title: Bulk_glomerulus_rep3

source_name: Glomerulus

growth_protocol: Glomeruli were isolated from human nephrectomy samples using a gradual sieving approach. Kidney tissue was minced and pushed through 300 um sieve, subsequently through a 212um sieve and glomeruli were collected using PBS+1% BSA on top of a 125 um sieve and used for total RNA extraction using RNAeasy (Qiagen, Germantown, Maryland).

extract_protocol: Sequencing was performed at Single Cell Discoveries, a (single cell) sequencing provider located in the Netherlands using an adapted version of the CEL-seq protocol. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq. Briefly, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina Nextseq500 platform.

value: Glomerulus:endothelial, mesangial and podocytes


title: Bulk_glomerulus_rep1

status: Public on Apr 25 2022

type: SRA

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

library_source: transcriptomic

data_processing:
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. Read 2 was aligned to the hg19 human RefSeq transcriptome using BWA (68). Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script1. Samples were normalized using RPM normalization.
Genome_build: GRCh38 for single-cell and hf19 for bulk RNA sequencing
Supplementary_files_format_and_content: barcodes.tsv.gz = barcodes present in input data
Supplementary_files_format_and_content: features.tsv.gz = a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively
Supplementary_files_format_and_content: matrix.mtx.gz = a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary_files_format_and_content: ReadCounts.tsv = Count matrix containing gene IDs and corresponding counts. Each column represents another sample (3x mutant (iPS134) and 3x repaired (iPS19))
Supplementary_files_format_and_content: counts.txt = Count matrix containing ENSEMBLE Ids and corresponding counts

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: genomic DNA from whole blood - 203239810248_R01C01

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

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

tag: tissue

value: whole blood

tag: batch


title: genomic DNA from whole blood - 203239810076_R08C01

description: Whole Blood sample


title: Bulk_wildtype podocytesno2_rep2

source_name: Kidney organoid

growth_protocol: iPSCs were cultured using Essential™ 8 (E8) medium (Gibco, ThermoFisher) supplemented with E8 supplement (50X, Gibco) and 0.5% antibiotic-antimycotic (Gibco) on Geltrex-coated (ThermoFisher) cell culture plates (Greiner, Alphen aan den Rijn, the Netherlands). For experimental seeding purposes iPSCs were washed 3 times with PBS and subsequently disassociated into single cells using TrypLE Select Enzyme (ThermoFisher) for 2 minutes at 37°C. iPSCs were seeded on Geltrex-coated cell culture plates using E8 medium supplemented with E8 supplement, 0.5% (v/v) antibiotic-antimycotic and 1X RevitaCell at a density between 18,750 - 22,900 cells/cm2. Twenty-four hours after seeding, culture medium was replaced by E6 medium supplemented with 6 µM CHIR (Tocris, Bio-Techne, Abingdon, United Kingdom) to initiate differentiation (defined as day 0). From day 3 onwards, half of the wells were cultured in  E6 medium supplemented with 200 ng/mL FGF9 (RD systems) and 1 µg/ml heparin (Sigma-Aldrich) until day 7 (anterior intermediate mesoderm, AIM), whereas the other wells remained on E6 medium with CHIR until day 5 (posterior intermediate mesoderm, PIM). From day 5 onward, all cells were cultured in E6 medium with FGF9 and heparin. At day 7, cell were harvested using trypsin-EDTA and a cell suspension was made consisting of AIM and PIM cells in a 1:2 ratio. Cells aggregates, consisting of 300K cells, were transferred to Transwell™ plates (Corning) and incubated for at least 1 hour at 37⁰C, 5% (v/v) CO2, with E6 medium supplemented with 5 uM CHIR to induce self-organizing nephrogenesis. After 1 hour, medium was replaced for E6 medium supplemented with FGF9 and heparin. At day 7+5 (i.e. 5 days later), medium was changed to E6 supplemented with EGF (10 ng/ml, RD systems) and BMP7 (50 ng/ml, RD systems). Organoids were used for experiments at day 7+17 or 7+18.

extract_protocol:
Organoids cultured on Transwell™ plates were washed twice in PBS, disassociated using accutase and transferred to sterile 6-wells plates (without Transwell™ inserts). Organoids from similar culture conditions were pooled and incubated for 15 minutes at 37oC. During incubation, the cell suspension was resuspended every 2 minutes for homogenization purposes. After incubation, the cell suspension was put on ice for 1 minute to inactivate the accutase, cells were strained using a 40 µm cell strainer (Corning) and the cell strainer was washed repeatedly with 10% (v/v) FCS in DMEM/F12 to collect all cells. The strained cell suspension was centrifuged for at 1500 rpm for 5 minutes at 4 oC and supernatant was discarded. Cells were washed using FACS buffer (PBS- 1% (v/v) BSA) once and incubated with primary antibodies for NPHS1 (1:100, RD systems, #AF4269) in FACS buffer for 45 minutes at 4 oC. After incubation, cells were centrifuged at 1500 rpm for 5 minutes at 4oC and again washed with FACS buffer. After washing, cells were again centrifuged at 1500 rpm for 5 minutes at 4oC and subsequently incubated with matching secondary antibodies (1:200, donkey a-sheep Alexa Fluor™ 647, ThermoFisher, #A-21448) for 30 minutes at 4oC. Cells were centrifuged at 1500 rpm for 5 minutes at 4oC and washed twice in FACS buffer. After washing, cells were incubated with DAPI (300nM, ThermoFisher) in FACS buffer 10 minutes prior to FACS (for live/dead gating). Detection events were gated to select cells and doublet control was performed for both forward and side scatter. Living cells (DAPI-) were selected and gated on NPHS1+ (podocytes). Cells were sorted by immune fluorescence using a fluorescent cell sorter (Biosciences; FACSAria™ II SORP 18-color) and DIVA8 software. After cell sorting, DAPI-/NPHS1+ cells were collected in RLT buffer (RNeasy, Qiagen, Germantown, Maryland) for further processing.
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (66, 67). Briefly, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina Nextseq500 platform.

value: Kidney organoid from iPS15


title: genomic DNA from whole blood - 203239810076_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203219760133_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810076_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810248_R02C01

description: Whole Blood sample

value: Female


title: Bulk_wildtype podocytes_rep2


title: genomic DNA from whole blood - 203239810076_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810076_R01C01

description: Whole Blood sample


title: Bulk_ciPOD_rep3

source_name: Conditionally immortalized podocyte cell line

growth_protocol: The conditionally immortalized podocyte cell line (ciPOD) used in this study was kindly provided by Prof. Saleem (Bristol, UK). ciPODs were cultured using uncoated 75 cm2 culture flasks (Greiner) at 33⁰C with 5% (v/v) CO2 in DMEM/F12 (Gibco) supplemented with 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL selenium (Sigma-Aldrich, Zwijndrecht, the Netherlands), 10% heat inactivated FCS (Gibco)  and 1% (v/v) penicillin/streptomycin (Gibco). Passaging and seeding of cells was performed by washing cells with PBS and subsequently detaching them using accutase (Sigma-Aldrich). For sequencing, ciPODs were seeded at 62,500/cm2 in 6-wells plates (Greiner) for total RNA isolation and incubated at 37⁰C with 5% (v/v) CO2, which initiated differentiation of the ciPODs. Extraction Protocol: Total RNA was extracted using RNAeasy (Qiagen, Germantown, Maryland).

extract_protocol: Total RNA was extracted using RNAeasy (Qiagen, Germantown, Maryland). Library construction protocol: Sequencing was performed at Single Cell Discoveries, a (single cell) sequencing provider located in the Netherlands using an adapted version of the CEL-seq protocol. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq. Briefly, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina Nextseq500 platform.

value: Conditionally immortalized podocytes


title: genomic DNA from whole blood - 203239690270_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690270_R06C01

description: Whole Blood sample


title: Bulk_repaired podocytes_rep2

description: ReadCounts.tsv [RNA_19-02]

source_name: Repaired kidney organoid

value: Kidney organoid from iPS19-00091

tag: mutation


title: Bulk_repaired podocytes_rep3

description: ReadCounts.tsv [RNA_19-03]


title: Bulk_glomerulus_rep2


title: Bulk_mutant podocytes_rep2

description: ReadCounts.tsv [RNA_134_02]

source_name: Mutant kidney organoid

value: Kidney organoid from emc-134


title: genomic DNA from whole blood - 203239690270_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690270_R03C01

description: Whole Blood sample


title: Bulk_mutant podocytes_rep3

description: ReadCounts.tsv [RNA_134_03]


title: genomic DNA from whole blood - 203239690270_R07C01

description: Whole Blood sample


title: Bulk_repaired podocytes_rep1

description: ReadCounts.tsv [RNA_19-01]


title: genomic DNA from whole blood - 203239690270_R05C01

description: Whole Blood sample


title: Bulk_wildtype podocytes_rep3


title: genomic DNA from whole blood - 203239690270_R02C01

description: Whole Blood sample


title: Bulk_mutant podocytes_rep1

description: ReadCounts.tsv [RNA_134_01]


title: genomic DNA from whole blood - 203239690119_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690119_R08C01

description: Whole Blood sample


title: Bulk_wildtype podocytes_rep1


title: WBC cluster from patient 2 at day_2 [Pat_WBC_DAY_2_060121]

