title: Figure 3, Donor 26, Untransduced (ntd), biol rep 2

description:
Library name: sample 64
Column name in all.gene_counts.tsv: sample.ntd_2

value: Untransduced


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain_and_BACH2_OE (28s_BACH2), biol rep 3

status: Public on Jan 21 2025

type: SRA

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

country: USA

institute: Washington University School of Medicine in St Louis

description:
Library name: sample 59
Column name in all.gene_counts.tsv: sample.28s.bach2_3

library_source: transcriptomic

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04
Assembly: figure 2, hg38 (GRCh38.76). figure 3, hg38 (GRCh38.101)
Supplementary files format and content: tab separated value file that contains the raw gene counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

growth_protocol: Primary Human T cells  were grown in RPMI media with 10% FBS, 1% Pen/Strep, 1% HEPES, 1% L-glutamine and 10ng/mL IL7+IL15 in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested from 1 million CAR positive Primary T cells using Quick-RNA™ Microprep Kit” from zymo research. 10ng of total RNA was used for creation of sequencing libraries.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Cells were stimulated on CD3/CD28 dynabeads at a ratio of 3 beads : 1 T cell. The following day, two different lentiviral vectors encoding CAR or BACH2 were co-transduced into T cells. Beads were removed on day 6 after bead stimulation and cells were expanded for 8 more days prior to collection for RNA purification.

tag: tissue

value: Peripheral blood mononuclear cells

tag: cell type

value: primary human T cells

tag: genotype

value: BACH2 overexpression

tag: treatment

value: CD22-targeted-CD28s-CD3z CAR, BACH2 overexpression


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 1

description:
Library name: sample 60
Column name in all.gene_counts.tsv: sample.bbs_1

value: WT

value: CD22-targeted-4-1BBs-CD3z CAR


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 3

description:
Library name: sample 62
Column name in all.gene_counts.tsv: sample.bbs_3


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain_and_BACH2_OE (28s_BACH2), biol rep 1

description:
Library name: sample 57
Column name in all.gene_counts.tsv: sample.28s.bach2_1


title: Figure 3, Donor 26, Untransduced (ntd), biol rep 1

description:
Library name: sample 63
Column name in all.gene_counts.tsv: sample.ntd_1


title: Figure 3, Donor 26, Untransduced (ntd), biol rep 3

description:
Library name: sample 65
Column name in all.gene_counts.tsv: sample.ntd_3


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 3,  biol rep 3

description:
Library name: sample 53
Column name in all_figure_2_donor_002.gene_counts.tsv: sample.28l3'


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 1

description:
Library name: sample 54
Column name in all.gene_counts.tsv: sample.28s_1

value: CD22-targeted-CD28s-CD3z CAR


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 1,  biol rep 3

description:
Library name: sample 52
Column name in all_figure_2_donor_002.gene_counts.tsv: sample.28l3'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 1,  biol rep 2

description:
Library name: sample 50
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs3'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 3,  biol rep 1

description:
Library name: sample 49
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs2'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 3,  biol rep 2

description:
Library name: sample 51
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs3'


title: ID4, CHLI-Tissue, Male, Young

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

description:
Library name: CHLI-Tissue
Column name in raw_counts.csv: CHLI-Tissue

data_processing:
Adapter trimming via Skewer (phred > 10)
Read alignment via Kallisto
Quality control monitoring via FastQC and MultiQC
Assembly: human transcriptome from Ensembl: GRCh38, release-111
Supplementary files format and content: csv text file includes raw counts for each sample

source_name: vastus lateralis muscle

extract_protocol:
TruSeq Stranded Total RNA Library Prep Gold Kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol and sequenced with 150-bp paired-end reads

value: vastus lateralis muscle

tag: Sex

value: Male

tag: age

value: Young


title: ID1, ANER-Tissue, Male, Young

description:
Library name: ANER-Tissue
Column name in raw_counts.csv: ANER-Tissue


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), Lane 1,  biol rep 1

description:
Library name: sample 48
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs2'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 3,  biol rep 3

description:
Library name: sample 47
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs1'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 1,  biol rep 3

description:
Library name: sample 46
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbs1'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 1,  biol rep 2

description:
Library name: sample 44
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl3'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 3,  biol rep 2

description:
Library name: sample 45
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl3'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 3,  biol rep 3

description:
Library name: sample 41
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl1'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 1,  biol rep 2

description:
Library name: sample 38
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s3'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 3,  biol rep 2

description:
Library name: sample 39
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s3'


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain_and_BACH2_OE (28s_BACH2), biol rep 2

description:
Library name: sample 58
Column name in all.gene_counts.tsv: sample.28s.bach2_2


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 1,  biol rep 3

description:
Library name: sample 40
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl1'


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 2

description:
Library name: sample 55
Column name in all.gene_counts.tsv: sample.28s_2


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 1,  biol rep 3

description:
Library name: sample 34
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s1'

value: CD22-targeted-long-linker-CD28-CD3z CAR


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 3,  biol rep 3

description:
Library name: sample 35
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s1'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 1,  biol rep 1

description:
Library name: sample 36
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s2'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 3,  biol rep 2

description:
Library name: sample 33
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28l2'


title: Figure 2,  Donor 002,  CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), Lane 3,  biol rep 1

description:
Library name: sample 37
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28s2'


title: Figure 3, Donor 26, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 3

description:
Library name: sample 56
Column name in all.gene_counts.tsv: sample.28s_3


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 3,  biol rep 1

description:
Library name: sample 31
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28l1'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 1,  biol rep 1

description:
Library name: sample 30
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28l1'


title: Figure 2, Donor 003, untransduced (ntd), biol rep 3

description:
Library name: sample 29
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_ntd3'


title: Figure 2, Donor 003, untransduced (ntd), biol rep 2

description:
Library name: sample 28
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_ntd2'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), Lane 1,  biol rep 2

description:
Library name: sample 32
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.28l2'


title: Figure 2, Donor 003, untransduced (ntd), biol rep 1

description:
Library name: sample 27
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_ntd1'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 3

description:
Library name: sample 26
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbs3'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 1

description:
Library name: sample 24
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbs1'


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), biol rep 3

description:
Library name: sample 23
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbl3'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 2

description:
Library name: sample 25
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbs2'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 3,  biol rep 1

description:
Library name: sample 43
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl2'


title: Figure 2,  Donor 002,  CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), Lane 1,  biol rep 1

description:
Library name: sample 42
Column name in all_figure_2_donor_002.gene_counts.tsv:  'sample.bbl2'


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), biol rep 2

description:
Library name: sample 22
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbl2'


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBl), biol rep 1

description:
Library name: sample 21
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_bbl1'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 3

description:
Library name: sample 20
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_28s3'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 1

description:
Library name: sample 18
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_28s1'


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), biol rep 3

description:
Library name: sample 17
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_28l2'


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), biol rep 2

description:
Library name: sample 16
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_28l1'


title: Figure 2, Donor 003, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 2

description:
Library name: sample 19
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_001_28s2'


title: Figure 2, Donor 001, Untransduced (ntd), biol rep 2

description:
Library name: sample 13
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_ntd2'


title: Figure 2, Donor 001, Untransduced (ntd), biol rep 1

description:
Library name: sample 12
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_ntd1'


title: Figure 2, Donor 001, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 3

description:
Library name: sample 8
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbl3'


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 1

description:
Library name: sample 9
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbs1'


title: Figure 2, Donor 001, Untransduced (ntd), biol rep 3

description:
Library name: sample 14
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_ntd3'


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 2

description:
Library name: sample 10
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbs2'


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 2

description:
Library name: sample 4
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_28s1'


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 3

description:
Library name: sample 5
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_28s2'


title: Figure 2, Donor 001, CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), biol rep 1

description:
Library name: sample 1
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_28l1'


title: Figure 2, Donor 001, CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), biol rep 2

description:
Library name: sample 2
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_28l2'


title: DU145,USF1 shRNA R2

city: Shanghai

first: Dandan

last: Dong

address: 130 Dongan Road, Xuhui

country: China

institute: Fudan University Shanghai Cancer Center

description: Library name: sample44

data_processing:
ChIP-seq: FastQC (v.0.11.9) was for quality assessment of raw data. Adapters and short reads were removed using TrimGalore (v.0.6.7, RRID: SCR_011847). The trimmed reads were mapped into the human genome hg38 using Bowtie2 (v.2.2.5) with the default parameters. Low-quality alignment reads were excluded via SAMtools (v.1.13) via applying the parameters “-q 30 -F 3844.” Duplicate reads were identified and removed using the Picard toolkit (v.2.25.1, RRID: SCR_006525). MACS2 (v.2.1.4) was employed for peak calling with default parameters. We utilized the Integrated Genome Viewer (IGV, v.2.12.3) for peak visualization and analysis.   RNA-seq: Raw sequence data were preprocessed using FastQC (v.0.11.9) for quality assessment. AdapterRemoval (v.2.3.2) was used for quality trimming and adapter removal with default parameters. The processed reads were aligned to the human genome (hg38) using STAR (v.2.7.9a) and the aligned BAM files were sorted using SAMtools (v.1.13). HTSeq (v.0.13.5) was employed to quantify aligned sequencing reads against UCSC gene annotation with the parameters “-s reverse, -i gene_id”. DESeq2 (v.1.30.1) was used for DEG analysis from the read count matrix.
Assembly: hg38
Supplementary files format and content: bigwig for ChIP-seq data

extract_protocol:
The immunoprecipitated and input DNA was purified using the MinElute PCR Purification Kit (#28006, Qiagen). Total RNA was isolated using the EZ-10 DNAaway RNA Mini-Preps Kit (#B618133, Sangon Biotech).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (#E7103L, NEB) according to the manufacturer’s instructions. RNA-seq libraries were prepared using the Stranded mRNA-seq Lib Prep Module (RK20349, Abclonal).

