title: Pre_competence_loss_RNASeq_rep4

data_processing:
Reads were pseudoaligned using kallisto 0.45.1 to transcripts from the human genome build hg38.
Abundance matrix was extracted with sleuth 0.30.0
Differentially expressed genes were identified using DESeq2 1.24.0 on R 3.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: abundance_genes.tsv contains the abundance estimates as output by sleuth for each gene; diff_expressed_by_gene.tsv contains the differentially expressed genes from DESeq2; both are in a tab-delimited format

extract_protocol:
Accutase-dissociated cells were sorted using a BD Aria III (BD Biosciences) using a 100 µm nozzle. Cells were gated such that the pre-competence-loss population was taken as the cells with the top 10-15% OCT4:RFP to SOX2:YFP ratio, and the post-competence-loss population was the bottom 10-15% OCT4:RFP to SOX2:YFP ratio. We sorted around 250,000 cells per subpopulation in a typical experiment. Populations were sorted into 1.5 mL centrifuge tubes (Eppendorf) filled with 500 µL of mTeSR supplemented with 10 µM γ-27632; by the end of the sort, ~800 µL of sheath and sorted cells had been added to each tube. After the sort had completed, we pelleted the cells in a microcentrifuge at 250 xg for 3 minutes, then resuspended in PBS. For each sorted sample, about 10% of the sorted cells were reserved for competence testing to confirm the pre-/post-competence-loss status of the sorted population. These cells were seeded back into glass-bottom 24-well plates (Ibidi) treated with Matrigel and filled with 1 mL of mTeSR supplemented with γ-27632 and allowed to recover for 3 hours. The media was then changed to mTeSR supplemented with BMP4 and Activin A for 36 hours. Cells were fixed and stained for OCT4 and SOX2. Total RNA was prepared from sorted or dissociated cells with an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. For the mesendoderm-derived outgroup samples, the input to the RNA extraction kit was a cell population directly after dissociation with Accutase; for FACS sorted populations, the input was sorted cells suspended in PBS. RNA integrity was quantified with a TapeStation 4200 (Agilent). All RINe scores were ≥ 9.9.
Libraries were constructed from total RNA using a Kapa mRNA HyperPrep Kit (Roche) by the Bauer Core at Harvard University.

treatment_protocol: Differentiation towards the ectoderm lineage was effected using mTeSR supplemented with 0.5 µM A83-01 (R&D Systems), a small molecule inhibitor of Activin and Nodal signaling. BMP4 + Activin A treatment was accomplished by treating cells with mTeSR supplemented with 3 ng/mL recombinant human BMP4 protein (R&D Systems) and 100 ng/mL recombinant human Activin A protein (R&D Systems).

value: hESC-derived ectoderm-directed differentiation, pre- mesendoderm competence loss

tag: passages


title: RNA-Seq neonate_ctrl_rep1

status: Public on Nov 08 2021

type: SRA

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

country: USA

institute: Cornell University

description:
neonate_ctrl_rep1
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

library_source: transcriptomic

data_processing:
trim_galore (with cutadapt v1.18) was used to trim and filter reads.
hisat2 (v2.2.0) was used to map reads to the mouse mm10.
featureCounts (v2.0.0) was used to count  reads to genes (-s 0 -Q 50).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: CD8+ T cells

growth_protocol: 2x105 magnetically-enriched CD8+ T cells from human PBMCs were plated per well in RPMI-1640 complete media with 10% FBS, Pen/strep and L-glut with IL-7 (2 ng/mL).

extract_protocol:
Naïve CD8+ T cells were FACS sorted by staining for CD8, CD4, CD45RA, CD45RO and Viability Dye. Cells were sorted into PBS + 2% BSA  + 2mM EDTA. Cells were placed in Trizol and RNA was purified following the manufacturer's instructions, with the addition of a chloroform extraction, GlycoBlue addition when precipitating, and a second wash of the pelleted RNA in 70% ethanol. RNA integrity was confirmed on a Fragment Analyzer.
Libraries were prepared by the TREx core at Cornell University as follows: RNAseq libraries were generated with the non-directional NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) using 10 ng of total RNA that was initially polyA-selected.

treatment_protocol: 100 µL of red blood cell EVs (RBCEVs) were added per well, and incubated at 37°C for 4-5 days. The media was changed every 48 hours.

tag: cell state

value: Naive

tag: tissue

value: Enriched Cord Blood Mononuclear Cells

tag: treatment

value: treat with EV loaded with negative control (NC) mimic for 4-5 days


title: RNA-Seq adult_miR29_ASO_rep1

description:
adult_miR29_ASO_rep1
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

value: Enriched Adult Peripheral Blood Mononuclear Cells

value: treat with EV loaded with miR-29 ASO for 4-5 days


title: Post_competence_loss_RNASeq_rep4

city: Cambridge

first: Sharad

last: Ramanathan

state: MA

address: 52 Oxford Street, Room 402

department: Molecular and Cellular Biology

institute: Harvard University

molecule: polyA RNA

source_name: OCT4:RFP; SOX2:YFP H1 hESCs

growth_protocol: Cells were grown on polyester membrane filters (Sterlitech) with 3 µm pores that had been treated with Matrigel.

tag: cell type

value: hESC-derived ectoderm-directed differentiation, post- mesendoderm competence loss


title: HN02_CD45+ cells

city: Pittsburgh

first: Robert

middle: L

last: Ferris

address: 5500 Center Ave

institute: University of Pittsburgh

data_processing:
BCL to Fastq: Cellranger mkfastq
Fastq to Counts: Cellranger count
Aggregation of counts: Cellranger aggr
Genome_build: hg38
Supplementary_files_format_and_content: Matrix, barcode and features files for each sample

source_name: Tumor

extract_protocol:
The Single Cell 3’ Reagent Kit Protocol
10x Genomics 3' kit v2

tag: tiisue

value: Tumor

tag: sorting


title: HN04_CD45+ cells


title: RNA-Seq adult_ctrl_rep2

description:
adult_ctrl_rep2
Samples collected by University of Rochester Pediatric Processing Core (PI: Gloria Pryhuber)

value: treat with EV loaded with negative control (NC) anti-sense oligonucleotides (ASO) for 4-5 days


title: Pre_competence_loss_RNASeq_rep3


title: Mesendoderm_outgroup_RNASeq_rep3


title: Pre_competence_loss_RNASeq_rep1


title: Mesendoderm_outgroup_RNASeq_rep1


title: Post_competence_loss_RNASeq_rep2


title: Pre_competence_loss_RNASeq_rep2


title: Mesendoderm_outgroup_RNASeq_rep2


title: b4_PFTeDA_6.7_695

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
targeted RNA
exp01
rawCountsBatch4wID.txt

data_processing:
Library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
"Description" column: ctrl01s are the control for exp01s, ctrl017s are the control for exp017s, ctrl03 are the control for exp03s.
Genome_build: Human TempO-Seq® Tox+ Surrogate (S1500+) custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample, grouped by exposure length

source_name: human liver spheroids Insphero

growth_protocol: 14 day in minimal media

extract_protocol:
not extracted, tempoSeq lysis buffer used to lyse cells, which were then frozen and 2ul used for TempO-Seq library building
[Assay Principle]  The TempO-Seq assay utilizes a detector oligo (DO) pool specific to the RNA targets to be monitored. BioSpyder offers fixed content and custom DO pools to measure focused sets of transcripts, up to whole transcriptomes. The assay can utilize purified RNA, cell lysates, tissue lysates, or FFPE tissue lysates (FFPE kit available separately). In addition, both positive and negative control samples can be included.
Samples are annealed to a matched pair of detector oligos (DOs), with each pair targeting a single gene. The DO pool targets up to tens of thousands of RNA sequences, depending on the targeted gene content of the assay, but all share the same pair of primer binding sequences (indicated in Fig 1. by the red and yellow sections of each DO). The DOs hybridize to sequences of the targeted RNA molecule such that their respective 3’ and 5’ ends are adjacent. Each UDO has an additional target-specific sequence at their 3’ end that hybridizes to the targeted RNA.
After DO annealing, excess oligos and mis-hybridized or weakly hybridized DOs are removed by nuclease digestion, and the annealed oligos are ligated to form amplifiable templates. The ligated DOs are amplified with one pair of primers (making each PCR reaction single-plex regardless of the number of genes measured), with a different combination of sample index/tag sequences assigned to each sample. The PCR products are pooled together into a sequencing library, which is then purified and run on an Illumina NGS to count the number of ligated detector oligo sequences per sample (ThermoFisher-compatible kit under development). Because TempO-Seq includes an end-point PCR reaction, quantitation of the amplified products before library pooling is not needed. Very low concentration and negative control samples are expected to show low reads in the sequencing data.
[Library construction protocol]  BioSyder -TempO-Seq protocol v2.1 sept 6,2017
Human S1500, index E,F,H,G were used for indexing

treatment_protocol: PFAS replenished every 3rd day with media change

tag: chemical

value: PFTeDA

tag: dose (um)

tag: time point (days)