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: BSSE_QGF_161983_HLWHKBGXH_1_Pat_WBC_DAY_2_060121_CAACTGCAAC_TGAACGCAAC_S335

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: WBC cluster from patient 2 at day_2

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: patient

tag: donor

value: Patient

tag: sample type

tag: number of ctcs

tag: number of wbcs attached

tag: timepoint

value: resting


title: WBC cluster from patient 2 at night_3 [Pat_WBC_NIGHT_3_060121]

description: BSSE_QGF_161963_HLWHKBGXH_1_Pat_WBC_NIGHT_3_060121_TGTGTTAGTA_TACTCTGTTA_S315

source_name: WBC cluster from patient 2 at night_3

value: active


title: WBC cluster from patient 2 at night_2 [Pat_WBC_NIGHT_2_060121]

description: BSSE_QGF_161960_HLWHKBGXH_1_Pat_WBC_NIGHT_2_060121_GGCACTAAGG_TCAGGTCAAC_S312

source_name: WBC cluster from patient 2 at night_2


title: WBC cluster from patient 2 at night_1 [Pat_WBC_NIGHT_1_060121]

description: BSSE_QGF_161952_HLWHKBGXH_1_Pat_WBC_NIGHT_1_060121_CACCTAGCAC_TGCTGGACAT_S304

source_name: WBC cluster from patient 2 at night_1


title: genomic DNA from whole blood - 203239690119_R06C01

description: Whole Blood sample


title: WBC cluster from patient 2 at day_1 [Pat_WBC_DAY_1_060121]

description: BSSE_QGF_161977_HLWHKBGXH_1_Pat_WBC_DAY_1_060121_CACCTGTTGC_ATTGACACAT_S329

source_name: WBC cluster from patient 2 at day_1


title: genomic DNA from whole blood - 203239690119_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690118_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690118_R04C01

description: Whole Blood sample


title: Single CTC from patient 2 at night_8 [Pat_Singles_NIGHT_18_060121]

description: BSSE_QGF_161964_HLWHKBGXH_1_Pat_Singles_NIGHT_18_060121_CAACGACCTA_GCGACTCGAT_S316

source_name: Single CTC from patient 2 at night_8


title: Single CTC from patient 2 at night_7 [Pat_Singles_NIGHT_17_060121]

description: BSSE_QGF_161961_HLWHKBGXH_1_Pat_Singles_NIGHT_17_060121_ATTCGGTACA_AGTCCGAGGA_S313

source_name: Single CTC from patient 2 at night_7


title: genomic DNA from whole blood - 203239690118_R03C01

description: Whole Blood sample


title: Brown preadipocytes-lgG

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
All libraries were sequenced using an Illumina Novaseq sequencer and 150 bp paired-end format.
CUT&TAG reads were aligned to the mm10 genome assembly using bowtie2 version 2.2.6 with "-end-to-end --very-sensitive --no-mixed --no-discordant".
Unmapped reads, low quality mapped reads and PCR duplicates were discarded by picard.
Peaks were called using MACS version 2.1.1  with "--pvalue 0.01 --keep-dup all --extsize -1 --shift 0"
Different peaks were used Manorm software
Assembly: mm10
Supplementary files format and content: Bigwig files were generated by bedGraphToBigWig
Supplementary files format and content: Tab-delimited text files include peak score for each sample
Library strategy: CUT&TAG

organism: Mus musculus

source_name: brown preadipocytes

growth_protocol: Lin−CD29+CD34+Sca1+ brown preadipocytes were obtained by flow cytometric cell sorting from male widetype mice(C57BL/6). Brown preadipocytes were maintained in Dulbecco’s modified Eagle’s medium/Ham’s F12 (DMEM/F12; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (#10091155, Gibco, CA, USA) and 1% penicillin/streptomycin (Sigma-Aldrich) at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
CUT&TAG assay was performed using ZFP410 antibodyor IgG and Hyperactive® Universal CUT&TAG Assay Kit for Illumina (#TD903, Vazyme Biotech, Nanjing, China) according to producer's instruction.
RNA libraries were prepared according to the protocol of the CUT&TAG Assay Kit for Illumina (#TD903, Vazyme Biotech, Nanjing, China). The quality of the tagmented DNA library was assessed using Bioanalyzer High Sensitivity DNA Analysis (Agilent). Final CUT&Tag libraries were sequenced with the Illumina NextSeq 550 sequencer.

treatment_protocol: Pre-adipocytes isolated from mouse BAT tissue were treated with or without brown adipocyte differentiation medium for 3 days.

value: brown preadipocytes

tag: strain

tag: chip antibody

value: lgG(#B900610, Proteintech)

tag: treatment

value: untreated


title: genomic DNA from whole blood - 203239690118_R02C01

description: Whole Blood sample


title: Single CTC from patient 2 at night_6 [Pat_Singles_NIGHT_16_060121]

description: BSSE_QGF_161959_HLWHKBGXH_1_Pat_Singles_NIGHT_16_060121_CATTCACGCT_GTTGTACTCA_S311

source_name: Single CTC from patient 2 at night_6


title: Brown preadipocytes-differentiation induction

value: ZFP410(#14529-1-AP, proteintech)

value: brown adipocyte differentiation induction


title: genomic DNA from whole blood - 203239580021_R07C01

description: Whole Blood sample

value: Male


title: Single CTC from patient 2 at night_5 [Pat_Singles_NIGHT_15_060121]

description: BSSE_QGF_161956_HLWHKBGXH_1_Pat_Singles_NIGHT_15_060121_TTCTCGTGCA_ATACACAGAG_S308

source_name: Single CTC from patient 2 at night_5


title: Single CTC from patient 2 at night_4 [Pat_Singles_NIGHT_14_060121]

description: BSSE_QGF_161955_HLWHKBGXH_1_Pat_Singles_NIGHT_14_060121_CACCTCTCTT_CTCGACTCCT_S307

source_name: Single CTC from patient 2 at night_4


title: Brown preadipocytes-control


title: In_n2_JAZF1_D8

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: mESC

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: mESC

tag: genotype

tag: treatment/genotype

value: Day 8 embryoid body formation

tag: ip antibody

value: none (input)


title: genomic DNA from whole blood - 203239690118_R01C01

description: Whole Blood sample

tag: Sex

value: Female

tag: age

value: whole blood


title: genomic DNA from whole blood - 203239580021_R05C01

description: Whole Blood sample

tag: tissue

tag: batch


title: Single CTC from patient 2 at night_3 [Pat_Singles_NIGHT_13_060121]

description: BSSE_QGF_161951_HLWHKBGXH_1_Pat_Singles_NIGHT_13_060121_TAGGTATGTT_CGAGACCAAG_S303

source_name: Single CTC from patient 2 at night_3

tag: cancer type


title: genomic DNA from whole blood - 203239580021_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580021_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580021_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690118_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690118_R07C01

description: Whole Blood sample


title: In_n2_JAZF1_D4

tag: cell type

value: Day 4 embryoid body formation


title: genomic DNA from whole blood - 203239580021_R03C01

description: Whole Blood sample


title: In_n2_JAZF1_D0

value: Day 0 embryoid body formation


title: genomic DNA from whole blood - 203239690118_R08C01

description: Whole Blood sample


title: Single CTC from patient 2 at day_5 [Pat_Singles_DAY_9_060121]

description: BSSE_QGF_161974_HLWHKBGXH_1_Pat_Singles_DAY_9_060121_GAGCTTGCCG_AGGTTGCAGG_S326

source_name: Single CTC from patient 2 at day_5

value: breast

tag: origin

value: patient

tag: donor


title: In_n2_JAZF1-SUZ12_D8


title: Bulk_wildtype podocytesno2_rep1

source_name: Kidney organoid

value: Kidney organoid from iPS15


title: Single CTC from patient 2 at day_3 [Pat_Singles_DAY_7_060121]

description: BSSE_QGF_161972_HLWHKBGXH_1_Pat_Singles_DAY_7_060121_TTGAATCCAA_GTCACGGTGT_S324

source_name: Single CTC from patient 2 at day_3

value: Patient

tag: sample type

tag: number of ctcs

value: resting


title: genomic DNA from whole blood - 203239690119_R01C01

description: Whole Blood sample


title: In_n2_JAZF1-SUZ12_D4


title: genomic DNA from whole blood - 203239690119_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239580021_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690119_R04C01

description: Whole Blood sample


title: In_n2_JAZF1-SUZ12_D0


title: Single CTC from patient 2 at day_1 [Pat_Singles_DAY_5_060121]

description: BSSE_QGF_161970_HLWHKBGXH_1_Pat_Singles_DAY_5_060121_ATATCTGCTT_TAGACAATCT_S322

source_name: Single CTC from patient 2 at day_1

tag: number of wbcs attached

tag: timepoint


title: genomic DNA from whole blood - 203249020116_R03C01

description: Whole Blood sample


title: WBC cluster from patient 2 at night_4 [Pat_WBC_NIGHT_4_060121]