tag: cell line

value: USF1 knockdown


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 3

description:
Library name: sample 11
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbs3'


title: DU145,USF1 shRNA R1

description: Library name: sample43


title: DU145,Control shRNA R2-1

description: Library name: sample42


title: Figure 2, Donor 001, CD22_targeted_short_linker_CAR_with_CD28-CD3z_signaling_domain (28s), biol rep 1

description:
Library name: sample 3
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_28l3'


title: LNCaP,USF1 shRNA R2

description: Library name: sample40

value: LNCaP


title: DU145,Control shRNA R1-1

description: Library name: sample41


title: PC3,NOL10 siRNA R1

description: Library name: sample37

value: NOL10 knockdown


title: LNCaP,USF1 shRNA R1

description: Library name: sample39


title: PC3,Control siRNA R1

description: Library name: sample35


title: PC3,Control siRNA R2

description: Library name: sample36


title: PC3,NOL10 siRNA R2

description: Library name: sample38


title: 22Rv1,NOL10 siRNA R1

description: Library name: sample33


title: 22Rv1,NOL10 siRNA R2

description: Library name: sample34


title: Figure 2, Donor 003, CD22_targeted_long_linker_CAR_with_CD28-CD3z_signaling_domain (28l), biol rep 1

description:
Library name: sample 15
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv: sample.donor_003_28s3'


title: 22Rv1,Control siRNA R2

description: Library name: sample32


title: 22Rv1,Control siRNA R1

description: Library name: sample31


title: DU145,NOL10 shRNA R2

description: Library name: sample30


title: Figure 2, Donor 001, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 2

description:
Library name: sample 7
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbl2'


title: Figure 2, Donor 001, CD22_targeted_long_linker_CAR_with_4-1-BB-CD3z_signaling_domain (BBs), biol rep 1

description:
Library name: sample 6
Column name in all_figure_2_donor_001_and_003.gene_counts.tsv:  'sample.donor_003_bbl1'


title: DU145,Control shRNA R2-2

description: Library name: sample28


title: DU145,NOL10 shRNA R1

description: Library name: sample29


title: LNCaP,NOL10 shRNA R2

description: Library name: sample26


title: DU145,Control shRNA R1-2

description: Library name: sample27


title: LNCaP,NOL10 siRNA R2

description: Library name: sample22


title: LNCaP,Control shRNA R2

description: Library name: sample24


title: LNCaP,NOL10 siRNA R1

description: Library name: sample21


title: LNCaP,Control shRNA R1

description: Library name: sample23


title: LNCaP,Control siRNA R2

description: Library name: sample20


title: LNCaP,Control siRNA R1

description: Library name: sample19

library_source: genomic

molecule: genomic DNA


title: patient4,H3K27ac

description: Library name: sample18

source_name: prostate

value: prostate


title: patient3,H3K27ac

description: Library name: sample17


title: patient2,H3K27ac

description: Library name: sample16


title: patient4,H3K4me3

description: Library name: sample14


title: patient2,H3K4me3

description: Library name: sample12


title: patient1,H3K4me3

description: Library name: sample11


title: patient3,H3K4me3

description: Library name: sample13


title: patient3,H3K4me1

description: Library name: sample9


title: VCaP,H3K27ac

description: Library name: sample6

value: VCaP


title: patient4,H3K4me1

description: Library name: sample10


title: VCaP,H3K4me3

description: Library name: sample4


title: LNCaP,H3K4me3

description: Library name: sample3


title: patient2,H3K4me1

description: Library name: sample8


title: LNCaP,H3K27ac

description: Library name: sample5


title: VCaP,H3K4me1

description: Library name: sample2


title: patient1,H3K4me1

description: Library name: sample7


title: LNCaP,NOL10 shRNA R1

description: Library name: sample25


title: blood, patient_108

city: Foligno

first: Nicola

last: Baldoni

state: PG

address: Via Maestà Formica, 12

country: Italy

institute: IRCCS Hospital San Raffaele

description: Library name: 96

data_processing:
Sequencing adapters and low-quality bases were removed using Trimmomatic (v0.39).
Quality of raw sequencing data was assessed using MultiQC version 1.9.
Reads were aligned to the GRCh38 using STAR (v2.5.3a) with default parameters.
Gene-level read counts were obtained using featureCounts (v1.6.4).
Assembly: The human genome assembly GRCh38, with Gencode release 43 and Ensembl release 108 annotations.
the analysis involved selecting the top 5000 most variable genes, which were then used in MOFA for multi-omics analysis.
Supplementary files format and content: CSV format with genes as rows and samples as columns include RNA-Seq RPKM values

source_name: blood

extract_protocol:
RNA was extracted from whole blood collected in in PAXgene® Blood RNA Tube (BD Biosciences) using the Maxwell® 16 LEV simplyRNA Blood Kit (Promega) and the AS2000 Maxwell® 16 Instrument (Promega).
NGS libraries were then constructed utilizing the TruSeq Stranded mRNA (Illumina) protocol, which permits library preparation starting from 50-100ng of total RNA.

value: blood

value: blood cells


title: blood, patient_106

description: Library name: 9


title: LNCaP,H3K4me1

description: Library name: sample1


title: blood, patient_105

description: Library name: 84


title: blood, patient_100

description: Library name: 73


title: blood, patient_99

description: Library name: 71


title: blood, patient_107

description: Library name: 93


title: blood, patient_103

description: Library name: 76


title: blood, patient_97

description: Library name: 69


title: blood, patient_96

description: Library name: 65


title: blood, patient_93

description: Library name: 44


title: blood, patient_91

description: Library name: 4


title: patient1,H3K27ac

description: Library name: sample15


title: blood, patient_92

description: Library name: 41


title: blood, patient_87

description: Library name: 381


title: blood, patient_90

description: Library name: 39


title: blood, patient_89

description: Library name: 383


title: blood, patient_83

description: Library name: 364


title: blood, patient_88

description: Library name: 382


title: blood, patient_80

description: Library name: 351


title: blood, patient_102

description: Library name: 75


title: blood, patient_101

description: Library name: 74


title: blood, patient_86

description: Library name: 380


title: blood, patient_85

description: Library name: 366


title: blood, patient_82

description: Library name: 36


title: blood, patient_79

description: Library name: 35


title: blood, patient_104

description: Library name: 8


title: blood, patient_75

description: Library name: 336


title: blood, patient_78

description: Library name: 349


title: blood, patient_73

description: Library name: 334


title: blood, patient_74

description: Library name: 335


title: blood, patient_71

description: Library name: 332


title: blood, patient_76

description: Library name: 337


title: blood, patient_77

description: Library name: 34


title: blood, patient_68

description: Library name: 317


title: blood, patient_98

description: Library name: 7


title: blood, patient_70

description: Library name: 331


title: blood, patient_69

description: Library name: 318


title: blood, patient_66

description: Library name: 315


title: blood, patient_67

description: Library name: 316


title: blood, patient_84

description: Library name: 365


title: blood, patient_64

description: Library name: 313


title: blood, patient_63

description: Library name: 301


title: blood, patient_81

description: Library name: 352


title: blood, patient_65

description: Library name: 314


title: blood, patient_61

description: Library name: 299


title: blood, patient_62

description: Library name: 300


title: blood, patient_58

description: Library name: 285


title: blood, patient_60

description: Library name: 298


title: blood, patient_59

description: Library name: 297


title: blood, patient_57

description: Library name: 284


title: blood, patient_55

description: Library name: 282


title: blood, patient_72

description: Library name: 333


title: blood, patient_54

description: Library name: 281


title: blood, patient_53

description: Library name: 28


title: blood, patient_56

description: Library name: 283


title: blood, patient_50

description: Library name: 267


title: blood, patient_52

description: Library name: 269


title: blood, patient_47

description: Library name: 262


title: blood, patient_49

description: Library name: 266


title: blood, patient_51

description: Library name: 268


title: blood, patient_43

description: Library name: 252


title: blood, patient_44

description: Library name: 255


title: blood, patient_45

description: Library name: 257


title: blood, patient_46

description: Library name: 258


title: blood, patient_42

description: Library name: 239


title: blood, patient_40

description: Library name: 237


title: blood, patient_39

description: Library name: 236


title: blood, patient_41

description: Library name: 238


title: blood, patient_37

description: Library name: 222


title: blood, patient_36

description: Library name: 221


title: blood, patient_35

description: Library name: 220


title: blood, patient_33

description: Library name: 218


title: blood, patient_31

description: Library name: 207


title: blood, patient_30

description: Library name: 206


title: blood, patient_34

description: Library name: 219


title: blood, patient_29

description: Library name: 205


title: blood, patient_27

description: Library name: 196


title: blood, patient_28

description: Library name: 204


title: blood, patient_26

description: Library name: 182


title: blood, patient_24

description: Library name: 179


title: blood, patient_22

description: Library name: 175


title: blood, patient_23

description: Library name: 178


title: blood, patient_25

description: Library name: 181


title: blood, patient_20

description: Library name: 167


title: blood, patient_19

description: Library name: 166


title: blood, patient_18

description: Library name: 160


title: blood, patient_21

description: Library name: 168


title: blood, patient_16

description: Library name: 157


title: blood, patient_17

description: Library name: 16


title: blood, patient_14

description: Library name: 152


title: blood, patient_15

description: Library name: 153


title: blood, patient_10

description: Library name: 138


title: blood, patient_13

description: Library name: 151


title: blood, patient_11

description: Library name: 139


title: blood, patient_9

description: Library name: 135


title: blood, patient_8

description: Library name: 127


title: blood, patient_12

description: Library name: 150


title: blood, patient_6

description: Library name: 112


title: blood, patient_7

description: Library name: 116


title: blood, patient_5

description: Library name: 110


title: blood, patient_4

description: Library name: 11


title: blood, patient_3

description: Library name: 102


title: DOPAC, replicate 3, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: DOPAC_3

data_processing:
The raw reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9).
Filtered reads were mapped against the mm10 assembly of the Mus musculus genome (National Center for Biotechnology Information) using hisat2 (Version 2.2.1).
Assembly: mm10
Supplementary files format and content: Raw count matrix with rows as genes and columns as samples

organism: Mus musculus

source_name: spleen

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Full-length cDNA was generated using SMART-Seq HT Kit (Takara), paired-end DNA libraries was generated and indexed using NexteraTM XT Library Prep Kit and then NexteraTM XT Index Kit.

