title: Bd21-3, Mutant, M1356, juvenile leaf tissue

description:
Library name: 471A1
Row name in SIEVE_M6_TPM.csv: M1356


title: Bd21-3, Mutant, M1274, juvenile leaf tissue

status: Public on Mar 09 2026

type: SRA

city: Aarhus

first: Guillaume

last: Ramstein

address: Moellers Alle

country: Denmark

institute: Aarhus University

description:
Library name: 472A1
Row name in SIEVE_M6_TPM.csv: M1274

library_source: transcriptomic

data_processing:
Sequencing reads were aligned using hisat2, with default options and converted into bam files using samtools.
The number of reads were counted using the featureCounts function of subread configured to count fragments instead of reads (-p), using the Bd21-3 genome annotations (-a BdistachyonBd21_3_537_v1.2.gene.gff3).
Assembly: BdistachyonBd21_3_537_v1.2
Supplementary files format and content: Tab-delimited file contained transcripts per million (TPM) for each sample

molecule: total RNA

organism: Brachypodium distachyon

source_name: leaf

growth_protocol: Seeds from Brachypodium distachyon accession Bd21-3 were treated with 0 mM (controls) or 7 mM (mutants) of the mutagen sodium azide at the M1 generation (first generation after seed mutagenesis). Then, plants were grown in the greenhouse (20h/4h light/dark, 21°C/18°C target temperature, at Aarhus University Flakkebjerg) and allowed to self-fertilize naturally across 6 generations, from M1 to M6.

extract_protocol:
Tissue sampling was performed in three independent biological replicates per line. The three replicates from each line were subsequently pooled for total RNA extraction. RNA extraction was conducted by Azenta GeneWiz (Leipzig, Germany).
Library preparation was performed using Poly(A) selection and paired-end sequencing (2 × 150 bp) was conducted on an Illumina NovaSeq platform at Azenta GeneWiz (Leipzig, Germany).

treatment_protocol: M6 seeds were pre-incubated for one week at 37°C and 20% relative humidity to enhance and synchronize germination. Germination and seedling growth were carried out in climate-controlled chambers at Aarhus University Flakkebjerg under a 16h/8h light/dark photoperiod, 23°C/21°C day/night temperatures, and 60% relative humidity. At the three-leaf stage (approximately 16 days post-germination), the blades of all three fully expanded leaves (excluding the cotyledons) were harvested and immediately frozen in liquid nitrogen, then stored at –80 °C until further processing.

tag: tissue

value: leaf

tag: cell line

tag: cell type

value: juvenile leaf tissue

tag: genotype

tag: treatment

value: Mutant

tag: batch


title: p53_null_MEFs_2

city: Toronto

first: Liam

middle: D

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: Library name: A2

data_processing:
Reads were QC'ed using fastqc (v 0.11.5) and multiqc (v 0.8) and aligned to the GRCm38 (mm10) mouse reference using STAR (v 2.5.2b).
Raw gene counts and transcripts per million (TPM) normalization were determined using RSEM (v 1.3.0).
Assembly: mm10
Supplementary files format and content: p53psi_all_RSEM_counts.txt: tab-delimited file containing RSEM outputs; expected gene counts, TPM normalized counts, and FPKM normalized counts for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Sarcoma

extract_protocol:
Tumor tissues from p53null or p53psiKI/KI E1A/RASV12 MEFs were collected in biological triplicates (for each genotype) and lysed in RNA lysis buffer and processed with PureLink™ RNA Mini Kit (Thermo Fisher) according to the manufacturer’s instructions. Total RNA (1ug) was resuspended in DNase- and RNase-free water.
mRNA library construction, quality control, and sequencing was performed by Novogene Co., Ltd. (Beijing, China).

treatment_protocol: Mouse embryonic fibroblasts were collected from p53null and p53psiKI/KI embryos between E14.5-E16.5. MEFs were transformed with the E1A and H-RasV12 oncogenes.

value: Sarcoma

tag: strain

value: mouse embryonic fibroblasts

tag: Sex

value: Male

tag: genetic modification


title: p53_psi_KiKi_MEFs_1

description: Library name: A4


title: Bd21-3, Mutant, M0915, juvenile leaf tissue

description:
Library name: 470A1
Row name in SIEVE_M6_TPM.csv: M0915


title: p53_null_MEFs_1

description: Library name: A1


title: Bd21-3, Mutant, M1174, juvenile leaf tissue

description:
Library name: 469A1
Row name in SIEVE_M6_TPM.csv: M1174


title: BoneRANKL-fm, fractured, index4

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: Library name: Frac_Tom_indx4

library_source: transcriptomic single cell

data_processing:
Basecalling was performed by Illumina RTA software in sequencer, further demultiplexing was performed by Illumina bcl2fastq 2.20 software based on index information.
Gene counting was performed using the Cell Ranger software v7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone, bone marrow, and callus

extract_protocol:
Tibiae were isolated at post-fracture day 14 and minced using scissors or tweezers. The fragmented bones were digested in DMEM containing Collagenase P, Liberase TH, and DNase I at 37 °C with gentle shaking for 1 h. Dissociated cells were collected every 20 min and passed through a 100 μm nylon mesh filter. Cells were pelleted by centrifugation and resuspended in FACS buffer (PBS containing 2% FBS and 2 mM EDTA). Red blood cells were lysed using 0.165 M ammonium chloride. The resulting single-cell suspension was stained with antibodies against CD45.2, Ter119, and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. CD45.2-Ter119-CD31-tdTomato+ cells were sorted for single-cell 3′ gene expression library preparation.
Library construction was performed according to the manufacturer’s instructions (Single Cell 3’ v3.1 protocol, 10x Genomics), with slight modifications.  Cells were directly sorted into the master mix and loaded, together with partitioning oil and gel beads, into the chip to generate gel bead-in-emulsions (GEMs).

treatment_protocol: RANKL fate-mapping mice (Tnfsf11-tTA; LC1; R26-tdTomato) were treated with doxycycline from embryonic day 0 to postnatal day 14 to suppress tdTomato labeling. A fracture was surgically induced in the right tibia at postnatal day 21.

value: Bone, bone marrow, and callus

value: tdTomato+

value: Tnfsf11-tTA; LC1; R26-tdTom

value: Doxycycline from E0 to P14, fractured at P21

tag: age

value: male


title: Bd21-3, Mutant, M0133, juvenile leaf tissue

description:
Library name: 46A1
Row name in SIEVE_M6_TPM.csv: M0133


title: Bd21-3, Mutant, M0927, juvenile leaf tissue

description:
Library name: 468A1
Row name in SIEVE_M6_TPM.csv: M0927


title: p53_psi_KiKi_MEFs_2

description: Library name: A5


title: BoneRANKL-fm, fractured, index3

description: Library name: Frac_Tom_indx3


title: Bd21-3, Mutant, M1150, juvenile leaf tissue

description:
Library name: 518A1
Row name in SIEVE_M6_TPM.csv: M1150


title: Bd21-3, Mutant, M1232, juvenile leaf tissue

description:
Library name: 467A1
Row name in SIEVE_M6_TPM.csv: M1232


title: BoneRANKL-fm, fractured, index1

description: Library name: Frac_Tom_indx1


title: Bd21-3, Mutant, M1189, juvenile leaf tissue

description:
Library name: 466A1
Row name in SIEVE_M6_TPM.csv: M1189


title: Bd21-3, Mutant, M0237, juvenile leaf tissue

description:
Library name: 47A1
Row name in SIEVE_M6_TPM.csv: M0237


title: Bd21-3, Mutant, M1300, juvenile leaf tissue

description:
Library name: 464A1
Row name in SIEVE_M6_TPM.csv: M1300


title: Bd21-3, Mutant, M1060, juvenile leaf tissue

description:
Library name: 465A1
Row name in SIEVE_M6_TPM.csv: M1060


title: MCPT5Cre x ST2f/f Hpb D14 3

city: Dundee

first: Henry

middle: J

last: McSorley

address: Dow Street

department: Cell Signalling & Immunology

country: United Kingdom

institute: University of Dundee

description: Library name: SH040-19-CrePos-D14

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the mouse GRCm39 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm39
Supplementary files format and content: TPM values for genes across all 16 samples

source_name: Upper duodenum

extract_protocol:
Total RNA was extracted from tissue samples using Qiagen RNeasy Plus universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Mice were infected with 200 L3 Heligmosomoides polygyrus bakeri larvae in water by oral gavage (except naïve controls)

value: Upper duodenum

value: MCPT5Cre x ST2f/f

value: Heligmosomoides polygyrus bakeri day 14

tag: age at_cull_(days)


title: MCPT5Cre x ST2f/f Hpb D14 4

description: Library name: SH040-20-CrePos-D14

value: Female


title: p53_null_MEFs_3

description: Library name: A3


title: MCPT5Cre x ST2f/f Hpb D14 1

description: Library name: SH040-17-CrePos-D14


title: Bd21-3, Mutant, M1132, juvenile leaf tissue

description:
Library name: 462A1
Row name in SIEVE_M6_TPM.csv: M1132


title: BoneRANKL-fm, fractured, index2

description: Library name: Frac_Tom_indx2


title: Bd21-3, Mutant, M0996, juvenile leaf tissue

description:
Library name: 461A1
Row name in SIEVE_M6_TPM.csv: M0996


title: Bd21-3, Mutant, M0309, juvenile leaf tissue

description:
Library name: 45A1
Row name in SIEVE_M6_TPM.csv: M0309


title: MCPT5WT x ST2f/f Hpb D14 2

description: Library name: SH040-12-CreNeg-D14

value: MCPT5WT x ST2f/f


title: MCPT5Cre x ST2f/f Naïve 4

description: Library name: SH040-9-CrePos-Naive

value: Naïve


title: Bd21-3, Mutant, M1126, juvenile leaf tissue

description:
Library name: 458A1
Row name in SIEVE_M6_TPM.csv: M1126

value: leaf


title: MCPT5Cre x ST2f/f Hpb D14 2

description: Library name: SH040-18-CrePos-D14


title: Bd21-3, Mutant, M1160, juvenile leaf tissue

description:
Library name: 459A1
Row name in SIEVE_M6_TPM.csv: M1160

value: juvenile leaf tissue


title: MCPT5Cre x ST2f/f Naïve 3

description: Library name: SH040-8-CrePos-Naive


title: MCPT5WT x ST2f/f Hpb D14 1

description: Library name: SH040-11-CreNeg-D14


title: Bd21-3, Mutant, M0917, juvenile leaf tissue

description:
Library name: 456A1
Row name in SIEVE_M6_TPM.csv: M0917

value: Mutant


title: Bd21-3, Mutant, M1019, juvenile leaf tissue

description:
Library name: 457A1
Row name in SIEVE_M6_TPM.csv: M1019


title: MCPT5Cre x ST2f/f Naïve 2

description: Library name: SH040-7-CrePos-Naive


title: Bd21-3, Mutant, M0955, juvenile leaf tissue

description:
Library name: 454A1
Row name in SIEVE_M6_TPM.csv: M0955


title: Bd21-3, Mutant, M1266, juvenile leaf tissue

description:
Library name: 460A1
Row name in SIEVE_M6_TPM.csv: M1266


title: MCPT5Cre x ST2f/f Naïve 1

description: Library name: SH040-6-CrePos-Naive


title: Bd21-3, Mutant, M1079, juvenile leaf tissue

description:
Library name: 463A1
Row name in SIEVE_M6_TPM.csv: M1079


title: MCPT5WT x ST2f/f Naïve 4

description: Library name: SH040-4-CreNeg-Naive


title: MCPT5WT x ST2f/f Naïve 1

description: Library name: SH040-1-CreNeg-Naive


title: Bd21-3, Mutant, M0930, juvenile leaf tissue

description:
Library name: 455A1
Row name in SIEVE_M6_TPM.csv: M0930


title: Bd21-3, Mutant, M1129, juvenile leaf tissue

description:
Library name: 453A1
Row name in SIEVE_M6_TPM.csv: M1129


title: MCPT5WT x ST2f/f Naïve 3

description: Library name: SH040-3-CreNeg-Naive


title: RNA_KO_cPAE_Vms-F1

city: St. Louis

first: Gabor

last: Egervari

email: gabor@wustl.edu, egervarilab@gmail.com

state: MO

address: 4515 McKinley Ave, Couch Building

department: Genetics, Biochemistry and Molecular Biophysics

country: USA

institute: Washington University School of Medicine

description:
Library name: KO_cPAE_Vms-F1
KO_EtOH_Vms-F1

data_processing:
Base calls and demultiplexing were performed with bcl2fastq (Illumina) with a maximum of 1 mismatch in the indexing read. This was done by  GTAC@MGI at WashU.
Adapters were trimmed from reads using Cutadapt 5.0 with parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Reads were aligned to the GRCm39 Mus musculus reference genome assembly using STAR 2.7.10a with parameters --runMode alignReads --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --quantMode TranscriptomeSAM GeneCounts
Counts were quantified using featureCounts 2.0.6 and the annotation from the NCBI RefSeq assembly GCF_000001635.27. Gene counts were quantified with parameters -t exon -g gene_id -s 2 -p -B -C -O -M ; Transcript isoform counts were quantified with parameters -t exon -g transcript_id -s 2 -p -B -C -O -M
Low counts were filtered out using the criteria of at least 2 samples in a group having counts of at least 5 each (groups defined by genotype, region, and condition).
Differential expression analysis was performed using DESeq2 in RStudio using the default Wald negative binomial test to determine DEGs or DETs for pairwise comparisons (cPAE vs cPSE within a genotype and region) and genotype × exposure interaction (within each region). An FDR cutoff of 0.1 was used in distinguishing differentially expressed from non-differing features.
Assembly: GRCm39
Supplementary files format and content: *_counts.csv files contain read counts ; *_counts_annotated.csv files contain read counts with additional annotation columns (* is 'gene' for gene level counts or 'transcript' for transcript isoform level counts; annotation data were derived from Mus_musculus.GRCm39.113.gtf).