description: BSSE_QGF_161966_HLWHKBGXH_1_Pat_WBC_NIGHT_4_060121_TCGACGCTAG_CCTCTTCGAA_S318

source_name: WBC cluster from patient 2 at night_4


title: genomic DNA from whole blood - 203249020116_R04C01

description: Whole Blood sample


title: Single CTC from patient 2 at night_1 [Pat_Singles_NIGHT_11_060121]

description: BSSE_QGF_161948_HLWHKBGXH_1_Pat_Singles_NIGHT_11_060121_GGAGAGACTC_TTGAAGCAGA_S300

source_name: Single CTC from patient 2 at night_1


title: In_n2_SUZ12D93_D4


title: genomic DNA from whole blood - 203249020116_R06C01

description: Whole Blood sample


title: Single CTC from patient 2 at day_7 [Pat_Singles_DAY_11_060121]

description: BSSE_QGF_161976_HLWHKBGXH_1_Pat_Singles_DAY_11_060121_CAATCCTTGT_CGAAGACGCA_S328

source_name: Single CTC from patient 2 at day_7


title: genomic DNA from whole blood - 203249020208_R01C01

description: Whole Blood sample


title: In_n2_SUZ12D93_D0


title: genomic DNA from whole blood - 203249020116_R07C01

description: Whole Blood sample


title: CTC cluster from patient 2 at night_9 [Pat_Clusters_NIGHT_9_060121]

description: BSSE_QGF_161968_HLWHKBGXH_1_Pat_Clusters_NIGHT_9_060121_AAGTTCTAGT_GGTAAGATAA_S320

source_name: CTC cluster from patient 2 at night_9


title: genomic DNA from whole blood - 203249020116_R08C01

description: Whole Blood sample


title: Single CTC from patient 2 at day_2 [Pat_Singles_DAY_6_060121]

description: BSSE_QGF_161971_HLWHKBGXH_1_Pat_Singles_DAY_6_060121_TGGATCTGGC_CAATGCTGAA_S323

source_name: Single CTC from patient 2 at day_2


title: genomic DNA from whole blood - 203239580021_R01C01

description: Whole Blood sample


title: In_n2_SUZ12_D8


title: genomic DNA from whole blood - 203249020208_R08C01

description: Whole Blood sample


title: In_n2_SUZ12_D4


title: CTC cluster from patient 2 at night_8 [Pat_Clusters_NIGHT_8_060121]

description: BSSE_QGF_161967_HLWHKBGXH_1_Pat_Clusters_NIGHT_8_060121_CTCGTAGGCA_TCATCCTCTT_S319

source_name: CTC cluster from patient 2 at night_8


title: CTC cluster from patient 2 at night_7 [Pat_Clusters_NIGHT_7_060121]

description: BSSE_QGF_161965_HLWHKBGXH_1_Pat_Clusters_NIGHT_7_060121_CGGTCGGCAT_CTAGGCAAGG_S317

source_name: CTC cluster from patient 2 at night_7


title: genomic DNA from whole blood - 203239690119_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020208_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020208_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020208_R05C01

description: Whole Blood sample


title: In_n2_SUZ12D93_D8


title: In_n2_SUZ12_D0


title: genomic DNA from whole blood - 203249020208_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020208_R03C01

description: Whole Blood sample


title: CTC cluster from patient 2 at night_6 [Pat_Clusters_NIGHT_6_060121]

description: BSSE_QGF_161962_HLWHKBGXH_1_Pat_Clusters_NIGHT_6_060121_ACTAATCTCC_CACTTAATCT_S314

source_name: CTC cluster from patient 2 at night_6

value: active


title: CTC cluster from patient 2 at night_5 [Pat_Clusters_NIGHT_5_060121]

description: BSSE_QGF_161958_HLWHKBGXH_1_Pat_Clusters_NIGHT_5_060121_TTAATAGCAC_ACCACGTCTG_S310

source_name: CTC cluster from patient 2 at night_5


title: genomic DNA from whole blood - 203249020208_R02C01

description: Whole Blood sample


title: Single CTC from patient 2 at day_6 [Pat_Singles_DAY_10_060121]

description: BSSE_QGF_161975_HLWHKBGXH_1_Pat_Singles_DAY_10_060121_AGCTAGCTTC_TAATACGGAG_S327

source_name: Single CTC from patient 2 at day_6


title: CTC cluster from patient 2 at night_4 [Pat_Clusters_NIGHT_4_060121]

description: BSSE_QGF_161957_HLWHKBGXH_1_Pat_Clusters_NIGHT_4_060121_GCTAGGAAGT_TCTCGGACGA_S309

source_name: CTC cluster from patient 2 at night_4


title: In_n2_GFP_D4

source_name: mESC


title: genomic DNA from whole blood - 203249020116_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020116_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810251_R08C01

description: Whole Blood sample


title: In_n2_GFP_D0


title: CTC cluster from patient 2 at night_3 [Pat_Clusters_NIGHT_3_060121]

description: BSSE_QGF_161954_HLWHKBGXH_1_Pat_Clusters_NIGHT_3_060121_TTAAGACAAG_GGCTTAATTG_S306

source_name: CTC cluster from patient 2 at night_3


title: CTC cluster from patient 2 at night_2 [Pat_Clusters_NIGHT_2_060121]

description: BSSE_QGF_161953_HLWHKBGXH_1_Pat_Clusters_NIGHT_2_060121_TTCAAGTATG_GATGGTATCG_S305

source_name: CTC cluster from patient 2 at night_2


title: In_n1_JAZF1_D8


title: genomic DNA from whole blood - 203239810251_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810095_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810095_R05C01

description: Whole Blood sample


title: In_n1_JAZF1_D4


title: genomic DNA from whole blood - 203239810095_R04C01

description: Whole Blood sample


title: In_n2_GFP_D8


title: genomic DNA from whole blood - 203239810095_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810095_R06C01

description: Whole Blood sample


title: CTC cluster from patient 2 at night_10 [Pat_Clusters_NIGHT_10_060121]

description: BSSE_QGF_161969_HLWHKBGXH_1_Pat_Clusters_NIGHT_10_060121_CCAAGAGGTG_AACGAGCCAG_S321

source_name: CTC cluster from patient 2 at night_10


title: CTC cluster from patient 2 at night_1 [Pat_Clusters_NIGHT_1_060121]

description: BSSE_QGF_161950_HLWHKBGXH_1_Pat_Clusters_NIGHT_1_060121_ATACATCACA_TCTCCATTGA_S302

source_name: CTC cluster from patient 2 at night_1


title: In_n1_JAZF1_D0


title: In_n1_JAZF1-SUZ12_D8


title: genomic DNA from whole blood - 203239690269_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203249020116_R02C01

description: Whole Blood sample


title: CTC cluster from patient 2 at day_7 [Pat_Clusters_DAY_7_060121]

description: BSSE_QGF_161985_HLWHKBGXH_1_Pat_Clusters_DAY_7_060121_GCAACCAGTC_CACCGAGGAA_S337

source_name: CTC cluster from patient 2 at day_7


title: genomic DNA from whole blood - 203239810095_R08C01

description: Whole Blood sample


title: In_n1_JAZF1-SUZ12_D0


title: CTC cluster from patient 2 at day_5 [Pat_Clusters_DAY_5_060121]

description: BSSE_QGF_161982_HLWHKBGXH_1_Pat_Clusters_DAY_5_060121_TGTAAGGTGG_AAGGCCTTGG_S334

source_name: CTC cluster from patient 2 at day_5


title: In_n1_JAZF1-SUZ12_D4


title: genomic DNA from whole blood - 203239810251_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810251_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690268_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810251_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690268_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810251_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239810251_R04C01

description: Whole Blood sample


title: In_n1_SUZ12D93_D8


title: CTC cluster from patient 2 at day_4 [Pat_Clusters_DAY_4_060121]

description: BSSE_QGF_161981_HLWHKBGXH_1_Pat_Clusters_DAY_4_060121_TTAGGCTCAA_TCGAATGGAA_S333

source_name: CTC cluster from patient 2 at day_4


title: genomic DNA from whole blood - 203239810251_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 203239690268_R05C01

description: Whole Blood sample


title: CTC cluster from patient 2 at day_3 [Pat_Clusters_DAY_3_060121]

description: BSSE_QGF_161980_HLWHKBGXH_1_Pat_Clusters_DAY_3_060121_ATGATTCCGG_CTCTGACGTG_S332

source_name: CTC cluster from patient 2 at day_3


title: genomic DNA from whole blood - 203239690268_R06C01

description: Whole Blood sample


title: CTC cluster from patient 2 at day_6 [Pat_Clusters_DAY_6_060121]

description: BSSE_QGF_161984_HLWHKBGXH_1_Pat_Clusters_DAY_6_060121_ACATGAGTGA_CCGCTTAGCT_S336

source_name: CTC cluster from patient 2 at day_6


title: In_n1_SUZ12D93_D4


title: genomic DNA from whole blood - 203239690268_R04C01

description: Whole Blood sample


title: CTC cluster from patient 2 at day_2 [Pat_Clusters_DAY_2_060121]