value: spleen

value: CD8+ T

value: lymphocyte

value: DOPAC


title: DOPAC, replicate 2, RNA_seq

description: Library name: DOPAC_2

value: WT


title: blood, patient_2

description: Library name: 10


title: DOOAC, replicate 1, RNA_seq

description: Library name: DOPAC_1


title: blood, patient_1

description: Library name: 1


title: Parse whole-transcriptome single-cell RNA-seq for all HCC1806 and MDA-MB-231 samples

city: Austin

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keeton St.

department: Biomedical Engineering

institute: The University of Texas at Austin

description:
Library name: CMDuo_SingleCell_WholeTranscriptome
whole-transcriptome sequencing library, from 7 sublibraries

library_source: transcriptomic single cell

data_processing:
All sequence alignment and sample annotation steps were performed with Parse Bioscience pipeline (v 1.3.1) in a Linux environment running Python version 3.10. Genome annotation and reference files containing eGFP and mCherry sequences were concatenated to the most recent human genome build (GRCh38, release 111). A Parse reference genome was built from the concatenated genome and annotation files. Each Parse whole transcriptome sublibrary was aligned to the built genome, then aligned sublibraries were combined for analysis.
Quality control steps were performed on the unfiltered outputs of the Parse pipeline using Seurat (v5.1.0). Cells in retained for analysis had total RNA counts between 1,500-100,000 genes, total feature counts between 800-50,000 counts, and mitochondrial percent between 2-18%. Cells were split by cell line and data from each cell line was independently normalized using a log transformation.
Barcodes were assigned to each cell using a probabilistic model accounting for sequencing noise in the data using the raw outputs from the Parse CRISPR detect pipeline. Assigned barcodes were first filtered to match the expected cell line, to have at least 3 reads per barcode in a cell, and to ensure that detected barcodes is present in at least 3 cells at this threshold within a sample. After this minimal filtering, the expected noise generated from each barcode was calculated based on overall barcode abundance in the population and the number of reads per cell. A negative binomial model was used to determine the probability that a barcode within a cell is noise. Barcodes with a p-adjusted value <= 0.05 were assigned to cells. Cells with multiple instances of green barcodes or multiple instances of red barcodes were indicated with underscores, e.g., gXXX_gYYY. Once barcodes were assigned, clone color was assigned as green, red, or fusion by presence of ‘g’ and/or ‘r’ in the assigned barcode name.
Assembly: GRCh38, release 111
Supplementary files format and content: count_matrix.mtx, cell_metadata.csv, and all_genes.csv are the unfiltered outputs from the Parse whole-transriptome pipeline from all samples combined (DGE_unfiltered).
Supplementary files format and content: count_matrix_CR.mtx, cell_metadata_CR.csv, and all_guides.csv are the unfiltered outputs from the Parse CRISPR detect pipeline from all samples combined (guide_RNAs_unfiltered).
Supplementary files format and content: sample-list.txt contains loading positions for each sample for the first stage of the Parse protocol.
Supplementary files format and content: CMDuo_seurat_raw.rds an unfiltered, unannotated Seurat object forged from the Parse whole-transcriptome outputs for all samples and both cell lines.
Supplementary files format and content: CMDuo_seurat_qc_barcodeAnnotated_HCC1806_samples.rds is a filtered and annotated Seurat object for containing all samples from the CMDuo-barcoded HCC1806 cell line experiment.
Supplementary files format and content: CMDuo_seurat_qc_barcodeAnnotated_MDAMB231_samples.rds is a filtered and annotated Seurat object for containing all samples from the CMDuo-barcoded MDA-MB-231 cell line experiment.

source_name: triple-negative breast cancer cell line

growth_protocol: For each CMDuo-barcoded cell line, five replicate plates were seeded, containing 1e6 cells each. HCC1806 cells were cultured in RPMI with 2.05 mM L-glutamine (HyClone, SH30027.01), supplemented with 10% FBS (Sigma, F0926-500mL). MDA-MB-231 cells were cultured in high glucose DMEM (Sigma D5796) supplemented with 10% FBS (Sigma, F0926-500mL) and 1X penicillin-streptomycin (ThermoFisher, 15140122). For each cell line, one plate was fixed for Parse scRNA-seq 2 days after seeding (“initial”), the other 4 plates were expanded in culture as independent replicates for one week before the first FACS enrichment for fusion cells.

extract_protocol:
Single-cell RNA preparation was performed according to manufacturer guidelines from Parse outlined in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025).
Library prep was performed according to manufacturer guidelines from Parse outlined in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025). As the WT kit can process 100,000 cells, samples from both cell lines were prepared with the same kit. For each cell line, the ‘initial’ sample was split over 4 wells targeting 13,000 cells total, each of the four ‘pre-sort’ samples were split over 3 wells targeting 6,250 cells per sample, and each of the sorted control and fusion-enriched samples received its own well, targeting 1500 cells per sample. 8 identical sublibraries were prepared, but one sublibrary (sublibrary 5) was lost during preparation, adjusting the expected cell number to 87,500 total and 11,375, 5,469, and 1312 per sample per cell line, respectively. ClonMapper Duo gRNA barcodes were amplified from sublibrary cDNA according to manufacture instructions for CRISPR Sequencing Library Preparation in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025). Whole transcriptome and CRISPR detect (CMDuo barcode) libraries were amplified separately from cDNA and sequenced independently across 8 sublibraries each. Whole transcriptome and CRISPR Detect sublibraries were sequenced at the UT Austin Genomic Sequencing and Analysis on a NovaSeq 6000 (S2 flow cell, paired-end, 200 cycles). 500e6 reads were targeted for each WT sublibrary and 50e6 reads for each CRIPSR Detect sublibrary, producing 41,973 mean reads per cell across transcriptomic libraries and 3,238 means reads per cell in the combined CRISPR Detect sublibraries.

treatment_protocol: At the time of sorting, 0.5e6 barcoded cells were fixed for Parse scRNA-seq fixation and 0.5e6 cells were pelleted for DNA and targeted barcode sequencing. These cells comprise the “pre-sort” samples. The remaining cells were FACS sorted for fusion cells (both GFP+ and mCherry+ cells) and control cells (single GFP+ or single mCherry+). Sorted cells were allowed to recover from cell sorting and expanded before undergoing repeat rounds of cell sorting until fusion populations were > 50% pure, then “fusion-enriched” and “control” cells were prepped for scRNA-seq and DNA extraction. From fixation of the “initial” timepoint to the time at which “fusion-enriched” and parallel “control” cells were fixed for scRNA-seq, HCC1806 cells underwent 3 enrichment sorts over 35 days and MDA-MB-231 underwent 4 enrichment sorts over 50 days.

value: triple-negative breast cancer cell line

value: cancer cell line


title: Parse CRISPR Detect single-cell barcode detection for all HCC1806 and MDA-MB-231 samples

description:
Library name: CMDuo_SingleCell_CRISPRDetectBarcodes
CRISPR detect sequencing library, from 7 sublibraries

library_source: other

molecule: other


title: Control, replicate 2, RNA_seq

description: Library name: Control_2

value: Control


title: Targeted barcode sequencing for FACS sorted fusion-enriched MDA-MB-231 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_4_fusion
targeted ClonMapper barcode sequencing from genomic DNA

data_processing:
The results of targeted barcode sequencing performed on bulk DNA extracted from each sample were combined into early and late timepoint groups for each cell line, with the early group containing the initial and pre-sort samples, and the fusion-enriched and control samples in the late group. The set of barcodes in each group was determined with pycashier56 (version 2024.1001+d20240221) (https://github.com/brocklab/pycashier/), setting the Levenshtein distance to 2 and the clustering ratio to 1. Post-processing on the pycashier outputs was performed to remove noisy sequences detected in both cell lines and ensure a minimum Levenshtein distance of 2 between all pairs of barcodes within each cell line. If any similar barcodes were detected, they were collapsed into the more abundant sequence. Barcode color assignment was performed by matching the first 5 nucleotides of each detected sequence to the designed index sequences (GFP = [’GACAA’, ‘GCTGT’, ‘ATCGC’, ‘ACGCA’]; mCherry = [’CATCC’, ‘CGAGA’, ‘TAGTG’, ‘TCAAC’]) and allowing a Levenshtein distance of 1 to account for sequencing errors. Unique nucleotide barcodes were assigned names according to their fluorescence reporter and their relative abundance in the ranking abundance, i.e. g001 and r001 represent the most abundant CMDuo-green and CMDuo-red clones in the early timepoint samples via targeted sequencing. Named barcodes and sequences were formatted into a reference list for input to the Parse CRISPR Detect alignment pipeline (v 1.3.1), setting the barcode name as the ‘Guide_Name’, the detected sequence as both the ‘Guide_Sequence’ and ‘Target_Gene’, and including flanking regions around the barcode as the ‘Prefix’ and ‘Suffix’ (ATCTTGTGGAAAGGACGAAACACCG; GTTTTAGAGCTAGAAATAGCAAGTT).
Supplementary files format and content: formatted_guide_list_hashed.csv contains the set of barcodes detected with pycashier from bulk sequencing, formatted for input into the Parse CRISPR detect pipeline