source_name: cerebellar vermis

growth_protocol: Following weaning (PND21), offspring were group housed (2-5 mice of matching genotype, sex, and condition per cage) on a 12h/12h light/dark cycle with food and water provided ad libitum until sacrificed (PND40-50 via cervical dislocation). Whole brains were immediately collected in cryogenic vials, snap-frozen, and stored at -80ºC until brain region dissections. Brain dissections were done on a -20ºC cold plate, and dissected tissue was stored at -80ºC until extraction.

extract_protocol:
Total RNA was extracted using TRIzol-chloroform and the Qiagen RNeasy Mini Kit (74104) with on-column RNase-free DNase (79254) digestion according to manufacturer protocols. Total RNA quality was assessed using the High Sensitivity RNA ScreenTape Assay on an Agilent 4200 TapeStation system.
mRNA was isolated from 10 ng total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) in coordination with NEBNext Multiplex Oligos (E6440) and HighPrep PCR Beads (MagBio AC-60050). Library quality was assessed using the D1000 ScreenTape Assay on an Agilent 4200 TapeStation system. Libraries were quantified using the NEBNext Library Quant Kit (E7630) on an Applied Biosystems QuantStudio 5 Real-Time PCR system. The concentration of amplifiable templates in each library was calculated using the NEBioCalculator qPCR Library Quantification Web Tool. Libraries were then pooled in equal concentrations and submitted for sequencing.

treatment_protocol: Female mice were housed with studs for 5 nights. Following night 1, female mice were administered 1 daily i.p. injection of 3 g/kg ethanol (20% [v/v] ethanol solution in saline; cPAE) or equivalent volume saline (cPSE) until they gave birth. Offspring were weaned at PND21 and sacrificed via cervical dislocation between PND40-50.

value: cerebellar vermis

value: ACSS2 KO

tag: prenatal exposure

value: ethanol

value: female

tag: mouse id


title: Bd21-3, Mutant, M1203, juvenile leaf tissue

description:
Library name: 452A1
Row name in SIEVE_M6_TPM.csv: M1203


title: RNA_KO_cPAE_Vms-M3

description:
Library name: KO_cPAE_Vms-M3
KO_EtOH_Vms-M3


title: RNA_KO_cPAE_Vms-M1

description:
Library name: KO_cPAE_Vms-M1
KO_EtOH_Vms-M1


title: Bd21-3, Mutant, M0987, juvenile leaf tissue

description:
Library name: 451A1
Row name in SIEVE_M6_TPM.csv: M0987


title: RNA_KO_cPAE_Vms-F3

description:
Library name: KO_cPAE_Vms-F3
KO_EtOH_Vms-F3


title: Bd21-3, Mutant, M1242, juvenile leaf tissue

description:
Library name: 450A1
Row name in SIEVE_M6_TPM.csv: M1242


title: Bd21-3, Mutant, M0430, juvenile leaf tissue

description:
Library name: 44A1
Row name in SIEVE_M6_TPM.csv: M0430


title: Bd21-3, Mutant, M1306, juvenile leaf tissue

description:
Library name: 449A1
Row name in SIEVE_M6_TPM.csv: M1306


title: Bd21-3, Mutant, M1180, juvenile leaf tissue

description:
Library name: 447A1
Row name in SIEVE_M6_TPM.csv: M1180


title: RNA_KO_cPSE_Vms-M3

description:
Library name: KO_cPSE_Vms-M3
KO_PBS_Vms-M3

value: saline


title: RNA_KO_cPSE_Vms-F3

description:
Library name: KO_cPSE_Vms-F3
KO_PBS_Vms-F3


title: Bd21-3, Mutant, M1186, juvenile leaf tissue

description:
Library name: 448A1
Row name in SIEVE_M6_TPM.csv: M1186


title: RNA_KO_cPSE_Vms-M1

description:
Library name: KO_cPSE_Vms-M1
KO_PBS_Vms-M1


title: Bd21-3, Mutant, M1199, juvenile leaf tissue

description:
Library name: 446A1
Row name in SIEVE_M6_TPM.csv: M1199


title: Bd21-3, Mutant, M1090, juvenile leaf tissue

description:
Library name: 445A1
Row name in SIEVE_M6_TPM.csv: M1090


title: RNA_WT_cPAE_Vms-F1

description:
Library name: WT_cPAE_Vms-F1
WT_EtOH_Vms-F1

value: WT


title: Bd21-3, Mutant, M1213, juvenile leaf tissue

description:
Library name: 444A1
Row name in SIEVE_M6_TPM.csv: M1213


title: RNA_WT_cPAE_Vms-M3

description:
Library name: WT_cPAE_Vms-M3
WT_EtOH_Vms-M3


title: RNA_WT_cPSE_Vms-F3

description:
Library name: WT_cPSE_Vms-F3
WT_PBS_Vms-F3


title: RNA_WT_cPAE_Vms-M1

description:
Library name: WT_cPAE_Vms-M1
WT_EtOH_Vms-M1


title: Bd21-3, Control, C70, juvenile leaf tissue

description:
Library name: 443A1
Row name in SIEVE_M6_TPM.csv: C70

value: Control


title: RNA_KO_cPSE_Vms-F1

description:
Library name: KO_cPSE_Vms-F1
KO_PBS_Vms-F1


title: Bd21-3, Mutant, M1291, juvenile leaf tissue

description:
Library name: 442A1
Row name in SIEVE_M6_TPM.csv: M1291


title: Bd21-3, Mutant, M1185, juvenile leaf tissue

description:
Library name: 441A1
Row name in SIEVE_M6_TPM.csv: M1185


title: Bd21-3, Mutant, M1279, juvenile leaf tissue

description:
Library name: 438A1
Row name in SIEVE_M6_TPM.csv: M1279


title: Bd21-3, Mutant, M1169, juvenile leaf tissue

description:
Library name: 440A1
Row name in SIEVE_M6_TPM.csv: M1169


title: Bd21-3, Mutant, M1197, juvenile leaf tissue

description:
Library name: 437A1
Row name in SIEVE_M6_TPM.csv: M1197


title: Bd21-3, Mutant, M1008, juvenile leaf tissue

description:
Library name: 439A1
Row name in SIEVE_M6_TPM.csv: M1008


title: RNA_KO_cPAE_dHPC-M3

description:
Library name: KO_cPAE_dHPC-M3
KO_EtOH_dHPC-M3

source_name: dorsal hippocampus

value: dorsal hippocampus

value: male


title: RNA_WT_cPSE_Vms-M3

description:
Library name: WT_cPSE_Vms-M3
WT_PBS_Vms-M3


title: RNA_KO_cPAE_dHPC-F3

description:
Library name: KO_cPAE_dHPC-F3
KO_EtOH_dHPC-F3


title: RNA_KO_cPAE_dHPC-F1

description:
Library name: KO_cPAE_dHPC-F1
KO_EtOH_dHPC-F1


title: Bd21-3, Mutant, M0992, juvenile leaf tissue

description:
Library name: 435A1
Row name in SIEVE_M6_TPM.csv: M0992


title: RNA_WT_cPSE_Vms-M1

description:
Library name: WT_cPSE_Vms-M1
WT_PBS_Vms-M1


title: RNA_WT_cPAE_Vms-F3

description:
Library name: WT_cPAE_Vms-F3
WT_EtOH_Vms-F3


title: Bd21-3, Mutant, M1121, juvenile leaf tissue

description:
Library name: 434A1
Row name in SIEVE_M6_TPM.csv: M1121


title: RNA_KO_cPSE_dHPC-F1

description:
Library name: KO_cPSE_dHPC-F1
KO_PBS_dHPC-F1


title: RNA_KO_cPSE_dHPC-M3

description:
Library name: KO_cPSE_dHPC-M3
KO_PBS_dHPC-M3


title: Bd21-3, Mutant, M1190, juvenile leaf tissue

description:
Library name: 429A1
Row name in SIEVE_M6_TPM.csv: M1190


title: RNA_WT_cPSE_Vms-F1

description:
Library name: WT_cPSE_Vms-F1
WT_PBS_Vms-F1


title: Bd21-3, Mutant, M1063, juvenile leaf tissue

description:
Library name: 430A1
Row name in SIEVE_M6_TPM.csv: M1063


title: RNA_KO_cPSE_dHPC-F3

description:
Library name: KO_cPSE_dHPC-F3
KO_PBS_dHPC-F3


title: RNA_KO_cPAE_dHPC-M1

description:
Library name: KO_cPAE_dHPC-M1
KO_EtOH_dHPC-M1


title: Bd21-3, Mutant, M1085, juvenile leaf tissue

description:
Library name: 431A1
Row name in SIEVE_M6_TPM.csv: M1085


title: Bd21-3, Mutant, M0423, juvenile leaf tissue

description:
Library name: 42A1
Row name in SIEVE_M6_TPM.csv: M0423


title: Bd21-3, Mutant, M1056, juvenile leaf tissue

description:
Library name: 428A1
Row name in SIEVE_M6_TPM.csv: M1056


title: RNA_KO_cPSE_dHPC-M1

description:
Library name: KO_cPSE_dHPC-M1
KO_PBS_dHPC-M1


title: RNA_WT_cPAE_dHPC-F1

description:
Library name: WT_cPAE_dHPC-F1
WT_EtOH_dHPC-F1


title: Bd21-3, Mutant, M1161, juvenile leaf tissue

description:
Library name: 426A1
Row name in SIEVE_M6_TPM.csv: M1161


title: RNA_WT_cPAE_dHPC-F3

description:
Library name: WT_cPAE_dHPC-F3
WT_EtOH_dHPC-F3


title: RNA_WT_cPAE_dHPC-M3

description:
Library name: WT_cPAE_dHPC-M3
WT_EtOH_dHPC-M3


title: RNA_WT_cPAE_dHPC-M1

description:
Library name: WT_cPAE_dHPC-M1
WT_EtOH_dHPC-M1


title: RNA_WT_cPSE_dHPC-F3

description:
Library name: WT_cPSE_dHPC-F3
WT_PBS_dHPC-F3


title: Bd21-3, Mutant, M1171, juvenile leaf tissue

description:
Library name: 424A1
Row name in SIEVE_M6_TPM.csv: M1171


title: RNA_WT_cPSE_dHPC-M3

description:
Library name: WT_cPSE_dHPC-M3
WT_PBS_dHPC-M3


title: Bd21-3, Mutant, M0967, juvenile leaf tissue

description:
Library name: 423A1
Row name in SIEVE_M6_TPM.csv: M0967


title: Bd21-3, Mutant, M0159, juvenile leaf tissue

description:
Library name: 41A1
Row name in SIEVE_M6_TPM.csv: M0159


title: RNA_WT_cPSE_dHPC-F1

description:
Library name: WT_cPSE_dHPC-F1
WT_PBS_dHPC-F1


title: Bd21-3, Mutant, M1351, juvenile leaf tissue

description:
Library name: 421A1
Row name in SIEVE_M6_TPM.csv: M1351


title: Bd21-3, Mutant, M1145, juvenile leaf tissue

description:
Library name: 427A1
Row name in SIEVE_M6_TPM.csv: M1145


title: Bd21-3, Mutant, M1089, juvenile leaf tissue

description:
Library name: 419A1
Row name in SIEVE_M6_TPM.csv: M1089


title: Bd21-3, Mutant, M0942, juvenile leaf tissue

description:
Library name: 420A1
Row name in SIEVE_M6_TPM.csv: M0942


title: YAP5SA_2

city: Cincinnati

first: Jeffrey

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description: Library name: Y2

data_processing:
RNA reads were aligned to the mouse genome (GRCm38.94) using STAR
Differential gene expression was performed in using limma and edgeR. Specifically, differential gene expression testing was performed using voomByGroup (doi: 10.1186/s13059-023-02949-2) function.
Assembly: GRCm38.94
Supplementary files format and content: YAPMEF_ReadSummary.txt: tab-delimited file containing genes (ensembl ID) and then gene counts from STAR for each of the libraries

source_name: Heart

extract_protocol:
RNA was isolated following manufacturer's guidelines for the Qiagen AllPrep Kit
Library construction was performed by Novogene Inc. Poly-A enriched, non-directional libraries

value: Heart

value: Cardiomyocyte

value: ICR


title: YAP5SA_MEF2A_1

description: Library name: YM1


title: YAP5SA_3

description: Library name: Y3


title: MEF2A_4

description: Library name: M4


title: Bd21-3, Control, C66, juvenile leaf tissue

description:
Library name: 415A1
Row name in SIEVE_M6_TPM.csv: C66


title: YAP5SA_MEF2A_2

description: Library name: YM2


title: Bd21-3, Mutant, M0908, juvenile leaf tissue

description:
Library name: 422A1
Row name in SIEVE_M6_TPM.csv: M0908


title: RNA_WT_cPSE_dHPC-M1

description:
Library name: WT_cPSE_dHPC-M1
WT_PBS_dHPC-M1


title: Bd21-3, Mutant, M1259, juvenile leaf tissue

description:
Library name: 417A1
Row name in SIEVE_M6_TPM.csv: M1259


title: YAP5SA_1

description: Library name: Y1


title: Bd21-3, Mutant, M1258, juvenile leaf tissue

description:
Library name: 425A1
Row name in SIEVE_M6_TPM.csv: M1258


title: Bd21-3, Mutant, M1278, juvenile leaf tissue

description:
Library name: 416A1
Row name in SIEVE_M6_TPM.csv: M1278


title: Bd21-3, Mutant, M0910, juvenile leaf tissue

description:
Library name: 418A1
Row name in SIEVE_M6_TPM.csv: M0910


title: Bd21-3, Mutant, M0980, juvenile leaf tissue

description:
Library name: 414A1
Row name in SIEVE_M6_TPM.csv: M0980


title: Bd21-3, Mutant, M1298, juvenile leaf tissue

description:
Library name: 413A1
Row name in SIEVE_M6_TPM.csv: M1298


title: MEF2A_2

description: Library name: M2


title: Bd21-3, Mutant, M1350, juvenile leaf tissue

description:
Library name: 412A1
Row name in SIEVE_M6_TPM.csv: M1350


title: MEF2A_3

description: Library name: M3


title: Bd21-3, Mutant, M0203, juvenile leaf tissue

description:
Library name: 40A1
Row name in SIEVE_M6_TPM.csv: M0203


title: MEF2A_1

description: Library name: M1


title: Bd21-3, Mutant, M1134, juvenile leaf tissue

description:
Library name: 411A1
Row name in SIEVE_M6_TPM.csv: M1134


title: Control_5

description: Library name: C5

value: No Virus


title: Control_4

description: Library name: C4


title: Bd21-3, Mutant, M1113, juvenile leaf tissue

description:
Library name: 409A1
Row name in SIEVE_M6_TPM.csv: M1113


title: TRF_2, (IP)

