title: MCF7_RNAseq_DMOG_aza_1day-Hypoxia_r2b

description: MCF7 DMOG aza 1day-Normoxia


title: heart_316s_N6

status: Public on Jun 18 2020

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol

tag: tissue

value: heart

tag: starin

tag: Sex

value: male

tag: age

value: 10-20 weeks

tag: cluster


title: Femoral homogenate - DO mouse 337

city: Charlottesville

first: Basel

last: Al-Barghouthi

state: VA

country: USA

institute: University of Virginia

data_processing:
Basecalls were performed using the Real-Time Analysis (RTA) software version 2.4.11
Each sample/run combination was aligned to GRCm38 using HISAT2 version 2.0.5, using the GRCm38_snp index. HISAT2 was run with the following parameters: --dta --trim3 1
Aligned files were sorted, merged by sample for all runs, and sorted again using samtools version 1.10
Assembly and quantification was performed with StringTie version 1.3.3, using the GRCm38.98 GTF annotation. The following StringTie parameters were used: -e -G
A single GTF was generated with all common transcripts, using StringTie --merge -G. Assembly and quantification were repeated as before, but using the merged GTF, with the -eB -G parameters.
A gene count matrix was generated using the prepDE.py script, sourced from the StringTie website (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual)
Gene counts were filtered to include genes that had more than 0.1 TPM and more than 6 reads in more than 38 samples (20%).
Gene read counts were transformed using the variance stabilizing transformation (VST) from the DESeq2 package (version 1.20.0). This was followed by a quantile- based inverse Normal transformation , as performed in Yang et al., Nature,  2012.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing filtered gene read counts for all 192 samples
Supplementary_files_format_and_content: CSV file containing transformed filtered gene read counts

source_name: Femur

extract_protocol:
Femurs were homogenated in TRIzol, and total RNA was extracted from homogenates using mirVana miRNA isolation kit (Life Technologies, Carlsbad, CA).
Libraries were prepared using the Illumina TruSeq Stranded Total RNA HT sample prep kits

treatment_protocol: Ends of femurs were cut, and marrow was flushed out.

value: Marrow-depleted left femur - homogenate

tag: strain

value: Diversity Outbred (J:DO)

value: 85 days


title: heart_316s_N5


title: MCF7_RNAseq_DMOG_aza_1day-Hypoxia_r2a

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

description: MCF7 DMOG aza 1day-Normoxia

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using tophat (version 2.0.10).
Counts were called byHTSeq (version 0.5.3p3)
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Breast cancer cell line

extract_protocol:
PolyA mRNA capture by using KAPA Stranded mRNA-Seq Kit (Illumina)
Strand specific library preparation

value: breast

tag: treatment

value: 2mM DMOG 24h, 1 µM aza 72h, 21% O2 24h

tag: growth protocol

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: heart_316s_N3


title: heart_316s_N24


title: MCF7_RNAseq_DMOG_aza_1day-Hypoxia_r1b

description: MCF7 DMOG aza 1day-Normoxia


title: Femoral homogenate - DO mouse 336

value: 84 days


title: heart_316s_N22


title: Femoral homogenate - DO mouse 335


title: Femoral homogenate - DO mouse 334


title: heart_316s_N20


title: MCF7_RNAseq_control_aza_1day-Normoxia_r3b

description: MCF7 DMSO aza 1day-Normoxia

value: DMSO 24h, 1 µM aza 72h, 21% O2 24h


title: heart_316s_N2


title: heart_316s_N18


title: heart_316s_N9


title: heart_316s_N16


title: MCF7_RNAseq_control_aza_1day-Normoxia_r2b

description: MCF7 DMSO aza 1day-Normoxia


title: Femoral homogenate - DO mouse 332

value: 83 days


title: Femoral homogenate - DO mouse 333


title: heart_316s_N13


title: Femoral homogenate - DO mouse 330


title: heart_316s_N14


title: Femoral homogenate - DO mouse 329


title: MCF7_RNAseq_control_aza_1day-Normoxia_r2a

description: MCF7 DMSO aza 1day-Normoxia


title: heart_316s_N10


title: heart_316s_N11


title: MCF7_RNAseq_control_aza_1day-Normoxia_r1b

description: MCF7 DMSO aza 1day-Normoxia


title: heart_316s_N23


title: heart_316s_N21


title: heart_316s_N12


title: MCF7_RNAseq_DMOG__aza_1day-Hypoxia_r1a

description: MCF7 DMOG aza 1day-Normoxia


title: heart_316s_N1


title: MCF7_RNAseq_control_aza_1day-Normoxia_r1a

description: MCF7 DMSO aza 1day-Normoxia


title: Femoral homogenate - DO mouse 327

value: 86 days


title: MCF7_RNAseq_control_aza_1day-Normoxia_r3a

description: MCF7 DMSO aza 1day-Normoxia


title: heart_316s_M9


title: Femoral homogenate - DO mouse 328


title: Femoral homogenate - DO mouse 326


title: heart_316s_M8


title: heart_316s_N15


title: heart_316s_M6


title: heart_316s_M5


title: Femoral homogenate - DO mouse 325


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r3b

description: MCF7 DMOG DMSO 1day-Normoxia

value: 2mM DMOG 24h, DMSO 72h, 21% O2 24h


title: heart_316s_M24


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r2b

description: MCF7 DMOG DMSO 1day-Normoxia


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r3a

description: MCF7 DMOG DMSO 1day-Normoxia


title: heart_316s_M3


title: heart_316s_M23


title: Femoral homogenate - DO mouse 323


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r2a

description: MCF7 DMOG DMSO 1day-Normoxia


title: heart_316s_M22


title: heart_316s_M21


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r1b

description: MCF7 DMOG DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 322