value: liver spheroids Insphero


title: b4_PFUnA_1.3_516

value: PFUnA


title: b4_PFTeDA_6.7_503


title: b4_PFTeDA_3.35_703


title: b4_PFUnA_1.3_708


title: b4_PFTeDA_6.7_407


title: b4_PFTeDA_6.7_599


title: b4_PFTeDA_3.35_415


title: b4_PFUnA_1.3_612


title: b4_PFUnA_1.3_420


title: b4_PFUnA_0.13_428


title: Post_competence_loss_RNASeq_rep3


title: b4_PFUnA_0.13_716


title: b4_PFTeDA_17_591

description:
targeted RNA
exp017
rawCountsBatch4wID.txt


title: b4_PFTeDA_17_687


title: b4_PFTeDA_17_495


title: b4_PFTeDA_3.35_607


title: b4_PFTeDA_3.35_511


title: b4_PFUnA_0.13_620


title: b4_PFTeDA_0.67_711


title: b4_PFTeDA_17_399


title: Post_competence_loss_RNASeq_rep1


title: b4_PFTeDA_0.67_519


title: b4_PFTeDA_0.06_719


title: b4_PFHxA_50_590

value: PFHxA


title: b4_PFTeDA_0.06_623


title: b4_PFHxA_50_686


title: b4_PFTeDA_0.06_431


title: b4_PFTeDA_0.67_615


title: b4_PFHxA_50_398


title: b4_PFHxA_2_614


title: b4_PFHxA_20_694


title: b4_PFHxA_2_422


title: b4_PFHxA_20_598


title: b4_PFHxA_100_678

description:
targeted RNA
exp03
rawCountsBatch4wID.txt


title: b4_PFHxA_2_518


title: b4_PFHxA_10_414


title: b4_PFHxA_10_606


title: b4_PFHxA_10_510


title: b4_PFHxA_0.2_622


title: b4_PFHxA_10_702


title: b4_PFHxA_0.2_526


title: b4_PFHxA_0.2_718


title: b4_PFHxA_50_494


title: b4_PFHxA_100_486


title: b4_nochemical_0_720

description:
targeted RNA
NA
rawCountsBatch4wID.txt

value: nochemical


title: b4_nochemical_0_728

description:
targeted RNA
NA
rawCountsBatch4wID.txt


title: b4_PFTeDA_0.06_527


title: b4_PFHxA_0.2_430


title: b4_Mix7_20_640


title: b4_Mix7_20_448


title: b4_PFHxA_100_390


title: b4_PFHxA_20_406


title: b4_PFHxA_2_710


title: b4_Mix7_2_752


title: b4_PFHxA_20_502


title: b4_Mix7_2_656


title: b4_Mix7_2_560


title: b4_Mix7_10_648


title: b4_Mix7_10_744


title: b4_Mix7_10_552


title: b4_Mix7_2_464


title: b4_Mix7_1_760


title: b4_Mix7_1_568


title: b4_Mix6_2_751


title: b4_Mix7_1_472


title: b4_Mix7_0.2_480


title: b4_Mix7_1_664


title: b4_Mix7_0.2_576


title: b4_Mix7_0.2_768


title: b4_Mix7_0.2_672


title: b4_Mix6_2_655


title: b4_Mix7_20_544


title: b4_Mix7_20_736


title: b4_Mix6_1_663


title: b4_Mix6_1_759


title: b4_Mix6_2_463


title: b4_Mix6_1_567


title: b4_Mix6_2_559


title: b4_Mix6_0.2_767


title: b4_Mix6_0.2_671


title: b4_Mix6_1_471


title: b4_Mix6_0.2_575


title: b4_Mix5_2_742


title: b4_Mix6_0.2_479


title: b4_Mix7_10_456


title: b4_Mix5_2_646


title: b4_Mix5_2_550


title: b4_Mix5_2_454


title: b4_Mix5_1_654


title: b4_Mix5_1_558


title: b4_Mix5_1_462


title: b4_Mix5_1_750


title: b4_Mix5_0.2_758


title: b4_Mix5_0.2_566


title: b4_Mix5_0.2_470


title: b4_Mix5_0.2_662


title: b4_Mix4_1_557


title: b4_Mix4_1_749


title: b4_Mix4_1_653


title: b4_Mix5_0.02_574


title: b4_Mix5_0.02_478


title: b4_Mix5_0.02_766


title: b4_Mix5_0.02_670


title: b4_Mix4_0.2_469


title: b4_Mix4_0.2_565


title: b4_Mix4_0.02_765


title: b4_Mix4_1_461


title: b4_Mix4_0.2_757


title: b4_Mix4_0.2_661


title: b4_Mix4_0.02_669


title: b4_Mix3_9_532


title: b4_Mix3_9_628


title: b4_Mix3_9_724


title: b4_Mix4_0.02_477


title: b4_Mix3_9_436


title: b4_Mix3_5_732


title: b4_Mix3_5_636


title: b4_Mix3_2_548


title: b4_Mix3_2_644


title: b4_Mix3_5_540


title: b4_Mix3_5_444


title: b4_Mix3_1_652


title: b4_Mix3_1_748


title: b4_Mix3_1_556


title: b4_Mix3_0.2_756


title: b4_Mix3_0.2_564


title: b4_Mix4_0.02_573


title: b4_Mix3_1_460


title: b4_Mix3_0.2_660


title: b4_Mix3_0.02_476


title: b4_Mix3_0.02_764


title: b4_Mix2_5_635


title: b4_Mix2_5_539


title: b4_Mix2_5_731


title: b4_Mix3_0.02_668


title: b4_Mix2_5_443


title: b4_Mix3_0.02_572


title: b4_Mix3_2_740


title: b4_Mix2_1_555


title: b4_Mix2_2_643


title: b4_Mix2_2_451


title: b4_Mix2_1_651


title: b4_Mix2_1_747


title: b4_Mix2_0.2_755


title: b4_Mix2_0.2_563


title: b4_Mix2_0.2_659


title: b4_Mix2_0.2_467


title: b4_Mix3_0.2_468


title: b4_Mix2_1_459


title: b4_Mix1_20_730


title: b4_Mix2_0.02_571


title: b4_Mix1_20_634


title: b4_Mix2_0.02_763


title: b4_Mix2_0.02_475


title: b4_Mix2_0.02_667


title: b4_Mix1_20_538


title: b4_Mix1_20_442


title: b4_Mix1_2_746


title: b4_Mix2_2_547


title: b4_Mix1_2_650


title: b4_Mix1_2_458


title: b4_Mix1_2_554


title: b4_Mix1_10_738


title: b4_Mix1_10_450


title: b4_Mix2_2_739


title: b4_Mix1_1_754


title: b4_Mix1_1_658


title: b4_Mix1_1_466


title: b4_Mix1_0.2_666


title: b4_Mix1_0.2_570


title: b4_Mix1_0.2_474


title: b4_FtS8_2_50_493

value: 8:2 FtS


title: b4_FtS8_2_50_685


title: b4_FtS8_2_50_589


title: b4_FtS8_2_50_397


title: b4_FtS8_2_20_693


title: b4_FtS8_2_20_597


title: b4_FtS8_2_2_709


title: b4_FtS8_2_20_405


title: b4_FtS8_2_20_501


title: b4_FtS8_2_2_421


title: b4_FtS8_2_10_701


title: b4_FtS8_2_2_613


title: b4_Mix1_10_642


title: b4_FtS8_2_10_509


title: b4_FtS8_2_10_413


title: b4_FtS8_2_10_605


title: b4_FtS8_2_0.2_717


title: b4_FtS6_2_50_682

value: 6:2 FtS


title: b4_FtS8_2_0.2_525


title: b4_FtS8_2_0.2_429


title: b4_FtS6_2_50_586


title: b4_Mix1_1_562


title: b4_FtS6_2_50_394


title: b4_FtS6_2_20_690


title: b4_FtS6_2_50_490


title: b4_FtS8_2_2_517


title: b4_FtS6_2_20_594


title: b4_FtS6_2_20_498


title: b4_FtS6_2_2_514


title: b4_FtS6_2_2_706


title: b4_FtS6_2_2_610


title: b4_Mix1_0.2_762


title: b4_FtS6_2_2_418


title: b4_FtS8_2_0.2_621


title: b4_FtS6_2_100_578


title: b4_FtS6_2_100_674


title: b4_FtS6_2_100_386


title: b4_FtS6_2_100_482


title: b4_FtS6_2_10_506


title: b4_FtS6_2_10_602


title: b4_FtS6_2_10_698


title: b4_FtS6_2_0.2_618


title: b4_FtS6_2_0.2_714


title: b4_FtS6_2_10_410


title: b4_FtS6_2_0.2_426


title: b4_FtOH6_2_50_683

value: 6:2 FtOH


title: b4_FtOH6_2_50_587


title: b4_FtOH6_2_20_691


title: b4_FtOH6_2_50_491


title: b4_FtS6_2_20_402


title: b4_FtOH6_2_20_403


title: b4_FtOH6_2_20_595


title: b4_FtOH6_2_20_499


title: b4_FtOH6_2_50_395


title: b4_FtOH6_2_2_707


title: b4_FtOH6_2_100_483


title: b4_FtOH6_2_100_675


title: b4_FtOH6_2_2_419


title: b4_FtOH6_2_2_611


title: b4_FtOH6_2_100_579


title: b4_FtOH6_2_10_603


title: b4_FtOH6_2_0.2_715


title: b4_FtOH6_2_10_699


title: b4_FtS6_2_0.2_522


title: b4_FtOH6_2_10_507


title: b4_FtOH6_2_10_411


title: b4_DMSO_0.00017_585

description:
targeted RNA
ctrl017
rawCountsBatch4wID.txt

value: DMSO


title: b4_FtOH6_2_0.2_427


title: b4_DMSO_0.00017_681


title: b4_DMSO_3e-04_577

description:
targeted RNA
ctrl03
rawCountsBatch4wID.txt


title: b4_DMSO_3e-04_481


title: b4_DMSO_3e-04_385


title: b4_FtOH6_2_0.2_619


title: b4_DMSO_0_761

description:
targeted RNA
ctrl01
rawCountsBatch4wID.txt


title: b4_DMSO_0_745


title: b4_DMSO_3e-04_673


title: b4_FtOH6_2_0.2_523


title: b4_DMSO_0.00017_489


title: b4_DMSO_0_737


title: b4_FtOH6_2_2_515


title: b4_DMSO_0.00017_393


title: b4_FtOH6_2_100_387


title: b4_DMSO_0_753


title: b4_DMSO_0_729


title: b4_DMSO_0_721


title: b4_DMSO_0_697


title: b4_DMSO_0_713


title: b4_DMSO_0_689


title: b4_DMSO_0_665


title: b4_DMSO_0_657


title: b4_DMSO_0_633


title: b4_DMSO_0_649


title: b4_DMSO_0_625


title: b4_DMSO_0_641


title: b4_DMSO_0_569


title: b4_DMSO_0_609


title: b4_DMSO_0_601


title: b4_DMSO_0_705


title: b4_DMSO_0_561


title: b4_DMSO_0_537


title: b4_DMSO_0_465


title: b4_DMSO_0_497


title: b4_DMSO_0_593


title: b4_DMSO_0_553


title: b4_DMSO_0_545


title: b4_DMSO_0_529


title: b4_DMSO_0_513


title: b4_DMSO_0_449


title: b4_DMSO_0_433


title: b4_DMSO_0_425


title: b4_DMSO_0_473


title: b4_DMSO_0_457


title: b4_DMSO_0_505


title: b4_DMSO_0_417


title: b3_PFPeA_50_638

description:
targeted RNA
exp017
rawCountsBatch3wID.txt

value: PFPeA


title: b4_DMSO_0_409


title: b4_DMSO_0_617


title: b3_PFPeA_20_742

description:
targeted RNA
exp01
rawCountsBatch3wID.txt


title: b4_DMSO_0_521


title: b4_DMSO_0_441


title: b3_PFPeA_20_550


title: b3_PFPeA_20_454


title: b3_PFPeA_2_758


title: b3_PFPeA_2_566


title: b3_PFPeA_2_662


title: b3_PFPeA_100_630

description:
targeted RNA
exp03
rawCountsBatch3wID.txt


title: b3_PFPeA_10_558


title: b3_PFPeA_100_534


title: b3_PFPeA_20_646


title: b3_PFPeA_2_470


title: b3_PFPeA_0.2_766


title: b3_PFPeA_0.2_670


title: b3_PFPeA_100_438


title: b3_PFPeA_100_726


title: b3_PFPeA_10_462


title: b4_DMSO_0_401


title: b3_PFOSA_2_709

value: PFOSA


title: b3_PFPeA_50_542


title: b3_PFPeA_10_750


title: b3_PFPeA_50_734


title: b3_PFOSA_10_701


title: b3_PFOSA_20_693


title: b3_PFPeA_0.2_478


title: b3_PFOSA_20_501


title: b3_PFPeA_50_446


title: b3_PFOSA_2_613


title: b3_PFOSA_20_405


title: b3_PFOSA_2_517


title: b3_PFOSA_10_413


title: b3_PFOSA_10_605


title: b3_PFOSA_0.2_717


title: b3_PFOSA_0.2_525


title: b3_PFOSA_0.2_621


title: b3_PFNA_2_757

value: PFNA


title: b3_PFOSA_0.2_429


title: b3_PFNA_2_661


title: b3_PFNA_2_565


title: b3_PFNA_0.2_669


title: b3_PFHxS_50_640

value: PFHxS


title: b3_PFNA_0.2_765


title: b3_PFHxS_50_448


title: b3_PFHxS_50_544


title: b3_PFOSA_2_421


title: b3_PFHxS_20_648


title: b3_PFHxS_20_552


title: b3_PFHxS_2_760


title: b3_PFHxS_20_744


title: b3_PFOSA_10_509


title: b3_PFHxS_2_664


title: b3_PFHxS_100_536


title: b3_PFHxS_100_632


title: b3_PFHxS_2_472


title: b3_PFHxS_100_728


title: b3_PFNA_2_469


title: b3_PFHxS_100_440


title: b3_PFNA_0.2_477


title: b3_PFHxS_10_560


title: b3_PFHxS_50_736


title: b3_PFHxS_10_464


title: b3_PFHpS_50_636