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent,

institute: Edinburgh university

description:
Library name: TRF_2, IP
TRF_ttaggg_2_2_Ratio_50.bw

library_source: genomic

data_processing:
The default mode of Bowtie 2 was used, which searches for mult(IP)le alignments and reports the best one or, if several alignments are deemed equally good, reports one of those randomly. The peaks were identified using MACS2 (version 2.2.7.1) broad peak call. The Ch(IP) samples were normalized to their respective (Input)s (ratio of Ch(IP) to (Input) reads) and the genome overview were using deeptools (Ramírez et al., 2016) with 50bp sliding window.
Assembly: Tb427V12
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Trypanosoma brucei brucei

source_name: bloodstream form

growth_protocol: Cell lines were grown at 37°C and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco), 1% 32 Penicillin-Streptomycin (Gibco) and selective drug(s) when required (Hirumi & Hirumi, 1989) . Cell cultures were maintained below 3 x 106 cells/ml. Selective drug(s) used Blasticidin 5 μg/ml Phleomycin 2.5 μg/ml G418 2.5 μg/ml Hygromycin 1 ug/ml Puromycin 0.5 μg/ml.

extract_protocol:
3.5 x 108 parasites were fixed with 0.8% formaldehyde for 20 min at room temperature. Cells were lysed and sonicated in the presence of 0.2% SDS for 30 cycles (30 sec on, 30 sec off) using the high setting on a Bioruptor sonicator (Diagenode). Cell debris were pelleted by centrifugation, and SDS in the lysate supernatants was diluted to 0.07%. (Input) samples were taken before incubating the rest of the cell lysates overnight with 10 μg rabbit anti-GFP antibody (Thermo Fisher Scientific A-11122) and Protein G Dynabeads. The beads were washed, and the DNA eluted from them was treated with RNase and Proteinase K. DNA was then purified using a QIAquick PCR purification kit (Qiagen).
libraries were prepared using NEXTflex barcoded adapters (Bio Scientific). The libraries were sequence on Illumina NextSeq (Western General Hospital, Edinburgh). In all cases, 75-bp paired-end sequencing was performed. Our subsequent analyses were based on two replicates for all TALEs.

value: bloodstream form

value: monomorphic cells

tag: chip antibody


title: Control_1

description: Library name: C1


title: NoTag_1, (Input)

description:
Library name: NoTag_1, Input
2_wt_IP_1_Ratio_50.bw


title: Control_3

description: Library name: C3


title: Bd21-3, Mutant, M1152, juvenile leaf tissue

description:
Library name: 407A1
Row name in SIEVE_M6_TPM.csv: M1152

value: leaf

value: juvenile leaf tissue


title: TRF_2, (Input)

description:
Library name: TRF_2, Input
TRF_ttaggg_2_2_Ratio_50.bw


title: NoTag_1, (IP)

description:
Library name: NoTag_1, IP
2_wt_IP_1_Ratio_50.bw

value: rabbit anti-GFP antibody (Thermo Fisher Scientific A-11122)


title: Bd21-3, Mutant, M1224, juvenile leaf tissue

description:
Library name: 406A1
Row name in SIEVE_M6_TPM.csv: M1224

value: Mutant


title: Bd21-3, Mutant, M0862, juvenile leaf tissue

description:
Library name: 400A1
Row name in SIEVE_M6_TPM.csv: M0862


title: Bd21-3, Mutant, M1288, juvenile leaf tissue

description:
Library name: 404A1
Row name in SIEVE_M6_TPM.csv: M1288


title: TelTALE.data2, (IP)

description:
Library name: TelTALE.data2, IP
TelTALE.data2.Ratio_50.bw


title: Bd21-3, Control, C64, juvenile leaf tissue

description:
Library name: 402A1
Row name in SIEVE_M6_TPM.csv: C64


title: TRF_1, (IP)

description:
Library name: TRF_1, IP
TRF_ttaggg_2_1_Ratio_50.bw


title: Bd21-3, Mutant, M0960, juvenile leaf tissue

description:
Library name: 401A1
Row name in SIEVE_M6_TPM.csv: M0960


title: Bd21-3, Mutant, M1211, juvenile leaf tissue

description:
Library name: 405A1
Row name in SIEVE_M6_TPM.csv: M1211


title: Control_2

description: Library name: C2


title: Bd21-3, Mutant, M0427, juvenile leaf tissue

description:
Library name: 3A1
Row name in SIEVE_M6_TPM.csv: M0427


title: TRF_1, (Input)

description:
Library name: TRF_1, Input
TRF_ttaggg_2_1_Ratio_50.bw


title: Bd21-3, Mutant, M1222, juvenile leaf tissue

description:
Library name: 403A1
Row name in SIEVE_M6_TPM.csv: M1222


title: TelTALE.data1, (Input)

description:
Library name: TelTALE.data1, Input
TelTALE.data1.Ratio_50.bw


title: Bd21-3, Mutant, M0410, juvenile leaf tissue

description:
Library name: 39A1
Row name in SIEVE_M6_TPM.csv: M0410


title: TelTALE.data1, (IP)

description:
Library name: TelTALE.data1, IP
TelTALE.data1.Ratio_50.bw


title: Bd21-3, Mutant, M1073, juvenile leaf tissue

description:
Library name: 408A1
Row name in SIEVE_M6_TPM.csv: M1073


title: Bd21-3, Mutant, M0897, juvenile leaf tissue

description:
Library name: 399A1
Row name in SIEVE_M6_TPM.csv: M0897


title: IngiTALE.data2, (IP)

description:
Library name: IngiTALE.data2, IP
IngiTALE.data2.Ratio_50.bw


title: TelTALE.data2, (Input)

description:
Library name: TelTALE.data2, Input
TelTALE.data2.Ratio_50.bw


title: Bd21-3, Mutant, M0587, juvenile leaf tissue

description:
Library name: 397A1
Row name in SIEVE_M6_TPM.csv: M0587


title: IngiTALE.data2, (Input)

description:
Library name: IngiTALE.data2, Input
IngiTALE.data2.Ratio_50.bw


title: Bd21-3, Mutant, M0556, juvenile leaf tissue

description:
Library name: 396A1
Row name in SIEVE_M6_TPM.csv: M0556


title: IngiTALE.data1, (Input)

description:
Library name: IngiTALE.data1, Input
IngiTALE.data1.Ratio_50.bw


title: IngiTALE.data1, (IP)

description:
Library name: IngiTALE.data1, IP
IngiTALE.data1.Ratio_50.bw


title: Bd21-3, Mutant, M0851, juvenile leaf tissue

description:
Library name: 395A1
Row name in SIEVE_M6_TPM.csv: M0851


title: CIR147-TALE.1, (IP)

description:
Library name: CIR147-TALE.1, IP
2_CIR147-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0823, juvenile leaf tissue

description:
Library name: 393A1
Row name in SIEVE_M6_TPM.csv: M0823


title: Bd21-3, Mutant, M0574, juvenile leaf tissue

description:
Library name: 394A1
Row name in SIEVE_M6_TPM.csv: M0574


title: CIR147-TALE.1, (Input)

description:
Library name: CIR147-TALE.1, Input
2_CIR147-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0561, juvenile leaf tissue

description:
Library name: 387A1
Row name in SIEVE_M6_TPM.csv: M0561


title: Bd21-3, Mutant, M0864, juvenile leaf tissue

description:
Library name: 389A1
Row name in SIEVE_M6_TPM.csv: M0864


title: Bd21-3, Mutant, M0047, juvenile leaf tissue

description:
Library name: 38A1
Row name in SIEVE_M6_TPM.csv: M0047


title: CIR147-TALE.2, (IP)

description:
Library name: CIR147-TALE.2, IP
3_CIR147-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0893, juvenile leaf tissue

description:
Library name: 386A1
Row name in SIEVE_M6_TPM.csv: M0893


title: Bd21-3, Mutant, M0744, juvenile leaf tissue

description:
Library name: 388A1
Row name in SIEVE_M6_TPM.csv: M0744


title: 70bp-TALE.2, (IP)

description:
Library name: 70bp-TALE.2, IP
2_70bp-TALE.Ratio_50.bw


title: MC177-TALE.1, (IP)

description:
Library name: MC177-TALE.1, IP
1_MC177-TALE.Ratio_50.bw


title: MC177-TALE.2, (Input)

description:
Library name: MC177-TALE.2, Input
MC177-TALE.Ratio_50.bw


title: MC177-TALE.1, (Input)

description:
Library name: MC177-TALE.1, Input
1_MC177-TALE.Ratio_50.bw


title: MC177-TALE.2, (IP)

description:
Library name: MC177-TALE.2, IP
MC177-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0670, juvenile leaf tissue

description:
Library name: 391A1
Row name in SIEVE_M6_TPM.csv: M0670


title: 70bp-TALE.1, (Input)

description:
Library name: 70bp-TALE.1, Input
1_70bp-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0846, juvenile leaf tissue

description:
Library name: 390A1
Row name in SIEVE_M6_TPM.csv: M0846


title: Bd21-3, Mutant, M0815, juvenile leaf tissue

description:
Library name: 384A1
Row name in SIEVE_M6_TPM.csv: M0815


title: Bd21-3, Mutant, M0491, juvenile leaf tissue

description:
Library name: 383A1
Row name in SIEVE_M6_TPM.csv: M0491


title: CIR147-TALE.2, (Input)

description:
Library name: CIR147-TALE.2, Input
3_CIR147-TALE.Ratio_50.bw


title: 70bp-TALE.1, (IP)

description:
Library name: 70bp-TALE.1, IP
1_70bp-TALE.Ratio_50.bw


title: 70bp-TALE.2, (Input)

description:
Library name: 70bp-TALE.2, Input
2_70bp-TALE.Ratio_50.bw


title: Bd21-3, Mutant, M0641, juvenile leaf tissue

description:
Library name: 392A1
Row name in SIEVE_M6_TPM.csv: M0641


title: ox40_batch-2_rep-1

city: Lund

first: Paula

last: Martos-Salvo

address: Sölvegatan 19

country: Sweden

institute: Lund University

description: Library name: ox40_batch-2_rep-1

data_processing:
RNAseq FASTQ files were processed using nf-core/rnaseq, version 3.22.2 (Patel et al., 2025), using the STAR aligner (ver 2.7.11b) and quantified by Salmon (ver 1.10.3).
Assembly: Samples were aligned against Drosophila melanogaster assembly version 54, Ensembl annotation release 115.
Supplementary files format and content: .sf files include transcript-level abundances

organism: Drosophila melanogaster

source_name: Midgut

extract_protocol:
Gut total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, #74134) following the manufacturer’s protocol at day 53.
DNBSEQ Eukaryotic Strand-specific mRNA library, as performed by BGI

treatment_protocol: Virgin females were introduced in hermetic cabinets at different concentrations of oxygen: 10% oxygen (hypoxia), 20% oxygen (normoxia) and 40% oxygen (hyperoxia).

value: Midgut

tag: oxygen percent


title: ox20_batch-2_rep-3

description: Library name: ox20_batch-2_rep-3


title: Bd21-3, Mutant, M0692, juvenile leaf tissue

description:
Library name: 381A1
Row name in SIEVE_M6_TPM.csv: M0692


title: Bd21-3, Mutant, M0748, juvenile leaf tissue

description:
Library name: 385A1
Row name in SIEVE_M6_TPM.csv: M0748


title: Bd21-3, Control, C28, juvenile leaf tissue

description:
Library name: 380A1
Row name in SIEVE_M6_TPM.csv: C28


title: ox20_batch-1_rep-2

description: Library name: ox20_batch-1_rep-2


title: ox20_batch-1_rep-1

description: Library name: ox20_batch-1_rep-1


title: Bd21-3, Mutant, M0279, juvenile leaf tissue

description:
Library name: 37A1
Row name in SIEVE_M6_TPM.csv: M0279


title: ox10_batch-1_rep-2

description: Library name: ox10_batch-1_rep-2


title: ox10_batch-2_rep-3

description: Library name: ox10_batch-2_rep-3


title: ox10_batch-1_rep-1

description: Library name: ox10_batch-1_rep-1


title: Bd21-3, Mutant, M0765, juvenile leaf tissue

description:
Library name: 376A1
Row name in SIEVE_M6_TPM.csv: M0765


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P4_3

city: Beijing

first: Gaoya

last: Su

address: Research Institute of Forestry Chinese Academy of Forestry No 1, Dong Xiao Fu Beijing , China

country: China

institute: Chinese Academy of Forestry

description:
Library name: P4_3
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P4, replicate 3

data_processing:
Clean reads were aligned to the Juglans regia reference genome (Jregia_v1.0) using STAR (v2.7.10a) with default parameters. Gene-level read counts were quantified using featureCounts (v2.0.3) based on the genome annotation.
Assembly: Juglans regia genome assembly v1.0
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample. Column headers formatted as "SampleID:read count".