title: Femoral homogenate - DO mouse 320


title: heart_316s_M19


title: MCF7_RNAseq_control_control_1day-Normoxia_r3b

description: MCF7 DMSO DMSO 1day-Normoxia

value: DMSO 24h, DMSO 72h, 21% O2 24h


title: Femoral homogenate - DO mouse 321


title: heart_316s_M14


title: MCF7_RNAseq_DMOG_control_1day-Hypoxia_r1a

description: MCF7 DMOG DMSO 1day-Normoxia


title: MCF7_RNAseq_control_control_1day-Normoxia_r3a

description: MCF7 DMSO DMSO 1day-Normoxia


title: heart_316s_M2


title: heart_316s_M13


title: heart_316s_M18


title: heart_316s_M7


title: heart_316s_M16


title: heart_316s_M15


title: Femoral homogenate - DO mouse 319


title: Femoral homogenate - DO mouse 318


title: MCF7_RNAseq_control_control_1day-Normoxia_r2a

description: MCF7 DMSO DMSO 1day-Normoxia


title: heart_316s_M20


title: MCF7_RNAseq_control_control_1day-Normoxia_r1b

description: MCF7 DMSO DMSO 1day-Normoxia


title: MCF7_RNAseq_control_control_1day-Normoxia_r2b

description: MCF7 DMSO DMSO 1day-Normoxia


title: heart_316s_M12


title: MCF7_RNAseq_control_control_1day-Normoxia_r1a

description: MCF7 DMSO DMSO 1day-Normoxia


title: heart_316s_L7


title: heart_316s_M11


title: Femoral homogenate - DO mouse 315


title: heart_316s_L6


title: Femoral homogenate - DO mouse 316


title: heart_316s_M1


title: Femoral homogenate - DO mouse 314


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r3b

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: Femoral homogenate - DO mouse 313


title: heart_316s_L9


title: Femoral homogenate - DO mouse 312

value: 87 days


title: heart_316s_L5


title: heart_316s_L8


title: heart_316s_L3


title: heart_316s_L4


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r3a

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: heart_316s_L24


title: heart_316s_M10


title: heart_316s_L21


title: Femoral homogenate - DO mouse 310


title: heart_316s_L22


title: heart_316s_L20


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r2a

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: Femoral homogenate - DO mouse 309


title: heart_316s_L19


title: Femoral homogenate - DO mouse 308


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r1b

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r1a

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: heart_316s_L18


title: Femoral homogenate - DO mouse 306


title: heart_316s_L16


title: heart_316s_L13


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Hypoxia_r2b

description: MCF7 HIF1B-KO aza 1day-Hypoxia


title: heart_316s_L12


title: heart_316s_L15


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Normoxia_r2b

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: heart_316s_L14


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Normoxia_r2a

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: heart_316s_L11


title: heart_316s_K9


title: heart_316s_L10


title: Femoral homogenate - DO mouse 303


title: Femoral homogenate - DO mouse 300


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Normoxia_r3a

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: heart_316s_L2


title: heart_316s_K8


title: Femoral homogenate - DO mouse 307


title: heart_316s_L17


title: heart_316s_K7


title: Femoral homogenate - DO mouse 304


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Normoxia_r3b

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: MCF7 HIF1B-KO_RNAseq_aza_1day-Normoxia_r1b

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: MCF7HIF1B-KO _RNAseq_aza_1day-Normoxia_r1a

description: MCF7 HIF1B-KO aza 1day-Normoxia


title: Femoral homogenate - DO mouse 302


title: heart_316s_K4


title: heart_316s_K5


title: Femoral homogenate - DO mouse 116


title: heart_316s_L1


title: Femoral homogenate - DO mouse 117


title: Femoral homogenate - DO mouse 115


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r3b

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r2b

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r3a

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 296


title: heart_316s_K3


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r2a

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: heart_316s_K20


title: heart_316s_K2


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r1b

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: heart_316s_K6


title: heart_316s_K17


title: heart_316s_K18


title: Femoral homogenate - DO mouse 112


title: MCF7 HIF1B-KO_RNAseq_control_1day-Hypoxia_r1a

description: MCF7 HIF1B-KO DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 113


title: heart_316s_K16


title: heart_316s_K23


title: heart_316s_K14


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r3b

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: heart_316s_K13


title: heart_316s_K12


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r3a

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: heart_316s_K21


title: Femoral homogenate - DO mouse 110


title: heart_316s_K11


title: Femoral homogenate - DO mouse 109


title: heart_316s_K10


title: heart_316s_K1


title: Femoral homogenate - DO mouse 294


title: heart_316s_K19


title: heart_316s_K24


title: heart_316s_J9


title: Femoral homogenate - DO mouse 107


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r2b

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r2a

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 106


title: Femoral homogenate - DO mouse 111


title: Femoral homogenate - DO mouse 105


title: heart_316s_J7


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r1b

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: heart_316s_J5


title: MCF7 HIF1B-KO_RNAseq_control_1day-Normoxia_r1a

description: MCF7 HIF1B-KO DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 104