value: PFHpS


title: b3_PFHpS_50_444


title: b3_PFHpS_20_644


title: b3_PFHxS_10_752


title: b3_PFHpS_20_452


title: b3_PFHpS_2_660


title: b3_PFHpS_2_468


title: b3_PFHpS_100_724


title: b3_PFHpS_20_548


title: b3_PFHpS_2_756


title: b3_PFHpS_100_532


title: b3_PFHpS_10_748


title: b3_PFHpS_100_436


title: b3_PFHpS_50_732


title: b3_PFHpS_100_628


title: b3_PFHxS_2_568


title: b3_PFHpS_10_556


title: b3_PFHpS_10_460


title: b3_PFHpA_50_635

value: PFHpA


title: b3_PFHpS_0.2_476


title: b3_PFHpS_0.2_764


title: b3_PFHpA_50_539


title: b3_PFHpS_20_740


title: b3_PFHpS_0.2_668


title: b3_PFHpA_20_739


title: b3_PFHpA_50_443


title: b3_PFHpA_20_451


title: b3_PFHpA_2_467


title: b3_PFHpA_2_659


title: b3_PFHpA_100_723


title: b3_PFHpA_100_627


title: b3_PFHpA_2_563


title: b3_PFHpS_10_652


title: b3_PFHxS_20_456


title: b3_PFHpA_10_459


title: b3_PFHpA_100_531


title: b3_PFHpA_2_755


title: b3_PFHpA_10_747


title: b3_PFHpA_100_435


title: b3_PFHpA_10_651


title: b3_PFHpS_0.2_572


title: b3_PFHpA_0.2_667


title: b3_PFHpA_50_731


title: b3_PFHpA_0.2_571


title: b3_PFHpA_20_643


title: b3_PFHpA_0.2_475


title: b3_PFHpA_20_547


title: b3_PFDA_2_711

value: PFDA


title: b3_PFDA_2_615


title: b3_PFDA_0.2_431


title: b3_PFDA_0.2_623


title: b3_PFDA_0.2_527


title: b3_PFDA_0.2_719


title: b3_PFDA_2_423


title: b3_PFBA_50_588

value: PFBA


title: b3_PFBA_50_492


title: b3_PFBA_20_596


title: b3_PFBA_50_684


title: b3_PFBA_20_500


title: b3_PFBA_2_708


title: b3_PFBA_20_692


title: b3_PFBA_20_404


title: b3_PFBA_100_580


title: b3_PFBA_2_420


title: b3_PFHpA_0.2_763


title: b3_PFBA_2_516


title: b3_PFBA_2_612


title: b3_PFBA_100_484


title: b3_PFBA_100_388


title: b3_PFBA_10_700


title: b3_PFBA_10_604


title: b3_PFDA_2_519


title: b3_PFBA_10_508


title: b3_PFBA_10_412


title: b3_PFBA_0.2_620


title: b3_PFBA_0.2_716


title: b3_FTS42_50_686

value: 4:2 FtS


title: b3_PFBA_0.2_428

value: liver spheroids Insphero


title: b3_PFBA_0.2_524


title: b3_FTS42_50_590


title: b3_FTS42_20_598


title: b3_FTS42_50_398


title: b3_FTS42_20_694


title: b3_FTS42_50_494


title: b3_FTS42_20_502


title: b3_FTS42_2_614


title: b3_FTS42_2_518


title: b3_FTS42_100_582


title: b3_FTS42_100_678


title: b3_FTS42_2_422


title: b3_FTS42_100_390


title: b3_FTS42_10_702


title: b3_FTS42_10_510


title: b3_FTS42_10_414


title: b3_FTS42_0.2_718


title: b3_FTS42_0.2_622


title: b3_FTS42_0.2_526


title: b3_FTS42_0.2_430


title: b3_FtOH82_50_683

value: FtOH 8:2


title: b3_FtOH82_50_491


title: b3_FtOH82_50_587


title: b3_FtOH82_20_691


title: b3_FtOH82_50_395


title: b3_FtOH82_20_595


title: b3_FtOH82_20_403


title: b3_FtOH82_20_499


title: b3_FtOH82_2_707


title: b3_FtOH82_2_515


title: b3_FTS42_20_406


title: b3_FtOH82_2_419


title: b3_FTS42_2_710


title: b3_FtOH82_100_579


title: b3_FtOH82_100_483


title: b3_FtOH82_10_603


title: b3_FtOH82_10_699


title: b3_FtOH82_0.2_427


title: b3_DMSO_30_577

description:
targeted RNA
ctrl03
rawCountsBatch3wID.txt


title: b3_FTS42_100_486


title: b3_FtOH82_10_507


title: b3_DMSO_30_481


title: b3_FtOH82_10_411


title: b3_DMSO_17_729

description:
targeted RNA
ctrl017
rawCountsBatch3wID.txt


title: b3_FtOH82_0.2_715


title: b3_DMSO_30_433


title: b3_FtOH82_0.2_523


title: b3_FtOH82_0.2_619


title: b3_DMSO_17_489


title: b3_DMSO_17_633


title: b3_DMSO_30_529


title: b3_DMSO_17_681


title: b3_DMSO_17_585


title: b3_DMSO_0_697

description:
targeted RNA
ctrl01
rawCountsBatch3wID.txt


title: b3_DMSO_0_713


title: b3_FtOH82_100_675


title: b3_DMSO_0_609


title: b3_DMSO_17_441


title: b3_FtOH82_100_387


title: b3_DMSO_0_737


title: b3_DMSO_0_521


title: b3_DMSO_0_601


title: b3_DMSO_0_617


title: b3_DMSO_30_625


title: b3_DMSO_17_393


title: b3_DMSO_0_513


title: b3_DMSO_0_505


title: b3_DMSO_0_449


title: b3_DMSO_0_425


title: b3_DMSO_0_417


title: b3_DMSO_0_401


title: b3_C82MonoPAP_50_688

value: 8:2 monoPAP


title: b3_DMSO_0_497


title: b3_DMSO_0_689


title: b3_C82MonoPAP_50_496


title: b3_DMSO_0_593


title: b3_DMSO_0_409


title: b3_C82MonoPAP_50_400


title: b3_C82MonoPAP_20_696


title: b3_C82MonoPAP_20_600


title: b3_C82MonoPAP_20_504


title: b3_C82MonoPAP_2_520


title: b3_C82MonoPAP_20_408


title: b3_C82MonoPAP_2_424


title: b3_C82MonoPAP_2_712


title: b3_C82MonoPAP_10_704


title: b3_C82MonoPAP_10_608


title: b3_C82MonoPAP_100_680


title: b3_C82MonoPAP_100_392


title: b3_C82MonoPAP_10_416


title: b3_C82MonoPAP_0.2_528


title: b3_C82MonoPAP_0.2_624


title: b3_C82MonoPAP_0.2_720


title: b3_C82MonoPAP_50_592


title: b3_C62monoPAP_50_639

value: 6:2 monoPAP


title: b3_C62monoPAP_50_735


title: b3_C62monoPAP_50_447


title: b3_C62monoPAP_20_551


title: b3_C62monoPAP_20_647


title: b3_C62monoPAP_20_455


title: b3_C62monoPAP_2_663


title: b3_C62monoPAP_2_567


title: b3_C62monoPAP_20_743


title: b3_C62monoPAP_2_759


title: b3_C62monoPAP_2_471


title: b3_C62monoPAP_100_439


title: b3_C62monoPAP_10_751


title: b3_C62monoPAP_100_727


title: b3_C82MonoPAP_10_512


title: b3_C62monoPAP_100_631


title: b3_C62monoPAP_100_535


title: b3_C62monoPAP_10_559


title: b3_C62monoPAP_10_655


title: b3_C62monoPAP_10_463


title: b3_C62monoPAP_0.2_479


title: b3_c53Acid_50_682

value: 5:3 Acid


title: b3_C62monoPAP_0.2_767


title: b3_C62monoPAP_50_543


title: b3_c53Acid_50_586


title: b3_c53Acid_20_690


title: b3_C82MonoPAP_0.2_432


title: b3_c53Acid_50_394


title: b3_c53Acid_2_610


title: b3_c53Acid_2_418


title: b3_c53Acid_100_674


title: b3_c53Acid_100_578


title: b3_c53Acid_100_482


title: b3_c53Acid_20_402


title: b3_c53Acid_10_506


title: b3_c53Acid_10_602


title: b3_c53Acid_20_498


title: b3_c53Acid_100_386


title: b3_c53Acid_10_410


title: b3_c53Acid_0.2_618


title: b3_c53Acid_0.2_522


title: b2_FtOH6_2_100_992

description:
targeted RNA
exp03
rawCountsBatch2wID.txt


title: b2_PFUnA_6.5_604

description:
targeted RNA
exp01
rawCountsBatch2wID.txt

value: PFUnA


title: b2_DMSO_3e-04_991

description:
targeted RNA
ctrl03
rawCountsBatch2wID.txt


title: b2_PFUnA_6.5_412


title: b2_DMSO_0.00017_994

description:
targeted RNA
ctrl017
rawCountsBatch2wID.txt


title: b2_PFUnA_6.5_700


title: b2_DMSO_3e-04_995


title: b2_FtOH6_2_100_988

value: 6:2 FtOH


title: b2_PFUnA_13_692


title: b3_c53Acid_0.2_426


title: b2_DMSO_0.00017_990

value: DMSO


title: b2_PFUnA_13_500


title: b2_PFUnA_1.3_708


title: b2_PFUnA_13_596


title: b3_c53Acid_2_514


title: b2_PFUnA_6.5_508


title: b2_PFUnA_0.13_620


title: b2_PFUnA_0.13_428


title: b3_c53Acid_10_698


title: b2_PFTeDA_6.7_695

value: PFTeDA


title: b2_PFUnA_1.3_612


title: b2_PFUnA_0.13_524


title: b2_PFUnA_1.3_420


title: b2_PFTeDA_6.7_503


title: b3_c53Acid_0.2_714


title: b2_PFTeDA_6.7_407


title: b2_PFTeDA_33_487


title: b2_PFTeDA_33_583


title: b2_PFTeDA_3.35_703


title: b2_PFTeDA_3.35_511


title: b2_PFTeDA_3.35_607


title: b2_PFTeDA_0.67_711


title: b2_PFTeDA_0.67_615


title: b2_PFTeDA_17_399

description:
targeted RNA
exp017
rawCountsBatch2wID.txt


title: b2_PFTeDA_3.35_415


title: b2_PFTeDA_17_495


title: b2_PFTeDA_17_591


title: b2_PFTeDA_0.67_519


title: b2_PFTeDA_0.06_719


title: b2_PFTeDA_0.06_527


title: b2_PFTeDA_0.06_623


title: b2_PFTeDA_0.06_431


title: b2_PFHxA_50_494

value: PFHxA


title: b2_PFHxA_50_590


title: b2_PFHxA_50_686


title: b2_PFHxA_50_398


title: b2_PFHxA_20_502


title: b2_PFTeDA_33_391


title: b2_PFHxA_20_694


title: b2_PFHxA_20_598


title: b2_PFHxA_2_518


title: b2_PFHxA_20_406


title: b2_PFHxA_2_710


title: b2_PFHxA_2_422


title: b2_PFTeDA_17_687


title: b2_PFHxA_100_486


title: b2_PFHxA_100_678


title: b2_PFHxA_10_702


title: b2_PFHxA_10_510


title: b2_PFHxA_100_390


title: b2_PFHxA_0.2_526


title: b2_PFHxA_0.2_718


title: b2_PFHxA_10_606


title: b2_PFHxA_0.2_622


title: b2_PFHxA_0.2_430


title: b2_Mix7_20_736


title: b2_Mix7_20_448


title: b2_Mix7_2_752


title: b2_Mix7_2_560


title: b2_Mix7_2_656


title: b2_PFHxA_2_614


title: b2_Mix7_10_744


title: b2_Mix7_2_464


title: b2_Mix7_10_456


title: b2_Mix7_1_760


title: b2_Mix7_1_664


title: b2_Mix7_1_568


title: b2_Mix7_1_472


title: b2_Mix7_0.2_768


title: b2_Mix7_0.2_672


title: b2_Mix7_0.2_576


title: b2_Mix7_0.2_480


title: b2_PFHxA_10_414


title: b2_Mix7_20_640


title: b2_Mix6_33.3_535


title: b2_Mix7_20_544


title: b2_Mix6_20_735


title: b2_Mix6_20_639


title: b2_Mix6_2_751


title: b2_Mix6_20_543


title: b2_Mix6_2_463


title: b2_Mix7_10_552


title: b2_Mix6_2_655


title: b2_Mix6_2_559


title: b2_Mix6_1_759


title: b2_Mix6_10_647


title: b2_Mix6_10_551


title: b2_Mix6_1_567


title: b2_Mix6_1_663


title: b2_Mix6_33.3_727


title: b2_Mix6_0.2_767


title: b2_Mix6_0.2_575


title: b2_Mix6_0.2_671


title: b2_Mix5_8_534


title: b2_Mix5_8_630


title: b2_Mix5_8_438


title: b2_Mix5_8_726


title: b2_Mix5_5_734


title: b2_Mix6_1_471


title: b2_Mix5_5_638


title: b2_Mix6_33.3_631


title: b2_Mix6_0.2_479


title: b2_Mix5_2_742


title: b2_Mix5_1_654


title: b2_Mix5_2_454


title: b2_Mix5_1_462


title: b2_Mix6_10_743


title: b2_Mix5_0.2_758


title: b2_Mix5_0.2_470


title: b2_Mix5_2_646


title: b2_Mix5_2_550


title: b2_Mix5_1_558


title: b2_Mix5_0.2_566


title: b2_Mix5_0.02_574


title: b2_Mix5_0.2_662


title: b2_Mix5_0.02_766


title: b2_Mix5_0.02_670


title: b2_Mix5_0.02_478


title: b2_Mix4_9_725


title: b2_Mix4_5_733


title: b2_Mix4_9_629


title: b2_Mix4_9_437