organism: Juglans regia

extract_protocol:
RNA sequencing (RNA-seq) libraries were constructed from 100 ng of total RNA of three biological replicates according to standard Illumina protocols
Strand-specific RNA-seq libraries were constructed from polyA-enriched mRNA. mRNA was fragmented to ~200-300 bp, reverse transcribed with random hexamers, and size-selected (~300-400 bp) prior to sequencing on an Illumina platform.


title: Bd21-3, Mutant, M0713, juvenile leaf tissue

description:
Library name: 377A1
Row name in SIEVE_M6_TPM.csv: M0713


title: Bd21-3, Mutant, M0676, juvenile leaf tissue

description:
Library name: 378A1
Row name in SIEVE_M6_TPM.csv: M0676


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P4_2

description:
Library name: P4_2
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P4, replicate 2


title: Bd21-3, Mutant, M0472, juvenile leaf tissue

description:
Library name: 374A1
Row name in SIEVE_M6_TPM.csv: M0472


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P3_3

description:
Library name: P3_3
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P3, replicate 3


title: Bd21-3, Mutant, M0572, juvenile leaf tissue

description:
Library name: 372A1
Row name in SIEVE_M6_TPM.csv: M0572


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P4_1

description:
Library name: P4_1
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P4, replicate 1


title: Bd21-3, Mutant, M0593, juvenile leaf tissue

description:
Library name: 371A1
Row name in SIEVE_M6_TPM.csv: M0593


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P3_2

description:
Library name: P3_2
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P3, replicate 2


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P2_3

description:
Library name: P2_3
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P2, replicate 3


title: Bd21-3, Mutant, M0648, juvenile leaf tissue

description:
Library name: 369A1
Row name in SIEVE_M6_TPM.csv: M0648


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P2_2

description:
Library name: P2_2
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P2, replicate 2


title: Bd21-3, Mutant, M0601, juvenile leaf tissue

description:
Library name: 373A1
Row name in SIEVE_M6_TPM.csv: M0601


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P2_1

description:
Library name: P2_1
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P2, replicate 1


title: Bd21-3, Control, C29, juvenile leaf tissue

description:
Library name: 370A1
Row name in SIEVE_M6_TPM.csv: C29


title: Bd21-3, Mutant, M0469, juvenile leaf tissue

description:
Library name: 367A1
Row name in SIEVE_M6_TPM.csv: M0469


title: Bd21-3, Mutant, M0731, juvenile leaf tissue

description:
Library name: 368A1
Row name in SIEVE_M6_TPM.csv: M0731


title: Bd21-3, Mutant, M0797, juvenile leaf tissue

description:
Library name: 366A1
Row name in SIEVE_M6_TPM.csv: M0797


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P3_1

description:
Library name: P3_1
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P3, replicate 1


title: Bd21-3, Mutant, M0894, juvenile leaf tissue

description:
Library name: 365A1
Row name in SIEVE_M6_TPM.csv: M0894


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P1_3

description:
Library name: P1_3
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P1, replicate 3


title: Bd21-3, Mutant, M0578, juvenile leaf tissue

description:
Library name: 363A1
Row name in SIEVE_M6_TPM.csv: M0578


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P1_2

description:
Library name: P1_2
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P1, replicate 2


title: Bd21-3, Mutant, M0490, juvenile leaf tissue

description:
Library name: 364A1
Row name in SIEVE_M6_TPM.csv: M0490


title: salt stress (100 mM NaCl) treatment3

description:
Library name: S3_RNAseq
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) treatment, replicate 3


title: water control3

description:
Library name: CK3
Leaf tissue from walnut seedling under water control, replicate 3


title: Bd21-3, Mutant, M0260, juvenile leaf tissue

description:
Library name: 35A1
Row name in SIEVE_M6_TPM.csv: M0260


title: Bd21-3, Mutant, M0775, juvenile leaf tissue

description:
Library name: 362A1
Row name in SIEVE_M6_TPM.csv: M0775


title: salt stress (100 mM NaCl) treatment2

description:
Library name: S2_RNAseq
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) treatment, replicate 2


title: salt stress (100 mM NaCl) treatment1

description:
Library name: S1_RNAseq
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) treatment, replicate 1


title: water control2

description:
Library name: CK2
Leaf tissue from walnut seedling under water control, replicate 2


title: Bd21-3, Mutant, M0900, juvenile leaf tissue

description:
Library name: 358A1
Row name in SIEVE_M6_TPM.csv: M0900


title: GTR1_2

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: Library name: GTR1_2

data_processing:
Reads were aligned to the Caenorhabditis elegans genome with STAR aligner. The reference genome version was WBcel235, with annotations from Ensembl release 113.  Quantification was done with htseq-count. Strand information was set to 'reverse'. Quantification was done with htseq-count. Strand information was set to 'reverse', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
Assembly: WBcel235
Supplementary files format and content: raw_counts_and_basemean_normalized_counts.xlsx
Supplementary files format and content: Raw and normalized counts per gene (row) per sample (collumn)

organism: Caenorhabditis elegans

source_name: pool of whole worms

growth_protocol: first generation of worms were treated either on EV expressing bacteria or gtr-1 3'UTR RNAi and kept at 20C. At day 1 of adulthood the worms were bleached for second generation progeny which continued to be exposed to the same treatment as their parental generation . the second generation worms were daily washed to get rid of progeny and harvested at day 6 of adulthood

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1μg was used for the library construction; library was eluted in 20μL of elution buffer. All DNA sample libraries were pooled into 10 nM samples.

treatment_protocol: both generations were exposed to the same treatment (either Ht115 expressin an empty vector (EV) or HT115 expressing gtr-1 3'UTR RNAi ). The worms were maintained and grown at 20C

value: pool of whole worms

tag: harvest time

value: second generation day 6 of adulthood

value: grown on gtr-1 3'UTR RNAi expressing Bactetria


title: Bd21-3, Mutant, M0755, juvenile leaf tissue

description:
Library name: 356A1
Row name in SIEVE_M6_TPM.csv: M0755


title: Bd21-3, Mutant, M0553, juvenile leaf tissue

description:
Library name: 355A1
Row name in SIEVE_M6_TPM.csv: M0553


title: Bd21-3, Mutant, M0662, juvenile leaf tissue

description:
Library name: 357A1
Row name in SIEVE_M6_TPM.csv: M0662


title: GTR1_3

description: Library name: GTR1_3


title: GTR1_1

description: Library name: GTR1_1


title: Bd21-3, Mutant, M0484, juvenile leaf tissue

description:
Library name: 382A1
Row name in SIEVE_M6_TPM.csv: M0484


title: Bd21-3, Mutant, M0566, juvenile leaf tissue

description:
Library name: 360A1
Row name in SIEVE_M6_TPM.csv: M0566


title: Bd21-3, Mutant, M0520, juvenile leaf tissue

description:
Library name: 361A1
Row name in SIEVE_M6_TPM.csv: M0520


title: Bd21-3, Mutant, M0543, juvenile leaf tissue

description:
Library name: 354A1
Row name in SIEVE_M6_TPM.csv: M0543


title: EV1

description: Library name: EV1

value: grown on EV expressing Bactetria


title: Bd21-3, Control, C37, juvenile leaf tissue

description:
Library name: 353A1
Row name in SIEVE_M6_TPM.csv: C37

value: Control


title: EV2

description: Library name: EV2


title: gtr1_4

description: Library name: JOUD_gtr_1_4_S10_R1_001.fastq.gz

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10. The processed reads were aligned to the Caenorhabditis elegans transcriptome and genome version WBcel235 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization, batch correction for experiment repeat number (2,3,4) and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: WBcel235
Supplementary files format and content: counts_norm_bcor.xlsx
Supplementary files format and content: DESeq2 raw, normalized and batch corrected counts per gene (rows) per sample(column)

growth_protocol: first generation of worms were treated either on EV expressing bacteria or gtr-1 3'UTR RNAi. At day 1 of adulthood the worms were bleached for second generation progeny which continued to be exposed to the same treatment as their parental generation . the second generation worms were daily washed to get rid of progeny and harvested at day 6 of adulthood

value: pCL12 (unc-54/human Abeta peptide 1-42 minigene) + pRF4


title: Bd21-3, Mutant, M0807, juvenile leaf tissue

description:
Library name: 352A1
Row name in SIEVE_M6_TPM.csv: M0807


title: salt stress (100 mM NaCl) inoculation with Pseudomonas P1_1

description:
Library name: P1_1
Leaf tissue from walnut seedling under salt stress (100 mM NaCl) inoculation with Pseudomonas P1, replicate 1


title: Bd21-3, Mutant, M0782, juvenile leaf tissue

description:
Library name: 351A1
Row name in SIEVE_M6_TPM.csv: M0782


title: Bd21-3, Mutant, M0809, juvenile leaf tissue

description:
Library name: 359A1
Row name in SIEVE_M6_TPM.csv: M0809


title: EV3

description: Library name: EV3


title: gtr1_3

description: Library name: JOUD_gtr_1_3_S8_R1_001.fastq.gz


title: gtr1_2

description: Library name: JOUD_gtr_1_2_S6_R1_001.fastq.gz


title: EV_2

description: Library name: JOUD_EV2_S5_R1_001.fastq.gz


title: Bd21-3, Mutant, M0825, juvenile leaf tissue

description:
Library name: 349A1
Row name in SIEVE_M6_TPM.csv: M0825


title: Bd21-3, Mutant, M0798, juvenile leaf tissue

description:
Library name: 348A1
Row name in SIEVE_M6_TPM.csv: M0798


title: Bd21-3, Mutant, M0264, juvenile leaf tissue

description:
Library name: 34A1
Row name in SIEVE_M6_TPM.csv: M0264


title: EV_4

description: Library name: JOUD_EV4_S9_R1_001.fastq.gz


title: EV_3

description: Library name: JOUD_EV3_S7_R1_001.fastq.gz


title: Bd21-3, Mutant, M0850, juvenile leaf tissue

description:
Library name: 346A1
Row name in SIEVE_M6_TPM.csv: M0850


title: Bd21-3, Mutant, M0712, juvenile leaf tissue

description:
Library name: 347A1
Row name in SIEVE_M6_TPM.csv: M0712


title: Bd21-3, Mutant, M0870, juvenile leaf tissue

description:
Library name: 350A1
Row name in SIEVE_M6_TPM.csv: M0870


title: Trim66_KO_homo_Olfr1507_OSN_ATAC_seq_rep_2

city: Shanghai

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University

description: Library name: sample 4

data_processing:
Reads were trimmed using Trimmomatic (version 0.39), then mapped to the mouse refer- ence genome (mm10) using Bowtie 2 (version 2.4.1) with the “very- sensitive –X 2000” parameters.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: Main Olfactory Epithelium (MOE)

extract_protocol:
The MOE from Olfr1507-ires-tdTomato; Trim66 -/- or Olfr1507-ires-tdTomato; Trim66 +/- mice was dissected and dissociated. Then more than 10,000 tdTomato-positive cells were sorted by flow cytometry
Libraries were prepared with the the TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and applied the index from the TruePrep® Index Kit V2 for Illumina (Vazyme, TD202).

value: Main Olfactory Epithelium (MOE)


title: Trim66_KO_het_Olfr1507_OSN_ATAC_seq_rep_2

description: Library name: sample 2


title: Bd21-3, Mutant, M0792, juvenile leaf tissue

description:
Library name: 345A1
Row name in SIEVE_M6_TPM.csv: M0792


title: Trim66_KO_homo_Olfr1507_OSN_ATAC_seq_rep_1

description:
Library name: sample 3
merge bw file of Homo 1 and 2


title: Bd21-3, Mutant, M0675, juvenile leaf tissue

description:
Library name: 343A1
Row name in SIEVE_M6_TPM.csv: M0675


title: Bd21-3, Mutant, M0660, juvenile leaf tissue

description:
Library name: 342A1
Row name in SIEVE_M6_TPM.csv: M0660


title: Trim66_KO_het_Olfr1507_OSN_ATAC_seq_rep_1

description:
Library name: sample 1
merge bw file of Het 1 and 2


title: MCE, heart, snRNA-seq

city: Nanjing

first: Ying

last: Wang

address: No. 2 Southeast University Road, Jiangning District, Nanjing

institute: Southeast University

description: Library name: MCE

data_processing:
Raw snRNA-seq data (FASTQ files) were processed using the CeleScope pipeline (v1.18.0) to generate gene expression matrices.
Assembly: mm10/GRCm38
Supplementary files format and content: Supplementary_files_format_and_content: *_ matrix.tar: Tar files include barcodes.tsv, features.tsv, matrix.mtx. Filtered counts of sequencing reads.