title: MCF7_RNAseq_aza_1day-Hypoxia_r3b

description: MCF7 aza 1day-Hypoxia


title: MCF7_RNAseq_aza_1day-Hypoxia_r3a

description: MCF7 aza 1day-Hypoxia


title: Femoral homogenate - DO mouse 101


title: heart_316s_J23


title: heart_316s_J21


title: heart_316s_J3


title: heart_316s_J24


title: MCF7_RNAseq_aza_1day-Hypoxia_r2b

description: MCF7 aza 1day-Hypoxia


title: heart_316s_J18


title: heart_316s_J20


title: heart_316s_J17


title: heart_316s_J15


title: Femoral homogenate - DO mouse 99


title: heart_316s_J13


title: MCF7_RNAseq_aza_1day-Hypoxia_r2a

description: MCF7 aza 1day-Hypoxia


title: heart_316s_J8


title: heart_316s_J16


title: Femoral homogenate - DO mouse 96


title: Femoral homogenate - DO mouse 98


title: heart_316s_J6


title: heart_316s_J11


title: Femoral homogenate - DO mouse 102


title: heart_316s_J14


title: heart_316s_J4


title: MCF7_RNAseq_aza_1day-Hypoxia_r1a

description: MCF7 aza 1day-Hypoxia


title: heart_316s_J12


title: Femoral homogenate - DO mouse 97


title: MCF7_RNAseq_aza_1day-Normoxia_r3b

description: MCF7 aza 1day-Normoxia


title: MCF7_RNAseq_aza_1day-Hypoxia_r1b

description: MCF7 aza 1day-Hypoxia


title: heart_316s_I9


title: MCF7_RNAseq_aza_1day-Normoxia_r2b

description: MCF7 aza 1day-Normoxia


title: heart_316s_J10


title: Femoral homogenate - DO mouse 95


title: Femoral homogenate - DO mouse 94


title: heart_316s_J1


title: heart_316s_I5


title: heart_316s_I3


title: Femoral homogenate - DO mouse 93


title: heart_316s_I7


title: MCF7_RNAseq_aza_1day-Normoxia_r1b

description: MCF7 aza 1day-Normoxia


title: MCF7_RNAseq_aza_1day-Normoxia_r2a

description: MCF7 aza 1day-Normoxia


title: heart_316s_I8


title: Femoral homogenate - DO mouse 89


title: heart_316s_I23


title: heart_316s_I4


title: Femoral homogenate - DO mouse 88

value: 80 days


title: heart_316s_I22

value: heart


title: MCF7_RNAseq_control_1day-Hypoxia_r3b

description: MCF7 DMSO 1day-Hypoxia


title: heart_316s_I21

value: male


title: heart_316s_I2

value: 10-20 weeks


title: MCF7_RNAseq_aza_1day-Normoxia_r1a

description: MCF7 aza 1day-Normoxia


title: MCF7_RNAseq_aza_1day-Normoxia_r3a

description: MCF7 aza 1day-Normoxia


title: heart_316s_I18


title: Femoral homogenate - DO mouse 83

value: Marrow-depleted left femur - homogenate

value: 79 days


title: Femoral homogenate - DO mouse 85

value: Diversity Outbred (J:DO)


title: heart_316s_I20


title: heart_316s_I16


title: heart_316s_I17


title: Femoral homogenate - DO mouse 82


title: Femoral homogenate - DO mouse 92


title: MCF7_RNAseq_control_1day-Hypoxia_r2b

description: MCF7 DMSO 1day-Hypoxia

value: breast


title: heart_316s_I14


title: MCF7_RNAseq_control_1day-Hypoxia_r2a

description: MCF7 DMSO 1day-Hypoxia


title: heart_316s_I24


title: MCF7_RNAseq_control_1day-Hypoxia_r1b

description: MCF7 DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 81


title: heart_316s_I12


title: heart_316s_I1


title: heart_316s_H8


title: MCF7_RNAseq_control_1day-Hypoxia_r3a

description: MCF7 DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 79

value: 77 days


title: Femoral homogenate - DO mouse 80


title: heart_316s_H9


title: heart_316s_I11


title: heart_316s_H22


title: MCF7_RNAseq_control_1day-Hypoxia_r1a

description: MCF7 DMSO 1day-Hypoxia

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: MCF7_RNAseq_control_1day-Normoxia_r3b

description: MCF7 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 77


title: MCF7_RNAseq_control_1day-Normoxia_r2a

description: MCF7 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 78


title: heart_316s_H20


title: MCF7_RNAseq_control_1day-Normoxia_r3a

description: MCF7 DMSO 1day-Normoxia


title: heart_316s_H23


title: heart_316s_H21


title: Femoral homogenate - DO mouse 76

value: 76 days


title: heart_316s_H24


title: heart_316s_I13


title: heart_316s_H18


title: heart_316s_H15


title: heart_316s_H16


title: MCF7_RNAseq_control_1day-Normoxia_r1b

description: MCF7 DMSO 1day-Normoxia


title: MCF7_RNAseq_control_1day-Normoxia_r2b

description: MCF7 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 75


title: heart_316s_H19


title: heart_316s_H14


title: heart_316s_H12


title: heart_316s_H13


title: Femoral homogenate - DO mouse 74


title: Femoral homogenate - DO mouse 73


title: Femoral homogenate - DO mouse 72


title: heart_316s_G9


title: MCF7_RNAseq_aza_Hypoxia_r3

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using tophat (version 2.0.10).
Counrs were called byHTSeq (version 0.5.3p3)
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample

source_name: MCF7 aza Hypoxia

extract_protocol:
RiboMinus Eukaryote System (Life technologies)
Briefly, total RNA was extracted using TRIzol (Invitrogen), and remaining DNA contaminants in 17-20ug of RNA was removed using Turbo DNase (Ambion) according to the manufacturers instruction. RNA was repurified using RNeasy Mini Kit (Qiagen).
Strand specific library preparation