title: b2_Mix4_9_533


title: b2_Mix4_5_637


title: b2_Mix4_5_541


title: b2_Mix4_5_445


title: b2_Mix4_2_741


title: b2_Mix4_1_749


title: b2_Mix4_1_653


title: b2_Mix4_2_453


title: b2_Mix4_2_549


title: b2_Mix4_1_557


title: b2_Mix4_0.2_469


title: b2_Mix4_0.2_565


title: b2_Mix3_9_724


title: b2_Mix4_0.02_765


title: b2_Mix4_0.02_573


title: b2_Mix3_9_532


title: b2_Mix3_9_628


title: b2_Mix3_5_636


title: b2_Mix3_2_548


title: b2_Mix3_2_740


title: b2_Mix3_5_540


title: b2_Mix3_1_748


title: b2_Mix3_5_444


title: b2_Mix3_1_556


title: b2_Mix4_1_461


title: b2_Mix4_0.2_661


title: b2_Mix3_5_732


title: b2_Mix3_0.2_468


title: b2_Mix3_1_460


title: b2_Mix3_2_452


title: b2_Mix3_0.02_668


title: b2_Mix3_0.2_660


title: b2_Mix4_0.2_757


title: b2_Mix3_1_652


title: b2_Mix4_0.02_477


title: b2_Mix3_0.2_756


title: b2_Mix3_9_436


title: b2_Mix4_0.02_669


title: b2_Mix3_0.2_564


title: b2_Mix3_0.02_572


title: b2_Mix3_0.02_476


title: b2_Mix3_0.02_764


title: b2_Mix2_2_547


title: b2_Mix2_5_635


title: b2_Mix3_2_644


title: b2_Mix2_5_539


title: b2_Mix2_5_731


title: b2_Mix2_5_443


title: b2_Mix2_2_739


title: b2_Mix2_1_459


title: b2_Mix2_0.2_563


title: b2_Mix2_2_643


title: b2_Mix2_0.02_571


title: b2_Mix2_0.02_475


title: b2_Mix2_0.02_763


title: b2_Mix2_2_451


title: b2_Mix2_1_747


title: b2_Mix2_11_531


title: b2_Mix2_0.2_467


title: b2_Mix1_20_634


title: b2_Mix2_1_555


title: b2_Mix2_1_651


title: b2_Mix2_11_723


title: b2_Mix2_0.2_755


title: b2_Mix2_11_435


title: b2_Mix4_2_645


title: b2_Mix1_20_442


title: b2_Mix1_2_554


title: b2_Mix1_2_650


title: b2_Mix1_2_746


title: b2_Mix2_0.02_667


title: b2_Mix1_10_738


title: b2_Mix1_10_642


title: b2_Mix1_50_722


title: b2_Mix1_50_626


title: b2_Mix1_50_530


title: b2_Mix1_20_730


title: b2_Mix1_10_546


title: b2_Mix1_20_538


title: b2_Mix1_10_450


title: b2_Mix1_50_434


title: b2_Mix1_1_658


title: b2_Mix1_1_754


title: b2_Mix1_0.2_666


title: b2_Mix1_0.2_762


title: b2_Mix1_1_562


title: b2_Mix1_0.2_474


title: b2_Mix1_0.2_570


title: b2_FtS8_2_50_493

value: 8:2 FtS


title: b2_FtS8_2_50_589


title: b2_FtS8_2_20_693


title: b2_Mix1_2_458


title: b2_FtS8_2_20_501


title: b2_FtS8_2_20_405


title: b2_FtS8_2_2_517


title: b2_FtS8_2_2_613


title: b2_FtS8_2_20_597


title: b2_FtS8_2_2_709


title: b2_FtS8_2_2_421


title: b2_FtS8_2_100_485


title: b2_FtS8_2_100_581


title: b2_Mix1_1_466


title: b2_FtS8_2_10_605


title: b2_FtS8_2_10_509


title: b2_FtS8_2_10_413


title: b2_FtS8_2_100_389


title: b2_FtS8_2_0.2_717


title: b2_FtS8_2_0.2_621


title: b2_FtS8_2_0.2_525


title: b2_FtS8_2_100_677


title: b2_FtS8_2_50_685


title: b2_FtS6_2_50_682

value: 6:2 FtS


title: b2_FtS6_2_20_594


title: b2_FtS6_2_20_402


title: b2_FtS6_2_50_490


title: b2_FtS6_2_50_586


title: b2_FtS6_2_20_498


title: b2_FtS8_2_10_701


title: b2_FtS6_2_2_514


title: b2_FtS6_2_50_394


title: b2_FtS6_2_2_610


title: b2_FtS6_2_2_418


title: b2_FtS6_2_100_482


title: b2_FtS6_2_10_698


title: b2_FtS6_2_10_506


title: b2_FtS6_2_0.2_714


title: b2_FtS6_2_100_386


title: b2_FtS6_2_10_602


title: b2_FtS8_2_0.2_429


title: b2_FtS6_2_0.2_522


title: b2_FtOH6_2_50_491


title: b2_FtOH6_2_50_683


title: b2_FtS6_2_0.2_426


title: b2_FtS6_2_10_410


title: b2_FtOH6_2_20_691


title: b2_FtOH6_2_50_587


title: b2_FtOH6_2_50_395


title: b2_FtOH6_2_20_403


title: b2_FtOH6_2_20_499


title: b2_FtOH6_2_20_595


title: b2_FtOH6_2_2_707


title: b2_FtOH6_2_2_611


title: b2_FtOH6_2_0.2_523


title: b2_FtOH6_2_10_411


title: b2_FtOH6_2_10_507


title: b2_FtOH6_2_10_699


title: b2_FtOH6_2_0.2_715


title: b2_FtOH6_2_10_603


title: b2_FtOH6_2_0.2_427


title: b2_DMSO_3e-04_481


title: b2_DMSO_3e-04_385


title: b2_DMSO_0.00017_585


title: b2_DMSO_0_745

description:
targeted RNA
ctrl01
rawCountsBatch2wID.txt


title: b2_DMSO_0_753


title: b2_DMSO_0.00017_489


title: b2_DMSO_0_729


title: b2_DMSO_0_761


title: b2_DMSO_0_721


title: b2_DMSO_0_737


title: b2_DMSO_0_705


title: b2_DMSO_0_697


title: b2_DMSO_0_713


title: b2_DMSO_0_665


title: b2_DMSO_0_689


title: b2_DMSO_0_657


title: b2_FtOH6_2_2_419


title: b2_FtOH6_2_0.2_619


title: b2_DMSO_0_649


title: b2_FtS6_2_0.2_618


title: b2_DMSO_0_593


title: b2_DMSO_0_617


title: b2_DMSO_0_601


title: b2_DMSO_0_553


title: b2_DMSO_0_569


title: b2_DMSO_0_625


title: b2_DMSO_0.00017_393


title: b2_DMSO_0_609


title: b2_DMSO_0_537


title: b2_DMSO_0_545


title: b2_DMSO_0_521


title: b2_DMSO_0_457


title: b2_DMSO_0_441


title: b2_DMSO_0_433


title: b2_DMSO_0_449


title: b2_DMSO_0_425


title: b2_DMSO_0_417


title: b2_DMSO_0_401


title: b2_DMSO_0_409


title: b1_PFPeA_50_638

description:
targeted RNA
exp017
rawCountsBatch1wID.txt

value: PFPeA


title: b1_PFPeA_50_446


title: b1_PFPeA_50_542


title: b1_PFPeA_20_646

description:
targeted RNA
exp01
rawCountsBatch1wID.txt


title: b1_PFPeA_20_742


title: b1_PFPeA_20_550


title: b2_DMSO_0_561


title: b1_PFPeA_2_758


title: b1_PFPeA_2_470


title: b1_PFPeA_100_726

description:
targeted RNA
exp03
rawCountsBatch1wID.txt


title: b1_PFPeA_100_630


title: b1_PFPeA_10_750


title: b1_PFPeA_100_534


title: b1_PFPeA_2_662


title: b1_PFPeA_10_654


title: b1_PFPeA_100_438


title: b1_PFPeA_50_734


title: b1_PFPeA_0.2_670


title: b1_PFPeA_0.2_574


title: b1_PFPeA_0.2_478


title: b1_PFOSA_20_693

value: PFOSA


title: b1_PFOSA_20_597


title: b1_PFOSA_20_501


title: b1_PFPeA_0.2_766


title: b1_PFOSA_20_405


title: b2_FtS8_2_50_397


title: b1_PFOSA_2_421


title: b1_PFOSA_2_517


title: b1_PFOSA_2_613


title: b1_PFOSA_10_605


title: b1_PFOSA_10_701


title: b1_PFOSA_10_413


title: b1_PFPeA_20_454


title: b1_PFOSA_0.2_717


title: b1_PFOSA_0.2_621


title: b1_PFPeA_10_462


title: b1_PFOSA_0.2_525


title: b1_PFOSA_0.2_429


title: b1_PFOSA_10_509


title: b1_PFNA_20_741

value: PFNA


title: b1_PFNA_50_541


title: b1_PFNA_50_445


title: b1_PFNA_50_637


title: b1_PFNA_20_645


title: b1_PFOSA_2_709


title: b1_PFNA_20_453


title: b1_PFNA_20_549


title: b1_PFNA_2_757


title: b1_PFNA_2_661


title: b1_PFNA_100_629


title: b1_PFNA_100_725


title: b1_PFNA_2_469


title: b1_PFNA_100_437


title: b1_PFNA_100_533


title: b1_PFNA_10_749


title: b1_PFNA_10_461


title: b1_PFNA_10_653


title: b1_PFNA_10_557


title: b1_PFNA_0.2_765


title: b1_PFNA_0.2_669


title: b1_PFNA_0.2_573


title: b1_PFNA_50_733


title: b1_PFNA_0.2_477


title: b1_PFHxS_50_640

value: PFHxS


title: b1_PFHxS_50_448


title: b1_PFHxS_20_744


title: b1_PFHxS_50_736


title: b1_PFNA_2_565


title: b1_PFHxS_2_760


title: b1_PFHxS_20_456


title: b1_PFHxS_100_728


title: b1_PFHxS_2_568


title: b1_PFHxS_2_472


title: b1_PFHxS_10_752


title: b1_PFHxS_2_664


title: b1_PFHxS_100_536


title: b1_PFHxS_100_632


title: b1_PFHxS_100_440


title: b1_PFHxS_0.2_768


title: b1_PFHxS_10_464


title: b1_PFHxS_0.2_672


title: b1_PFHxS_0.2_576


title: b1_PFHxS_0.2_480


title: b1_PFHpS_50_540

value: PFHpS


title: b1_PFHpS_50_444

value: liver spheroids Insphero


title: b1_PFHxS_50_544


title: b1_PFHpS_20_740


title: b1_PFHxS_20_552


title: b1_PFHxS_20_648


title: b1_PFHpS_20_548


title: b1_PFHpS_20_644


title: b1_PFHpS_2_756


title: b1_PFHpS_2_564


title: b1_PFHpS_2_468


title: b1_PFHpS_100_724


title: b1_PFHpS_100_628


title: b1_PFHpS_100_532


title: b1_PFHpS_100_436


title: b1_PFHpS_10_748


title: b1_PFHpS_10_556


title: b1_PFHxS_10_656


title: b1_PFHpS_10_652


title: b1_PFHpS_10_460


title: b1_PFHpS_0.2_668


title: b1_PFHpS_0.2_764


title: b1_PFHpS_0.2_572


title: b1_PFHpS_0.2_476


title: b1_PFHpS_50_732


title: b1_PFHpS_50_636


title: b1_PFHpA_50_731

value: PFHpA


title: b1_PFHpA_50_539


title: b1_PFHpA_50_443


title: b1_PFHpA_50_635


title: b1_PFHpA_20_739


title: b1_PFHpA_20_643


title: b1_PFHpS_2_660


title: b1_PFHpA_20_547


title: b1_PFHpA_2_755


title: b1_PFHpA_20_451


title: b1_PFHpA_2_659


title: b1_PFHpA_2_563


title: b1_PFHpA_100_723


title: b1_PFHpA_2_467


title: b1_PFHpA_100_531


title: b1_PFHpA_100_627


title: b1_PFHpA_100_435


title: b1_PFHpA_0.2_667


title: b1_PFHpA_10_459


title: b1_PFHpA_10_651


title: b1_PFHpA_0.2_763


title: b1_PFDA_20_695

value: PFDA


title: b1_PFHpA_0.2_475


title: b1_PFHpA_0.2_571


title: b1_PFDA_20_503


title: b1_PFDA_50_687


title: b1_PFHpA_10_747


title: b1_PFHpA_10_555


title: b1_PFDA_50_399


title: b1_PFDA_50_591


title: b1_PFDA_2_519


title: b1_PFDA_2_615


title: b1_PFDA_2_423


title: b1_PFDA_10_703


title: b1_PFDA_10_607


title: b1_PFDA_10_415


title: b1_PFDA_10_511


title: b1_PFDA_0.2_719


title: b1_PFDA_0.2_623


title: b1_PFBA_50_588

value: PFBA


title: b1_PFBA_50_684


title: b1_PFDA_0.2_431


title: b1_PFDA_0.2_527


title: b1_PFBA_50_492


title: b1_PFDA_20_407


title: b1_PFBA_20_692


title: b1_PFBA_20_404


title: b1_PFBA_2_708


title: b1_PFBA_20_500


title: b1_PFBA_100_676


title: b1_PFBA_2_612


title: b1_PFBA_100_580


title: b1_PFBA_100_388


title: b1_PFBA_0.2_620


title: b1_PFBA_2_420


title: b1_PFDA_2_711


title: b1_PFBA_10_604


title: b1_PFBA_0.2_716


title: b1_PFBA_0.2_524


title: b1_PFBA_10_508


title: b1_FTS42_50_686

value: FtS 4:2


title: b1_PFBA_0.2_428


title: b1_PFBA_2_516


title: b1_PFBA_50_396


title: b1_PFBA_10_700


title: b1_FTS42_50_590


title: b1_PFBA_100_484


title: b1_FTS42_2_422


title: b1_FTS42_2_710


title: b1_FTS42_100_678


title: b1_FTS42_20_598


title: b1_FTS42_2_518