extract_protocol:
DNA was extracted from frozen cell pellets containg ~0.5e6 cells using the Invitrogen PureLink Genomic DNA kit (ThermoFisher, K182001) according to manufacturer’s instructions.
Amplification steps were performed following published ClonMapper barcode amplification procedures (up-to-date web protocol: https://docs.brocklab.com/clonmapper/protocol/, published protocol:https://doi.org/10.1007/978-1-0716-1811-0_8). Briefly, DNA was quantified with NanoDrop, then 1 µg of DNA was loaded into the first PCR reaction. Amplified DNA was cleaned with SPRI beads, then 4 ng of cleaned stage 1 product was loaded into the next PCR reaction to add unique Illumina i7/i5 indices to each sample. Stage 2 samples were cleaned with SPRI beads, then quantified Qubit using the 1X dsDNA high-sensitivity assay (ThermoFisher, Q33231). Illumina indexed samples were run on a NovaSeq 6000 (S1 flow cell, single read, 100 cycles) by the UT Genome Analysis and Sequencing Facility, targeting 100e6 reads for all samples and biasing more reads toward the earlier timepoint samples. ∼14e6 reads were obtained for each initial population, ∼6e6 for each pre-sort sample, and ∼3e6 for each control and fusion sample in each cell line.

value: fusion-enriched


title: Targeted barcode sequencing for FACS sorted fusion-enriched MDA-MB-231 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_3_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for FACS sorted fusion-enriched MDA-MB-231 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_2_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: Control, replicate 1, RNA_seq

description: Library name: Control_1


title: Meibomian glands, transgene, replicate 2

city: New York

first: Sarah

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
For data analysis, reads were mapped to GRCm38/mm10. Salmon (v0.9.1) was used to count data against the transcriptome defined inGencodevM18. Wethen annotated and summarized the transcriptome count data to the gene level withtximeta3and performed further annotation withbiomaRt (v0.7.0). Normalizations and statistical analyses were carried out withDESeq2 (v1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: Normalized counts for each sample

source_name: Meibomian glands

extract_protocol:
RNA was extracted using the Qiagen All Prep DNA/RNA FFPE Kit according to the manufacturer’s instructions. 50ng RNA from each laser-captured sample was used for RNA-seq library construction.
RNA-seq library construction were prepared with Trio RNA-Seq™ library preparation kit from Nugene

value: Meibomian glands

value: K5-rtTA tetO-GLI2{delta}N


title: Targeted barcode sequencing for FACS sorted fusion-enriched MDA-MB-231 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_1_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for FACS sorted control MDA-MB-231 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_4_ctrl
targeted ClonMapper barcode sequencing from genomic DNA

value: sort-control


title: Meibomian glands, transgene, replicate 3


title: Meibomian glands, wildtype, replicate 3

value: control; wild type


title: Targeted barcode sequencing for FACS sorted control MDA-MB-231 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_2_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: Meibomian glands, wildtype, replicate 1


title: Targeted barcode sequencing for FACS sorted control MDA-MB-231 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_1_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for FACS sorted control MDA-MB-231 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_3_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: Rat embryonic cortical cells at E18

city: Tokyo

first: Ikuo

middle: K

last: Suzuki

address: Bunkyo-ku, Hongo7-3-1

country: Japan

institute: The University of Tokyo

description:
Library name: Sample3
Rat embryonic cortical cells at E18

data_processing:
Read data generated from samples labeled with Cell Multiplexing Oligo were processed with cellranger v6.0.1 with “multi” option.
Assembly: mRatBN7.2
Supplementary files format and content: Cellranger output, tab-delimitted barcodes, features, and matrix files.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Cerebral cortex

growth_protocol: Freshly prepared primary rat cortical cells

extract_protocol:
RNA extraction was integrated in "library construction protocol" process.
Whole-cell suspensions harvested from the expansion culture were pelleted and were subjected to Cell Multiplexing Oligo labeling.  Alternatively, samples for analysis were cryopreserved as follows: whole-cell suspensions harvested from the expansion culture were pelleted and were resuspended in Cell Banker Type 1 Plus for cryopreservation at −80˚C.  For Cell Multiplexing Oligo labeling, after thawing in the water bath at 37℃ if needed, collected cells were resuspended in Cell Multiplexing Oligo solution and were incubated for 5 minutes at room temperature.  After the incubation, cells were washed with 1% BSA (SIGMA, A1519)-PBS (−) and were collected by centrifugation at 200g for 10 minutes.  Collected cells were resuspended in 1% BSA-PBS (−) containing anti-TRA-1-85 antibody (BD Bioscience, 563302, 1:20) and placed on ice for 30 minutes in the dark.  Then, the cells were washed with PBS once and were resuspended in 1% BSA-PBS (−) containing 3 μM DRAQ7 (abcam, ab109202).  To isolate live human cells, TRA-1-85 (+) DRAQ7(−) cells were sorted into DMEM/F12 (GIBCO, 10565-018) + 1% BSA by FACS Aria III.  Sorted cells were subjected to the subsequent library construction using 10X Genomics Single Cell 3’ Kit v. 3.1, followed by sequencing on an Illumina NovaSeq 6000 platform.  All steps were performed in accordance with the manufacturer's instructions.

treatment_protocol: Rat cortical tissues are dissociated with papaine and washed with PBS

value: Cerebral cortex

value: wildtype


title: Meibomian glands, wildtype, replicate 2


title: Targeted barcode sequencing for pre-sort MDA-MB-231 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_4_presort
targeted ClonMapper barcode sequencing from genomic DNA

value: pre-sort


title: Targeted barcode sequencing for pre-sort MDA-MB-231 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_2_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for pre-sort MDA-MB-231 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_3_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: Rat embryonic cortical cells at E14

description:
Library name: Sample1
Rat embryonic cortical cells at E14


title: Control, replicate 3, RNA_seq

description: Library name: Control_3


title: rc_p26_tum_IgG_3

city: Moscow

first: Ekaterina

last: Serebrovskaya

address: Ostrovityanova st., 1

country: Russia

institute: Russian National Research Medical University

description: Library name: rc_p26_tum_IgG_3

data_processing:
The alignment of samples was performed using STAR with GRCh38.p13 genome assembly and GRCh38.109 gene annotation, filtering out multimappers. The quality of aligned reads was evaluated using Qualimap 2 software.
Gene quantification was performed using featureCounts from the Subread package. Resulting table of counts was used for differential expression (DE) analysis. Samples with zero counts, and samples with less than 50% reads aligned to exons were excluded.
Assembly: GRCh38.p13 genome assembly and GRCh38.109 gene annotation

source_name: tumor

extract_protocol:
Trizol
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TakaraBio, 634893)

value: tumor


title: rc_p26_tum_IgG_2

description: Library name: rc_p26_tum_IgG_2


title: Targeted barcode sequencing for pre-sort MDA-MB-231 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_1_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: Rat embryonic cortical cells at E16

description:
Library name: Sample2
Rat embryonic cortical cells at E16


title: rc_p26_tum_IgG_1

description: Library name: rc_p26_tum_IgG_1


title: Targeted barcode sequencing for initial MDA-MB-231 sample

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_MDAMB231_0_initial
targeted ClonMapper barcode sequencing from genomic DNA

value: initial


title: rc_p26_tum_IgA

description: Library name: rc_p26_tum_IgA


title: rc_p25_tum_IgG_3

description: Library name: rc_p25_tum_IgG_3


title: Targeted barcode sequencing for FACS sorted fusion-enriched HCC1806 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_3_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for FACS sorted fusion-enriched HCC1806 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_4_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: Meibomian glands, transgene, replicate 1


title: rc_p25_tum_IgG_2

description: Library name: rc_p25_tum_IgG_2


title: Targeted barcode sequencing for FACS sorted fusion-enriched HCC1806 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_1_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p25_tum_IgA_3

description: Library name: rc_p25_tum_IgA_3


title: Targeted barcode sequencing for FACS sorted control HCC1806 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_3_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p25_tum_IgG_1

description: Library name: rc_p25_tum_IgG_1


title: Targeted barcode sequencing for FACS sorted control HCC1806 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_2_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for FACS sorted control HCC1806 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_1_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p23_tum_IgG_1

description: Library name: rc_p23_tum_IgG_1


title: Targeted barcode sequencing for pre-sort HCC1806 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_4_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p23_tum_IgA_2

description: Library name: rc_p23_tum_IgA_2


title: Targeted barcode sequencing for pre-sort HCC1806 sample, replicate 3

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_3_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p23_tum_IgA_1

description: Library name: rc_p23_tum_IgA_1


title: Targeted barcode sequencing for pre-sort HCC1806 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_2_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p22_tum_IgG_1

description: Library name: rc_p22_tum_IgG_1


title: rc_p22_tum_IgG_2

description: Library name: rc_p22_tum_IgG_2


title: Targeted barcode sequencing for pre-sort HCC1806 sample, replicate 1

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_1_presort
targeted ClonMapper barcode sequencing from genomic DNA


title: Targeted barcode sequencing for initial HCC1806 sample

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_0_initial
targeted ClonMapper barcode sequencing from genomic DNA


title: 769-P_sgKDM5C_5

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Hospital Freiburg

description: Library name: 769-P_sgKDM5C_5

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using trimmomatic (v 0.38) (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:3 TRAILING:10 MINLEN:25)
Sequences were aligned using the STAR aligner (v 2.5.2b) (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --quantMode GeneCounts)
Raw counts were generated using STAR --quantMode GeneCounts
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file of raw counts for each sample

source_name: kidney

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey Nagel).
RNA libraries were prepared using the Illumina TruSeq Stranded RNA library preparation kit.