tag: cell line

tag: cell type

value: Breast cancer cell line


title: MCF7_RNAseq_control_1day-Normoxia_r1a

description: MCF7 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 70


title: heart_316s_G8


title: MCF7_RNAseq_aza_Normoxia_r3

source_name: MCF7 aza Normoxia


title: heart_316s_G7


title: Femoral homogenate - DO mouse 68


title: heart_316s_G5


title: MCF7_RNAseq_aza_Normoxia_r2


title: heart_316s_G6


title: MCF7_RNAseq_aza_Hypoxia_r2


title: heart_316s_G4


title: heart_316s_G3


title: MCF7_RNAseq_aza_Hypoxia_r1


title: heart_316s_G23


title: Femoral homogenate - DO mouse 66


title: heart_316s_G21


title: MCF7_RNAseq_aza_Normoxia_r1


title: Femoral homogenate - DO mouse 65


title: SK-MEL-28_RNAseq_Hypoxia_r3

source_name: SK-MEL-28 Hypoxia

value: skin

value: Melanoma cell line


title: Femoral homogenate - DO mouse 64


title: heart_316s_G20


title: heart_316s_G22


title: Femoral homogenate - DO mouse 63


title: heart_316s_H11


title: heart_316s_G18


title: heart_316s_G2


title: heart_316s_G17


title: Femoral homogenate - DO mouse 62


title: SK-MEL-28_RNAseq_Normoxia_r3

source_name: SK-MEL-28 Normoxia


title: RCC4_RNAseq_Hypoxia_r3

source_name: RCC4 Hypoxia

value: kidney

value: Renal cell carcinoma


title: heart_316s_G16


title: heart_316s_G13


title: heart_316s_G14


title: RCC4_RNAseq_Normoxia_r3

source_name: RCC4 Normoxia


title: heart_316s_G12


title: RCC4_RNAseq_Hypoxia_r2


title: RCC4_RNAseq_Normoxia_r2


title: heart_316s_G10


title: heart_316s_F9


title: heart_316s_F8


title: Femoral homogenate - DO mouse 60


title: heart_316s_G11


title: Femoral homogenate - DO mouse 59


title: heart_316s_F7


title: heart_316s_G1


title: Femoral homogenate - DO mouse 57


title: heart_316s_F6


title: Femoral homogenate - DO mouse 56

value: 94 days


title: RCC4_RNAseq_Hypoxia_r1


title: heart_316s_F5


title: heart_316s_F4


title: Femoral homogenate - DO mouse 55


title: heart_316s_F24


title: Femoral homogenate - DO mouse 61


title: Femoral homogenate - DO mouse 53


title: SK-MEL-28_RNAseq_Normoxia_r2

value: cultured at 37°C in Roswell Park Memorial Institut 1640 Medium (RPMI) 10% FBS 1% Pen Strep and 1% L-Glutamine.


title: heart_316s_F20

value: heart


title: heart_316s_F18

value: male


title: SK-MEL-28_RNAseq_Hypoxia_r1


title: heart_316s_F19

value: 10-20 weeks


title: Femoral homogenate - DO mouse 52

value: Marrow-depleted left femur - homogenate


title: heart_316s_F17


title: SK-MEL-28_RNAseq_Normoxia_r1


title: heart_316s_F15


title: Femoral homogenate - DO mouse 51

value: 92 days


title: SK-MEL-28_Input_r4

description:
SK-MEL-28
processed data file: SKMEL28.macs.peaks.txt

library_source: genomic

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using bowtie (version 0.12.8; settings -v 2 -m 1 -p --best -S).
Peaks were called by model-based analysis of ChIP-sequencing (MACS) using pooled data for each cell line and using the correspondent input as background set.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: MACS called peaks for each cell line

molecule: genomic DNA

growth_protocol: cultured at 37°C in Roswell Park Memorial Institut 1640 Medium (RPMI) 10% FBS 1% Pen Strep and 1% L-Glutamine.

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 µM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
Five µg of input and all of the immunoprecipitated DNA were converted into sequencing libraries using the NEBNext Ultra DNA library prep kit.

tag: tissue source

tag: type of sample

value: Input

tag: chip antibody


title: heart_316s_F16


title: heart_316s_F12


title: RCC4_RNAseq_Normoxia_r1


title: heart_316s_F13


title: Femoral homogenate - DO mouse 54

value: Diversity Outbred (J:DO)


title: heart_316s_F11


title: SK-MEL-28_RNAseq_Hypoxia_r2


title: Femoral homogenate - DO mouse 46

value: 90 days


title: Femoral homogenate - DO mouse 47


title: heart_316s_F10


title: Femoral homogenate - DO mouse 49


title: SK-MEL-28_Input_r1


title: heart_316s_E9


title: SK-MEL-28_Input_r2


title: heart_316s_F2


title: heart_316s_F1


title: RCC4_Input_r3

description:
RCC4
processed data file: RCC4.macs.peaks.txt

growth_protocol: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.

value: Renal cell carcinoma cell line


title: heart_316s_E7


title: Femoral homogenate - DO mouse 43


title: RCC4_Input_r2


title: heart_316s_F14


title: heart_316s_E4


title: Femoral homogenate - DO mouse 44


title: heart_316s_E8


title: Femoral homogenate - DO mouse 42


title: heart_316s_E24


title: heart_316s_E6


title: heart_316s_E22


title: SK-MEL-28_Input_r3


title: heart_316s_E20


title: RCC4_Input_r1


title: Femoral homogenate - DO mouse 40


title: Femoral homogenate - DO mouse 39


title: heart_316s_E23


title: heart_316s_E16


title: SK-MEL-28_HIF1bChIPseq_r4

value: ChIP

value: ARNT/HIF-1β monoclonal antibody (NB100-124, Novus)