title: b1_FTS42_20_502


title: b1_FTS42_20_694


title: b1_FTS42_20_406


title: b1_FTS42_50_494


title: b1_FTS42_10_702


title: b1_FTS42_100_390


title: b1_FTS42_2_614


title: b1_FTS42_50_398


title: b1_FTS42_10_414


title: b1_FTS42_10_510


title: b1_FTS42_10_606


title: b1_FTS42_0.2_526


title: b1_FTS42_0.2_622


title: b1_FTS42_0.2_430


title: b1_FtOH82_50_683

value: FtOH 8:2


title: b1_FtOH82_50_587


title: b1_FTS42_100_486


title: b1_FtOH82_20_595


title: b1_FtOH82_50_395


title: b1_FtOH82_50_491


title: b1_FtOH82_20_691


title: b1_PFBA_20_596


title: b1_FtOH82_20_403


title: b1_FtOH82_2_515


title: b1_FtOH82_2_611


title: b1_FtOH82_100_483


title: b1_FtOH82_2_707


title: b1_FtOH82_20_499


title: b1_FtOH82_10_507


title: b1_FtOH82_0.2_715


title: b1_FtOH82_2_419


title: b1_FtOH82_10_411


title: b1_FtOH82_100_387


title: b1_FtOH82_100_579


title: b1_FtOH82_10_603


title: b1_FtOH82_0.2_619


title: b1_FtOH82_0.2_523


title: b1_FtOH82_100_675


title: b1_DMSO_3e-04_625

description:
targeted RNA
ctrl03
rawCountsBatch1wID.txt


title: b1_DMSO_3e-04_721


title: b1_FtOH82_0.2_427


title: b1_DMSO_3e-04_577


title: b1_DMSO_3e-04_481


title: b1_DMSO_3e-04_433


title: b1_FTS42_0.2_718


title: b1_FTS42_100_582


title: b1_DMSO_3e-04_385


title: b1_DMSO_0.00017_633

description:
targeted RNA
ctrl017
rawCountsBatch1wID.txt


title: b1_DMSO_0.00017_729


title: b1_DMSO_0.00017_585


title: b1_DMSO_0.00017_537


title: b1_DMSO_0.00017_489


title: b1_DMSO_0.00017_441


title: b1_DMSO_0_737

description:
targeted RNA
ctrl01
rawCountsBatch1wID.txt


title: b1_DMSO_0.00017_393


title: b1_DMSO_0_641


title: b1_DMSO_0_601


title: b1_DMSO_0_609


title: b1_DMSO_0_593


title: b1_DMSO_0_617


title: b1_DMSO_0_505


title: b1_DMSO_0_705


title: b1_DMSO_0_449


title: b1_DMSO_0_521


title: b1_DMSO_0_425


title: b1_DMSO_0_409


title: b1_DMSO_0_417


title: b1_DMSO_0_401


title: b1_DMSO_0_497


title: b1_C82MonoPAP_50_688

value: 8:2 monoPAP


title: b1_C82MonoPAP_50_592


title: b1_C82MonoPAP_50_400


title: b1_C82MonoPAP_20_696


title: b1_C82MonoPAP_20_600


title: b1_C82MonoPAP_20_504


title: b1_C82MonoPAP_20_408


title: b1_C82MonoPAP_2_712


title: b1_C82MonoPAP_50_496


title: b1_C82MonoPAP_2_616


title: b1_C82MonoPAP_2_520


title: b1_C82MonoPAP_2_424


title: b1_DMSO_0_545

value: DMSO


title: b1_DMSO_0_513


title: b1_C82MonoPAP_100_680


title: b1_C82MonoPAP_100_488


title: b1_C82MonoPAP_10_704


title: b1_C82MonoPAP_10_416


title: b1_C82MonoPAP_10_608


title: b1_C82MonoPAP_0.2_528


title: b1_C82MonoPAP_0.2_624


title: b1_C82MonoPAP_100_392


title: b1_C82MonoPAP_0.2_432


title: b1_C62monoPAP_50_735

value: 6:2 monoPAP


title: b1_C62monoPAP_50_639


title: b1_C62monoPAP_50_543


title: b1_C62monoPAP_50_447


title: b1_C62monoPAP_20_647


title: b1_C62monoPAP_2_471


title: b1_C62monoPAP_2_759


title: b1_C62monoPAP_2_567


title: b1_C62monoPAP_100_727


title: b1_C62monoPAP_100_631


title: b1_C62monoPAP_2_663


title: CP-CML M044 input

city: Milwaukee

first: Michael

last: Deininger

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Versiti Blood Research Institute

description: 15825X14_190222_D00550_0547_BCD3D6ANXX_S28_L007

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 1*10-10 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized fragment coverage bigWig tracks derived from MACS2

molecule: genomic DNA

source_name: peripheral blood

extract_protocol:
Cryo-preserved cells were thawed and immediately resuspended in 1% formaldehyde (diluted in PBS from a 37% stock, with 10-15% methanol, F8775-500ML, Sigma-Aldrich, St. Louis, MO) and incubated at room temperature for 10 minutes without shaking. Glycine was added to 125 mM to quench formaldehyde and cells were centrifuged at 2,400g for 5 minutes. The cell pellet was washed in 1 mL of cold PBS and centrifuged again. The supernatant was discarded and the cells were stored at -80°C until further processing. Chromatin immunoprecipitation was performed as previously described 11. Cells were sonicated for 8 cycles of 30 seconds with 30 seconds of rest on an Epishear probe-in sonicator (Active Motif). An antibody against H3K27me3 (Active Motif, cat # 39155) was used for pulldown and input DNA was used as controls for each sample.
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina

tag: age

value: adult

tag: disease

value: CML

value: peripheral blood


title: BP-CML M050 input

description: 15825X15_190222_D00550_0547_BCD3D6ANXX_S27_L007


title: CB M082 input

description: 15825X17_190222_D00550_0547_BCD3D6ANXX_S11_L007

value: neonatal

value: normal


title: BP-CML M033 input

description: 15825X10_190222_D00550_0547_BCD3D6ANXX_S22_L007


title: CP-CML M041 input

description: 15825X11_190222_D00550_0547_BCD3D6ANXX_S25_L007


title: CB M083 input

description: 15825X18_190222_D00550_0547_BCD3D6ANXX_S12_L007


title: CB M081 input

description: 15825X16_190222_D00550_0547_BCD3D6ANXX_S26_L007


title: CP-CML M043 input

description: 15825X13_190222_D00550_0547_BCD3D6ANXX_S23_L007


title: b1_C82MonoPAP_100_584


title: b1_C62monoPAP_10_751


title: b1_C62monoPAP_10_655


title: b1_C62monoPAP_100_439


title: CB M081 ChIP

description: 15825X7_190222_D00550_0547_BCD3D6ANXX_S19_L006

tag: chip antibody

value: H3K27me3 (Active Motif, cat # 39155)


title: CB M082 ChIP

description: 15825X8_190222_D00550_0547_BCD3D6ANXX_S20_L006


title: b1_C62monoPAP_100_535


title: BP-CML M033 ChIP

description: 15825X1_190222_D00550_0547_BCD3D6ANXX_S13_L006


title: b1_C62monoPAP_0.2_767


title: CP-CML M044 ChIP

description: 15825X5_190222_D00550_0547_BCD3D6ANXX_S17_L006


title: b1_C62monoPAP_0.2_671

description:
targeted RNA
exp01
rawCountsBatch1wID.txt


title: CP-CML M043 ChIP

description: 15825X4_190222_D00550_0547_BCD3D6ANXX_S16_L006


title: b1_C62monoPAP_20_551


title: b1_C62monoPAP_0.2_575


title: b1_C62monoPAP_0.2_479


title: b1_c53Acid_50_682

description:
targeted RNA
exp017
rawCountsBatch1wID.txt

value: 5:3 Acid


title: b1_c53Acid_50_586


title: CB M083 ChIP

description: 15825X9_190222_D00550_0547_BCD3D6ANXX_S21_L006


title: b1_c53Acid_20_690


title: b1_c53Acid_2_610


title: b1_c53Acid_50_394


title: b1_c53Acid_2_706


title: b1_c53Acid_20_498


title: b1_c53Acid_20_402


title: b1_c53Acid_50_490


title: b1_c53Acid_100_674

description:
targeted RNA
exp03
rawCountsBatch1wID.txt


title: b1_c53Acid_100_386


title: b1_c53Acid_10_698


title: b1_c53Acid_10_602


title: b1_c53Acid_10_506


title: b1_C62monoPAP_10_463


title: b1_c53Acid_0.2_714


title: b1_c53Acid_20_594


title: b1_c53Acid_2_418


title: b1_c53Acid_0.2_522


title: b1_c53Acid_0.2_426


title: BP-CML M050 ChIP

description: 15825X6_190222_D00550_0547_BCD3D6ANXX_S18_L006


title: b1_c53Acid_100_578


title: b1_c53Acid_2_514


title: b1_c53Acid_10_410


title: b1_c53Acid_0.2_618


title: KF16_Ptprca_M19_SPL_VEHICLE_PCR2

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
mCH
KF16_filtered_collapsed_CPM.txt

data_processing:
Library strategy: DNA-Seq
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR GFP reference library
Supplementary_files_format_and_content: Filtered and normalized table of barcode counts per million

organism: Mus musculus

growth_protocol: c-Kit positive hematopoietic progenitor cells were cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

extract_protocol: Viable barcoded cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA. Cells were then spun down and resuspended in PBS + 0.04% BSA + 0.4 U/ uL RNase Inhibitor (Roche) to a final cell concentrationof >1500 cells per uL. The final cell suspension was put through a cell strainer then onto a 10X Chromium Chip

treatment_protocol: Cells were transduced with SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g). Following expansion 1 million cells were transplanted into Ptprca mice. After 9 days mice were treated with chemotherapy (5+3 Cytarabine + Doxorubicin). Mice were culled across the treatment window.

value: SPL

tag: donor mouse

tag: strain

value: Ptprca

tag: timepoint

value: VEHICLE


title: b1_c53Acid_100_482

value: liver spheroids Insphero


title: KF16_Ptprca_M08_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M16_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: CP-CML M041 ChIP

description: 15825X2_190222_D00550_0547_BCD3D6ANXX_S14_L006


title: KF16_Ptprca_M08_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: BM


title: tertiary MLL-AF9 #2

description: low coverage wgs of purified leukemic cells from bone marrow

data_processing:
raw sequencing reads were cleaned with cutadapt (v1.9.1) and aligned with BWA (v0.7.13) to reference genome GRCm38.78. PCR duplicates were marked with picard (v2.17.3) and removed using Samtools (v1.9). Copy number analysis was performed using QDNASeq (version 1.26.0). The genome was divided into nonoverlapping 15-kb bins, and the number of reads mapping within each bin was counted and adjusted with a simultaneous 2D locally estimated scatterplot smoothing (LOESS) correction accounting for read mappability and GC content. All other QDNASeq parameters were set as default. Copy number changes were reported as transformed absolute copy number values (log2(absolute copy number) −1).
Genome_build: mm10
Supplementary_files_format_and_content: log2 normalized genome segment files

source_name: tertiary MLL-AF9 #2

growth_protocol: tertiary MLL-AF9 leukemic cells were harvested from the bone marrow of secondary recipient C57BL/6 mice.