value: kidney


title: rc_p22_tum_IgA_1

description: Library name: rc_p22_tum_IgA_1


title: Targeted barcode sequencing for FACS sorted fusion-enriched HCC1806 sample, replicate 2

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_2_fusion
targeted ClonMapper barcode sequencing from genomic DNA


title: rc_p21_tum_IgA

description: Library name: rc_p21_tum_IgA


title: 769-P_sgKDM5C_4

description: Library name: 769-P_sgKDM5C_4


title: A498_sgKDM5C_5

description: Library name: A498_sgKDM5C_5


title: rc_p21_tum_IgG

description: Library name: rc_p21_tum_IgG


title: Targeted barcode sequencing for FACS sorted control HCC1806 sample, replicate 4

description:
Library name: CMDuo_Bulk_TargetedBarcodeSequencing_HCC1806_4_ctrl
targeted ClonMapper barcode sequencing from genomic DNA


title: A498_sgKDM5C_4

description: Library name: A498_sgKDM5C_4


title: 769-P_sgCtrl

description: Library name: 769-P_sgCtrl

value: sgCtrl


title: rc_p20_tum_IgG

description: Library name: rc_p20_tum_IgG


title: rc_p20_tum_IgA

description: Library name: rc_p20_tum_IgA


title: rc_p23_tum_IgG_2

description: Library name: rc_p23_tum_IgG_2


title: rc_p25_tum_IgA_2

description: Library name: rc_p25_tum_IgA_2


title: rc_p19_tum_IgG

description: Library name: rc_p19_tum_IgG


title: rc_p19_tum_IgA

description: Library name: rc_p19_tum_IgA


title: CAKI-2_sgKDM5D_4

description: Library name: CAKI-2_sgKDM5D_4


title: rc_p18_tum_IgG_2

description: Library name: rc_p18_tum_IgG_2


title: CAKI-2_sgKDM5C_5

description: Library name: CAKI-2_sgKDM5C_5


title: CAKI-2_sgKDM5D_2

description: Library name: CAKI-2_sgKDM5D_2


title: CAKI-2_sgKDM5C_4

description: Library name: CAKI-2_sgKDM5C_4


title: rc_p18_tum_IgA_2

description: Library name: rc_p18_tum_IgA_2


title: rc_p18_tum_IgG_1_star

description: Library name: rc_p18_tum_IgG_1_star


title: CAKI-2_sgCtrl

description: Library name: CAKI-2_sgCtrl


title: rc_p22_tum_IgA_2

description: Library name: rc_p22_tum_IgA_2


title: rc_p17_tum_IgG

description: Library name: rc_p17_tum_IgG


title: rc_p18_tum_IgA_1_star

description: Library name: rc_p18_tum_IgA_1_star


title: rc_p17_tum_IgA

description: Library name: rc_p17_tum_IgA


title: rc_p16_tum_IgG1

description: Library name: rc_p16_tum_IgG1


title: A498_sgCtrl

description: Library name: A498_sgCtrl


title: 786-O_sgKDM5C_4

description: Library name: 786-O_sgKDM5C_4


title: rc_p12_tum_IgG

description: Library name: rc_p12_tum_IgG


title: 786-O_sgKDM5C_5_sgKDM5D_4_rep3

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_4_rep3


title: rc_p12_tum_IgA

description: Library name: rc_p12_tum_IgA


title: Lcp9_tum_IgG_2

description: Library name: Lcp9_tum_IgG_2


title: rc_p16_tum_IgA

description: Library name: rc_p16_tum_IgA


title: 786-O_sgKDM5C_5_sgKDM5D_4_rep2

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_4_rep2


title: 786-O_sgKDM5C_5_sgKDM5D_2_rep3

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_2_rep3


title: Lcp9_tum_IgG_1

description: Library name: Lcp9_tum_IgG_1


title: 786-O_sgKDM5C_5_sgKDM5D_2_rep2

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_2_rep2


title: Lcp9_tum_IgA_2

description: Library name: Lcp9_tum_IgA_2


title: 786-O_sgKDM5C_5_sgKDM5D_2_rep1

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_2_rep1


title: 786-O_sgKDM5D_2

description: Library name: 786-O_sgKDM5D_2


title: Lcp8_tum_IgG_2

description: Library name: Lcp8_tum_IgG_2


title: Lcp9_tum_IgA_1

description: Library name: Lcp9_tum_IgA_1


title: 786-O_sgKDM5D_4

description: Library name: 786-O_sgKDM5D_4


title: Lcp8_tum_IgG_1

description: Library name: Lcp8_tum_IgG_1


title: 786-O_sgKDM5C_4_sgKDM5D_4_rep2

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_4_rep2


title: 786-O_sgKDM5C_4_sgKDM5D_4_rep1

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_4_rep1


title: Lcp8_tum_IgA_2

description: Library name: Lcp8_tum_IgA_2


title: 786-O_sgKDM5C_5

description: Library name: 786-O_sgKDM5C_5


title: 786-O_sgKDM5C_4_sgKDM5D_2_rep3

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_2_rep3


title: 786-O_sgKDM5C_5_sgKDM5D_4_rep1

description: Library name: 786-O_sgKDM5C_5_sgKDM5D_4_rep1


title: 786-O_sgKDM5C_4_sgKDM5D_4_rep3

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_4_rep3


title: 786-O_sgCtrl

description: Library name: 786-O_sgCtrl


title: 786-O_sgKDM5C_4_sgKDM5D_2_rep2

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_2_rep2


title: Lcp8_tum_IgA_1

description: Library name: Lcp8_tum_IgA_1


title: Lcp7_tum_IgA

description: Library name: Lcp7_tum_IgA


title: Lcp12_tum_IgG

description: Library name: Lcp12_tum_IgG


title: 786-O_sgKDM5C_4_sgKDM5D_2_rep1

description: Library name: 786-O_sgKDM5C_4_sgKDM5D_2_rep1


title: Lcp12_tum_IgA

description: Library name: Lcp12_tum_IgA


title: Lcp_20_tum_IgG_2

description: Library name: Lcp_20_tum_IgG_2


title: Lcp_20_tum_IgG_1

description: Library name: Lcp_20_tum_IgG_1


title: 786-O_sgKDM5D_4_rep2

description: Library name: 786-O_sgKDM5D_4_rep2


title: 786-O_sgKDM5D_4_rep3

description: Library name: 786-O_sgKDM5D_4_rep3


title: Lcp_20_tum_IgA_2

description: Library name: Lcp_20_tum_IgA_2


title: Lcp_20_tum_IgA_1

description: Library name: Lcp_20_tum_IgA_1


title: 786-O_sgKDM5D_2_rep1

description: Library name: 786-O_sgKDM5D_2_rep1


title: Lcp_17_tum_IgG_2

description: Library name: Lcp_17_tum_IgG_2


title: 786-O_sgKDM5C_5_rep3

description: Library name: 786-O_sgKDM5C_5_rep3


title: Lcp7_tum_IgG

description: Library name: Lcp7_tum_IgG


title: Lcp_17_tum_IgG_1

description: Library name: Lcp_17_tum_IgG_1


title: 786-O_sgKDM5C_5_rep1

description: Library name: 786-O_sgKDM5C_5_rep1


title: Lcp_16_tum_IgG_2

description: Library name: Lcp_16_tum_IgG_2


title: Lcp_17_tum_IgA_1

description: Library name: Lcp_17_tum_IgA_1


title: 786-O_sgKDM5C_4_rep2

description: Library name: 786-O_sgKDM5C_4_rep2


title: Lcp_16_tum_IgG_1

description: Library name: Lcp_16_tum_IgG_1


title: 786-O_sgKDM5D_2_rep3

description: Library name: 786-O_sgKDM5D_2_rep3


title: Lcp_16_tum_IgA_2

description: Library name: Lcp_16_tum_IgA_2


title: Lcp_16_tum_IgA_1

description: Library name: Lcp_16_tum_IgA_1


title: Lcp_15_tum_IgG_2

description: Library name: Lcp_15_tum_IgG_2


title: 786-O_sgKDM5C_5_rep2

description: Library name: 786-O_sgKDM5C_5_rep2


title: 786-O_sgCtrl_rep1

description: Library name: 786-O_sgCtrl_rep1


title: 786-O_sgKDM5C_4_rep1

description: Library name: 786-O_sgKDM5C_4_rep1


title: 786-O_sgKDM5D_4_rep1

description: Library name: 786-O_sgKDM5D_4_rep1


title: exp3_786O_sgKDM5C_5_KDM5D

description: Library name: exp3_786O_sgKDM5C_5_KDM5D

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality sequences using Trim Galore (v 0.6.6) with default settings.
Sequences were aligned to UCSC hg19 using Bowtie2 (v 2.4.5) (parameters: --dovetail, --local, --very-sensitive-local, --no-unal, --no-mixed, --no-discordant, -I 10, -X 700). Spike-in sequences were aligned to UCSC dm6 for exp1 and exp2 and to E. coli NCBI K12 MG1655 for exp3.
BigWig files were generated using bamCoverage from deepTools (v 3.5.0)
Tag directories were generated using makeTagDirectory with the option -totalReads from Homer (v 4.11)
Peaks were called using Homer's findPeaks with -style histone and -C 0 and experimental samples were compared to the corresponding IgG control. Peaks with 4-fold more tags in the experimental sample compared to the control and cumulative Poisson p-value ≤ 0.0001 were kept, while peaks within blacklisted regions from ENCODE were excluded using intersectBed from BEDTools.
Unique and overlapping peaks were determined using Homer's mergePeaks with -d given.
Assembly: hg19
Supplementary files format and content: bigWig of coverage, peaks (.Clean.bed) (except for IgG controls)
Library strategy: CUT&RUN