source_name: Whole heart

extract_protocol:
Harvested heart tissues were washed in pre-cooled PBSE (PBS buffer supplemented with 2 mM EGTA). Nuclei were isolated using the GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies, Nanjing, China) according to the manufacturer's instructions. To reduce technical variability, heart tissues from three mice per group were pooled into a single sample for nuclei isolation. Isolated nuclei were resuspended in PBSE (106 nuclei per 400 μl), filtered through a 40 μm cell strainer, and counted with Trypan blue. Nuclear integrity and viability were confirmed by DAPI (1:1,000, TermoFisher Scientific, D1306) staining, and only preparations with high viability (>80%) were processed further. Nuclei were defined as DAPI-positive singlets
Single nucleus suspensions were adjusted to a concentration of 3-4 × 105 nuclei/mL in PBS and then loaded onto a microfluidic chip (GEXSCOPE® Single Nucleus RNA-seq Kit, Singleron Biotechnologies) for library construction according to the manufacturer's protocol. The resulting snRNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

value: Whole heart

value: 16° C for 7 days, 12° C for 14 days and 6° C for 14 days


title: Bd21-3, Mutant, M0629, juvenile leaf tissue

description:
Library name: 341A1
Row name in SIEVE_M6_TPM.csv: M0629


title: RT, heart, snRNA-seq

description: Library name: RT

value: Room temperature 22° C


title: Bd21-3, Mutant, M0781, juvenile leaf tissue

description:
Library name: 338A1
Row name in SIEVE_M6_TPM.csv: M0781


title: LLC, CD47 KO Clone E3, Replicate 3

first: Kelsie

last: Thu

state: ON

address: 209 Victoria Street

institute: Keenan Research Centre for Biomedical Science

description:
Library name: LLC CD47 KO E3 in vitro 3
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E3_in_vitro_3

data_processing:
Quality control for the raw sequence data was done using FastQC.
Trimmomatic was used to trim adapter sequences and filter out low-quality reads.
Cleaned reads were aligned to the Mus musculus GRCm39 transcriptome using the STAR aligner.
Assembly: GRCm39
Supplementary files format and content: csv file contains raw counts for each sample

source_name: Lung adenocarcinoma

growth_protocol: LLC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Total RNA was extractioned using Rneasy Plus Mini Kit (Qiagen, #74104) followed by DNase treatment.
Library preparation (NEB Ultra II Directional polyA mRNA) and paired-end sequencing was done at The Centre for Applied Genomics (Toronto, Canada) generating 30-40 million reads per sample on an Illumina Novaseq.

value: Lewis Lung Carcninoma

value: CD47 KO


title: LLC CD47 KO Clone E5, Replicate 3

description:
Library name: LLC CD47 KO E5 in vitro 3
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E5_in_vitro_3


title: LLC CD47 KO Clone E5, Replicate 2

description:
Library name: LLC CD47 KO E5 in vitro 2
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E5_in_vitro_2


title: LLC CD47 KO Clone E5, Replicate 1

description:
Library name: LLC CD47 KO E5 in vitro 1
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E5_in_vitro_1


title: LLC, CD47 KO Clone E3, Replicate 2

description:
Library name: LLC CD47 KO E3 in vitro 2
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E3_in_vitro_2


title: Bd21-3, Mutant, M0612, juvenile leaf tissue

description:
Library name: 339A1
Row name in SIEVE_M6_TPM.csv: M0612

value: leaf


title: LLC, CD47 KO Clone E3, Replicate 1

description:
Library name: LLC CD47 KO E3 in vitro 1
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_KO_E3_in_vitro_1


title: Bd21-3, Mutant, M0569, juvenile leaf tissue

description:
Library name: 344A1
Row name in SIEVE_M6_TPM.csv: M0569

value: juvenile leaf tissue


title: LLC, WT, Replicate 3

description:
Library name: LLC WT in vitro 3
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_WT_in_vitro_3

value: WT


title: Bd21-3, Mutant, M0761, juvenile leaf tissue

description:
Library name: 337A1
Row name in SIEVE_M6_TPM.csv: M0761

value: Mutant


title: LLC, WT, Replicate 2

description:
Library name: LLC WT in vitro 2
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_WT_in_vitro_2


title: Bd21-3, Mutant, M0169, juvenile leaf tissue

description:
Library name: 33A1
Row name in SIEVE_M6_TPM.csv: M0169


title: Bd21-3, Mutant, M0889, juvenile leaf tissue

description:
Library name: 334A1
Row name in SIEVE_M6_TPM.csv: M0889


title: LLC, WT, Replicate 1

description:
Library name: LLC WT in vitro 1
Column name in THU27608_Vitro_AllGenes_Raw_Counts.csv: LLC_WT_in_vitro_1


title: Bd21-3, Mutant, M0877, juvenile leaf tissue

description:
Library name: 340A1
Row name in SIEVE_M6_TPM.csv: M0877


title: water control1

description:
Library name: CK1
Leaf tissue from walnut seedling under water control, replicate 1


title: Bd21-3, Mutant, M0804, juvenile leaf tissue

description:
Library name: 331A1
Row name in SIEVE_M6_TPM.csv: M0804


title: Bd21-3, Mutant, M0619, juvenile leaf tissue

description:
Library name: 336A1
Row name in SIEVE_M6_TPM.csv: M0619


title: Bd21-3, Mutant, M0542, juvenile leaf tissue

description:
Library name: 332A1
Row name in SIEVE_M6_TPM.csv: M0542


title: T12 Tumor, Erlotinib, CP-4359

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description:
Library name: T12_CP-4359
Column name in processed files: T12_CP-4359

data_processing:
STAR aligner algorithm was used to aligned the fastq files to the mouse mm10 reference genome.
Resulting BAM files were sorted and indexed using Samtools. Quality control was completed using Picard.
Salmon was used to determine the transcript read counts.
The raw counts were upper quartile-normalized.
Assembly: mm10
Supplementary files format and content: Salmon-quantified, upper quartile-normalized read-counts. First column is the gene name, subsequent columns are individual samples.

source_name: mammary tumor

extract_protocol:
Cryopreserved tumors were homogenized using a tissue homogenizer. The RNeasy Mini Kit (#74104, Qiagen) was used to isolate the RNA according to the manufacturer's protocol.
The Agilent Bioanalyzer was used to asses the mRNA quality and libraries for mRNA-seq were constructed using total RNA and the Illumina TruSeq mRNA sample preparation kit.

value: mammary tumor

tag: tumor model

value: Erlotinib


title: Bd21-3, Mutant, M0688, juvenile leaf tissue

description:
Library name: 330A1
Row name in SIEVE_M6_TPM.csv: M0688

tag: tissue


title: T12 Tumor, Erlotinib, CP-4360

description:
Library name: T12_CP-4360
Column name in processed files: T12_CP-4360


title: Bd21-3, Mutant, M0686, juvenile leaf tissue

description:
Library name: 335A1
Row name in SIEVE_M6_TPM.csv: M0686

tag: cell line


title: T12 Tumor, Trametinib, CP-4358

description:
Library name: T12_CP-4358
Column name in processed files: T12_CP-4358

value: Trametinib


title: Bd21-3, Mutant, M0142, juvenile leaf tissue

description:
Library name: 32A1
Row name in SIEVE_M6_TPM.csv: M0142

tag: cell type


title: T12 Tumor, Trametinib, CP-4357

description:
Library name: T12_CP-4357
Column name in processed files: T12_CP-4357


title: Bd21-3, Mutant, M0818, juvenile leaf tissue

description:
Library name: 329A1
Row name in SIEVE_M6_TPM.csv: M0818

tag: genotype


title: Bd21-3, Mutant, M0734, juvenile leaf tissue

description:
Library name: 333A1
Row name in SIEVE_M6_TPM.csv: M0734

tag: treatment


title: T11-APOBEC Tumor, Erlotinib, CP-3604

description:
Library name: T11-APOBEC_CP-3604
Column name in processed files: T11-APOBEC_CP-3604


title: T12 Tumor, Erlotinib, CP-4361

description:
Library name: T12_CP-4361
Column name in processed files: T12_CP-4361


title: Bd21-3, Mutant, M0510, juvenile leaf tissue

description:
Library name: 325A1
Row name in SIEVE_M6_TPM.csv: M0510

tag: batch


title: T11-APOBEC Tumor, Erlotinib, CP-3605

description:
Library name: T11-APOBEC_CP-3605
Column name in processed files: T11-APOBEC_CP-3605


title: Bd21-3, Mutant, M0890, juvenile leaf tissue

description:
Library name: 324A1
Row name in SIEVE_M6_TPM.csv: M0890


title: Bd21-3, Mutant, M0628, juvenile leaf tissue

description:
Library name: 326A1
Row name in SIEVE_M6_TPM.csv: M0628


title: T11-APOBEC Tumor, Erlotinib, CP-3603

description:
Library name: T11-APOBEC_CP-3603
Column name in processed files: T11-APOBEC_CP-3603


title: T11-APOBEC Tumor, Trametinib, CP-3611

description:
Library name: T11-APOBEC_CP-3611
Column name in processed files: T11-APOBEC_CP-3611


title: T12 Tumor, Trametinib, CP-4356

description:
Library name: T12_CP-4356
Column name in processed files: T12_CP-4356


title: Bd21-3, Mutant, M0535, juvenile leaf tissue

description:
Library name: 323A1
Row name in SIEVE_M6_TPM.csv: M0535


title: T11 Tumor, Erlotinib, CP-3590

description:
Library name: T11_CP-3590
Column name in processed files: T11_CP-3590


title: T11 Tumor, Erlotinib, CP-3589

description:
Library name: T11_CP-3589
Column name in processed files: T11_CP-3589


title: Bd21-3, Mutant, M0760, juvenile leaf tissue

description:
Library name: 322A1
Row name in SIEVE_M6_TPM.csv: M0760


title: T11-APOBEC Tumor, Trametinib, CP-3610

description:
Library name: T11-APOBEC_CP-3610
Column name in processed files: T11-APOBEC_CP-3610


title: Bd21-3, Mutant, M0497, juvenile leaf tissue

description:
Library name: 327A1
Row name in SIEVE_M6_TPM.csv: M0497


title: Bd21-3, Control, C35, juvenile leaf tissue

description:
Library name: 320A1
Row name in SIEVE_M6_TPM.csv: C35


title: T11 Tumor, Erlotinib, CP-3588

description:
Library name: T11_CP-3588
Column name in processed files: T11_CP-3588


title: Bd21-3, Mutant, M0715, juvenile leaf tissue

description:
Library name: 328A1
Row name in SIEVE_M6_TPM.csv: M0715


title: Bd21-3, Mutant, M0650, juvenile leaf tissue

description:
Library name: 321A1
Row name in SIEVE_M6_TPM.csv: M0650


title: T11 Tumor, Trametinib, CP-3596

description:
Library name: T11_CP-3596
Column name in processed files: T11_CP-3596


title: p53RB-626 Tumor, Erlotinib, CP-4099

description:
Library name: p53RB-626_CP-4099
Column name in processed files: p53RB-626_CP-4099


title: p53RB-626 Tumor, Erlotinib, CP-4098

description:
Library name: p53RB-626_CP-4098
Column name in processed files: p53RB-626_CP-4098


title: Bd21-3, Mutant, M0803, juvenile leaf tissue

description:
Library name: 317A1
Row name in SIEVE_M6_TPM.csv: M0803


title: T11 Tumor, Trametinib, CP-3594

description:
Library name: T11_CP-3594
Column name in processed files: T11_CP-3594


title: Bd21-3, Mutant, M0701, juvenile leaf tissue

description:
Library name: 318A1
Row name in SIEVE_M6_TPM.csv: M0701


title: Bd21-3, Mutant, M0790, juvenile leaf tissue

description:
Library name: 316A1
Row name in SIEVE_M6_TPM.csv: M0790


title: Bd21-3, Mutant, M0288, juvenile leaf tissue

description:
Library name: 31A1
Row name in SIEVE_M6_TPM.csv: M0288


title: Bd21-3, Mutant, M0820, juvenile leaf tissue

description:
Library name: 319A1
Row name in SIEVE_M6_TPM.csv: M0820


title: T11 Tumor, Trametinib, CP-3595

description:
Library name: T11_CP-3595
Column name in processed files: T11_CP-3595


title: Bd21-3, Mutant, M0568, juvenile leaf tissue

description:
Library name: 315A1
Row name in SIEVE_M6_TPM.csv: M0568


title: T11-APOBEC Tumor, Trametinib, CP-3609

description:
Library name: T11-APOBEC_CP-3609
Column name in processed files: T11-APOBEC_CP-3609


title: p53RB-626 Tumor, Erlotinib, CP-4097

description:
Library name: p53RB-626_CP-4097
Column name in processed files: p53RB-626_CP-4097


title: Bd21-3, Mutant, M0571, juvenile leaf tissue

description:
Library name: 313A1
Row name in SIEVE_M6_TPM.csv: M0571


title: Bd21-3, Mutant, M0479, juvenile leaf tissue

description:
Library name: 311A1
Row name in SIEVE_M6_TPM.csv: M0479


title: p53RB-626 Tumor, Trametinib, CP-4100

description:
Library name: p53RB-626_CP-4100
Column name in processed files: p53RB-626_CP-4100


title: Bd21-3, Mutant, M0740, juvenile leaf tissue

description:
Library name: 312A1
Row name in SIEVE_M6_TPM.csv: M0740


title: p53RB-624 Tumor, Erlotinib, CP-4528

description:
Library name: p53RB-624_CP-4528
Column name in processed files: p53RB-624_CP-4528