description: BSSE_QGF_161979_HLWHKBGXH_1_Pat_Clusters_DAY_2_060121_AATGACTGGT_TCTCACGCGT_S331

source_name: CTC cluster from patient 2 at day_2


title: LM2 CTC-WBC cluster at 22h [LM2_WBC_2200_2_060121]

description: BSSE_QGF_161835_HLWHKBGXH_1_LM2_WBC_2200_2_060121_CAACACCGCA_GGCAGTAGCA_S189

source_name: LM2 CTC-WBC cluster at 22h

value: xenograft


title: In_n1_SUZ12_D8


title: genomic DNA from whole blood - 203239690268_R03C01

description: Whole Blood sample


title: CTC cluster from patient 2 at day_1 [Pat_Clusters_DAY_1_060121]

description: BSSE_QGF_161978_HLWHKBGXH_1_Pat_Clusters_DAY_1_060121_CGTCACCTTG_CAGCCGATTG_S330

source_name: CTC cluster from patient 2 at day_1


title: In_n1_SUZ12_D0


title: In_n1_SUZ12_D4


title: genomic DNA from whole blood - 203219760168_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110061_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110061_R05C01

description: Whole Blood sample


title: LM2 CTC-WBC cluster at 22h [LM2_WBC_2200_1_060121]

description: BSSE_QGF_161834_HLWHKBGXH_1_LM2_WBC_2200_1_060121_TGCTACTGCC_CAACCGGAGG_S188


title: genomic DNA from whole blood - 202163110061_R03C01

description: Whole Blood sample


title: In_n1_GFP_D8


title: In_n1_SUZ12D93_D0


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_8_060121]

description: BSSE_QGF_161896_HLWHKBGXH_1_LM2_WBC_1000_8_060121_GTTGTGACTA_ACATAACGGA_S249

source_name: LM2 CTC-WBC cluster at 10h


title: genomic DNA from whole blood - 202163110061_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110061_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110061_R01C01

description: Whole Blood sample


title: In_n1_GFP_D4


title: In_n1_GFP_D0


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_7_060121]

description: BSSE_QGF_161895_HLWHKBGXH_1_LM2_WBC_1000_7_060121_GCGTATTAAT_TGCGGTGTTG_S248


title: genomic DNA from whole blood - 203219760168_R02C01

description: Whole Blood sample


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_6_060121]

description: BSSE_QGF_161894_HLWHKBGXH_1_LM2_WBC_1000_6_060121_CAACGTTCGG_GGATCCGCAT_S247


title: genomic DNA from whole blood - 202163110061_R08C01

description: Whole Blood sample


title: FLAG_n2_JAZF1_D4

value: FLAG A8592 Sigma


title: genomic DNA from whole blood - 202163110059_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110059_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110059_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110061_R06C01

description: Whole Blood sample


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_3_060121]

description: BSSE_QGF_161891_HLWHKBGXH_1_LM2_WBC_1000_3_060121_ATGGCGTGCC_CGCTTGAAGT_S244


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_4_060121]

description: BSSE_QGF_161892_HLWHKBGXH_1_LM2_WBC_1000_4_060121_TCCAGAGATC_CTGCACTTCA_S245


title: genomic DNA from whole blood - 202163110059_R04C01

description: Whole Blood sample


title: FLAG_n2_JAZF1_D0


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_2_060121]

description: BSSE_QGF_161890_HLWHKBGXH_1_LM2_WBC_1000_2_060121_ATTATCCACT_TACGCACGTA_S243


title: genomic DNA from whole blood - 202163110059_R03C01

description: Whole Blood sample


title: FLAG_n2_JAZF1-SUZ12_D8


title: genomic DNA from whole blood - 202163110053_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110059_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110059_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110059_R07C01

description: Whole Blood sample


title: LM2 CTC-WBC cluster at 10h [LM2_WBC_1000_1_060121]

description: BSSE_QGF_161889_HLWHKBGXH_1_LM2_WBC_1000_1_060121_CACTAGACCA_ACTGCCTTAT_S242


title: LM2 single CTC at 22h [LM2_Singles_2200_9_060121]

description: BSSE_QGF_161905_HLWHKBGXH_1_LM2_Singles_2200_9_060121_AGCGAATTAG_AGCCGGAACA_S258

source_name: LM2 single CTC at 22h


title: FLAG_n2_JAZF1-SUZ12_D4


title: FLAG_n2_JAZF1_D8


title: genomic DNA from whole blood - 203239690270_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110053_R07C01

description: Whole Blood sample


title: FLAG_n2_JAZF1-SUZ12_D0


title: genomic DNA from whole blood - 202163110053_R04C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_6_060121]

description: BSSE_QGF_161902_HLWHKBGXH_1_LM2_Singles_2200_6_060121_CAGCGGTAGA_GCAACAGGTG_S255


title: genomic DNA from whole blood - 202163110053_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110053_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110053_R01C01

description: Whole Blood sample


title: FLAG_n2_SUZ12D93_D8


title: LM2 single CTC at 22h [LM2_Singles_2200_8_060121]

description: BSSE_QGF_161904_HLWHKBGXH_1_LM2_Singles_2200_8_060121_GGCGCCATTG_ACCGCGCAAT_S257


title: genomic DNA from whole blood - 202163110053_R03C01

description: Whole Blood sample


title: FLAG_n2_SUZ12D93_D4


title: genomic DNA from whole blood - 202163110037_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110037_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110037_R07C01

description: Whole Blood sample


title: FLAG_n2_SUZ12_D8


title: FLAG_n2_SUZ12D93_D0


title: LM2 single CTC at 22h [LM2_Singles_2200_5_060121]

description: BSSE_QGF_161901_HLWHKBGXH_1_LM2_Singles_2200_5_060121_GTAACAATCT_CTCTGTATAC_S254


title: genomic DNA from whole blood - 202163110037_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110037_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110053_R06C01

description: Whole Blood sample


title: FLAG_n2_SUZ12_D4


title: LM2 single CTC at 22h [LM2_Singles_2200_4_060121]

description: BSSE_QGF_161900_HLWHKBGXH_1_LM2_Singles_2200_4_060121_TGCAAGATAA_TTGAGGACGG_S253


title: genomic DNA from whole blood - 202163110037_R02C01

description: Whole Blood sample


title: FLAG_n2_SUZ12_D0


title: FLAG_n2_GFP_D8


title: LM2 single CTC at 22h [LM2_Singles_2200_28_060121]

description: BSSE_QGF_161924_HLWHKBGXH_1_LM2_Singles_2200_28_060121_AGATTAAGTG_CACCTCTTGG_S277


title: genomic DNA from whole blood - 202163110037_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202163110037_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260086_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260086_R08C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_27_060121]

description: BSSE_QGF_161923_HLWHKBGXH_1_LM2_Singles_2200_27_060121_AACAAGTACA_GGATATATCC_S276


title: genomic DNA from whole blood - 202135260086_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260086_R06C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_26_060121]

description: BSSE_QGF_161922_HLWHKBGXH_1_LM2_Singles_2200_26_060121_GTGGACAAGT_CCGTGGCCTT_S275


title: LM2 single CTC at 22h [LM2_Singles_2200_3_060121]

description: BSSE_QGF_161899_HLWHKBGXH_1_LM2_Singles_2200_3_060121_TCAGTCTCGT_CACGGATTAT_S252


title: genomic DNA from whole blood - 202135260086_R04C01

description: Whole Blood sample


title: FLAG_n2_GFP_D4


title: genomic DNA from whole blood - 202135260086_R02C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_24_060121]

description: BSSE_QGF_161920_HLWHKBGXH_1_LM2_Singles_2200_24_060121_CTTCCTAGGA_CCTAGAGTAT_S273


title: genomic DNA from whole blood - 202135260086_R03C01

description: Whole Blood sample


title: FLAG_n2_GFP_D0


title: genomic DNA from whole blood - 202135260086_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260084_R08C01

description: Whole Blood sample


title: FLAG_n1_JAZF1_D4


title: LM2 single CTC at 22h [LM2_Singles_2200_25_060121]

description: BSSE_QGF_161921_HLWHKBGXH_1_LM2_Singles_2200_25_060121_CGATCTGTGA_TAGGAAGACT_S274


title: LM2 single CTC at 22h [LM2_Singles_2200_29_060121]

description: BSSE_QGF_161925_HLWHKBGXH_1_LM2_Singles_2200_29_060121_TATCACTCTG_AACGTTACAT_S278


title: FLAG_n1_JAZF1_D8


title: LM2 single CTC at 22h [LM2_Singles_2200_23_060121]

description: BSSE_QGF_161919_HLWHKBGXH_1_LM2_Singles_2200_23_060121_AGCTAAGCGG_ATTAATACGC_S272


title: genomic DNA from whole blood - 202135260084_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260084_R06C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_22_060121]

description: BSSE_QGF_161918_HLWHKBGXH_1_LM2_Singles_2200_22_060121_GAGGCCTATT_CTAGTCCGGA_S271


title: FLAG_n1_JAZF1_D0


title: genomic DNA from whole blood - 202135260084_R04C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_21_060121]