title: heart_316s_E15


title: heart_316s_E18


title: heart_316s_E14


title: SK-MEL-28_HIF1bChIPseq_r2

value: skin


title: heart_316s_E19


title: SK-MEL-28_HIF1bChIPseq_r1

value: Melanoma cell line


title: heart_316s_E2


title: Femoral homogenate - DO mouse 38


title: Femoral homogenate - DO mouse 37


title: SK-MEL-28_HIF1bChIPseq_r3


title: heart_316s_E13


title: RCC4_HIF1bChIPseq_r3

value: kidney


title: Femoral homogenate - DO mouse 36


title: heart_316s_E11


title: Femoral homogenate - DO mouse 35


title: heart_316s_E10


title: heart_316s_E12


title: heart_316s_E1


title: Femoral homogenate - DO mouse 41


title: RCC4_HIF1bChIPseq_r2


title: RCC4_HIF1bChIPseq_r1


title: Femoral homogenate - DO mouse 34


title: MCF7_control_HIF1bChIPseq_r4 (Re-sequencing)

description:
MCF7 DMSO (Re-sequencing)
processed data file: MCF7.dmso.macspeaks.txt

value: breast

value: Breast cancer cell line


title: heart_316s_D22


title: heart_316s_D24


title: heart_316s_D21


title: Femoral homogenate - DO mouse 33


title: MCF7_aza_Input_r3

description:
MCF7 aza
processed data file: MCF7.AZA.macs.peaks.txt


title: heart_316s_D19


title: heart_316s_D18


title: Femoral homogenate - DO mouse 32


title: MCF7_control_HIF1bChIPseq_r3

description:
MCF7 DMSO
processed data file: MCF7.dmso.macspeaks.txt


title: heart_316s_D1


title: Femoral homogenate - DO mouse 31


title: heart_316s_B1


title: MCF7_control_Input_r3


title: Femoral homogenate - DO mouse 30


title: heart_203s_P9


title: heart_204s_E22


title: Femoral homogenate - DO mouse 29


title: Femoral homogenate - DO mouse 28

value: 87 days


title: MCF7_aza_Input_r2


title: heart_203s_P8

value: heart


title: heart_203s_P4

value: male


title: MCF7_aza_HIF1bChIPseq_r4


title: Femoral homogenate - DO mouse 27


title: heart_316s_D20

value: 10-20 weeks


title: heart_203s_P3


title: heart_203s_P22


title: heart_316s_D17


title: MCF7_aza_Input_r4


title: heart_203s_P2


title: Femoral homogenate - DO mouse 25

value: Marrow-depleted left femur - homogenate


title: heart_203s_P18


title: heart_203s_P19


title: heart_203s_P16


title: heart_203s_P17


title: Femoral homogenate - DO mouse 24


title: MCF7_aza_HIF1bChIPseq_r2 (Re-sequencing)

description:
MCF7 aza (Re-sequencing)
processed data file: MCF7.AZA.macs.peaks.txt


title: heart_203s_P7


title: heart_203s_P14


title: heart_203s_P15


title: MCF7_aza_HIF1bChIPseq_r3


title: heart_203s_P12


title: MCF7_aza_HIF1bChIPseq_r2


title: Femoral homogenate - DO mouse 22


title: heart_203s_P5


title: heart_203s_P13


title: Femoral homogenate - DO mouse 21

value: 86 days


title: Femoral homogenate - DO mouse 26


title: heart_203s_O9


title: MCF7_control_HIF1bChIPseq_r4


title: MCF7_IgG_input

description:
MCF7
MCF7.IgG.peaks.txt

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 mM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
One µg of input and all of the immunoprecipitated DNA were converted into sequencing libraries using the NEBNext Ultra DNA library prep kit.

value: Input


title: heart_203s_O8


title: MCF7_HIF1bChIP-BSseq

data_processing:
FastQ files were mapped to the mouse genome ((human:build GRCh37/hg19; mouse:mm10) using bismark (version 0.10.1).
Read counts at HIF peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain read numbers overlapping HIF peaks both in MCF7 and Tet-TKO mouse

source_name: Beast cancer cell line

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 µM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. DNA libraries were bisulfite converted using the EZ DNA Methylation-Lightning™ kit (Zymo) prior to library amplification using HiFi Uracil+ (KAPA).

value: Beast cancer cell line

value: ChIP-BS


title: heart_203s_O7


title: MCF7_control_Input_r4


title: MCF7_IgG_ChIPseq

description:
MCF7
MCF7.IgG.peaks.txt


title: Femoral homogenate - DO mouse 20

value: Diversity Outbred (J:DO)


title: Femoral homogenate - DO mouse 19


title: heart_203s_O4


title: A549_HIF1bChIPseq_r3

description:
A549
A549.macs.peaks.txt

source_name: Adenocarcinomic human alveolar basal epithelial cell line

value: lung

value: ChIP


title: Femoral homogenate - DO mouse 23


title: A549_HIF1bChIPseq_r2

description:
A549
A549.macs.peaks.txt

value: ARNT/HIF-1β monoclonal antibody (NB100-124, Novus)