extract_protocol:
Samples were processed following the EpiCypher® CUTANATM CUT&RUN Protocol (for histone PTMs, transcription factors (TFs), and chromatin regulators).
RNA libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit and NEBNext® Multiplex Oligos Set (New England Biolabs).

tag: antibody


title: Lcp_15_tum_IgG_1

description: Library name: Lcp_15_tum_IgG_1


title: Lcp_15_tum_IgA_2

description: Library name: Lcp_15_tum_IgA_2


title: exp3_786O_sgKDM5D_4_KDM5D

description: Library name: exp3_786O_sgKDM5D_4_KDM5D


title: Lcp_15_tum_IgA_1

description: Library name: Lcp_15_tum_IgA_1


title: 786-O_sgKDM5D_2_rep2

description: Library name: 786-O_sgKDM5D_2_rep2


title: 786-O_sgCtrl_rep2

description: Library name: 786-O_sgCtrl_rep2


title: exp3_786O_sgCtrl_KDM5D

description: Library name: exp3_786O_sgCtrl_KDM5D


title: exp3_786O_sgKDM5D_2_KDM5D

description: Library name: exp3_786O_sgKDM5D_2_KDM5D


title: Lcp_17_tum_IgA_2

description: Library name: Lcp_17_tum_IgA_2


title: HEC1B Abema replicate 2 (batch 1)

city: Boston

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw fastq data were aligned and preprocessed using the VIPER pipeline
Reads were aligned to hg19 using STAR v2.7.0f
Multimapping reads (mapq=0) were filtered out using samtools v1.19 and PCR duplicates removed with picard MarkDuplicates v2.21.8
Aligned read counts were extracted and analysed; differential expression analysis was performed with DESeq2 v1.40.2
Assembly: hg19

source_name: Endometrial Cancer

growth_protocol: ARK1 and ARK2 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 (Gibco Cat. #11875-093), 10% FBS (Sigma Cat. #F2442), and 1% penicillin/streptomycin (P/S) (Gibco Cat. #15140-122). HEC1B and AN3CA cells were grown in Minimum Essential Medium (MEM, Corning Cat. #10-010-CV), 10% FBS, and 1% P/S. KLE cells were grown in Dulbecco's Modified Eagle Medium (DMEM)/F12 1:1 (Gibco Cat. # 11320-033), 10% FBS, and 1% P/S. Organoids were grown in advanced DMEM/F12 (Gibco Cat. #12634-028), supplemented with 1% P/S, 1% HEPES (Gibco Cat. # 15630080), 1X Glutamax (Gibco Cat. # 35050061), 500nM A83-01 (BioGems Cat. #9094360), 10µM SB202190 (BioGems Cat. #1523072), 10mM Nicotinamide (Sigma Aldrich Cat. #N0636), 1X B-27 (Gibco Cat. #17504044), 1.25mM N-acetylcysteine (Sigma Aldrich Cat. #A9165), 1µM Prostaglandin E2 (BioGems Cat. # 3632464), 10% Noggin and 10% R-Spondin1 conditioned media, 10ng/mL FGF-10 (Peprotech Cat. #100-26), 50ng/mL EGF (Peprotech Cat. #100-15), and 10ng/mL FGF2 (Peprotech Cat. #100-18B). Cells were treated as described in the Overall Design and Treatment protocol sections.

extract_protocol:
Cell lines were trypsinized and organoids scraped. Cells were pelleted and stored at -80°C until RNA was prepared. RNA was prepared using Qiagen's RNEasy Mini kit (Qiagen Cat #74104) with on-column DNASE digest (Qiagen Cat. #79254) according to the manufacturer's protocol. RNA was snap frozen and sent to GENEWIZ (South Plainfield, NJ) for Standard RNA sequencing.
RNA libraries for RNA-seq were prepared by GENEWIZ.

treatment_protocol: For cell lines, doubling times were calculated. For HEC1B and ARK1 models, cells were treated for one doubling time (approximately 26 hours for ARK1 and 33.5 hours for HEC1B) with either 0.25µM Abemaciclib methanesulfonate (referred to as "Abemaciclib" henceforth) or media containing DMSO vehicle (used for analysis as batch 1). For organoids, a subset of the organoids were treated with media containing either 0.25µM Abemaciclib or media containing DMSO vehicle for 24 hours (used for analysis as batch 2). For additional cell lines and organoids to be used only for baseline transcriptomic comparisons, the cells were treated with media containing DMSO at 1:100,000 for 24 hours (used for analysis as batch 3). After treatments, cell lines and organoids were harvested and stored at -80°C until RNA was prepared. RNA was prepared using Qiagen's RNEasy Mini kit (Qiagen Cat #74104) with on-column DNASE digest (Qiagen Cat. #79254) according to the manufacturer's protocol. RNA was snap frozen and sent to GENEWIZ (South Plainfield, NJ) for Standard RNA sequencing. Each individual sample was sequenced in duplicate to provide technical replicates for validation.

value: Endometrial Cancer

value: Abemaciclib

tag: batch


title: HEC1B DMSO control replicate 2 (batch 1)

value: DMSO


title: 786-O_sgKDM5C_4_rep3

description: Library name: 786-O_sgKDM5C_4_rep3


title: exp3_786O_sgKDM5C_5_KDM5C

description: Library name: exp3_786O_sgKDM5C_5_KDM5C


title: 786-O_sgCtrl_rep3

description: Library name: 786-O_sgCtrl_rep3


title: ARK1 DMSO control replicate 1 (batch 1)


title: ARK1 DMSO control replicate 2 (batch 1)


title: exp3_786O_sgKDM5D_2_KDM5C

description: Library name: exp3_786O_sgKDM5D_2_KDM5C


title: HEC1B Abema replicate 1 (batch 1)


title: exp3_786O_sgKDM5C_4_KDM5C

description: Library name: exp3_786O_sgKDM5C_4_KDM5C


title: ARK1 Abema replicate 2 (batch 1)


title: exp3_786O_sgKDM5D_4_KDM5C

description: Library name: exp3_786O_sgKDM5D_4_KDM5C


title: exp3_786O_sgCtrl_KDM5C

description: Library name: exp3_786O_sgCtrl_KDM5C


title: exp3_786O_sgCtrl_IgG_for_Ab_KDM5C_KDM5D

description: Library name: exp3_786O_sgCtrl_IgG_for_Ab_KDM5C_KDM5D


title: exp3_786O_sgKDM5C_5_sgKDM5D_4_H3K4me1

description: Library name: exp3_786O_sgKDM5C_5_sgKDM5D_4_H3K4me1


title: Smoking utero exposition [F7]

city: Zaragoza

first: Ana

last: Gascón-Catalán

address: Domingo Miral s/n

country: Spain

institute: Universidad de Zaragoza

data_processing:
Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on  alignment statistical analysis (mapping ratio), we determine whether the results can be used for subsequent  data analysis.
Aligned reads were used for peak calling, LncRNA, mRNA and Small ncRNA associated  MeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value  threshold of 10􀀀4 by MACS2.
LncRNA, mRNA and Small ncRNA associated MeDIP enriched regions (peaks)  were annotated by the nearest gene using the newest UCSC RefSeq database
LncRNA, mRNA and Small ncRNA associated differentially  Methylated regions (DMRs) within promoter between two groups with statistically significant were identified  by diffReps(Cut-off: log2FC_x0015_1, p-value_x0014_10􀀀4)
Enhancer & SuperEnhancer associated Intergenic DMRs were  annotated by the nearest gene using the UCSC RefSeq database
Assembly: hg19
Supplementary files format and content: DNA Methylation profiles are saved as UCSC binary wig format files. DNA Methylation in each bin is determined by the extended read counts  of each sample

source_name: umbilical cord blood

extract_protocol:
DNA was isolated using Norgen’s Blood DNA Isolation Midi Kit
DNA libraries for meDIP-seq were prepared using Genomic DNA Sample Kit (#FC-102-1002, Illumina) following manufacturer's protocols.