description: BSSE_QGF_161917_HLWHKBGXH_1_LM2_Singles_2200_21_060121_CCAATGATAC_GAGTGTGCCG_S270


title: genomic DNA from whole blood - 202135260084_R03C01

description: Whole Blood sample


title: FLAG_n1_JAZF1-SUZ12_D4


title: FLAG_n1_JAZF1-SUZ12_D0


title: genomic DNA from whole blood - 202135260077_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260084_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260077_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260077_R02C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_19_060121]

description: BSSE_QGF_161915_HLWHKBGXH_1_LM2_Singles_2200_19_060121_ATTATGTCTC_AGTTAAGAGC_S268


title: genomic DNA from whole blood - 202135260077_R03C01

description: Whole Blood sample


title: FLAG_n1_JAZF1-SUZ12_D8


title: FLAG_n1_SUZ12D93_D4


title: LM2 single CTC at 22h [LM2_Singles_2200_20_060121]

description: BSSE_QGF_161916_HLWHKBGXH_1_LM2_Singles_2200_20_060121_TATAACAGCT_TCGCGTATAA_S269


title: LM2 single CTC at 22h [LM2_Singles_2200_17_060121]

description: BSSE_QGF_161913_HLWHKBGXH_1_LM2_Singles_2200_17_060121_GTAGGCGAGC_TAGGAGCGCA_S266


title: LM2 single CTC at 22h [LM2_Singles_2200_18_060121]

description: BSSE_QGF_161914_HLWHKBGXH_1_LM2_Singles_2200_18_060121_AACTTATCCT_GTACTGGCGT_S267


title: genomic DNA from whole blood - 202135260084_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260077_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260077_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260040_R04C01

description: Whole Blood sample


title: FLAG_n1_SUZ12D93_D8


title: genomic DNA from whole blood - 202135260040_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260040_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260077_R04C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_16_060121]

description: BSSE_QGF_161912_HLWHKBGXH_1_LM2_Singles_2200_16_060121_AAGAGAGTCT_TACGAATCTT_S265


title: FLAG_n1_SUZ12D93_D0


title: FLAG_n1_SUZ12_D8


title: FLAG_n1_SUZ12_D4


title: LM2 single CTC at 22h [LM2_Singles_2200_2_060121]

description: BSSE_QGF_161898_HLWHKBGXH_1_LM2_Singles_2200_2_060121_AAGCATCTTG_CATTCAACAA_S251


title: LM2 single CTC at 22h [LM2_Singles_2200_15_060121]

description: BSSE_QGF_161911_HLWHKBGXH_1_LM2_Singles_2200_15_060121_TAACCGGCGA_GCTACATTAG_S264


title: genomic DNA from whole blood - 202135260077_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260084_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202135260040_R01C01

description: Whole Blood sample


title: FLAG_n1_SUZ12_D0


title: genomic DNA from whole blood - 202081130134_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R06C01

description: Whole Blood sample


title: FLAG_n1_GFP_D0


title: genomic DNA from whole blood - 202081130134_R05C01

description: Whole Blood sample


title: FLAG_n1_GFP_D4


title: LM2 single CTC at 22h [LM2_Singles_2200_11_060121]

description: BSSE_QGF_161907_HLWHKBGXH_1_LM2_Singles_2200_11_060121_CACACAGTAT_TTGAGCCTAA_S260


title: FLAG_n1_GFP_D8


title: genomic DNA from whole blood - 202081130109_R07C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_13_060121]

description: BSSE_QGF_161909_HLWHKBGXH_1_LM2_Singles_2200_13_060121_TACCGCCTCG_CCTCGCAACC_S262


title: genomic DNA from whole blood - 202081130109_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130109_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130134_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130109_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130109_R04C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_10_060121]

description: BSSE_QGF_161906_HLWHKBGXH_1_LM2_Singles_2200_10_060121_TTAGACCATG_TCCTAGGAAG_S259


title: LM2 single CTC at 22h [LM2_Singles_2200_14_060121]

description: BSSE_QGF_161910_HLWHKBGXH_1_LM2_Singles_2200_14_060121_CTGTTATATC_GTATAGCTGT_S263


title: LM2 single CTC at 22h [LM2_Singles_2200_12_060121]

description: BSSE_QGF_161908_HLWHKBGXH_1_LM2_Singles_2200_12_060121_TCTTGTCGGC_CCACCTGTGT_S261


title: genomic DNA from whole blood - 202081130109_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202081130109_R02C01

description: Whole Blood sample


title: LM2 single CTC at 22h [LM2_Singles_2200_1_060121]

description: BSSE_QGF_161897_HLWHKBGXH_1_LM2_Singles_2200_1_060121_TCTCAATACC_GACGTTCGCG_S250


title: LM2 single CTC at 10h [LM2_Singles_1000_7_060121]

description: BSSE_QGF_161843_HLWHKBGXH_1_LM2_Singles_1000_7_060121_CGCACGACTG_GGACCAACAG_S196

source_name: LM2 single CTC at 10h


title: genomic DNA from whole blood - 202066270103_R08C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_9_060121]

description: BSSE_QGF_161845_HLWHKBGXH_1_LM2_Singles_1000_9_060121_AACCGAGTTC_GATCTCTGGA_S198


title: genomic DNA from whole blood - 202081130109_R08C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_6_060121]

description: BSSE_QGF_161842_HLWHKBGXH_1_LM2_Singles_1000_6_060121_TAATTCTGCT_TCTCATCAAT_S195


title: genomic DNA from whole blood - 202066270103_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270103_R05C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_5_060121]

description: BSSE_QGF_161841_HLWHKBGXH_1_LM2_Singles_1000_5_060121_TCCTGGTTGT_CTGACCGGCA_S194


title: genomic DNA from whole blood - 202066270103_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270103_R06C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_30_060121]

description: BSSE_QGF_161866_HLWHKBGXH_1_LM2_Singles_1000_30_060121_CTATTACTAC_GAGTCTCTCC_S219


title: LM2 single CTC at 10h [LM2_Singles_1000_4_060121]

description: BSSE_QGF_161840_HLWHKBGXH_1_LM2_Singles_1000_4_060121_GCGTGGATGG_TTGACCAATG_S193


title: genomic DNA from whole blood - 202066270103_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270101_R08C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_29_060121]

description: BSSE_QGF_161865_HLWHKBGXH_1_LM2_Singles_1000_29_060121_TAGTTCGGTA_CCATGTGTAG_S218


title: genomic DNA from whole blood - 202066270101_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270101_R05C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_3_060121]

description: BSSE_QGF_161839_HLWHKBGXH_1_LM2_Singles_1000_3_060121_TTCACGAGAC_AGATTGTTAC_S192


title: genomic DNA from whole blood - 202066270101_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270103_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270101_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270103_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270101_R02C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_28_060121]

description: BSSE_QGF_161864_HLWHKBGXH_1_LM2_Singles_1000_28_060121_CTAAGTACGC_AACATACCTA_S217


title: LM2 single CTC at 10h [LM2_Singles_1000_27_060121]

description: BSSE_QGF_161863_HLWHKBGXH_1_LM2_Singles_1000_27_060121_TTACAGTTAG_ACATGCATAT_S216


title: genomic DNA from whole blood - 202066270101_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202066270101_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330278_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330278_R08C01

description: Whole Blood sample


title: 2.3Gy_5508020_D7.txt

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

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: LM2 single CTC at 10h [LM2_Singles_1000_26_060121]

description: BSSE_QGF_161862_HLWHKBGXH_1_LM2_Singles_1000_26_060121_TTGCTCTATT_GTGACCTTGA_S215


title: 2.3Gy_5508305_D1.txt


title: 2.3Gy_5508305_D3.txt


title: 2.3Gy_5503036_D7.txt


title: 2.3Gy_5508020_D3.txt


title: 2.3Gy_5508305_D7.txt


title: genomic DNA from whole blood - 202128330278_R05C01

description: Whole Blood sample

tag: Sex


title: genomic DNA from whole blood - 202128330278_R03C01

description: Whole Blood sample

tag: age


title: genomic DNA from whole blood - 202128330278_R04C01

description: Whole Blood sample

value: Male

tag: tissue


title: LM2 single CTC at 10h [LM2_Singles_1000_25_060121]

description: BSSE_QGF_161861_HLWHKBGXH_1_LM2_Singles_1000_25_060121_CACTATCAAC_TCAGTTAATG_S214


title: 2.3Gy_5508020_Ctrl.txt

value: Control

value: day -1

tag: batch


title: genomic DNA from whole blood - 202128330278_R02C01

description: Whole Blood sample

value: Female

value: whole blood


title: LM2 single CTC at 10h [LM2_Singles_1000_24_060121]

description: BSSE_QGF_161860_HLWHKBGXH_1_LM2_Singles_1000_24_060121_CCGAAGCGCT_TGCTAACTAT_S213

tag: cancer type


title: genomic DNA from whole blood - 202128330278_R01C01

description: Whole Blood sample


title: 2.3Gy_5508020_D1.txt


title: 2.3Gy_5503036_D1.txt


title: 2.3Gy_5508305_Ctrl.txt


title: LM2 single CTC at 10h [LM2_Singles_1000_23_060121]