title: heart_203s_O3


title: heart_203s_O6


title: heart_203s_O23


title: A549_HIF1bChIPseq_r1

description:
A549
A549.macs.peaks.txt


title: heart_203s_P1


title: Femoral homogenate - DO mouse 17

value: 85 days


title: Femoral homogenate - DO mouse 16


title: A549_Input_r3

description:
A549
A549.macs.peaks.txt


title: heart_203s_O20


title: heart_203s_O2


title: heart_203s_O21


title: heart_203s_O18


title: Femoral homogenate - DO mouse 14


title: heart_203s_O19


title: A549_Input_r2

description:
A549
A549.macs.peaks.txt


title: A549_Input_r1

description:
A549
A549.macs.peaks.txt


title: heart_203s_O17


title: heart_203s_O16


title: Femoral homogenate - DO mouse 11


title: Femoral homogenate - DO mouse 10


title: heart_203s_O5


title: heart_203s_O22


title: Femoral homogenate - DO mouse 18


title: heart_203s_O15


title: Femoral homogenate - DO mouse 8


title: Femoral homogenate - DO mouse 9


title: heart_203s_O10


title: heart_203s_O12


title: heart_203s_O11


title: heart_203s_O13


title: heart_203s_O14


title: Femoral homogenate - DO mouse 6


title: heart_203s_N7


title: heart_203s_N9


title: heart_203s_N8


title: Femoral homogenate - DO mouse 4


title: heart_203s_N6


title: heart_203s_N3


title: Femoral homogenate - DO mouse 1

value: 84 days


title: Femoral homogenate - DO mouse 2


title: heart_203s_O1


title: Femoral homogenate - DO mouse 5


title: heart_203s_N4


title: heart_203s_N22


title: Blood samples 126181

type: genomic

city: Ningbo

first: cao

last: yuhao

state: Zhejiang Province

address: 818 Fenghua Road, Jiangbei District, Ningbo City, Zhejiang Province

country: China

institute: Medical School of Ningbo University

description:
126181
200109370006_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP284BeadChip

hyb_protocol: Hybridization of DNA and chip: After the DNA sample obtained  is hybridized with the chip, it is placed in a hybridization furnace to fully react.Chip extension and staining: Wash unbound and non-specifically bound DNA with a cleaning solution.Coated chip: Place the above chip in XC4 reagent, apply the coating solution, and place it under vacuum for 1h.

scan_protocol: Chip scanning: Put the chip processed in step (8) into the scanner to perform chip scanning.

data_processing: Genotyping of individual SNPs was performed using the Ovine SNP50BeadChip

label: C-Bio and A-DNP

organism: Ovis aries

label_protocol: (1) Sample standardization: Dilute the DNA concentration to 50ng / µL.2) DNA amplification: add 1N NaOH solution to the sample, and then add the reagents required for genome amplification, and then leave it at room temperature for 12 h.(3) Fragmentation of DNA: Use enzyme preparation to turn DNA into fragments.4) Precipitate DNA: Use anhydrous isopropyl alcohol to deposit DNA on the wall of the tube.(5) Resuspend the DNA: after drying at room temperature, add the corresponding buffer solvent to dissolve it completely.

extract_protocol: Blood samples were collected from the posterior venous plexus of Hu sheep to extract genomic DNA using the standard phenol/chloroform method

tag: gender

value: Famale

tag: g

tag: father

tag: mother

tag: sibling number

tag: birth weight

tag: weaning weight

tag: six-month weight


title: Blood samples 129170

description:
129170
200109370006_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP283BeadChip


title: Blood samples 129189

description:
129189
200109370006_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP287BeadChip


title: heart_203s_N21

tag: tissue

tag: starin

tag: Sex

tag: age

tag: cluster


title: Blood samples 129201

description:
129201
200109370006_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP285BeadChip


title: heart_203s_N19


title: Blood samples 129223

description:
129223
200109370006_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP282BeadChip


title: Blood samples 126179

description:
126179
200109370006_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP286BeadChip


title: heart_203s_N18


title: heart_203s_N20


title: heart_203s_N5


title: Blood samples 127243

description:
127243
200109370006_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP281BeadChip


title: heart_203s_N23


title: RNA-Seq-Clone21-CTCF&TSS-CRISPR#1-rep2

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
RNA-Seq
RNA-Seq_near_insertions_CRISPR.tar

data_processing:
Two biological replicates were performed for each cell line. For differential expression (DE) analysis, reads were mapped to the indexed Ensembl hg19 transcriptome (GRCh37.67) and quantified using Salmon (Patro et al., Nat. Methods, 2017). Transcript-level quantifications were then imported, using tximport (Soneson et al., F1000Res, 2015), for gene-level (EnsDb.Hsapiens.v75) measurements with DESeq2 (Love et al., Genome Biol., 2014). Genes with less than 10 reads were excluded from downstream DE analysis. DESeq2 was performed to identify DE genes between Clone 21 and non-Clone 21, and between Clone 25 and non-Clone 25, at an FDR < 0.01. For RNA-seq analysis for genome tracks visualization, the sequence reads were processed using the ENCODE long RNA-Seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). Briefly, raw sequencing reads were initially accessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Mapping to hg19 was performed using STAR (Dobin et al., Bioinformatics, 2013). Resulting bedGraph files were then converted to bigWig format for genome browser visualization with strand specificity.
Genome_build: hg19
Supplementary_files_format_and_content: "C21_DESeq_res" and "C25_DESeq_res" are quantification results using Salmon (Patro et al., Nat. Methods, 2017), also catagorizing whether each gene is within a distance range centered around each insertion site. "RNA-Seq_near_insertions.tar" are extracted bedgraphs from alignment bigwig file for visualization purposes.

growth_protocol: HAP1 cells (Carette et al., Nature 477, 340-343 (2011)), derived from KBM7 cells, a chronic myelogenous leukemia cell line, were cultured in IMDM with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2 (as described in Carette et al., 2011).