title: Bd21-3, Mutant, M0200, juvenile leaf tissue

description:
Library name: 30A1
Row name in SIEVE_M6_TPM.csv: M0200


title: p53RB-626 Tumor, Trametinib, CP-4101

description:
Library name: p53RB-626_CP-4101
Column name in processed files: p53RB-626_CP-4101


title: p53RB-626 Tumor, Trametinib, CP-4102

description:
Library name: p53RB-626_CP-4102
Column name in processed files: p53RB-626_CP-4102


title: Bd21-3, Mutant, M0532, juvenile leaf tissue

description:
Library name: 310A1
Row name in SIEVE_M6_TPM.csv: M0532


title: p53RB-624 Tumor, Erlotinib, CP-4526

description:
Library name: p53RB-624_CP-4526
Column name in processed files: p53RB-624_CP-4526


title: p53RB-624 Tumor, Erlotinib, CP-4527

description:
Library name: p53RB-624_CP-4527
Column name in processed files: p53RB-624_CP-4527


title: p53RB-624 Tumor, Trametinib, CP-4531

description:
Library name: p53RB-624_CP-4531
Column name in processed files: p53RB-624_CP-4531


title: Bd21-3, Mutant, M0541, juvenile leaf tissue

description:
Library name: 314A1
Row name in SIEVE_M6_TPM.csv: M0541


title: Bd21-3, Mutant, M0845, juvenile leaf tissue

description:
Library name: 307A1
Row name in SIEVE_M6_TPM.csv: M0845


title: p53RB-624 Tumor, Trametinib, CP-4530

description:
Library name: p53RB-624_CP-4530
Column name in processed files: p53RB-624_CP-4530


title: Bd21-3, Mutant, M0677, juvenile leaf tissue

description:
Library name: 309A1
Row name in SIEVE_M6_TPM.csv: M0677


title: Bd21-3, Control, C42, juvenile leaf tissue

description:
Library name: 306A1
Row name in SIEVE_M6_TPM.csv: C42


title: Bd21-3, Mutant, M0728, juvenile leaf tissue

description:
Library name: 308A1
Row name in SIEVE_M6_TPM.csv: M0728


title: p53RB-426 Tumor, Erlotinib, CP-4263

description:
Library name: p53RB-426_CP-4263
Column name in processed files: p53RB-426_CP-4263


title: p53RB-426 Tumor, Erlotinib, CP-4261

description:
Library name: p53RB-426_CP-4261
Column name in processed files: p53RB-426_CP-4261


title: Bd21-3, Mutant, M0698, juvenile leaf tissue

description:
Library name: 303A1
Row name in SIEVE_M6_TPM.csv: M0698


title: Bd21-3, Mutant, M0895, juvenile leaf tissue

description:
Library name: 302A1
Row name in SIEVE_M6_TPM.csv: M0895


title: p53RB-426 Tumor, Erlotinib, CP-4262

description:
Library name: p53RB-426_CP-4262
Column name in processed files: p53RB-426_CP-4262


title: Bd21-3, Mutant, M0808, juvenile leaf tissue

description:
Library name: 301A1
Row name in SIEVE_M6_TPM.csv: M0808


title: PY-Hi

city: Bronx

first: Russell

last: Scharf

state: New York

address: 1945 Eastchester Rd

institute: Albert Einstein College of Medicine

description:
Library name: Sample 2
10x genomics

data_processing:
Reads were processed with Cell Ranger with the GRCh38 reference transcriptome
Assembly: GRCh38
Supplementary files format and content: HDF5 files containing filtered single-cell gene-barcode count matrices

organism: Homo sapiens

source_name: Peripheral blood leukocytes

growth_protocol: HL60 cells were cultured and maintained in RPMI + 10% FBS + 1% PenStrap

extract_protocol:
scRNA-seq 975 libraries using the 10x Genomics GEM-X Single Cell 3ʹ Kit v4.1.
Single-cell suspensions were loaded onto the 10x Genomics Chromium GEM-X platform for droplet-based partitioning and barcoding. cDNA synthesis and library preparation were performed using the Chromium Single Cell 3′ Reagent Kit v4.1 according to the manufacturer’s protocol.

treatment_protocol: HL60 cells were treated with 250nM AraC for 1 day. Cells were then stained for Pyronin Y and Hoechst and Pyronin Y low and high fraction within G0/G1 gated cells were sorted using flow cytometry for RNA seq analysis

value: Peripheral blood leukocytes

value: Promyeloblast

value: AraC 250nM 1 day

tag: fraction

value: PY-Hi


title: p53RB-624 Tumor, Trametinib, CP-4529

description:
Library name: p53RB-624_CP-4529
Column name in processed files: p53RB-624_CP-4529


title: Bd21-3, Mutant, M0066, juvenile leaf tissue

description:
Library name: 2A1
Row name in SIEVE_M6_TPM.csv: M0066


title: p53RB-426 Tumor, Trametinib, CP-4260

description:
Library name: p53RB-426_CP-4260
Column name in processed files: p53RB-426_CP-4260


title: p53RB-426 Tumor, Trametinib, CP-4139

description:
Library name: p53RB-426_CP-4139
Column name in processed files: p53RB-426_CP-4139


title: Bd21-3, Mutant, M0844, juvenile leaf tissue

description:
Library name: 300A1
Row name in SIEVE_M6_TPM.csv: M0844


title: PY-Lo

description:
Library name: Sample 1
10x genomics

value: PY-Lo


title: Bd21-3, Mutant, M0559, juvenile leaf tissue

description:
Library name: 299A1
Row name in SIEVE_M6_TPM.csv: M0559


title: V5(MORC3) ChIP-Seq in MORC3.AID.V5 SPI1.dTAG cells treated with dTAGV1, Replicate 2

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: Library name: MORC3-V5_dTAGV1_M3AID-SPI1dTAG_REP2

data_processing:
ChIP-Seq: nf-core/chipseq v2.1.0 was run with default parameters to quality check and align the data, create coverage tracks (bigWig) and call peaks.
Assembly: GRCh38
Supplementary files format and content: .bigWig: genome-wide read coverage track

growth_protocol: BLaER1 cells were cultured in RPMI Medium 1640 supplemented with L-glutamine, sodium pyruvate, 100U/ml penicillin-streptomycin (Thermo Fisher) and 10% (v/v) FCS (Omega Scientific).

extract_protocol:
BLaER1 cells were washed with PBS and fixed with 1% formaldehyde for 10 min at RT before quenching the reaction with 0.6 M glycine. Fixed cells were washed with cold PBS and lysed in 50mM TRIS pH 8, 10mM EDTA and 1% SDS. Lysates were sonicated using the Bioruptor (Diagenode) with cycles of 30s ON / 30s OFF in the high-power mode until a fragment length of 200-500bp was achieved. Lysates were mixed with dilution buffer to a final concentration of 20 mM TRIS pH 8, 150 mM NaCl, 2 mM EDTA ,1% Triton-X100 and 0.1% SDS. 2.5% drosophila melanogaster S2 cell derived chromatin (prepared similarly) was spiked into the samples. Lysates were pre-incubated at 4°C for 2 h with ProteinA-coated magnetic beads (G&E) previously blocked in TE with 1% BSA. After removal of the beads, target and spike-in antibodies were added to the lysates and incubated at 4°C overnight. Fresh blocked beads were added and incubated with the lysates for 2h at 4°C. Beads were washed with RIPA buffer (150 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 0.5% Na-deoxycholate, 1% Igepal), high salt buffer (500 mM NaCl, 50 mM TRIS pH 8, 0.1% SDS, 1% Igepal), LiCl buffer (250 mM LiCl, 50 mM TRIS pH 8, 0.5% Na-deoxycholate, 1% Igepal) and TE wash buffer (10 mM TRIS-HCl, 1 mM EDTA, 50 mM NaCl) and protein DNA complexes were eluted with 100mM NaHCO3 + 1% SDS. ChIP and input samples were incubated overnight at 55°C with 200mM NaCl, 10mM EDTA, 20mM Tris-HCl pH 6.5 and 300 µg/ml Proteinase K (Thermo Fisher). DNA was isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research).
NEBNext Ultra II liabrary prep was performed accoring to manufacturer's instructions

treatment_protocol: 1.4 million BLaER1 cells per well of a 6-well plate were trans-differentiated into monocytes for 5 days in medium containing 10 ng/ml of hrIL-3, 10 ng/ml hr-CSF-1 (M-CSF) (both PeproTech) and 100 nM β-estradiol (Sigma-Aldrich)

value: monocytes

value: IFNAR1-/- / IFNAR2-/- MORC3.AID.V5 TIR1(F74G) sgSPI1 + SPI1.dTAG

value: 500nM dTAGV1

value: anti-PU.1 antibody, 9G7, Cell Siganling Technology


title: MMTV-PyMT Tumor, Erlotinib, CP-4948

description:
Library name: MMTV-PyMT_CP-4948
Column name in processed files: MMTV-PyMT_CP-4948

value: MMTV-PyMT


title: Bd21-3, Mutant, M0614, juvenile leaf tissue

description:
Library name: 298A1
Row name in SIEVE_M6_TPM.csv: M0614

data_processing:
Sequencing reads were aligned using hisat2, with default options and converted into bam files using samtools.
The number of reads were counted using the featureCounts function of subread configured to count fragments instead of reads (-p), using the Bd21-3 genome annotations (-a BdistachyonBd21_3_537_v1.2.gene.gff3).
Assembly: BdistachyonBd21_3_537_v1.2
Supplementary files format and content: Tab-delimited file contained transcripts per million (TPM) for each sample

value: leaf


title: MMTV-PyMT Tumor, Erlotinib, CP-4947

description:
Library name: MMTV-PyMT_CP-4947
Column name in processed files: MMTV-PyMT_CP-4947


title: Bd21-3, Mutant, M0471, juvenile leaf tissue

description:
Library name: 297A1
Row name in SIEVE_M6_TPM.csv: M0471

value: juvenile leaf tissue


title: Bd21-3, Mutant, M0588, juvenile leaf tissue

description:
Library name: 293A1
Row name in SIEVE_M6_TPM.csv: M0588


title: V5(MORC3) ChIP-Seq in MORC3.AID.V5 SPI1.dTAG cells treated with dTAGV1, Replicate 1

description: Library name: MORC3-V5_dTAGV1_M3AID-SPI1dTAG_REP1


title: p53RB-426 Tumor, Trametinib, CP-4205

description:
Library name: p53RB-426_CP-4205
Column name in processed files: p53RB-426_CP-4205


title: Bd21-3, Mutant, M0752, juvenile leaf tissue

description:
Library name: 296A1
Row name in SIEVE_M6_TPM.csv: M0752


title: Bd21-3, Mutant, M0795, juvenile leaf tissue

description:
Library name: 292A1
Row name in SIEVE_M6_TPM.csv: M0795


title: V5(MORC3) ChIP-Seq in MORC3.AID.V5 SPI1.dTAG cells treated with DMSO, Replicate 2

description: Library name: MORC3-V5_DMSO_M3AID-SPI1dTAG_REP2

value: DMSO


title: Bd21-3, Mutant, M0777, juvenile leaf tissue

description:
Library name: 294A1
Row name in SIEVE_M6_TPM.csv: M0777

value: Mutant


title: V5(MORC3) ChIP-Seq in MORC3.AID.V5 SPI1.dTAG cells treated with DMSO, Replicate 1

description: Library name: MORC3-V5_DMSO_M3AID-SPI1dTAG_REP1


title: Bd21-3, Mutant, M0538, juvenile leaf tissue

description:
Library name: 304A1
Row name in SIEVE_M6_TPM.csv: M0538


title: Bd21-3, Mutant, M0736, juvenile leaf tissue

description:
Library name: 291A1
Row name in SIEVE_M6_TPM.csv: M0736


title: MMTV-PyMT Tumor, Erlotinib, CP-4946

description:
Library name: MMTV-PyMT_CP-4946
Column name in processed files: MMTV-PyMT_CP-4946

value: mammary tumor


title: Bd21-3, Mutant, M0034, juvenile leaf tissue

description:
Library name: 28A1
Row name in SIEVE_M6_TPM.csv: M0034


title: Bd21-3, Mutant, M0666, juvenile leaf tissue

description:
Library name: 290A1
Row name in SIEVE_M6_TPM.csv: M0666


title: ChIP-Seq Input for V5(MORC3) ChIP in MORC3.AID.V5 SPI1.dTAG cells, Replicate 2

description: Library name: Input_DMSO_M3AID-SPI1dTAG_REP2


title: MMTV-PyMT Tumor, Trametinib, CP-4945

description:
Library name: MMTV-PyMT_CP-4945
Column name in processed files: MMTV-PyMT_CP-4945


title: Bd21-3, Mutant, M0706, juvenile leaf tissue

description:
Library name: 287A1
Row name in SIEVE_M6_TPM.csv: M0706


title: MMTV-PyMT Tumor, Trametinib, CP-4944

description:
Library name: MMTV-PyMT_CP-4944
Column name in processed files: MMTV-PyMT_CP-4944


title: MMTV-Neu Tumor, Erlotinib, CP-4941

description:
Library name: MMTV-Neu_CP-4941
Column name in processed files: MMTV-Neu_CP-4941

value: MMTV-Neu

value: Erlotinib


title: Bd21-3, Mutant, M0527, juvenile leaf tissue

description:
Library name: 286A1
Row name in SIEVE_M6_TPM.csv: M0527


title: ChIP-Seq Input for V5(MORC3) ChIP in MORC3.AID.V5 SPI1.dTAG cells, Replicate 1

description: Library name: Input_DMSO_M3AID-SPI1dTAG_REP1


title: Bd21-3, Mutant, M0839, juvenile leaf tissue

description:
Library name: 284A1
Row name in SIEVE_M6_TPM.csv: M0839


title: PU.1 ChIP-Seq in MORC3.AID.V5 cells treated with 5Ph-IAA (Auxin), Replicate 2