description: BSSE_QGF_161859_HLWHKBGXH_1_LM2_Singles_1000_23_060121_CGCTTAGAAT_CAGAGTGATA_S212


title: genomic DNA from whole blood - 202128330269_R08C01

description: Whole Blood sample


title: 2.3Gy_5503036_D3.txt


title: genomic DNA from whole blood - 202128330269_R07C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_22_060121]

description: BSSE_QGF_161858_HLWHKBGXH_1_LM2_Singles_1000_22_060121_TTATACGCGA_GCCGTCTGTT_S211


title: LM2 single CTC at 10h [LM2_Singles_1000_21_060121]

description: BSSE_QGF_161857_HLWHKBGXH_1_LM2_Singles_1000_21_060121_TTAGGATATC_TATACCATGG_S210


title: 2.3Gy_5502439_D7.txt


title: genomic DNA from whole blood - 202128330269_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330269_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330269_R04C01

description: Whole Blood sample


title: 2.3Gy_5503036_Ctrl.txt


title: 2.3Gy_5502439_D1.txt


title: 2.3Gy_5502439_Ctrl.txt


title: genomic DNA from whole blood - 202123800264_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800264_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330269_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330269_R06C01

description: Whole Blood sample


title: 2.3Gy_5502439_D3.txt


title: genomic DNA from whole blood - 202123800264_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330269_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800264_R06C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_19_060121]

description: BSSE_QGF_161855_HLWHKBGXH_1_LM2_Singles_1000_19_060121_CCACCGGAGT_GCCTGCCATG_S208


title: genomic DNA from whole blood - 202123800264_R04C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_18_060121]

description: BSSE_QGF_161854_HLWHKBGXH_1_LM2_Singles_1000_18_060121_AGCTACTATA_GTTATATGGC_S207


title: 2.3Gy_5493758_D7.txt


title: LM2 single CTC at 10h [LM2_Singles_1000_20_060121]

description: BSSE_QGF_161856_HLWHKBGXH_1_LM2_Singles_1000_20_060121_CTTACCGCAC_TAAGACCTAT_S209


title: LM2 single CTC at 10h [LM2_Singles_1000_2_060121]

description: BSSE_QGF_161838_HLWHKBGXH_1_LM2_Singles_1000_2_060121_CGAGGCCAAG_GTGTTACCGG_S191


title: genomic DNA from whole blood - 202123800264_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800264_R02C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_16_060121]

description: BSSE_QGF_161852_HLWHKBGXH_1_LM2_Singles_1000_16_060121_GATCGGATAA_GTATCGGCCG_S205


title: LM2 single CTC at 10h [LM2_Singles_1000_17_060121]

description: BSSE_QGF_161853_HLWHKBGXH_1_LM2_Singles_1000_17_060121_GCTAGACTAT_AATACGACAT_S206


title: genomic DNA from whole blood - 202128330248_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330248_R04C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_15_060121]

description: BSSE_QGF_161851_HLWHKBGXH_1_LM2_Singles_1000_15_060121_GAATATGCGG_ACGAGACTGA_S204


title: genomic DNA from whole blood - 202123800264_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330248_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330248_R05C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_14_060121]

description: BSSE_QGF_161850_HLWHKBGXH_1_LM2_Singles_1000_14_060121_CTGGAACTGT_CGTAATTAAC_S203


title: genomic DNA from whole blood - 202128330248_R06C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_13_060121]

description: BSSE_QGF_161849_HLWHKBGXH_1_LM2_Singles_1000_13_060121_TCCTCGGACT_AACGCCAGAG_S202


title: genomic DNA from whole blood - 202128330248_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330248_R02C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_11_060121]

description: BSSE_QGF_161847_HLWHKBGXH_1_LM2_Singles_1000_11_060121_AGTATGCTAC_TTAATAGACC_S200


title: genomic DNA from whole blood - 202128330248_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330239_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330239_R08C01

description: Whole Blood sample


title: 2.3Gy_5493758_Ctrl.txt


title: 2.3Gy_5493758_D3.txt


title: 2.3Gy_5492336_D1.txt


title: 2.1Gy_5507457_D3.txt


title: 2.3Gy_5492336_D7.txt


title: genomic DNA from whole blood - 202128330239_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330239_R06C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_10_060121]

description: BSSE_QGF_161846_HLWHKBGXH_1_LM2_Singles_1000_10_060121_TGTGATAACT_CAGGCGCCAT_S199


title: 2.3Gy_5492336_Ctrl.txt


title: genomic DNA from whole blood - 202128330239_R04C01

description: Whole Blood sample


title: LM2 single CTC at 10h [LM2_Singles_1000_1_060121]

description: BSSE_QGF_161837_HLWHKBGXH_1_LM2_Singles_1000_1_060121_TCTCATGATA_AACACGTGGA_S190


title: genomic DNA from whole blood - 202128330239_R03C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_8_060121]

description: BSSE_QGF_161816_HLWHKBGXH_1_LM2_Clusters_2200_8_060121_GCACCACCAA_TGGTACTGAT_S170

source_name: LM2 CTC cluster at 22h


title: genomic DNA from whole blood - 202128330239_R01C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_7_060121]

description: BSSE_QGF_161815_HLWHKBGXH_1_LM2_Clusters_2200_7_060121_ATGTTGTTGG_CAATCTATGA_S169


title: genomic DNA from whole blood - 202128330234_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330239_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R04C01

description: Whole Blood sample


title: 2.3Gy_5493758_D1.txt


title: genomic DNA from whole blood - 202128330234_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330234_R01C01

description: Whole Blood sample


title: 2.3Gy_5492336_D3.txt


title: 2.1Gy_5507457_D1.txt


title: genomic DNA from whole blood - 202128330207_R08C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_5_060121]

description: BSSE_QGF_161931_HLWHKBGXH_1_LM2_Clusters_2200_5_060121_ATTGGCTTCT_TGGCTCGCAG_S284


title: genomic DNA from whole blood - 202128330207_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330207_R05C01

description: Whole Blood sample


title: 2.1Gy_5507457_Ctrl.txt


title: 2.1Gy_5507457_D7.txt


title: 2.1Gy_5502552_D3.txt


title: genomic DNA from whole blood - 202128330207_R03C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_24_060121]

description: BSSE_QGF_161832_HLWHKBGXH_1_LM2_Clusters_2200_24_060121_GTAACTTGGT_CGCCATACCT_S186


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_23_060121]

description: BSSE_QGF_161831_HLWHKBGXH_1_LM2_Clusters_2200_23_060121_ACGGTCCAAC_TCTTACATCA_S185


title: 2.1Gy_5502145_D7.txt


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_3_060121]

description: BSSE_QGF_161929_HLWHKBGXH_1_LM2_Clusters_2200_3_060121_TGATAACGAG_GTTCCGCAGG_S282


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_4_060121]

description: BSSE_QGF_161930_HLWHKBGXH_1_LM2_Clusters_2200_4_060121_CATAGTAAGG_ACCAAGTTAC_S283


title: 2.1Gy_5502552_D1.txt


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_25_060121]

description: BSSE_QGF_161833_HLWHKBGXH_1_LM2_Clusters_2200_25_060121_AGCGCCACAC_CTAATGTCTT_S187


title: genomic DNA from whole blood - 202128330207_R02C01

description: Whole Blood sample


title: 2.1Gy_5502145_D3.txt


title: 2.1Gy_5502145_Ctrl.txt


title: genomic DNA from whole blood - 202128330207_R01C01

description: Whole Blood sample


title: 2.1Gy_5502552_D7.txt


title: genomic DNA from whole blood - 202128330182_R08C01

description: Whole Blood sample


title: 2.1Gy_5502552_Ctrl.txt


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_21_060121]

description: BSSE_QGF_161829_HLWHKBGXH_1_LM2_Clusters_2200_21_060121_TTCCTACAGC_GGCGAATTCT_S183


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_22_060121]

description: BSSE_QGF_161830_HLWHKBGXH_1_LM2_Clusters_2200_22_060121_ATCCAGGTAT_CAACGTCAGC_S184


title: 2.1Gy_5502145_D1.txt


title: 2.1Gy_5493766_D1.txt


title: 2.1Gy_5493766_D3.txt


title: genomic DNA from whole blood - 202128330182_R05C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_20_060121]

description: BSSE_QGF_161828_HLWHKBGXH_1_LM2_Clusters_2200_20_060121_AATTCTTGGA_TTGTCAACTT_S182


title: genomic DNA from whole blood - 202128330182_R07C01

description: Whole Blood sample


title: 2.1Gy_5493766_Ctrl.txt


title: 2.1Gy_5493766_D7.txt


title: genomic DNA from whole blood - 202128330182_R03C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_2_060121]

description: BSSE_QGF_161928_HLWHKBGXH_1_LM2_Clusters_2200_2_060121_AGCTGGAATG_ACGGAATGCG_S281


title: 2.1Gy_5491003_D7.txt


title: genomic DNA from whole blood - 202128330182_R02C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_18_060121]

description: BSSE_QGF_161826_HLWHKBGXH_1_LM2_Clusters_2200_18_060121_CGCTGTCTCA_ATTACTCACC_S180


title: genomic DNA from whole blood - 202128330182_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330182_R06C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_19_060121]

description: BSSE_QGF_161827_HLWHKBGXH_1_LM2_Clusters_2200_19_060121_AATGCGAACA_AATTGGCGGA_S181