extract_protocol:
Viable leukemic cells were sorted on the BD FACSAria III. Genomic DNA was purified with the Qiagen Dneasy blood and tissue kit.
300 ng of DNA was fragmented to approximately 200 bp using a focal acoustic device (Covaris S2, Sage Sciences). Libraries were prepared with NEB-Next Ultra II Kit (NEB) according to the manufacturer’s instructions
low coverage wgs

value: bone marrow

tag: genotype

value: baseline


title: wild type C57BL/6 #1

description: low coverage wgs of purified bone marrow

source_name: wild type C57BL/6 #1

value: sex age matched wild type

value: purified bone marrow


title: KF16_Ptprca_M11_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: chemo disease endpoint scRNA-seq pool 1 hashtag library

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10X Genomics Cell Ranger v3.1.0 count pipeline against the mm10/GRCm38 genome.
scRNA-seq quality control was performed using Seurat v3.2 in R. Low quality cells were removed by filtering out cells that had fewer than 500 genes or 1000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial content were also removed.
For detection of the SPLINTR barcodes from single cell data, unmapped reads (which contain reads corresponding to barcode transcripts) were extracted from BAM alignment files for each scRNAseq library using SAMtools v1.9.
BAM entries containing SPLINTR barcode reads were identified and extracted using a regular expression specific to the barcode structure.
Barcode reads were mapped to the corresponding reference library using Bowtie v1.2.2 end-to-end alignment allowing a maximum of two mismatches.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene names, matrix of gene names, matrix of 10x cell barcodes
Supplementary_files_format_and_content: matrix of gene counts - hashtag libraries, matrix of gene names - hashtag libraries, matrix of 10x cell barcodes - hashtag libraries

molecule: protein

growth_protocol: Secondary bone marrow cells from MLL-AF9 KRASG12D (KRAStm4Tyj/J) mice were cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA. Cells were then spun down and resuspended in PBS + 0.04% BSA + 0.4 U/ uL RNase Inhibitor (Roche) to a final cell concentrationof >1500 cells per uL. The final cell suspension was put through a cell strainer then onto a 10X Chromium Chip
Single cells were captured in droplet emulsions using the 10X Chromium Single-Cell Instrument and reverse transcription, cDNA amplification and library preparation were performed based on the manufacturer’s protocol using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)

treatment_protocol: Cells were transduced with GFP SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g). After the expansion period, barcoded cells were transplanted into either sub-lethally irradiated (5.5 Gy) Ptprca or non-irradiated NSG mice via lateral tail vein injection. Each mouse received 1x106 barcoded cells.

tag: disease state

value: disease endpoint - hashtags

tag: molecule type

value: Hashtag PCR amplicon


title: KF16_Ptprca_M15_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

tag: tissue


title: KF16_Ptprca_M13_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: wild type C57BL/6 #2

source_name: wild type C57BL/6 #2


title: tertiary MLL-AF9 #1

source_name: tertiary MLL-AF9 #1

value: purified leukemic cells from bone marrow


title: KF16_Ptprca_M04_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M11_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M08_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M15_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M16_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M05_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M19_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M18_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M04_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M16_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M15_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M08_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M14_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M19_SPL_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M11_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M10_BM_MRD_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: MRD


title: KF16_Ptprca_M12_BM_RELAPSE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: RELAPSE


title: KF16_Ptprca_M13_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M16_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M09_BM_MRD_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M19_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M14_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M12_BM_RELAPSE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M13_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M04_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M18_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M05_BM_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M11_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M04_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M05_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M09_BM_MRD_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M15_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: PB


title: KF16_Ptprca_M14_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M11_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M08_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M07_PB_MRD_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M05_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M10_BM_MRD_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M02_PB_RELAPSE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_TP0-01_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M04_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M01_PB_MRD_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M08_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M03_PB_RELAPSE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M01_PB_MRD_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M15_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M14_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M15_BM_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M04_PB_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M11_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_TP0-02_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF15_GMP_T0_GMP_T0_TP0_GMP_T0_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt
KF15_Ptprca_filtered_collapsed_CPM.txt

data_processing:
Library strategy: DNA-Seq
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR GFP & mCHERRY reference libraries
Supplementary_files_format_and_content: Filtered and normalized table of barcode counts per million

growth_protocol: Cells were isolated from the bone marrow of 6-8week old female C57BL/6 mice. LSK were sorted based on Lin-, c-Kit +, Sca-1+ and GMPs sorted on Lin-, c-Kit +, CD34+, FcγRHI. Both pools of primary hematopoietic progenitor cells were transduced with MLL-AF9 retrovirus and cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

extract_protocol: Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA. Cells were then spun down and resuspended in PBS + 0.04% BSA + 0.4 U/ uL RNase Inhibitor (Roche) to a final cell concentration of >1500 cells per uL. The final cell suspension was put through a cell strainer then onto a 10X Chromium Chip

treatment_protocol: Cells were transduced with SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g).

value: Baseline (T0)

tag: mouse

tag: tumor


title: KF15_GMPLSK_T0_GMPLSK_T0_TP0_GMPLSK_T0_PCR1

description:
GFP_mCH
KF15_NSG_filtered_collapsed_CPM.txt
KF15_Ptprca_filtered_collapsed_CPM.txt


title: KF15_LSK_T0_LSK_T0_TP0_LSK_T0_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt
KF15_Ptprca_filtered_collapsed_CPM.txt


title: KF16_Ptprca_TP0-01_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M07_PB_MRD_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF15_GMP_T0_GMP_T0_TP0_GMP_T0_PCR1


title: KF16_Ptprca_M03_PB_RELAPSE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF16_Ptprca_TP0-02_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF15_NSG_M24_SPL_LSK_GMP_PCR2

description:
GFP_mCH
KF15_NSG_filtered_collapsed_CPM.txt

value: Spleen

value: NSG


title: KF16_Ptprca_M05_PB_VEHICLE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: Ptprca


title: KF15_NSG_M23_SPL_LSK_GMP_PCR2


title: KF16_Ptprca_M02_PB_RELAPSE_PCR1

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF15_NSG_M24_SPL_LSK_GMP_PCR1


title: KF15_NSG_M23_SPL_LSK_GMP_PCR1


title: KF15_NSG_M22_SPL_LSK_GMP_PCR2


title: KF15_NSG_M22_SPL_LSK_GMP_PCR1


title: KF15_LSK_T0_LSK_T0_TP0_LSK_T0_PCR2


title: KF15_NSG_M21_SPL_LSK_GMP_PCR2


title: KF15_NSG_M21_SPL_LSK_GMP_PCR1


title: KF15_Ptprca_M20_SPL_LSK_GMP_PCR1

description:
GFP_mCH
KF15_Ptprca_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M20_SPL_LSK_GMP_PCR2


title: KF15_GMPLSK_T0_GMPLSK_T0_TP0_GMPLSK_T0_PCR2


title: KF15_Ptprca_M19_SPL_LSK_GMP_PCR2


title: KF15_Ptprca_M19_SPL_LSK_GMP_PCR1


title: KF15_Ptprca_M18_SPL_LSK_GMP_PCR2


title: KF15_Ptprca_M18_SPL_LSK_GMP_PCR1


title: KF15_NSG_M14_SPL_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt

value: GMP


title: KF15_Ptprca_M17_SPL_LSK_GMP_PCR1


title: KF15_NSG_M16_SPL_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M13_SPL_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M14_SPL_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M16_SPL_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M15_SPL_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M13_SPL_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M12_SPL_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt

value: LSK


title: KF15_NSG_M12_SPL_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M11_SPL_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M11_SPL_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M8_SPL_GMP_PCR1

description:
mCH
KF15_Ptprca_filtered_collapsed_CPM.txt


title: KF15_NSG_M10_SPL_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M10_SPL_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M9_SPL_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M9_SPL_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M8_SPL_GMP_PCR2


title: KF15_Ptprca_M7_SPL_GMP_PCR2


title: KF15_Ptprca_M6_SPL_GMP_PCR2


title: KF15_Ptprca_M5_SPL_GMP_PCR2


title: KF16_Ptprca_M05_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt

value: SPL

value: VEHICLE


title: KF15_Ptprca_M6_SPL_GMP_PCR1


title: KF15_NSG_M15_SPL_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M3_SPL_LSK_PCR2

description:
GFP
KF15_Ptprca_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M7_SPL_GMP_PCR1


title: KF15_Ptprca_M5_SPL_GMP_PCR1


title: KF15_Ptprca_M3_SPL_LSK_PCR1


title: KF15_Ptprca_M17_SPL_LSK_GMP_PCR2


title: KF15_Ptprca_M2_SPL_LSK_PCR2


title: KF15_NSG_M23_BM_LSK_GMP_PCR1

value: Bone Marrow


title: KF15_Ptprca_M2_SPL_LSK_PCR1


title: KF15_NSG_M22_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M1_SPL_LSK_PCR1


title: KF15_NSG_M23_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M1_SPL_LSK_PCR2


title: KF15_NSG_M21_BM_LSK_GMP_PCR1


title: KF15_NSG_M21_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M20_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M19_BM_LSK_GMP_PCR1


title: KF15_Ptprca_M18_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M18_BM_LSK_GMP_PCR1


title: KF15_Ptprca_M19_BM_LSK_GMP_PCR2


title: KF15_Ptprca_M17_BM_LSK_GMP_PCR2


title: KF15_NSG_M16_BM_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M16_BM_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M15_BM_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M14_BM_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M14_BM_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M13_BM_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M12_BM_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M22_BM_LSK_GMP_PCR1


title: KF15_NSG_M12_BM_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M20_BM_LSK_GMP_PCR1


title: KF15_Ptprca_M8_BM_GMP_PCR2


title: KF15_NSG_M10_BM_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M11_BM_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M9_BM_LSK_PCR2

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_NSG_M9_BM_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M8_BM_GMP_PCR1


title: KF15_Ptprca_M7_BM_GMP_PCR2


title: KF15_Ptprca_M7_BM_GMP_PCR1


title: KF15_Ptprca_M17_BM_LSK_GMP_PCR1


title: KF15_Ptprca_M5_BM_GMP_PCR2


title: KF15_Ptprca_M5_BM_GMP_PCR1


title: KF15_NSG_M15_BM_GMP_PCR2

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M6_BM_GMP_PCR2


title: KF15_NSG_M10_BM_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: KF16_Ptprca_M13_SPL_VEHICLE_PCR2

description:
mCH
KF16_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M3_BM_LSK_PCR1


title: KF15_NSG_M13_BM_GMP_PCR1

description:
mCH
KF15_NSG_filtered_collapsed_CPM.txt


title: KF15_Ptprca_M2_BM_LSK_PCR1


title: KF15_Ptprca_M1_BM_LSK_PCR1


title: KF15_Ptprca_M6_BM_GMP_PCR1


title: KF15_Ptprca_M2_BM_LSK_PCR2


title: 2_TCR_CD45_m1

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
library strategy: scTCR seq
We performed two sequencing runs, therefore each sample hast two pairs of fastq files ending with 001 and 002.
Using CellRanger analysis pipeline (v6.0) from 10x Genomics, we performed the multi-modal analysis of gene expression and TCR data simultaneously.
The pipeline workflow includes the following steps:
(1) alignment to the murine genome reference sequence,
(2) cell inference,
(3) saturation analysis and
(4) various QC metrics. Only cells tagged with 'high_confidence', 'productive' and 'full_length' were
Genome_build: GRCm38 (pre-processed release refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 - downloaded from the website of 10x Genomics)
Supplementary_files_format_and_content: two csv for each; the first is for the annotated contigs in each cell and the other a summary table for the clonotypes.