extract_protocol:
HAP1 cells were washed with PBS, and resuspended in 1mL TRIzol (Thermo Fisher), with 200µL chloroform then added. RNA was extracted using RNeasy Mini Kit (Qiagen). For sample ID #s 1732-1737, sequencing libraries were constructed from 500 ng of DNase-treated, total RNA using the ScriptSeqv2 Complete Kit (Illumina BHMR1224). Later samples (ID #s 2564-2565, 2694-2697), Illumina Truseq Stranded Total RNA kit was used, as ScriptSeqv2 was discontinued. Briefly, the RNA was depleted of rRNA using the Ribo-Zero removal reagents and fragmented. First strand cDNA was then synthesized using a 5’ tagged random hexamer and reverse transcription, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo and second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles. Libraries were quality checked and quantified prior to 2 x 76 bp sequencing on the Illumina NextSeq 500.
rRNA-depleted RNA

treatment_protocol: HAP1 cells were co-transfected with the two components of the Sleeping Beauty transposon system: pSA-MCS-2kb, the transposon vector with the 2kb insert containing a CTCF binding site and the TSS of PARL gene, and the transposase vector, pCMV(CAT)T7-SB100. Clonal lines were established following transposon genome editing. Hi-C was then performed for two clones (Clone 21 and Clone 25) with the highest numbers of insertions. Where indicated, CRISPR editing using a gRNA targeting the CTCF binding site within ectopic insertions was performed, and Capture-C was used to characterize effects upon CTCF binding site disruption.

tag: cell type

value: KBM7-derived near haploid cells


title: RNA-Seq-Clone21-CTCF&TSS-CRISPR#1-rep1


title: RNA-Seq-Clone21-TSS-CRISPR-rep2


title: heart_203s_N15


title: heart_203s_N17


title: RNA-Seq-Clone21-TSS-CRISPR-rep1


title: mouse ESC

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Bioinformatics

country: Japan

institute: Soka University, Graduate School of Engineering

data_processing:
Illumina bcl2fastq ver2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using StrandNGS (Agilent Technologies)
DeSeq normalization was calculated using StrandNGS (Agilent Technologies)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include  DeSeq values for ESCs

source_name: Embryonic stem cells

growth_protocol: ESC medium consisting of DMEM (Gibco) supplemented with 15% fetal bovine serum (FBS) (Nichirei Biosciences), 1% penicillin/streptomycin (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 0.1 mM nonessential amino acids (Gibco), and 1000 U/mL LIF (Chemicon International).

extract_protocol:
RNA was purified using a RNeasy Mini Kit with an RNase-free DNase Set (QIAGEN, Venlo, Netherlands), according to the supplier’s manual.
One ug of total RNA for the construction of sequencing libraries using QuantSeq 3 mRNA Seq Library Prep Kit for Illumina (FWD) (LEXOGEN, Vienna, Austria).
3'-end specific RNA seq

value: Embryonic stem cells

tag: strain

tag: genotype

value: wild type


title: Blood samples 129215

description:
129215
200109370006_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP280BeadChip


title: Blood samples 123128

description:
123128
200109370006_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP279BeadChip


title: Blood samples 129213

description:
129213
200109370006_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP278BeadChip


title: heart_203s_N13

value: heart

value: male


title: Blood samples 121121

description:
121121
200109370006_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP277BeadChip


title: heart_203s_N10

value: 10-20 weeks


title: heart_203s_N14


title: Blood samples 126178

description:
126178
200109370006_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP276BeadChip


title: heart_203s_M7


title: heart_203s_M6


title: RNA-Seq-Clone21-CTCF-CRISPR-rep2


title: heart_203s_N11


title: ChIP-seq-WT-2kb-CRISPR-Rad21-rep1

description:
ChIP-seq
ChIP-insertions_or_edited_endo_bedgraphs.tar

data_processing:
Raw sequencing reads were mapped to hg19 using Bowtie. SAM files were converted to BAM files using SAMtools. For transcription factor (or other targets with narrow peaks, such as CTCF and Rad21 here), MACS (Zhang et al., Genome Biol., 2008) was used for generating Wiggle and for peak calling. For histone marks (H3K27Ac), BAM files were converted to Wiggle using MACS and subsequently converted to bigWig. Subsequent peak calling was performed using Sicer (Xu et al., Methods Mol Biol., 2014). For the data tracks visualized in the figures, bamCoverage from Deeptools (Ramírez., Nucleic Acids Research, 2016) was used to generate counts-per-million (CPM)-normalized bigwig files from bam files. The CPM-normalized bigwig files were later converted to bedgraphs for insertion-proximal regions.
Basecalls using bcl2fastq2 v2.15.0.4, and parameters  --barcode-mismatches 1
Mapping to reference genome hg19 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 2615371906 --tsize 36 --bw 120 --mfold 12 --wig --space 1
For CTCF and Rad21 (factors with narrow binding profiles): peaks were called with MACS using MFOLD=12, PVALUE="" --format BAM --gsize $EFFGENSIZE --tsize 36 --bw 120 --mfold $MFOLD --wig --space 1 $PVALUE
Genome_build: Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Supplementary_files_format_and_content: bw alignment files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Hsiung, et al., Genes Dev., 2016), using the H3K27Ac antibody (Active Motif 39685), CTCF antibody (Millipore 07-729), and Rad21 antibody (abcam ab992). Briefly, ~20 million HAP1 cells were fixed in 1% formaldehyde in fresh culture medium at room temperature for 10 minutes, followed by quenching in 1M glycine for 5 minutes. Crosslinked cells were lysed for 10 minutes in 1mL cold Cell Lysis Buffer (10mM Tris pH 8.0, 10mM NaCl, and 0.2% NP-40/Igepal), supplied with Protease Inhibitors (Sigma-Aldrich P8340) and phenylmethylsulfonyl fluoride (PMSF). Nuclei were pelleted, resuspended in 1mL room temperature Nuclei Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS), with Protease Inhibitors and PMSF, and were incubated on ice for 20 minutes. The samples were sonicated at 100% amplitude, 30 seconds on/30 seconds off, for 45 minutes, in a bath sonicator (QSonica Q800R3). Sonicated materials were centrifuged, with the supernatant subsequently collected, and diluted with 4mL IP Dilution Buffer (20mM Tris pH 8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS), with Protease Inhibitors and PMSF. 50µL protein A/G agarose beads (Thermo Fisher 15918014, Thermo Fisher 15920010) and 50µg isotype-matched IgG control were added to sonicated chromatin to pre-clear it for >2 hours at 4°C. Beads were then spun down, with 200µL supernatant containing pre-cleared chromatin saved as “input” before immunoprecipitation. The remaining pre-cleared chromatin was split into equal volumes, each incubated with antibody or isotype-matched control (IgG) pre-bound protein A/G beads, and rotated overnight at 4°C. Chromatin-bound beads were washed on ice, once with IP Wash 1 (20mM Tris pH 8, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20mM Tris pH 8, 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash 2 (10mM Tris pH 8, 1mM EDTA, 0.25M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate), and twice with TE. Beads were then moved to room temperature, and were eluted twice with a total volume of freshly prepared 200µL Elution Buffer (100mM NaHCO3, 1% SDS). Into each IP and input, 12µL 5M NaCl and 2µL RNase A (10mg/mL, Roche through Sigma 10109169001) were added, and samples were incubated at 65°C overnight. 3µL proteinase K (20mg/mL, Roche through Sigma 3115879) was then added, for an additional 2 hours at 65°C. DNA was column cleaned up using a QIAquick PCR Purification Kit (QIAGEN 28106). For ChIP-sequencing, library construction was performed using Illumina’s TruSeq ChIP sample preparation kit (Illumina IP-202-1012), followed by size selection using SPRIselect beads (Beckman Coulter, B23318). Libraries were quality checked, quantified prior to 1 x 75 bp sequencing on the Illumina NextSeq 500.
See "extract protocol"