value: umbilical cord blood

value: leukocytes

tag: subject status

value: newborns of smoking mother


title: exp3_786O_sgKDM5C_5_sgKDM5D_2_H3K4me1

description: Library name: exp3_786O_sgKDM5C_5_sgKDM5D_2_H3K4me1


title: Smoking utero exposition [F2]


title: HEC1B DMSO control replicate 1 (batch 1)


title: Smoking utero exposition [E6]


title: exp3_786O_sgKDM5C_4_sgKDM5D_2_H3K4me1

description: Library name: exp3_786O_sgKDM5C_4_sgKDM5D_2_H3K4me1


title: exp3_786O_sgKDM5C_4_sgKDM5D_4_H3K4me1

description: Library name: exp3_786O_sgKDM5C_4_sgKDM5D_4_H3K4me1


title: Smoking utero exposition [E7]


title: Smoking utero exposition [E5]


title: exp3_786O_sgKDM5C_5_H3K4me1

description: Library name: exp3_786O_sgKDM5C_5_H3K4me1


title: exp3_786O_sgKDM5D_2_H3K4me1

description: Library name: exp3_786O_sgKDM5D_2_H3K4me1


title: exp3_786O_sgCtrl_H3K4me1

description: Library name: exp3_786O_sgCtrl_H3K4me1


title: exp3_786O_sgCtrl_IgG_for_Ab_H3K4me1

description: Library name: exp3_786O_sgCtrl_IgG_for_Ab_H3K4me1


title: Non-smoking utero exposition  [A1]

value: newborns of non-smoking mother


title: Non-smoking utero exposition  [A4]


title: exp3_786O_sgKDM5D_4_H3K4me1

description: Library name: exp3_786O_sgKDM5D_4_H3K4me1


title: Non-smoking utero exposition  [A2]


title: IMR90 fibroblast, 2 kPa hydrogel culture, 250nM doxorubicin treatment, rep3

city: novato

first: HUIXUN

last: DU

state: CALIFORNIA

address: 8001 Redwood Blvd

institute: Buck Institute

data_processing:
RNA quantification, preparation of RNA library, and mRNA sequencing were conducted by Novogene Co., LTD (CA, US). About 20 million paired-end 150 bp reads per sample were generated from Illumina NovaSeq 6000 Sequencing System. FASTQ raw reads were analyzed using seqWorkflows (https://github.com/natmurad/seqWorkflows). Briefly, raw files were trimmed using trimmomatic, aligned using STAR and annotated using RSEM. RSEM output file contains counts, TPM and FPKM information, and it has the following '[ID].gene.results' format. Differential gene expression analysis between groups was done by DESeq2 R package (version 1.36.0). Genes with adjusted p-value < 0.05 and |log2(FoldChange)| > 0.5 were considered as significantly differentially expressed
Assembly: GRCh38
Supplementary files format and content: raw

growth_protocol: IMR-90 primary human lung fibroblasts (ATCC, Manassas, VA; #CCL186) were cultured in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific, Waltham, MA; #12430054) supplemented with penicillin-streptomycin (5,000 U/mL; Thermo Fisher Scientific, Waltham, MA; #15070063) and 10% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA; #2614079). Cells were seeded on either conventional polystyrene cell-culture treated 6-well plate (Nunc, Thermo Fisher Scientific, Waltham, MA; #140675), 2 kPa or 50 kPa PDMS-coated plates for overnight before any following treatment.

extract_protocol:
Collected cell pellets were stored in TRIzol Reagent (Invitrogen, Waltham, MA; #15596026) for long-term storage at -80°C.
Total RNA was prepared using the Zymo Research Direct-zol RNA Miniprep kit (Irvine, CA; #R2050).

treatment_protocol: Cells were cultured in above mentioned media containing either 50, 100, or 250 μM doxorubicin, or vehicle (DMSO) for 24 hours. Subsequently, cells were cultured for at least 8 days to allow development of the senescent phenotype. Proliferating control cells were cultured in complete media for 4 days. Quiescence was induced in control cells by culturing in complete media for 1 day and 0.2% FBS serum media for the subsequent 2 days.

value: Lung fibroblast

value: WT

value: 2 kPa gel, 250nM doxo


title: ARK1 Abema replicate 1 (batch 1)


title: Vehicle_Day5_S3 (Liver-Chip)

first: Lorna

last: Ewart

address: 27 Drydock Avenue

institute: Emulate Inc.

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 Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Primary Human Hepatocytes

growth_protocol: Liver-Chips were seeded with primary human hepatocytes  (introduced in the top channel of an Organ-on-Chip) and human liver sinusoidal microvascular endothelial cells (LSECs), Kupffer cells and stellate cells (introduced into the bottom channel). Cryopreserved primary human hepatocytes, purchased from Gibco (Thermo Fisher Scientific), and cryopreserved primary human liver sinusoidal endothelial cells (LSECs), purchased from Cell Systems, were cultured according to their respective vendor/Emulate protocols. The LSECs were expanded at a 1:1 ratio in 10-15 T-75 flasks (Corning) that were pre-treated with 5mL of Attachment Factor (Cell Systems). Complete LSEC medium includes Cell Systems medium with final concentrations of 1% Pen/Strep (Sigma), 2% CultureBoost (Cell Systems), and 10% Fetal Bovine Serum (FBS) (Sigma). Media was refreshed every other day until cells were ready for use. Cryopreserved human Kupffer cells (Samsara Sciences) and human Stellate cells (IXCells) were thawed according to their respective vendor/Emulate protocols on the day of seeding. The top channel media comprised of William's E media (WEM), with final concentrations of 1% Pen/Strep (Sigma), 1% L-GlutaMAX (Gibco), 1% ITS+ premix (Corning), 50 µg/mL Ascorbic acid (Sigma), 100nM Dexamethasone (Sigma). The bottom channel media comprised of  1 part of William's E media (WEM), 1% Pen/Strep (Sigma), 1% L-GlutaMAX (Gibco), 1% ITS+ premix (Corning), 50 µg/mL Ascorbic acid (Sigma), and 1 part of Cell Systems medium with final concentrations of 1% Pen/Strep (Sigma), 2% CultureBoost (Cell Systems); supplemeted with 2% Fetal Bovine Serum (FBS) (Sigma).

extract_protocol:
RNA was extracted from chips using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary Human Hepatocytes

tag: day


title: exp3_786O_sgKDM5C_4_H3K4me1

description: Library name: exp3_786O_sgKDM5C_4_H3K4me1


title: Vehicle_Day5_S2 (Liver-Chip)


title: IMR90 fibroblast, 2 kPa hydrogel culture, 250nM doxorubicin treatment, rep2


title: Vehicle_Day5_S4 (Liver-Chip)


title: exp3_786O_sgKDM5C_4_KDM5D

description: Library name: exp3_786O_sgKDM5C_4_KDM5D


title: IMR90 fibroblast, 2 kPa hydrogel culture, 250nM doxorubicin treatment, rep1


title: Vehicle_Day5_S1 (Liver-Chip)


title: Vehicle_Day3_S4 (Liver-Chip)


title: IMR90 fibroblast, plastic culture, 250nM doxorubicin treatment, rep3

value: plastic culture, 250nM doxo


title: Vehicle_Day3_S3 (Liver-Chip)


title: IMR90 fibroblast, plastic culture, 250nM doxorubicin treatment, rep2


title: IMR90 fibroblast, plastic culture, 250nM doxorubicin treatment, rep1


title: Vehicle_Day3_S2 (Liver-Chip)


title: Non-smoking utero exposition  [B13]


title: Non-smoking utero exposition  [A3]


title: Vehicle_Day3_S1 (Liver-Chip)


title: IMR90 fibroblast, 2 kPa hydrogel culture, 100nM doxorubicin treatment, rep2

value: 2 kPa gel, 100nM doxo


title: LNCaP, HTO

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

description:
DNA-seq
LIB5458340_SAM24418231

data_processing:
scMultiome data processing of sequencing reads was performed using our Single Cell Multiome ATAC + Gene Expression (ARCSeq) - 10X Cellranger bioinformatics pipeline (martian v4.0.5)which implements the CellRanger ARC seq (cellranger-arc count ) workflow (cellranger-arc_2.0.0) using the GRCh38 genome reference. ATAC-seq (atac_fragments.tsv.gz) and scRNA-seq (raw_feature_bc_matrix.h5) matrices were generated from fastq files.
The cell hashing (hashed-tag oligonucleotide (HTO)) (*.hashing.tsv) feature count matrices were generated with  cumulus_feature_barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding) (v0.11.1). This  barcode count matrix was then used to demultiplex the scRNAseq data using a DropleUtils (v1.21.0)-based  workflow with the emptyDrops(test.ambient = TRUE, by.rank=30000) and hashedDrops(  doublet.nmads=3, doublet.min=2, confident.nmads=1, confident.min=1) key steps and parameters. ATAC-seq data was processed with ArchR v1.0.3. Briefly, low quality cells were removed (minTSS>=4 and  minFrags>=1000) and arrow files were generated followed by generation of Tile and Gene Score matrices  using a tile size of 500 bp. Doublets were identified and filtered out using ArchR’s addDoubletScores()  function with default parameters.  Filtered ATACSeq data was merged with the libary-size normalized scRNAseq using the function addGeneIntegrationMatrix. For both modalities we used addIterativeLSI to reduce dimensionality. The results were combined into single space in which cell clusters were identified. Peaks were generated using addReproduciblePeakSet() with macs2. Peaks were annotated with addPeakAnnotations()(using public cisBP database) followed by  addDeviationsMatrix().  The peaks.mtx.gz and gex.mtx.gz files contains processed peaks and normalized gene expression data.
Assembly: GRCh38-2020-A
Supplementary files format and content: matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz - output of Cellranger
Supplementary files format and content: gex.mtx.gz, peaks.mtx.gz, gex_peaks_barcodes.tsv, peaks_features.tsv, gex_features.tsv - files representing ArchR GeneExpressionMatrix (normalized counts) and PeakMatrix assays, row names (genes or peaks) and column names (barcodes)
Supplementary files format and content: <library name>.hashing.csv cell hashing count matrix generated by cumulus_feature_barcoding with the first column storing HTO ID and other column names being barcodes
Library strategy: Single cell multiome (scMultiome)