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_16_060121]

description: BSSE_QGF_161824_HLWHKBGXH_1_LM2_Clusters_2200_16_060121_GATCGTCGCG_CTGGATATGT_S178


title: genomic DNA from whole blood - 202128330163_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330182_R04C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R03C01

description: Whole Blood sample


title: 2.1Gy_5491003_D1.txt


title: genomic DNA from whole blood - 202128330207_R07C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_17_060121]

description: BSSE_QGF_161825_HLWHKBGXH_1_LM2_Clusters_2200_17_060121_TATCCGAGGC_GGCCAATAAG_S179


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_15_060121]

description: BSSE_QGF_161823_HLWHKBGXH_1_LM2_Clusters_2200_15_060121_CTCGAATATA_GAGATGTCGA_S177


title: 2.1Gy_5491003_Ctrl.txt


title: genomic DNA from whole blood - 202128330163_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800150_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330163_R08C01

description: Whole Blood sample


title: 2.1Gy_5489637_D1.txt


title: genomic DNA from whole blood - 202123800150_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800150_R05C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_13_060121]

description: BSSE_QGF_161821_HLWHKBGXH_1_LM2_Clusters_2200_13_060121_GGACCAGTGG_CGCGAGCCTA_S175


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_12_060121]

description: BSSE_QGF_161820_HLWHKBGXH_1_LM2_Clusters_2200_12_060121_ATTGTTCGTC_TCTCTAGATT_S174


title: 2.1Gy_5489637_D3.txt


title: genomic DNA from whole blood - 202123800150_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_11_060121]

description: BSSE_QGF_161819_HLWHKBGXH_1_LM2_Clusters_2200_11_060121_GTCCACCGCT_TCCTATTAGC_S173


title: 2.1Gy_5489637_D7.txt


title: genomic DNA from whole blood - 202123800150_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800150_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800149_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800150_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800149_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800150_R08C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_14_060121]

description: BSSE_QGF_161822_HLWHKBGXH_1_LM2_Clusters_2200_14_060121_CCTTCTAACA_GATAAGCTCT_S176


title: 1.9Gy_5507384_D7.txt


title: genomic DNA from whole blood - 202123800149_R06C01

description: Whole Blood sample


title: LM2 CTC cluster at 22h [LM2_Clusters_2200_10_060121]

description: BSSE_QGF_161818_HLWHKBGXH_1_LM2_Clusters_2200_10_060121_CCTCCGGTTG_CATAACACCA_S172


title: 2.1Gy_5491003_D3.txt


title: genomic DNA from whole blood - 202123800149_R05C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_9_060121]

description: BSSE_QGF_161875_HLWHKBGXH_1_LM2_Clusters_1000_9_060121_TGACGGCCGT_AGTCAACCAT_S228

source_name: LM2 CTC cluster at 10h


title: 1.9Gy_5507384_D1.txt


title: 1.9Gy_5507384_Ctrl.txt


title: genomic DNA from whole blood - 202123800149_R03C01

description: Whole Blood sample


title: 1.9Gy_5507384_D3.txt


title: genomic DNA from whole blood - 202123800149_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_7_060121]

description: BSSE_QGF_161873_HLWHKBGXH_1_LM2_Clusters_1000_7_060121_GCTCTTAACT_CACGTCCACC_S226


title: 2.1Gy_5489637_Ctrl.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_6_060121]

description: BSSE_QGF_161872_HLWHKBGXH_1_LM2_Clusters_1000_6_060121_ACTAGCGCTA_TTACTTCCTC_S225


title: genomic DNA from whole blood - 202123800149_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800149_R02C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_5_060121]

description: BSSE_QGF_161871_HLWHKBGXH_1_LM2_Clusters_1000_5_060121_GCTTCATATT_CGTTCAGCCT_S224


title: genomic DNA from whole blood - 202123800148_R06C01

description: Whole Blood sample


title: 1.9Gy_5503532_D7.txt


title: genomic DNA from whole blood - 202123800148_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800148_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800148_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202123800148_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_3_060121]

description: BSSE_QGF_161869_HLWHKBGXH_1_LM2_Clusters_1000_3_060121_TAGTGGAAGC_AGTACCTATA_S222


title: genomic DNA from whole blood - 202123800148_R03C01

description: Whole Blood sample


title: 1.9Gy_5503532_D3.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_22_060121]

description: BSSE_QGF_161888_HLWHKBGXH_1_LM2_Clusters_1000_22_060121_ATCCTCTCAA_TCCGCAAGGC_S241


title: genomic DNA from whole blood - 202123800148_R02C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_21_060121]

description: BSSE_QGF_161887_HLWHKBGXH_1_LM2_Clusters_1000_21_060121_TTCATGGTTC_GACATTGTCA_S240


title: genomic DNA from whole blood - 202128330219_R08C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330219_R06C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_20_060121]

description: BSSE_QGF_161886_HLWHKBGXH_1_LM2_Clusters_1000_20_060121_CCTGCAACCT_GTAGAGTCAG_S239


title: genomic DNA from whole blood - 202123800148_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330219_R05C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330219_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_2_060121]

description: BSSE_QGF_161868_HLWHKBGXH_1_LM2_Clusters_1000_2_060121_ACTCTATTGT_ATCGCATATG_S221


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_4_060121]

description: BSSE_QGF_161870_HLWHKBGXH_1_LM2_Clusters_1000_4_060121_CGCCATATCT_GACCGGAGAT_S223


title: 1.9Gy_5503346_D7.txt


title: 1.9Gy_5503532_Ctrl.txt


title: 1.9Gy_5503346_D3.txt


title: 1.9Gy_5503532_D1.txt


title: genomic DNA from whole blood - 202128330219_R03C01

description: Whole Blood sample


title: 1.9Gy_5503346_D1.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_19_060121]

description: BSSE_QGF_161885_HLWHKBGXH_1_LM2_Clusters_1000_19_060121_TGAACGCGGA_CTTCGAAGGA_S238


title: genomic DNA from whole blood - 202128330219_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330219_R01C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330210_R08C01

description: Whole Blood sample


title: 1.9Gy_5493112_D7.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_18_060121]

description: BSSE_QGF_161884_HLWHKBGXH_1_LM2_Clusters_1000_18_060121_GGAAGGAGAC_TGGTGAGTCT_S237


title: 1.9Gy_5503346_Ctrl.txt


title: genomic DNA from whole blood - 202128330219_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330210_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330210_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330210_R05C01

description: Whole Blood sample


title: 1.9Gy_5493112_D1.txt


title: genomic DNA from whole blood - 202128330210_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_17_060121]

description: BSSE_QGF_161883_HLWHKBGXH_1_LM2_Clusters_1000_17_060121_AAGGAAGAGT_CACGTTAGGC_S236


title: genomic DNA from whole blood - 202128330210_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330210_R02C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330207_R04C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_15_060121]

description: BSSE_QGF_161881_HLWHKBGXH_1_LM2_Clusters_1000_15_060121_ATAGGTCTTA_GTCACCACAG_S234


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_16_060121]

description: BSSE_QGF_161882_HLWHKBGXH_1_LM2_Clusters_1000_16_060121_TTCTTAACCA_TCTACATACC_S235


title: genomic DNA from whole blood - 202128330210_R01C01

description: Whole Blood sample


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_13_060121]

description: BSSE_QGF_161879_HLWHKBGXH_1_LM2_Clusters_1000_13_060121_CTCCACTAAT_TGTACTTGTT_S232


title: genomic DNA from whole blood - 202128330189_R06C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330189_R08C01

description: Whole Blood sample


title: 1.9Gy_5492565_Ctrl.txt


title: genomic DNA from whole blood - 202128330189_R05C01

description: Whole Blood sample


title: 1.9Gy_5492565_D1.txt


title: 1.9Gy_5493112_D3.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_12_060121]

description: BSSE_QGF_161878_HLWHKBGXH_1_LM2_Clusters_1000_12_060121_CTGTGGTGAC_GACAGACAGG_S231


title: genomic DNA from whole blood - 202128330189_R03C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330189_R04C01

description: Whole Blood sample


title: 1.9Gy_5492565_D3.txt


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_10_060121]

description: BSSE_QGF_161876_HLWHKBGXH_1_LM2_Clusters_1000_10_060121_CAGTAATTAC_CGAGGCGGTA_S229


title: genomic DNA from whole blood - 202128330189_R02C01

description: Whole Blood sample


title: 1.9Gy_5493112_Ctrl.txt


title: genomic DNA from whole blood - 202128330189_R07C01

description: Whole Blood sample


title: genomic DNA from whole blood - 202128330189_R01C01

description: Whole Blood sample


title: 1.9Gy_5490775_D3.txt


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_9_060121]

description: BSSE_QGF_161803_HLWHKBGXH_1_BR16_WBC_2200_9_060121_CTAGATTGCG_AGATATGGCG_S157

source_name: BR16 CTC-WBC cluster at 22h


title: genomic DNA from whole blood - 202128330184_R08C01

description: Whole Blood sample


title: 1.9Gy_5492565_D7.txt


title: 1.9Gy_5490775_Ctrl.txt


title: genomic DNA from whole blood - 202128330184_R07C01

description: Whole Blood sample


title: 1.9Gy_5490775_D7.txt


title: FleQ_C

city: Seattle

first: Joseph

last: Mougous

state: WA

address: 1959 NE Pacific St Box 357710

institute: University of Washington /HHMI

description:
Sample 5 C
Immunoprecipitated DNA was not size-selected during library construction
FleQ-V_AllPeaks.bed

