFGF (Sigma)).

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid containing gRNAs targeting the first exon of ZNF519


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq SantaCruz Ab, rep4

value: Antibody name:Anti-CTCF Antibody; Vendor:Santa Cruz; Catalog#:sc-271514X Lot#:J619


title: RNA_h9coD14_ZNF519_EV7-1


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq SantaCruz Ab, rep3


title: NRVM_THZ1_PE_1


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq SantaCruz Ab, rep2


title: NRVM_PE_2


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq SantaCruz Ab, rep1


title: WT naive CD8, CTCF ChIP-seq CellSignaling Ab, rep2


title: RNA_h9ESC_ZNF519_KO92


title: RNA_h9ESC_ZNF519_KO31


title: RNA_h9ESC_ZNF519_EV7

treatment_protocol: h9ESCs were transfected with the pX330-U6-Chimeric_BB-CBh-hSpCas9 plasmid


title: WT naive CD8, CTCF ChIP-seq CellSignaling Ab, rep1


title: Tcf1/Lef1-deficient CD8, CTCF ChIP-seq Milipore Ab, rep2


title: NRVM_THZ1_PE_3


title: RNA_h9coD14_ZNF519_EV7-3


title: WT naive CD8, CTCF ChIP-seq Milipore Ab, rep1


title: RNA_h9ESC_ZNF519_EV2


title: WT naive CD8, CTCF ChIP-seq Milipore Ab, rep2


title: RNA_h9ESC_ZNF519_EV6


title: BR16 CTC cluster at 22h [BR16_Clusters_2200_15_060121]

description: BSSE_QGF_161779_HLWHKBGXH_1_BR16_Clusters_2200_15_060121_AACGAGGCCG_ATACCTGGAT_S133

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.6.5; parameters : –q 20 –length 20).
Trimmed reads were aligned to human (GRCh38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) with splice junctions from the human GENCODE annotation (release 35). To eliminate residual contamination from mouse RNA, reads derived from xenograft models were also aligned to mouse (GRCm38) genome reference using STAR (v.2.7.3a; parameters: --twopassMode Basic --outSAMmapqUnique 60 --sjdbGTFfile) , with splice junctions from the mouse GENCODE annotation (release M25), and assigned to either human or mouse using Disambiguate (v1.0.0).
The gene-level expression counts were computed with featureCounts (v.2.0.1; parameters: -t exon -g gene_id --minOverlap 10 -Q 10) using the human gene annotations from GENCODE (release 35).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing per sample raw counts as obtained from featureCounts.

source_name: BR16 CTC cluster at 22h

extract_protocol:
Using the CellCelector, an automated single-cell picking system (ALS), single CTCs, CTC clusters and CTC-WBC clusters were collected and immediately transferred into individual tubes (Axygen, 321-032-501) containing 2.5 μl RLT Plus lysis buffer and 1U SUPERase IN RNA inhibitor (Invitrogen, AM2694). Samples were immediately frozen and kept at 800C until further processing.
cDNA was amplifiead and libraries prepared according to the Smart-seq2 protocol.

value: breast

tag: origin

value: xenograft

tag: donor

tag: sample type

tag: number of wbcs attached

tag: timepoint

value: active


title: NRVM_PE_3


title: WT naive CD8, IgG Cut&Run

data_processing:
Library strategy: Cut&Run
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
Naïve CD8+ T cells were sort-purified from the spleen, and stimulated with IL-7 and IL-15 in vitro for 0 or 72 hrs. The live cells were permeabilized, and then incubated with CTCF antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.

tag: time point


title: WT naive CD8, CTCF ChIP-seq SantaCruz Ab, rep2

tag: genotype


title: WT naive CD8, CTCF ChIP-seq SantaCruz Ab, rep3

tag: chip antibody


title: WT naive CD8, CTCF ChIP-seq SantaCruz Ab, rep1


title: WT naive CD8, CTCF Cut&Run, rep1


title: d3-m6A-P7-rep2

city: Hangzhou

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

country: China

institute: Zhejiang University

data_processing:
adapter, low quality reads and short reads were trimed with fastp v0.19.7 with following parameters: -f 10 -F 10 -x --detect_adapter_for_pe -l 25
clean reads were aligned with hg38 genome using hisat2 v2.1.0 with parameters: --rna-strandness RF
sam files were converted and sorted into bam files using samtools with parameters: samtools sort -@ 4 sam -o bam
bam files were counted using featureCounts
differentially expressed genes were obtained using a R package DESeq2
Assembly: hg38
Supplementary files format and content: txt file presents the counting result of bam files, csv file shows the tpm results used for heatmap,xlsx files mark the differentially expressed gene sets

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high-glucose media(HyCloneSH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco 10270) , 1% 100× Pen Strep (HyClone SV30010) at 37 °C with 5 % CO2

extract_protocol:
total RNA was extracted with TRIZOL Reagent following protocol (thermofisher)
total RNA was used as input, and libraries were constructed following illumina's protocol. Briefly, polyA-RNA was first extracted using oligd(T) conjungated beads, fagmented into about 100 nt, reverse transcribed into cDNA and amplified by PCR.

treatment_protocol: 100mM d3-m6A was used as stock and added into DMEM at a final concentration of 500 μM, HeLa cells were incubated with d3-m6A containing DMEM for different time courses

tag: treatment

value: treated with d3-m6A for 168 hours

tag: cell line

value: HeLa


title: WT naive CD8, CTCF Cut&Run, rep2


title: NRVM_Veh_WCE

data_processing:
Each ChIP-seq sample was processed and aligned using bowtie 1. Each sample was aligned against the rn5 reference genome using bowtie with options “-k 1 -m1”. All gene track and ChIP-seq quantifications were normalized by the number of (uniquely) mapped reads to estimate the “reads per million” (rpm) quantity.
Genome_build: rn5
Supplementary_files_format_and_content: WIG files of ChIP-seq density across the genome

extract_protocol:
NRVM were plated in 15 cm dishes at 4 x 10^6 cells/dish. Total of 15 million cells were used for each immunoprecipitation. After indicated treatments, cells were crosslinked with 1% formaldehyde for 10 min at room temperature followed by quenching with 0.125M glycine for 5 min. Cells were then lysed and chromatin was extracted. Isolated chromatin was subjected to shearing with Bioruptor (Diagenode) for 16 cycles (30sec on and 30 sec off/cycle) at high intensity. Small volume of sheared chromatin (50 uL) from each was stored at -80 °C as input. The rest of sheared chromatin was then incubated with 5mg RNAPII antibody (clone 8WG16, BioLegend 920102 lot B217159) with 50uL Dynabeads (Invitrogen) overnight at 4 °C. Chromatin was washed, eluted and reverse crosslinked overnight at 65 °C. Genomic DNA was purified from both immunoprecipitated samples and input samples.
The library was prepared with TrueSeq ChIP kit (Illumina)

treatment_protocol: 48 hours of treatment: 1. Vehicle ; 2. PE (100 μM); 3. PE (100 μM)+THZ1(10 nM)


title: NRVM_Veh_RNAPII

value: RNAPII antibody (clone 8WG16, BioLegend 920102 lot B217159)


title: WT naive CD8, CTCF ChIP-seq SantaCruz Ab, rep4


title: NRVM_Veh_1


title: NRVM_Veh_2


title: NRVM_PE_THZ1_WCE


title: NRVM_Veh_3


title: NRVM_PE_WCE


title: NRVM_PE_THZ1_RNAPII


title: NRVM_PE_RNAPII


title: NRVM_PE_1


title: WT stim CD8 72h, CTCF Cut&Run, rep2