source_name: Large intestinal T cells

extract_protocol:
T cells were FACS sorted and library preparation was performed accroding to the 10X Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 for murine T cells
DNA libraries were prepared for sequencing using the 10X Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1 for murine T cells

treatment_protocol: 2 RAG2 KO mice received naive CD4+ FoxP3- T cells and CD4+ FoxP3+ regulatory T cells in an adoptive T cell transfer. 7 weeks later, large intestinal FoxP3- and FoxP3+ were isolated by FACS and scTCR-Profiles were prepared

tag: host strain

value: RAG2 KO

tag: cell type

value: Large intestinal T cells

tag: cell subtype

value: effector T cell


title: 3_TCR_GFP_m2

value: regulatory T cell


title: 4_TCR_CD45_m2


title: chemo disease endpoint scRNA-seq pool 2 hashtag library

value: bone marrow

value: disease endpoint - hashtags

value: Hashtag PCR amplicon


title: KF15_NSG_M11_BM_LSK_PCR1

description:
GFP
KF15_NSG_filtered_collapsed_CPM.txt


title: 1_TCR_GFP_m1


title: Pool 1 - MLL-AF9 KRAS M8 & MLL M2

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10X Genomics Cell Ranger v3.1.0 count pipeline against the mm10/GRCm38 genome.
scRNA-seq quality control was performed using Seurat v3.2 in R. Low quality cells were removed by filtering out cells that had fewer than 500 genes or 1000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial content were also removed.
For detection of the SPLINTR barcodes from single cell data, unmapped reads (which contain reads corresponding to barcode transcripts) were extracted from BAM alignment files for each scRNAseq library using SAMtools v1.9.
BAM entries containing SPLINTR barcode reads were identified and extracted using a regular expression specific to the barcode structure.
Barcode reads were mapped to the corresponding reference library using Bowtie v1.2.2 end-to-end alignment allowing a maximum of two mismatches.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene counts
Supplementary_files_format_and_content: matrix of gene names
Supplementary_files_format_and_content: matrix of 10x cell barcodes
Supplementary_files_format_and_content: Hashtag sequences

source_name: Bone marrow and spleen cells

growth_protocol: Secondary bone marrow cells from MLL-AF9 mice were cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng/mL), human IL-6 (10 ng/mL), mouse SCF (50 ng/mL) 20% fetal bovine serum (FBS), streptomycin (100 ug/mL), penicillin (100 units/mL) and 2 mM glutamax in 5% CO2 at 37 °C.

treatment_protocol: Cells were transduced with SPLINTR barcode libraries in polybrene (8.5 mg/mL) via spinfection (90 minutes at 1250 g). After the expansion period, barcoded cells were transplanted into sub-lethally irradiated (5.5 Gy) Ptprca via lateral tail vein injection. Each mouse received 1.5 x106 barcoded cells.

value: bone marrow and spleen cells

value: Disease


title: Pool 5 - KRAS M10 & COMBO 80-15-5 M24


title: Pool 3 - MLL M3 & FLT3 M12


title: lancelet_juvenile_ACEseq_rep2

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

data_processing:
Library strategy: ACE-seq
Adapter clipping and read quality trimming using Trimmomatic (ILLUMINACLIP:NEXTflex.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:50 CROP:140 HEADCROP:10) (Bolger et al, 2014)
Trimmed reads were mapped to Spur_v3.1, Bl71nemr, danRer10 and mm10 genome references for sea urchin, lancelet, zebrafish and mouse, respectively, (all containing the λ phage genome as chrLambda and pUC19 plasmid genome as chrPUC) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
Reads with more than three consecutive non-converted cytosines in the CC, CA and CT context were removed using Picard Tools’ function FilterSamReads, in order to eliminate DNA molecules not efficiently deaminated by APOBEC3A
The numbers of hydroxymethylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Additional MethylDackel extract parameters --minOppositeDepth 5 --maxVariantFrac 0.5 were used for the genotype correction (in order to exclude C-to-T nucleotide transitions in the genomic DNA of interest, which could be incorrectly considered as unmodified cytosines) (https://github.com/dpryan79/MethylDackel)
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bed / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

organism: Branchiostoma lanceolatum

source_name: lancelet juvenile DNA subjected to ACE-seq rep2

extract_protocol: ACE-seq library preparation for the DNA hydroxymethylation profiling was performed as previously described {Schutsky et al, 2018 PMID: 30295673;Wang et al, 2021 PMID: 32822044}. Briefly, 100 ng of genomic DNA extracted from sea urchin, lancelet and zebrafish embryos and adult tissues was spiked with 1ng of CpG methylated λ phage DNA (Wisegene) and 0.5 ng of all-C hydroxymethylated pUC19 plasmid DNA (Wisegene) and sonicated to ~300 bp fragments using a M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA (125 ul total volume) was concentrated to 16.6 ul using AMPure beads (1 volume DNA : 2 volumes AMPure beads). 5hmC protection reaction was performed using β-glucosetransferase (10U/ul, New England Biolabs) in Cutsmart Buffer according to manufacturer’s instructions at 37°C for 1 hr, followed by 10 min at 65°C. The DNA was denatured in DMSO at 95°C for 10 min and immediately placed on dry ice for 2 mins allowing the samples to freeze. C and 5mC deamination reaction was performed using the APOBEC3A enzyme (NEBNext® Enzymatic Methyl-seq Kit, New England Biolabs) with the following ramping conditions: 4°C for 10 min, 4°C - 50°C 2:15 min per degree of the ramp, 50°C for 10 min. Deaminated DNA was then purified using AMPure beads (1 volume DNA : 1 volume AMPure beads) and subjected to low input library preparation using Accel-NGS Methyl-Seq DNA kit (Swift Biosciences). Briefly, DNA was denatured and subjected to an adaptase reaction, followed by primer extension, adapter ligation, and 15 cycles of indexing PCR. Library size and consistency was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche).

value: juvenile

value: whole organism


title: mll-af9 + flt3 itd/itd (KF09)

source_name: cKit + progenitors

value: haematopoietic progenitors

tag: mutation

value: MLL-AF9 Flt3 ITD/ITD

value: Baseline

tag: barcode library

value: BFP


title: Pool 4 - COMBO 1-1-1 M19 & COMBO 80-15-5 M22


title: lancelet_larvae_ACEseq_rep2

source_name: lancelet larvae DNA subjected to ACE-seq rep2

tag: age

value: larvae


title: KF15_Ptprca_M3_BM_LSK_PCR2

value: Bone Marrow

value: Ptprca

value: LSK


title: mll-af9 + kras g12d/+ (KF09)

value: MLL-AF9 KRAS G12D/+

value: mCHERRY


title: mll-af9 (KF09)

value: GFP


title: 80-15-5_Baseline

description: KF09_COMBO-80-15-5_filtered_collapsed_CPM.txt

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR reference library

extract_protocol:
Viable cells were sorted on the BD FACSAria III directly into Eppendorf tubes. The cells were then washed twice with PBS + 0.04% BSA.
Cells were lysed in 40 uL Viagen lysis buffer containing 0.5 mg/mL Proteinase K (Invitrogen) and split into technical replicates. Barcodes in cell lysate were then amplified following two rounds of PCR using Q5 polymerase (NEB). The first PCR amplified barcode specific DNA and added partial Illumina sequencing primer binding sites. PCR primers containing staggers to account for low sequence diversity during sequencing. In the second round PCR, the sequencing primer binding sites were completed, P5 and P7 flow cell regions were added and samples received a well-specific 8bp dual index (96 different indices in total).
DNA-Seq


title: 80-15-5_MOUSE25_BM

value: BM


title: Pool 2 - FLT3 M11 & COMBO 1-1-1 M17


title: lancelet_juvenile_ACEseq_rep1

source_name: lancelet juvenile DNA subjected to ACE-seq rep1


title: lancelet_larvae_ACEseq_rep1

source_name: lancelet larvae DNA subjected to ACE-seq rep1


title: KF15_Ptprca_M1_BM_LSK_PCR2


title: 80-15-5_MOUSE23_BM


title: 80-15-5_MOUSE24_BM


title: S1_Vehicle

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

country: China

institute: Wuhan University

data_processing:
Illumina ® TruSeq ® Stranded Total RNA Sample Preparation kits
Illumina Real Time Analysis software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome
RNA-seq analysis was performed using Illumina Real Time Analysis software, STAR, and Cufflinks.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: primary hepatic stellate cells

growth_protocol: DMEM with 10% FBS

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit
Libraries were prepared according to Illumina's instructions

treatment_protocol: HSCs were treated with PFD for four days

value: primary hepatic stellate cells

tag: culture method

value: culture activation

tag: treatment

value: vehicle


title: S2_PFD

value: pirfenidone


title: 80-15-5_MOUSE22_BM

value: Disease


title: 80-15-5_MOUSE24_SPL

value: SPL


title: 80-15-5_MOUSE23_SPL


title: 80-15-5_MOUSE22_SPL


title: MLL_Baseline

value: MLL


title: 80-15-5_MOUSE25_SPL


title: SP_6W_1

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Danio rerio

source_name: spinal cord

extract_protocol:
Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tg(tph2:GFP) line by FAC-sorting, flash frozen on dry ice. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spinal cord segment in the injury site

value: serotonergic neuron

value: 6-8 week post injury


title: SP_6W_2


title: SP_6W_4


title: SP_SC_1

value: spinal cord segments distal to the injury site


title: SP_6W_3


title: SP_6W_6


title: SP_SC_2


title: SP_SC_5


title: SP_SC_3


title: SP_6W_5


title: SP_SC_4


title: MLL_MOUSE4_SPL


title: W6_C5

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Spinal cord segments were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

value: 5 spinal segment caudal to the injury site

value: 6 week post injury


title: W6_C3


title: W6_C2


title: W6_C1


title: MLL_MOUSE3_SPL


title: MLL_MOUSE2_SPL


title: W6_R5

value: 5 spinal segment rostral to the injury site


title: MLL_MOUSE1_SPL


title: MLL_MOUSE4_BM


title: W6_R2


title: MLL_MOUSE3_BM


title: W6_R3


title: MLL_MOUSE2_BM


title: W6_R1


title: W4_C5

value: 4 week post injury


title: W4_C2


title: W4_C4


title: W4_C3


title: W6_R4


title: W4_C1


title: W4_R4


title: MLL_MOUSE1_BM

value: BM


title: FLT3_Baseline

value: Baseline


title: W4_R5


title: W4_R3


title: FLT3_MOUSE15_SPL


title: FLT3_MOUSE14_SPL


title: FLT3_MOUSE13_SPL 1


title: FLT3_MOUSE13_SPL 2


title: FLT3_MOUSE12_SPL


title: FLT3_MOUSE11_SPL


title: W4_R2


title: W2_R4

value: 2 week post injury


title: W2_R3


title: W4_R1


title: W2_C2


title: W2_C4


title: W2_R1


title: W2_C1


title: W2_R2


title: W2_C3


title: W2_R5


title: W2_C5


title: FLT3_MOUSE15_BM


title: FLT3_MOUSE14_BM


title: W1_C3

value: 1 week post injury


title: W1_C5


title: W1_C4


title: FLT3_MOUSE13_BM


title: W1_R5


title: FLT3_MOUSE12_BM


title: W1_C1


title: W1_R2


title: W1_R4


title: W1_R1


title: C_C5

value: uninjured


title: Genomic DNA from ferrostatin-1 control MM1R cells replicate 3

type: genomic

city: Wilrijk

first: Emilie

last: Logie

state: Antwerp

address: Universiteitsplein 1

department: Biomedical Sciences

country: Belgium

institute: University of Antwerp

description: Control MM1R cells pre-treated with 2 µM Ferrostatin-1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium 850K Human MethylationEPIC Array using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina Hi-Scan system according to the manufacturer's recommendations

data_processing: Minfi (v1.36.0) and Limma (v3.46.0) R packages

label: Cy3 and Cy5

source_name: MM1R cell line

label_protocol: Standard Illumina Protocol

growth_protocol: MM1 cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% PenStrep

extract_protocol: genomic DNA was extracted and purified from MM1 cells using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Cells were treated with 1 µM RSL3 for 72hrs with or without pre-treatment with 2 µM Ferrostatin-1 (for 2 hours)

value: 2 microM Ferrostatin-1 for 2 hrs, followed by 1 microM RSL3 for 72 hrs


title: KRAS_Baseline

value: KRAS


title: KRAS_MOUSE9_SPL

value: SPL

value: Disease


title: C_C4


title: Untreated MM1S cells, rep 3

data_processing:
Quality of sequencing reads was evaluated using FastQC v0.11.5
Alignment to the human reference genome build 37 was performed with the STAR V2.7.3a tool
Differential gene expression analysis was performed using the DESeq2 R package
Genome_build: hg19
Supplementary_files_format_and_content: The raw_readcounts_allsamples.txt file contains the matrix table with all raw gene counts of all samples
Supplementary_files_format_and_content: The normalized_readcounts_allsamples.txt file contains the matrix table with all (DSEq2) normalized gene counts of all samples

source_name: MM1S cells

growth_protocol: MM1 cells were grown in RPMI-1640 medium supplemented with 10 % FBS and 1% PenStrep

extract_protocol:
RNA was extracted using the Rneasy Mini kit (#74104, Qiagen)
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Cells were treated with 5 µM RSL3 with or without 2hr pre-treatment with Fer-1