description: Library name: PU1_Auxin_M3AID_REP2

value: IFNAR1-/- / IFNAR2-/- MORC3.AID.V5 TIR1(F74G)

value: 1µM 5Ph-IAA

value: anti-V5 antibody; SV-Pk5, Thermo Fisher


title: Bd21-3, Mutant, M0859, juvenile leaf tissue

description:
Library name: 288A1
Row name in SIEVE_M6_TPM.csv: M0859


title: MMTV-PyMT Tumor, Trametinib, CP-4943

description:
Library name: MMTV-PyMT_CP-4943
Column name in processed files: MMTV-PyMT_CP-4943

value: Trametinib


title: MMTV-Neu Tumor, Erlotinib, CP-4942

description:
Library name: MMTV-Neu_CP-4942
Column name in processed files: MMTV-Neu_CP-4942


title: PU.1 ChIP-Seq in MORC3.AID.V5 cells treated with DMSO, Replicate 1

description: Library name: PU1_DMSO_M3AID_REP1


title: Bd21-3, Mutant, M0882, juvenile leaf tissue

description:
Library name: 279A1
Row name in SIEVE_M6_TPM.csv: M0882


title: Bd21-3, Mutant, M0549, juvenile leaf tissue

description:
Library name: 289A1
Row name in SIEVE_M6_TPM.csv: M0549


title: Bd21-3, Mutant, M0560, juvenile leaf tissue

description:
Library name: 285A1
Row name in SIEVE_M6_TPM.csv: M0560


title: PU.1 ChIP-Seq in MORC3.AID.V5 cells treated with 5Ph-IAA (Auxin), Replicate 1

description: Library name: PU1_Auxin_M3AID_REP1


title: Bd21-3, Mutant, M0868, juvenile leaf tissue

description:
Library name: 283A1
Row name in SIEVE_M6_TPM.csv: M0868


title: Bd21-3, Mutant, M0361, juvenile leaf tissue

description:
Library name: 27A1
Row name in SIEVE_M6_TPM.csv: M0361


title: Input for PU.1 ChIP-Seq in MORC3.AID.V5 cells, Replicate 2

description: Library name: Input_DMSO_M3AID_REP2


title: MMTV-Neu Tumor, Trametinib, CP-4938

description:
Library name: MMTV-Neu_CP-4938
Column name in processed files: MMTV-Neu_CP-4938


title: Bd21-3, Mutant, M0613, juvenile leaf tissue

description:
Library name: 277A1
Row name in SIEVE_M6_TPM.csv: M0613


title: PU.1 ChIP-Seq in MORC3.AID.V5 cells treated with DMSO, Replicate 2

description: Library name: PU1_DMSO_M3AID_REP2


title: Bd21-3, Mutant, M0523, juvenile leaf tissue

description:
Library name: 282A1
Row name in SIEVE_M6_TPM.csv: M0523


title: Bd21-3, Mutant, M0887, juvenile leaf tissue

description:
Library name: 280A1
Row name in SIEVE_M6_TPM.csv: M0887


title: Bd21-3, Mutant, M0784, juvenile leaf tissue

description:
Library name: 276A1
Row name in SIEVE_M6_TPM.csv: M0784


title: Bd21-3, Mutant, M0618, juvenile leaf tissue

description:
Library name: 275A1
Row name in SIEVE_M6_TPM.csv: M0618


title: MMTV-Neu Tumor, Trametinib, CP-4937

description:
Library name: MMTV-Neu_CP-4937
Column name in processed files: MMTV-Neu_CP-4937


title: Input for PU.1 ChIP-Seq in MORC3.AID.V5 cells, Replicate 1

description: Library name: Input_DMSO_M3AID_REP1


title: Bd21-3, Mutant, M0842, juvenile leaf tissue

description:
Library name: 274A1
Row name in SIEVE_M6_TPM.csv: M0842


title: MMTV-Neu Tumor, Trametinib, CP-4939

description:
Library name: MMTV-Neu_CP-4939
Column name in processed files: MMTV-Neu_CP-4939


title: Bd21-3, Mutant, M0718, juvenile leaf tissue

description:
Library name: 271A1
Row name in SIEVE_M6_TPM.csv: M0718


title: Bd21-3, Mutant, M0762, juvenile leaf tissue

description:
Library name: 272A1
Row name in SIEVE_M6_TPM.csv: M0762


title: Bd21-3, Mutant, M0863, juvenile leaf tissue

description:
Library name: 270A1
Row name in SIEVE_M6_TPM.csv: M0863


title: pool-9, well-4, GEX

city: San Francisco

first: Ravi

last: Patel

state: CA

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

description:
Library name: XHLT2-POOL-DB9-SCG4_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1

data_processing:
Sequencer-obtained bcl files were demultiplexed using mkfastq program from Cell Ranger v6.0.2 (10x Genomics). Feature-barcode matrices were obtained for each library by aligning the raw fastqs of gene expression to GRCh38 reference genome (Gencode v32-primary assembly) and the raw fastqs of surface protein expression to a TotalSeq-C antibody reference panel using the Cell Ranger count. Raw feature-barcode matrices were imported and analyzed using Seurat (v4.0.3).
Each library was demultiplexed to map individual cells to their sample of origin using freemuxlet (vAug2021), SNP profiles were mapped to the genotypes of individual participants from bulk RNA-seq using bcftools gtcheck (v1.10.2), and inter-sample doublets and empty droplets were removed.
DoubletFinder (v2.0.3) was used to filter barcodes containing heterotypic intra-sample doublets.
Barcodes containing less than 100 genes and genes that are detected in fewer than 3 cells were removed. We further filtered out the barcodes based on library-specific cutoffs for the number of genes per cell (nFeature_RNA <300-800 and >6,000), the number of unique molecular indexes (UMIs) per cell (nCount_RNA <400-2,000 and >40,000), mitochondrial content (>15%), and ribosomal content (<8-15% and >60%) to remove poor quality cells. The RNA and ADT count data for the resulting high-quality cell-barcodes are provided here.
For processing of follow-up timepoint, the baseline samples were reanalyzed along with the the follow-up timepoint (separated by ~19 months). After generating single-cell count data from sequencing reads and performing quality control, the identification of cell subsets in the follow-up data was performed using Azimuth. The Seurat object from original baseline data was converted to Azimuth reference, and the follow-up dataset was mapped onto it using Azimuth, which provided predicted cell subset labels for single cells.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain raw count data in 10X H5 format for the high-quality single-cells
Supplementary files format and content: cell_metadata_baseline.rds and cell_metadata_followup.rds are R object files containing metadata for single-cells in baseline and follow-up datasets, respectively. The metadata include sample id (donor id + timepoint id), library id, cell annotations, and timepoint.
Library strategy: CITE-seq

source_name: PBMC

extract_protocol:
Blood was collected in EDTA tubes within a 90 min window for all participants of the study. Peripheral blood mononuclear cells (PBMC) were obtained by density gradient centrifugation of whole blood at 800g for 30 min at room temperature without brake, using Ficoll-Paque (Cytiva). Isolated cells were cryopreserved in a solution containing fetal Bovine Serum and 10% DMSO (Sigma). Thawed PBMC suspensions from 14-16 individuals were pooled together with equivalent numbers to a total of 1 million live cells. Pools were resuspended in Cell Staining Buffer (Biolegend) and incubated with Fc Receptor Blocking Solution (Biolegend) at 20mg/mL for 10 minutes on ice. Cells were then stained with a cocktail of 140 TotalSeq-C oligo-tagged antibodies (Biolegend) for 30 minutes at 4°C. Stained cells were washed in PBS containing 1% BSA, filtered through a 70uM filter, and re-suspended in a final solution of PBS containing 0.04% BSA.
Stained cells (n=60,000) were loaded on the Chromium Controller (10X Genomics) for GEM generation. The cDNA libraries were generated using the Chromium Next GEM Single Cell 5’ v1.1 Library Kit for gene expression (GEX) and the Chromium Single Cell 5’ Feature Barcode Library kit for antibody derived tag (ADT) according to manufacturer’s instructions (10X Genomics). Each batch of 14-16 samples was sampled four times to prepare four independent cDNA libraries per batch to obtain a sufficient number of cells per sample. The libraries were subsequently sequenced on a NovaSeq 6000 S4 platform (Illumina).

value: PBMC

tag: library type

value: mRNA


title: pool-9, well-3, ADT

description:
Library name: XHLT2-POOL-DB9-SCG3_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1

library_source: other

molecule: protein

value: ADT


title: pool-9, well-4, ADT

description:
Library name: XHLT2-POOL-DB9-SCG4_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: Bd21-3, Mutant, M0631, juvenile leaf tissue

first: Guillaume

last: Ramstein

address: Moellers Alle

institute: Aarhus University

description:
Library name: 273A1
Row name in SIEVE_M6_TPM.csv: M0631

extract_protocol:
Tissue sampling was performed in three independent biological replicates per line. The three replicates from each line were subsequently pooled for total RNA extraction. RNA extraction was conducted by Azenta GeneWiz (Leipzig, Germany).
Library preparation was performed using Poly(A) selection and paired-end sequencing (2 × 150 bp) was conducted on an Illumina NovaSeq platform at Azenta GeneWiz (Leipzig, Germany).


title: KPB25L Tumor, Erlotinib, CP-3817

description:
Library name: KPB25L_CP-3817
Column name in processed files: KPB25L_CP-3817


title: Bd21-3, Mutant, M0555, juvenile leaf tissue

description:
Library name: 267A1
Row name in SIEVE_M6_TPM.csv: M0555


title: MMTV-Neu Tumor, Erlotinib, CP-4940

description:
Library name: MMTV-Neu_CP-4940
Column name in processed files: MMTV-Neu_CP-4940


title: Bd21-3, Mutant, M0114, juvenile leaf tissue

description:
Library name: 26A1
Row name in SIEVE_M6_TPM.csv: M0114


title: pool-9, well-3, GEX

description:
Library name: XHLT2-POOL-DB9-SCG3_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: Bd21-3, Mutant, M0656, juvenile leaf tissue

description:
Library name: 269A1
Row name in SIEVE_M6_TPM.csv: M0656


title: KPB25L Tumor, Erlotinib, CP-3816

description:
Library name: KPB25L_CP-3816
Column name in processed files: KPB25L_CP-3816


title: KPB25L Tumor, Trametinib, CP-3812

description:
Library name: KPB25L_CP-3812
Column name in processed files: KPB25L_CP-3812


title: pool-9, well-2, ADT

description:
Library name: XHLT2-POOL-DB9-SCG2_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: Bd21-3, Mutant, M0499, juvenile leaf tissue

description:
Library name: 263A1
Row name in SIEVE_M6_TPM.csv: M0499


title: Bd21-3, Mutant, M0679, juvenile leaf tissue

description:
Library name: 264A1
Row name in SIEVE_M6_TPM.csv: M0679


title: Bd21-3, Mutant, M0737, juvenile leaf tissue

description:
Library name: 265A1
Row name in SIEVE_M6_TPM.csv: M0737


title: Bd21-3, Mutant, M0547, juvenile leaf tissue

description:
Library name: 268A1
Row name in SIEVE_M6_TPM.csv: M0547


title: KPB25L Tumor, Trametinib, CP-3810

description:
Library name: KPB25L_CP-3810
Column name in processed files: KPB25L_CP-3810


title: KPB25L Tumor, Trametinib, CP-3811

description:
Library name: KPB25L_CP-3811
Column name in processed files: KPB25L_CP-3811


title: KPB25L Tumor, Erlotinib, CP-3818

description:
Library name: KPB25L_CP-3818
Column name in processed files: KPB25L_CP-3818


title: pool-9, well-1, GEX

description:
Library name: XHLT2-POOL-DB9-SCG1_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: pool-9, well-2, GEX

description:
Library name: XHLT2-POOL-DB9-SCG2_GEX
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: Bd21-3, Mutant, M0054, juvenile leaf tissue

description:
Library name: 25A1
Row name in SIEVE_M6_TPM.csv: M0054


title: KPB1-B Tumor, Erlotinib, CP-4516

description:
Library name: KPB1-B_CP-4516
Column name in processed files: KPB1-B_CP-4516


title: Bd21-3, Mutant, M0754, juvenile leaf tissue

description:
Library name: 266A1
Row name in SIEVE_M6_TPM.csv: M0754


title: Bd21-3, Mutant, M0515, juvenile leaf tissue

description:
Library name: 259A1
Row name in SIEVE_M6_TPM.csv: M0515


title: Bd21-3, Control, C36, juvenile leaf tissue

description:
Library name: 262A1
Row name in SIEVE_M6_TPM.csv: C36

value: Control


title: pool-8, well-2, ADT

description:
Library name: XHLT2-POOL-DB8-SCG2_ADT
Pool of XHLT2-HS32-BLE1, XHLT2-HS6-BLE1, XHLT2-HS94-AAE6


title: Bd21-3, Mutant, M0821, juvenile leaf tissue

description:
Library name: 261A1
Row name in SIEVE_M6_TPM.csv: M0821


title: pool-9, well-1, ADT

description:
Library name: XHLT2-POOL-DB9-SCG1_ADT
Pool of XHLT2-HS10-BLE1, XHLT2-HS16-AAE6, XHLT2-HS24-AAE6, XHLT2-HS46-BLE1, XHLT2-HS86-AAE6, XHLT2-HS88-BLE1