source_name: prostate adenocarcinoma

growth_protocol: LNCap Clone FGC, VCAP and DU145 cells were obtained from ATCC and cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine; NCI-H660 cells were obtained from ATCC and cultured with DMEM/F12 with 0.005 mg/ml insulin,0.01 mg/ml Transferrin, 30nM Sodium selenite,10nM Hydrocortisone,10nM beta-estradiol, 4mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density. For the drug response assay, cells were seeded in 6 well format.The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
After 24 hours from treatment, the cells were harvested for the single-cell RNA-ATAC Co-assay.
The library construction was following the standard 10X protocol with the following modifications to the protocol:  1) 1µl of 10µM HTO additive primer was spiked in during the pre-AMP and cDNA PCR steps; 2) during the 0.6X cDNA cleanup, the supernatant was saved to amplify the HTO library. Along with the transcriptome library, the HTO library was amplified from the supernatant using the HTO-specific primer. The detailed protocol can be found on the cell hashing website (https://cite-seq.com/cell-hashing/).

treatment_protocol: 1.5E5 DU145 cells were seeded into each well of a 6 well plate and 5E3 DU145 cells were seeded into each well of a 96 well plate; 1.5-2E6 LNCAP or VCAP cells were seeded into T75 flasks; 5E5 cells NCI-H660 cells were seeded into each well of a 6 well plate. After 48 hours, the media was removed and cells were treated with DMSO, 1uM Enzalutamide, 0.1 uM SMARCA2.4_1 or 1 uM ARV-110 in complete media.

value: prostate adenocarcinoma

value: LNCaP clone FGC


title: IMR90 fibroblast, 2 kPa hydrogel culture, 100nM doxorubicin treatment, rep3


title: IMR90 fibroblast, 2 kPa hydrogel culture, 100nM doxorubicin treatment, rep1


title: VCaP, HTO

description:
DNA-seq
LIB5458339_SAM24418230

value: VCaP


title: IMR90 fibroblast, plastic culture, 100nM doxorubicin treatment, rep3

value: plastic culture, 100nM doxo


title: IMR90 fibroblast, plastic culture, 100nM doxorubicin treatment, rep1


title: Shotgun sequencing of WT after O/N culture, rep 2

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

country: France

institute: Institut Pasteur

description:
Library name: FG0689
BY4741 without 2 micron transformed with plasmid pKanMX-REP1-STB-p (RSGB1057)

data_processing:
Reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against the reference genomes.
Assembly: GCF_000146045.2 for S. cerevisiae , J01347.1 for the 2µ plasmid.
Supplementary files format and content: Reads from S. cerevisiae chromosomes and reads from 2µ plasmid were counted using bash commands.

organism: Saccharomyces cerevisiae

extract_protocol:
After the O/N incubation, a 1 mL aliquot from each culture was collected for subsequent shotgun sequencing. DNA was extracted using zymolyase, proteinase K and phenol and processed with Collibri kit.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

tag: background

tag: strain


title: IMR90 fibroblast, plastic culture, 100nM doxorubicin treatment, rep2


title: Shotgun sequencing of WT after O/N culture, rep 3

description:
Library name: FG0690
BY4741 without 2 micron transformed with plasmid pKanMX-REP1-STB-p (RSGB1057)


title: Shotgun sequencing of 5toA mutant after O/N culture, rep 3

description:
Library name: FG0681
5toA + pKAN


title: TOV21-G cell line, BLU-222 (1200nM), Biol Rep 3

city: Cambridge

first: Maxine

last: Chen

state: Massachusetts

address: 45 Sidney St.

institute: Blueprint Medicines

data_processing:
nf-core/rna-seq (Ewels et al. Nat Bioetechnol. 2020, doi: 10.5281/zenodo.1400710)
Read processing, alignment, and count were peformed using nf-core/rna-seq.
Briefly, adaptor sequence/low-quality reads were trimmed using Trim Galore! (--min-trimmed-reads 10000)
Read alignment was performed using STAR v2.7.11b (--min-mapped-reads 5)
Read count was performed using salmon 1.2
Assembly: hg38
Supplementary files format and content: count matrix csv

source_name: ovarian

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit, following manufacturer's instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions

value: ovarian


title: Shotgun sequencing of 5toA mutant after O/N culture, rep 2

description:
Library name: FG0680
5toA + pKAN


title: TOV21-G cell line, BLU-222 (1200nM), Biol Rep 2


title: TOV21-G cell line, BLU-222 (1200nM), Biol Rep 1


title: TOV21-G cell line, DMSO, Biol Rep 3


title: TOV21-G cell line, DMSO, Biol Rep 2


title: Shotgun sequencing of 5toA mutant after O/N culture, rep 1

description:
Library name: FG0679
5toA + pKAN


title: NKL10-delta-hda1_insitu-HiC_MseI

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description:
Library name: NKL10-delta-hda1_insitu-HiC_MseI
processed matrices contain the contact probability value between genomic loci in defined bin sizes

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.5 for all analyses. Briefly, raw fastq files were mapped to the Neurospora genome (version 14 [Rodriguez et al., 2022 [Pubmed ID: 35244156]) using bowtie2 (version 2.3), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with both DpnII [GATC] and MseI [TTAA] restriction sites used for quality control), and resulting images of the contact matrix images were made with hicPlotMatrix; (total) merged matrices were constructed by first merging all replicates using the cat command and processing them in an identical manner. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. Differences between wild type datasets (from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and mutant datasets were performed with hicCompareMatrices in which the experimental (mutant) matrix was listed first and the control (wild type) matrix was listed second; all compare matrices used the --log2diff flag to obtain the log2 difference in contact strength. Wild type (Rodriguez et al., 2022) and mutant matrices that were compared were generated to contain approximately the same number of valid reads, which was accomplished by selecting the appropriate number of total reads from fastq files of the dataset that had the highest number of valid reads using the sed command, such that the number of valid reads in both datasets were approximately equal, and these reads were mapped to the nc14 genome, and the contact matrix built with hicBuildMatrix as above.
Assembly: Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156])
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts, Knight-Ruiz corrected contact counts, or the calculated log2 difference in contacts between a wild type strain (wild type data from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and the mutant strains presented here.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: To grow WT Neurospora culture, 25 mL cultures containing 1x Vogel’s medium + 1.5% sucrose were inoculated with 1.25x10^8 conidia, (harvested from ~six baby slants by vortexing with water; conidia were washed twice prior to use) and grown at 32 °C with shaking at 200 revolutions per minute (RPM) for ~four hours until ~90% of conidia had germinated, and growth tubes were ~4x the length of the initial conidia.

extract_protocol:
First, the concentration of genomic DNA per spheroplast aliquot was determined by resuspending one aliquot per culture replicate in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 mg proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 mg RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Spheroplasts containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x restriction enzyme buffer (either DpnII, above) and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Spheroplasts were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII or MseI buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII and MseI (double digest) for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used eight and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced on an Illumina NovaSeq 6000 at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon as 100 nucleotide (nt) paired-end (PE100) sequencing runs.

treatment_protocol: Methanol-free formaldehyde was added to a final concentration of 1% and cultures were incubated 10 minutes at room temperature (RT; ~25°C) with shaking at 100 RPM for crosslinking; 1 M Tris-HCl [pH 8 at 25°C] (Hoffman et al. 2015) was added to a final concentration of 125 mM and cultures were incubated at RT for 10 minutes, shaking at 100 RPM, to quench the reaction. Conidia were harvested by centrifugation (4000 RPM, 3 min) and resuspended gently in 20 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4 [pH 7.5]) with b-mercaptoethanol added to 30mM. Conidia were pelleted again and resuspended in 20 mL spheroplasting buffer with b-mercaptoethanol added to 1mM. VinoTaste (Novozymes; powder dissolved in water to a stock solution of 50 mg/mL) was added to 50mg and strains were digested at 30°C, shaking at 100 RPM, for 60 min. Spheroplasts were harvested by centrifugation (3500 RPM, 2 min) and pellets were washed twice with 20 mL Spheroplasting buffer, followed by three washes of the buffer of the 1x restriction enzyme to be used for digestion, here DpnII buffer (100 mM NaCl, 50 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL BSA). Washed pellets were resuspended in 3.5 mL of the same restriction enzyme buffer, split into four – 1 mL aliquots in 1.7 mL Eppendorf tubes, pelleted (10,000 rpm, 5 min), whereupon the supernatant was removed, and spheroplast pellets were stored at -80°C.

value: germinated conidia

value: hyphae

value: mat ?; delta hda1::hph


title: TOV21-G cell line, DMSO, Biol Rep 1

value: DMSO


title: NKL9-delta-hda1_insitu-HiC_MseI

description:
Library name: NKL9-delta-hda1_insitu-HiC_MseI
processed matrices contain the contact probability value between genomic loci in defined bin sizes


title: TOV-112D cell line, BLU-222 (350nM), Biol Rep 3