tag: cell line

value: Untreated control

tag: cell passage


title: W1_R3

tag: strain


title: C_C2


title: FLT3_MOUSE11_BM

tag: timepoint


title: KRAS_MOUSE8_SPL


title: C_C1

tag: disease state


title: C_C3


title: Genomic DNA from ferrostatin-1 control MM1S cells replicate 3

description: Control MM1S cells pre-treated with 2 µM Ferrostatin-1

source_name: MM1S cell line


title: KRAS_MOUSE6_SPL


title: KRAS_MOUSE7_SPL


title: Untreated MM1S cells, rep 2


title: Genomic DNA from ferroptotic MM1R cells replicate 1

description: Ferroptotic MM1R cells

value: 1 microM RSL3 for 72 hrs


title: Genomic DNA from ferroptotic MM1S cells replicate 3

description: Ferroptotic MM1S cells


title: Genomic DNA from ferrostatin-1 control MM1S cells replicate 1


title: MM1S cells treated with RSL3, rep 3

value: 3 hr treatment with 5 microM RSL3


title: C_R3

value: AB


title: MM1S cells treated with Fer-1 and RSL3, rep 3

value: 2 hr pre-treatment with 2 microM Fer-1, followed by 3 hr treatment with 5 microM RSL3


title: KRAS_MOUSE7_BM


title: MM1S cells treated with Fer-1 and RSL3, rep 2


title: MM1S cells treated with RSL3, rep 2


title: Donor Mouse 2 baseline

data_processing:
Barcode sequences were extracted from fastq files based on the known constant sequences flanking the random barcodes and subsequently trimmed to remove these regions such that only the random barcode sequences remained.
Barcode containing reads were further filtered to keep only those barcodes that (a) showed a correct upstream constant region (5’- CGATTGACTA-3’), (b) showed the expected barcode pattern (c) did not contain N residues, and (d) possessed an average phred quality of 30 or higher across the length of the barcode.
Barcode reads were then mapped to the respective SPLINTR reference library using bowtie v1.2.2 allowing up to 2 mismatches.
Barcode count data were imported into R v3.6 for further analysis.
Genome_build: SPLINTR GFP reference library
Supplementary_files_format_and_content: Table of barcode CPM

source_name: Donor Mouse 2 baseline

tag: donor mouse

value: mouse 2


title: MM1S cells treated with RSL3, rep 1


title: Untreated MM1S cells, rep 1


title: Genomic DNA from ferroptotic MM1S cells replicate 2

description: Ferroptotic MM1S cells


title: MM1S cells treated with Fer-1 and RSL3, rep 1


title: Genomic DNA from ferrostatin-1 control MM1S cells replicate 2


title: Donor Mouse 1 baseline

source_name: Donor Mouse 1 baseline

value: mouse 1


title: KRAS_MOUSE9_BM

tag: tissue


title: Donor Mouse 1 PTPRCA Spleen

source_name: Donor Mouse 1 PTPRCA Spleen

value: Spleen

value: PTPRCA


title: C_R2

value: 5 spinal segment rostral to the injury site


title: NW075-E4

city: Stockholm

first: Anita

last: Göndör

address: Nobels väg 16, KI Solna Campus, Karolinska Institutet, Box 280

department: MTC

country: Sweden

institute: Karolinska Institutet

description:
Nodewalk DNA
Biological replicate 3

data_processing:
Sequence reads were mapped using bwa to a reference genome composed of PhiX, BDGP5 (Drosophila), K12 (E. coli) and human (HG19). Alignments with mapping quality greater than 10 of the read 2 were used to determine the probe position. An extension region (region from the probe’s end to the first restriction site) was used to discriminate valid from mis-annealing events. The total number of alignments in the read 1 with the proper probe extension in the second read was reported by restriction fragment. Next the number of distinct transposon integration sites was also reported to remove PCR duplicates.
Genome_build: hg19/BDGP5/PhiX/K12
Supplementary_files_format_and_content: tab-delimited text files

source_name: Colon cancer cells

growth_protocol: Human colon cancer cells (HCT-116 cells from clone 28) were grown in McCoys' 5A medium with GlutaMAX supplement (Gibco, ThermoFisher) in T-175 flasks (Sarstedt).

extract_protocol:
Cells were crosslinked with freshly prepared 1% PFA and were then used for Nodewalk. The initial part of this technique is based on the 3C protocol with enzymatic digestion with Hind-III, and ligation using T4 DNA polymerase, generating ligated 3C DNA that is then used for Nodewalk library preparation.
Nodewalk library preparation involves tagmentation using Illumina's transposome-linked beads from the Illumina® DNA Prep, (M) Tagmentation (cat.no. 20018704) kit. It is then followed by in vitro transcription for conversion to RNA, subsequent generation of cDNA and amplification of a specific region of interest (with interactors) using a specifically designed bait/primer. The final Nodewalk DNA is then sequenced using the Illumina MiSeq sequencing platform.
Nodewalk-seq

treatment_protocol: Cells used for Nodewalk experiments were untreated. The D3 and E4 clones with a mutated CTCFBS within the OSE region were generated from the HCT-116 cells using the CRISPR/Cas9 technology and gRNA cutting at chr8:127,215,101. The cell pool generated by CRISPR/Cas9 was used to generate the two clones (D3 and E4) from single cells, and the clones were verified by Sanger sequencing.

value: clone 28 of HCT-116 colon cancer cells

value: untreated

tag: genotype

value: E4 clone:mutated CTCFBS within OSE region


title: Untreated MM1R cells, rep 3

source_name: MM1R cells


title: KRAS_MOUSE6_BM

value: BM

tag: mouse


title: C_R1

value: uninjured


title: Genomic DNA from ferroptotic MM1S cells replicate 1

description: Ferroptotic MM1S cells


title: MM1R cells treated with RSL3, rep 3


title: NW075-WT

description:
Nodewalk DNA
Biological replicate 3

value: WT


title: NW074-D3

description:
Nodewalk DNA
Biological replicate 2

value: D3 clone:mutated CTCFBS within OSE region


title: C_R5


title: NW075-D3

description:
Nodewalk DNA
Biological replicate 3


title: Genomic DNA from ferroptotic MM1R cells replicate 2

description: Ferroptotic MM1R cells


title: Genomic DNA from ferrostatin-1 control MM1R cells replicate 2

value: 2 microM Ferrostatin-1 for 2 hrs, followed by 1 microM RSL3 for 72 hrs


title: Genomic DNA from ferroptotic MM1R cells replicate 3

description: Ferroptotic MM1R cells

value: 1 microM RSL3 for 72 hrs


title: MM1R cells treated with RSL3, rep 2

value: 3 hr treatment with 5 microM RSL3


title: Donor Mouse 2 PTPRCA Bone Marrow

source_name: Donor Mouse 2 PTPRCA Bone Marrow

value: Bone Marrow

value: Disease


title: Genomic DNA from ferrostatin-1 control MM1R cells replicate 1


title: NW074-WT

description:
Nodewalk DNA
Biological replicate 2


title: NW074-E4

description:
Nodewalk DNA
Biological replicate 2


title: MM1R cells treated with Fer-1 and RSL3, rep 2

value: 2 hr pre-treatment with 2 microM Fer-1, followed by 3 hr treatment with 5 microM RSL3


title: MM1R cells treated with Fer-1 and RSL3, rep 3


title: Untreated MM1R cells, rep 1

value: Untreated control


title: NW073-D3

description:
Nodewalk DNA
Biological replicate 1


title: W1_C2

value: AB

value: 5 spinal segment caudal to the injury site

value: 1 week post injury


title: Untreated MM1R cells, rep 2


title: NW073-WT

description:
Nodewalk DNA
Biological replicate 1

value: clone 28 of HCT-116 colon cancer cells


title: Donor Mouse 1 NSG Spleen

source_name: Donor Mouse 1 NSG Spleen

value: Spleen

value: mouse 1

value: NSG


title: Donor Mouse 2 NSG Spleen

source_name: Donor Mouse 2 NSG Spleen

value: mouse 2


title: Donor Mouse 2 PTPRCA Spleen

source_name: Donor Mouse 2 PTPRCA Spleen

value: PTPRCA


title: Donor Mouse 1 NSG Bone Marrow

source_name: Donor Mouse 1 NSG Bone Marrow


title: CPF3_45-1y

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: Litter 45, pup no. 1y

data_processing:
Expression values were computed using STAR and featureCounts
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: text files holding kallisto expression estimates

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

value: Long Evans

tag: Sex

value: Male

value: Dorsal Hippocampus

tag: developmental stage

value: Postnatal day 6

tag: time of day (lights on 07.00-19.00)

tag: experimental group

value: Chlorpyrifos 3 mg/kg body wt, injected subcutaneously to dam during pregnancy and lactation.


title: Donor Mouse 2 NSG Bone Marrow

source_name: Donor Mouse 2 NSG Bone Marrow

value: Bone Marrow

value: Disease


title: NW073-E4

description:
Nodewalk DNA
Biological replicate 1

tag: cell type

value: untreated

value: E4 clone:mutated CTCFBS within OSE region


title: MM1R cells treated with Fer-1 and RSL3, rep 1

value: 2 hr pre-treatment with 2 microM Fer-1, followed by 3 hr treatment with 5 microM RSL3


title: Donor Mouse 1 PTPRCA Bone Marrow

source_name: Donor Mouse 1 PTPRCA Bone Marrow


title: CPF3_44-2y

description: Litter 44, pup no. 2y


title: CPF3_43-6y

description: Litter 43, pup no. 6y


title: MLL-AF9 baseline ATAC

data_processing:
Count matrices were generated from demultiplexed scRNA-seq fastq files using the 10X Genomics Cell Ranger v3.1.0 count pipeline against the mm10/GRCm38 genome.
scRNA-seq quality control was performed using Seurat v3.2 in R. Low quality cells were removed by filtering out cells that had fewer than 500 genes or 1000 unique molecular identifiers (UMIs). Cells with greater than 15% mitochondrial content were also removed.
For detection of the SPLINTR barcodes from single cell data, unmapped reads (which contain reads corresponding to barcode transcripts) were extracted from BAM alignment files for each scRNAseq library using SAMtools v1.9.
BAM entries containing SPLINTR barcode reads were identified and extracted using a regular expression specific to the barcode structure.
Barcode reads were mapped to the corresponding reference library using Bowtie v1.2.2 end-to-end alignment allowing a maximum of two mismatches.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene counts
Supplementary_files_format_and_content: matrix of gene names
Supplementary_files_format_and_content: matrix of 10x cell barcodes

source_name: Bone marrow cells

value: haematopoietic progenitors


title: NSG Disease mouse 6

source_name: Bone marrow and spleen cells

value: bone marrow and spleen cells


title: CPF3_40-3y

description: Litter 40, pup no. 3y


title: MM1R cells treated with RSL3, rep 1

value: 3 hr treatment with 5 microM RSL3


title: B24h2

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

data_processing:
Sequencing was performed on a NovaSeq 6000 S2 flow cell.
The function cellranger count from Cell Ranger31was used to transform the fastq files.
The functioncellranger mat2csv was used to generatethe UMI matrix.
Genome_build: The reference genome was the mm10 available at Illumina Cell Ranger webpage.
Supplementary_files_format_and_content: barcode sequences
Supplementary_files_format_and_content: gene expression features
Supplementary_files_format_and_content: UMI matrix

source_name: Peritoneal buttons 24h post-injury

growth_protocol: Mice were kept under SPF condition wich free access to food and water

extract_protocol:
After 24h mice were euthanized by injection anesthesia and subsequent intracardial perfusion with ice cold PBS with 2mM EDTA. Peritoneal buttons were excised and digested for 30 minutes at 37°C in IMDM containing Ca, 25mM Hepes, 2% FCS, 1mg/mL Colagenase 1a (Sigma C9891-1g) and 0.1mg/mL DNAseI (Roche 10104159001). IMDM with 2mM EDTA was used to stop the reaction and wash the cells. Then, samples were resuspended in 40% Percoll and pipetted on top of 80% Percoll solution to create a gradient. After centrifugation (2000rpm, 20min), the interface was transferred again and washed in DPBS + 0.04% BSA. Finally, the sample was resuspended in DPBS + 0.04% BSA for library preparation.
Library preparationscRNA-seq libraries were prepared from 10000cells using the Chromium Single Cell 3’ Library & Gel Bead Kit v3(10xGenomics). Libraries were prepared according to the manufacturers protocol.

treatment_protocol: Mice (C57/Bl6) underwent surgery to receive injury alone (PB) or in combination with bacterial contamination (PB + CLP).

value: female

tag: protocol

value: peritoneal injury

tag: time pont

value: intervention 24h


title: B24h1


title: PtprcaDisease mouse 2

value: Ptprca


title: CPF3_38-1y

description: Litter 38, pup no. 1y

value: Long Evans