title: Bd21-3, Mutant, M0657, juvenile leaf tissue

description:
Library name: 260A1
Row name in SIEVE_M6_TPM.csv: M0657


title: KPB1-B Tumor, Erlotinib, CP-4515

description:
Library name: KPB1-B_CP-4515
Column name in processed files: KPB1-B_CP-4515


title: KPB1-B Tumor, Erlotinib, CP-4514

description:
Library name: KPB1-B_CP-4514
Column name in processed files: KPB1-B_CP-4514


title: Bd21-3, Mutant, M0904, juvenile leaf tissue

description:
Library name: 258A1
Row name in SIEVE_M6_TPM.csv: M0904


title: pool-8, well-2, GEX

description:
Library name: XHLT2-POOL-DB8-SCG2_GEX
Pool of XHLT2-HS32-BLE1, XHLT2-HS6-BLE1, XHLT2-HS94-AAE6


title: Bd21-3, Mutant, M0540, juvenile leaf tissue

description:
Library name: 257A1
Row name in SIEVE_M6_TPM.csv: M0540


title: pool-8, well-1, ADT

description:
Library name: XHLT2-POOL-DB8-SCG1_ADT
Pool of XHLT2-HS32-BLE1, XHLT2-HS6-BLE1, XHLT2-HS94-AAE6


title: Bd21-3, Mutant, M0879, juvenile leaf tissue

description:
Library name: 256A1
Row name in SIEVE_M6_TPM.csv: M0879


title: KPB1-B Tumor, Trametinib, CP-4519

description:
Library name: KPB1-B_CP-4519
Column name in processed files: KPB1-B_CP-4519


title: Bd21-3, Mutant, M0669, juvenile leaf tissue

description:
Library name: 254A1
Row name in SIEVE_M6_TPM.csv: M0669


title: pool-8, well-1, GEX

description:
Library name: XHLT2-POOL-DB8-SCG1_GEX
Pool of XHLT2-HS32-BLE1, XHLT2-HS6-BLE1, XHLT2-HS94-AAE6


title: Bd21-3, Mutant, M0638, juvenile leaf tissue

description:
Library name: 253A1
Row name in SIEVE_M6_TPM.csv: M0638


title: KPB1-B Tumor, Trametinib, CP-4518

description:
Library name: KPB1-B_CP-4518
Column name in processed files: KPB1-B_CP-4518


title: pool-14, well-4, ADT

description:
Library name: XHLT2-POOL-DB14-SCG4_ADT
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: KPB1-B Tumor, Trametinib, CP-4517

description:
Library name: KPB1-B_CP-4517
Column name in processed files: KPB1-B_CP-4517


title: Bd21-3, Mutant, M0847, juvenile leaf tissue

description:
Library name: 252A1
Row name in SIEVE_M6_TPM.csv: M0847


title: Bd21-3, Mutant, M0558, juvenile leaf tissue

description:
Library name: 250A1
Row name in SIEVE_M6_TPM.csv: M0558


title: KPB1-A Tumor, Erlotinib, CP-4287

description:
Library name: KPB1-A_CP-4287
Column name in processed files: KPB1-A_CP-4287


title: Bd21-3, Mutant, M0682, juvenile leaf tissue

description:
Library name: 255A1
Row name in SIEVE_M6_TPM.csv: M0682


title: pool-14, well-2, ADT

description:
Library name: XHLT2-POOL-DB14-SCG2_ADT
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: KPB1-A Tumor, Trametinib, CP-4284

description:
Library name: KPB1-A_CP-4284
Column name in processed files: KPB1-A_CP-4284


title: Bd21-3, Mutant, M0805, juvenile leaf tissue

description:
Library name: 247A1
Row name in SIEVE_M6_TPM.csv: M0805


title: KPB1-A Tumor, Trametinib, CP-4283

description:
Library name: KPB1-A_CP-4283
Column name in processed files: KPB1-A_CP-4283


title: Bd21-3, Mutant, M0667, juvenile leaf tissue

description:
Library name: 243A1
Row name in SIEVE_M6_TPM.csv: M0667


title: pool-14, well-2, GEX

description:
Library name: XHLT2-POOL-DB14-SCG2_GEX
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: Bd21-3, Mutant, M0816, juvenile leaf tissue

description:
Library name: 244A1
Row name in SIEVE_M6_TPM.csv: M0816


title: Bd21-3, Mutant, M0750, juvenile leaf tissue

description:
Library name: 245A1
Row name in SIEVE_M6_TPM.csv: M0750


title: Bd21-3, Mutant, M0727, juvenile leaf tissue

description:
Library name: 251A1
Row name in SIEVE_M6_TPM.csv: M0727


title: Bd21-3, Mutant, M0874, juvenile leaf tissue

description:
Library name: 241A1
Row name in SIEVE_M6_TPM.csv: M0874


title: Bd21-3, Mutant, M0810, juvenile leaf tissue

description:
Library name: 242A1
Row name in SIEVE_M6_TPM.csv: M0810


title: pool-14, well-3, GEX

description:
Library name: XHLT2-POOL-DB14-SCG3_GEX
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: pool-14, well-1, ADT

description:
Library name: XHLT2-POOL-DB14-SCG1_ADT
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: Bd21-3, Mutant, M0514, juvenile leaf tissue

description:
Library name: 240A1
Row name in SIEVE_M6_TPM.csv: M0514


title: KPB1-A Tumor, Trametinib, CP-4282

description:
Library name: KPB1-A_CP-4282
Column name in processed files: KPB1-A_CP-4282


title: Bd21-3, Mutant, M0265, juvenile leaf tissue

description:
Library name: 23A1
Row name in SIEVE_M6_TPM.csv: M0265


title: pool-14, well-1, GEX

description:
Library name: XHLT2-POOL-DB14-SCG1_GEX
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: KPB25L-UV Tumor, Erlotinib, CP-3835

description:
Library name: KPB25L-UV_CP-3835
Column name in processed files: KPB25L-UV_CP-3835


title: Bd21-3, Mutant, M0663, juvenile leaf tissue

description:
Library name: 239A1
Row name in SIEVE_M6_TPM.csv: M0663


title: Bd21-3, Mutant, M0633, juvenile leaf tissue

description:
Library name: 238A1
Row name in SIEVE_M6_TPM.csv: M0633


title: Bd21-3, Mutant, M0596, juvenile leaf tissue

description:
Library name: 237A1
Row name in SIEVE_M6_TPM.csv: M0596


title: pool-13, well-4, ADT

description:
Library name: XHLT2-POOL-DB13-SCG4_ADT
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: pool-13, well-4, GEX

description:
Library name: XHLT2-POOL-DB13-SCG4_GEX
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: KPB1-A Tumor, Erlotinib, CP-4286

description:
Library name: KPB1-A_CP-4286
Column name in processed files: KPB1-A_CP-4286


title: Bd21-3, Mutant, M0714, juvenile leaf tissue

description:
Library name: 249A1
Row name in SIEVE_M6_TPM.csv: M0714


title: KPB25L-UV Tumor, Erlotinib, CP-3834

description:
Library name: KPB25L-UV_CP-3834
Column name in processed files: KPB25L-UV_CP-3834


title: Bd21-3, Mutant, M0878, juvenile leaf tissue

description:
Library name: 248A1
Row name in SIEVE_M6_TPM.csv: M0878


title: Bd21-3, Mutant, M0504, juvenile leaf tissue

description:
Library name: 234A1
Row name in SIEVE_M6_TPM.csv: M0504


title: Bd21-3, Mutant, M0835, juvenile leaf tissue

description:
Library name: 235A1
Row name in SIEVE_M6_TPM.csv: M0835


title: KPB25L-UV Tumor, Erlotinib, CP-3833

description:
Library name: KPB25L-UV_CP-3833
Column name in processed files: KPB25L-UV_CP-3833


title: pool-13, well-3, ADT

description:
Library name: XHLT2-POOL-DB13-SCG3_ADT
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: Bd21-3, Mutant, M0691, juvenile leaf tissue

description:
Library name: 232A1
Row name in SIEVE_M6_TPM.csv: M0691


title: Bd21-3, Mutant, M0837, juvenile leaf tissue

description:
Library name: 231A1
Row name in SIEVE_M6_TPM.csv: M0837


title: KPB25L-UV Tumor, Trametinib, CP-3829

description:
Library name: KPB25L-UV_CP-3829
Column name in processed files: KPB25L-UV_CP-3829


title: Bd21-3, Mutant, M0723, juvenile leaf tissue

description:
Library name: 246A1
Row name in SIEVE_M6_TPM.csv: M0723


title: Bd21-3, Mutant, M0524, juvenile leaf tissue

description:
Library name: 230A1
Row name in SIEVE_M6_TPM.csv: M0524


title: pool-13, well-3, GEX

description:
Library name: XHLT2-POOL-DB13-SCG3_GEX
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: Bd21-3, Mutant, M0449, juvenile leaf tissue

description:
Library name: 24A1
Row name in SIEVE_M6_TPM.csv: M0449


title: Bd21-3, Mutant, M0002, juvenile leaf tissue

description:
Library name: 22A1
Row name in SIEVE_M6_TPM.csv: M0002


title: Bd21-3, Mutant, M0529, juvenile leaf tissue

description:
Library name: 229A1
Row name in SIEVE_M6_TPM.csv: M0529


title: Bd21-3, Mutant, M0517, juvenile leaf tissue

description:
Library name: 233A1
Row name in SIEVE_M6_TPM.csv: M0517


title: KPB25L-UV Tumor, Trametinib, CP-3827

description:
Library name: KPB25L-UV_CP-3827
Column name in processed files: KPB25L-UV_CP-3827


title: pool-14, well-4, GEX

description:
Library name: XHLT2-POOL-DB14-SCG4_GEX
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: Bd21-3, Mutant, M0654, juvenile leaf tissue

description:
Library name: 228A1
Row name in SIEVE_M6_TPM.csv: M0654


title: KPB25L-UV Tumor, Trametinib, CP-3828

description:
Library name: KPB25L-UV_CP-3828
Column name in processed files: KPB25L-UV_CP-3828


title: pool-13, well-2, GEX

description:
Library name: XHLT2-POOL-DB13-SCG2_GEX
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: pool-14, well-3, ADT

description:
Library name: XHLT2-POOL-DB14-SCG3_ADT
Pool of XHLT2-HS12-AAE6, XHLT2-HS28-AAE6, XHLT2-HS30-BLE1, XHLT2-HS32-AAE6, XHLT2-HS86-BLE1, XHLT2-HS94-BLE1


title: Bd21-3, Mutant, M0531, juvenile leaf tissue

description:
Library name: 227A1
Row name in SIEVE_M6_TPM.csv: M0531


title: E0771 Tumor, Erlotinib, CP-4299

description:
Library name: E0771_CP-4299
Column name in processed files: E0771_CP-4299


title: Bd21-3, Mutant, M0896, juvenile leaf tissue

description:
Library name: 223A1
Row name in SIEVE_M6_TPM.csv: M0896


title: pool-13, well-2, ADT

description:
Library name: XHLT2-POOL-DB13-SCG2_ADT
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: Bd21-3, Mutant, M0486, juvenile leaf tissue

description:
Library name: 225A1
Row name in SIEVE_M6_TPM.csv: M0486


title: pool-13, well-1, ADT

description:
Library name: XHLT2-POOL-DB13-SCG1_ADT
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: pool-13, well-1, GEX

description:
Library name: XHLT2-POOL-DB13-SCG1_GEX
Pool of XHLT2-HS22-BLE1, XHLT2-HS30-AAE6, XHLT2-HS48-BLE1, XHLT2-HS6-AAE6


title: Bd21-3, Mutant, M0565, juvenile leaf tissue

description:
Library name: 226A1
Row name in SIEVE_M6_TPM.csv: M0565


title: E0771 Tumor, Erlotinib, CP-4298

description:
Library name: E0771_CP-4298
Column name in processed files: E0771_CP-4298


title: E0771 Tumor, Erlotinib, CP-4297

description:
Library name: E0771_CP-4297
Column name in processed files: E0771_CP-4297


title: Bd21-3, Mutant, M0708, juvenile leaf tissue

description:
Library name: 221A1
Row name in SIEVE_M6_TPM.csv: M0708


title: Bd21-3, Mutant, M0251, juvenile leaf tissue

description:
Library name: 21A1
Row name in SIEVE_M6_TPM.csv: M0251


title: E0771 Tumor, Trametinib, CP-4296

description:
Library name: E0771_CP-4296
Column name in processed files: E0771_CP-4296


title: pool-12, well-4, GEX

description:
Library name: XHLT2-POOL-DB12-SCG4_GEX
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1


title: Bd21-3, Mutant, M0866, juvenile leaf tissue

description:
Library name: 220A1
Row name in SIEVE_M6_TPM.csv: M0866


title: pool-12, well-4, ADT

description:
Library name: XHLT2-POOL-DB12-SCG4_ADT
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1


title: Bd21-3, Mutant, M0562, juvenile leaf tissue

description:
Library name: 219A1
Row name in SIEVE_M6_TPM.csv: M0562


title: E0771 Tumor, Trametinib, CP-4295

description:
Library name: E0771_CP-4295
Column name in processed files: E0771_CP-4295


title: Bd21-3, Mutant, M0060, juvenile leaf tissue

description:
Library name: 20A1
Row name in SIEVE_M6_TPM.csv: M0060


title: pool-12, well-3, ADT

description:
Library name: XHLT2-POOL-DB12-SCG3_ADT
Pool of XHLT2-HS10-AAE6, XHLT2-HS16-BLE1, XHLT2-HS47-BLE1, XHLT2-HS75-AAE6, XHLT2-HS93-BLE1