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: fleQ-vsvG

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.

tag: genotype

value: fleQ-vsvG

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: FleQ_B

description:
Sample 5 B
Immunoprecipitated DNA was not size-selected during library construction
FleQ-V_AllPeaks.bed


title: 1.7Gy_5507236_D7.txt


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_8_060121]

description: BSSE_QGF_161802_HLWHKBGXH_1_BR16_WBC_2200_8_060121_GCAATATTCA_GGCGCCAATT_S156

value: breast

tag: origin

tag: donor

tag: sample type


title: GacA_C

description:
Sample 4 C
Immunoprecipitated DNA was not size-selected during library construction
GacA-V_AllPeaks.bed

source_name: PAO1 ∆retS gacA-vsvG

value: PAO1 {delta}retS gacA-vsvG


title: 1.7Gy_5507236_D3.txt


title: 1.7Gy_5507236_D1.txt


title: FleQ_A

description:
Sample 5 A
Immunoprecipitated DNA was not size-selected during library construction
FleQ-V_AllPeaks.bed


title: genomic DNA from whole blood - 202128330184_R06C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_7_060121]

description: BSSE_QGF_161801_HLWHKBGXH_1_BR16_WBC_2200_7_060121_ATAGCGGAAT_GCGCAGAGTA_S155

tag: number of ctcs

tag: number of wbcs attached

tag: timepoint


title: GacA_B

description:
Sample 4 B
Immunoprecipitated DNA was not size-selected during library construction
GacA-V_AllPeaks.bed


title: genomic DNA from whole blood - 202128330184_R05C01

description: Whole Blood sample


title: GacA_A

description:
Sample 4 A
Immunoprecipitated DNA was not size-selected during library construction
GacA-V_AllPeaks.bed


title: retS_Mock_C

description:
Sample 3 C
Immunoprecipitated DNA was not size-selected during library construction

source_name: PAO1 ∆retS

value: PAO1 {delta}retS


title: LM2 CTC cluster at 10h [LM2_Clusters_1000_1_060121]

description: BSSE_QGF_161867_HLWHKBGXH_1_LM2_Clusters_1000_1_060121_TAGCATAACC_GCTATGCGCA_S220

value: resting


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_6_060121]

description: BSSE_QGF_161800_HLWHKBGXH_1_BR16_WBC_2200_6_060121_GTTCGGAGTT_CGCCTTCTGA_S154

value: xenograft

value: active


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_5_060121]

description: BSSE_QGF_161799_HLWHKBGXH_1_BR16_WBC_2200_5_060121_CCACGCTGAA_TATTCCTCAG_S153


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_4_060121]

description: BSSE_QGF_161798_HLWHKBGXH_1_BR16_WBC_2200_4_060121_CACAGCGGTC_ATTCCTATTG_S152


title: retS_Mock_B

description:
Sample 3 B
Immunoprecipitated DNA was not size-selected during library construction


title: genomic DNA from whole blood - 202128330184_R04C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_3_060121]

description: BSSE_QGF_161797_HLWHKBGXH_1_BR16_WBC_2200_3_060121_TTGTATCAGG_ACAGAGGCCA_S151


title: retS_Mock_A

description:
Sample 3 A
Immunoprecipitated DNA was not size-selected during library construction


title: 1.7Gy_5506302_D3.txt

value: Blood

tag: breed

tag: gender

tag: animal id


title: 1.7Gy_5507236_Ctrl.txt

value: Gottingen minipigs

tag: dose

tag: time point


title: genomic DNA from whole blood - 202128330184_R01C01

description: Whole Blood sample

tag: Sex

tag: age

tag: tissue


title: genomic DNA from whole blood - 202128330176_R08C01

description: Whole Blood sample

tag: batch


title: 1.7Gy_5506302_Ctrl.txt

value: male


title: GcsR_C

description:
Sample 2 C
Immunoprecipitated DNA was not size-selected during library construction
GcsR-V_AllPeaks.bed

source_name: gcsR-vsvG

tag: genotype

value: gcsR-vsvG

tag: growth phase


title: genomic DNA from whole blood - 202128330184_R03C01

description: Whole Blood sample


title: 1.7Gy_5506302_D1.txt


title: 1.7Gy_5503117_D7.txt


title: Mock_2_C

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

source_name: wild-type

value: wild-type

tag: chip antibody


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_16_060121]

description: BSSE_QGF_161810_HLWHKBGXH_1_BR16_WBC_2200_16_060121_CGTGTACCAG_AGGATAAGTT_S164

tag: cancer type

tag: origin

tag: donor


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_17_060121]

description: BSSE_QGF_161811_HLWHKBGXH_1_BR16_WBC_2200_17_060121_TTAACCTTCG_AGGCCAGACA_S165

tag: sample type

tag: number of ctcs

tag: number of wbcs attached


title: genomic DNA from whole blood - 202128330176_R06C01

description: Whole Blood sample

value: Male


title: GcsR_A

description:
Sample 2 A
Immunoprecipitated DNA was not size-selected during library construction
GcsR-V_AllPeaks.bed


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_15_060121]

description: BSSE_QGF_161809_HLWHKBGXH_1_BR16_WBC_2200_15_060121_ACTTGTTATC_CGCGCCTAGA_S163

tag: timepoint


title: 1.7Gy_5503117_D3.txt

tag: breed

tag: gender

tag: animal id


title: 1.7Gy_5503117_D1.txt

tag: dose

tag: time point


title: 1.7Gy_5506302_D7.txt

tag: tissue


title: genomic DNA from whole blood - 202128330176_R07C01

description: Whole Blood sample

tag: Sex

tag: age

tag: batch


title: genomic DNA from whole blood - 202128330184_R02C01

description: Whole Blood sample


title: GcsR_B

description:
Sample 2 B
Immunoprecipitated DNA was not size-selected during library construction
GcsR-V_AllPeaks.bed

tag: genotype

tag: growth phase

tag: chip antibody


title: genomic DNA from whole blood - 202128330176_R05C01

description: Whole Blood sample


title: 1.7Gy_5503117_Ctrl.txt

value: Control

value: day -1


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_18_060121]

description: BSSE_QGF_161812_HLWHKBGXH_1_BR16_WBC_2200_18_060121_CATATGCGAT_CCTTGAACGG_S166

tag: cancer type

tag: origin

tag: donor


title: Mock_2_A

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


title: 1.7Gy_5501815_D7.txt


title: genomic DNA from whole blood - 202128330176_R04C01

description: Whole Blood sample

value: Female

value: whole blood


title: genomic DNA from whole blood - 202128330176_R03C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_13_060121]

description: BSSE_QGF_161807_HLWHKBGXH_1_BR16_WBC_2200_13_060121_AATTCCATCT_CTTCAGTTAC_S161

tag: sample type

tag: number of ctcs

tag: number of wbcs attached


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_14_060121]

description: BSSE_QGF_161808_HLWHKBGXH_1_BR16_WBC_2200_14_060121_TTAACGGTGT_TCCTGACCGT_S162

tag: timepoint


title: MtWOX9-1 overexpressing callus, 35th day of cell culture, biol rep 2

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.

value: Callus from leaf explant

tag: cell type

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_D3.txt

tag: breed

tag: gender

tag: animal id

tag: dose

tag: time point


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_12_060121]

description: BSSE_QGF_161806_HLWHKBGXH_1_BR16_WBC_2200_12_060121_GTGACGGAGC_TGGCGGTCCA_S160

value: breast


title: genomic DNA from whole blood - 202128330176_R02C01

description: Whole Blood sample

tag: Sex

tag: age

tag: tissue

tag: batch


title: genomic DNA from whole blood - 202128330176_R01C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_11_060121]

description: BSSE_QGF_161805_HLWHKBGXH_1_BR16_WBC_2200_11_060121_TCCGGACTAG_GACGAACAAT_S159

tag: cancer type

tag: origin

value: xenograft


title: Wildtype callus, 35th day of cell culture, biol rep 2

tag: genotype


title: genomic DNA from whole blood - 202128330165_R07C01

description: Whole Blood sample


title: BR16 CTC-WBC cluster at 22h [BR16_WBC_2200_10_060121]

description: BSSE_QGF_161804_HLWHKBGXH_1_BR16_WBC_2200_10_060121_CGATGCGGTT_CCTGCTTGGT_S158

tag: donor

tag: sample type

tag: number of ctcs

value: active


title: Wildtype callus, 35th day of cell culture, biol rep 1

tag: cell type