title: ChIP-seq-WT-2kb-CRISPR-CTCF-rep2


title: heart_203s_N16


title: Blood samples 1413076

description:
1413076
200109370014_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP274BeadChip

tag: yearling weight


title: heart_203s_M8


title: heart_203s_N1


title: heart_203s_M9


title: ChIP-seq-WT-2kb-CRISPR-Rad21-rep2


title: RNA-Seq-Clone21-CTCF-CRISPR-rep1


title: Blood samples 1414083

description:
1414083
200109370014_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP275BeadChip

tag: gender


title: heart_203s_M5


title: heart_203s_N12


title: heart_203s_M4


title: Blood samples 1413075

description:
1413075
200109370014_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP272BeadChip

tag: g


title: Blood samples 1413088

description:
1413088
200109370014_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP271BeadChip

tag: father


title: heart_203s_M3


title: ChIP-seq-WT-2kb-CRISPR-CTCF-rep1


title: heart_203s_M24


title: heart_203s_M23


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#2-CTCF-rep2


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#2-Rad21-rep1


title: Blood samples 1413072

description:
1413072
200109370014_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP270BeadChip

tag: mother


title: Blood samples 1413083

description:
1413083
200109370014_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP269BeadChip

tag: sibling number


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#2-Rad21-rep2


title: heart_203s_M21


title: Blood samples 1413068

description:
1413068
200109370014_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP268BeadChip

tag: birth weight


title: heart_203s_M22


title: heart_203s_M20


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#2-CTCF-rep1


title: heart_203s_M17


title: heart_203s_M19


title: Blood samples 1413081

description:
1413081
200109370014_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP267BeadChip

tag: weaning weight


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#1-Rad21-rep2


title: heart_203s_M16


title: Blood samples 1413089

description:
1413089
200109370014_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP273BeadChip

tag: six-month weight


title: heart_203s_M15

tag: tissue


title: heart_203s_M13

tag: starin


title: heart_203s_M14

tag: Sex


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#1-CTCF-rep2


title: heart_203s_M2

tag: age


title: heart_203s_M18

tag: cluster


title: heart_203s_M12


title: heart_203s_M1


title: heart_203s_L9


title: heart_203s_L7


title: heart_203s_L8


title: heart_203s_M11


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#1-Rad21-rep1

tag: cell type


title: heart_203s_L6


title: heart_203s_M10


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#1-CTCF-rep1


title: Blood samples 1413064

description:
1413064
200109370014_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP266BeadChip


title: Blood samples 1413077

description:
1413077
200109370014_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP265BeadChip


title: heart_203s_L4


title: Blood samples 1413115

description:
1413115
200109370014_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP264BeadChip


title: heart_203s_L5


title: ChIP-seq-Clone21-TSS-CRISPR-Rad21-rep2


title: heart_203s_L3


title: ChIP-seq-Clone21-TSS-CRISPR-CTCF-rep1


title: ChIP-seq-Clone21-TSS-CRISPR-Rad21-rep1


title: ChIP-seq-Clone21-TSS-CRISPR-CTCF-rep2


title: heart_203s_L24


title: heart_203s_L23


title: ChIP-seq-Clone21-CTCF-CRISPR-CTCF-rep2


title: Blood samples 125124

description:
125124
200109370003_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP261BeadChip


title: heart_203s_L22


title: Blood samples 125146

description:
125146
200109370003_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP262BeadChip


title: Blood samples 1414N02

description:
1414N02
200109370003_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP263BeadChip


title: Blood samples 127184

description:
127184
200109370003_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP258BeadChip


title: Blood samples 127230

description:
127230
200109370003_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP259BeadChip


title: heart_203s_L21


title: ChIP-seq-Clone21-CTCF-CRISPR-Rad21-rep2

description:
ChIP-seq
ChIP-insertions_or_edited_endo_bedgraphs.tar


title: heart_203s_L2


title: Blood samples 129151

description:
129151
200109370003_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP257BeadChip


title: ChIP-seq-Clone21-CTCF-CRISPR-Rad21-rep1


title: heart_203s_L20


title: heart_203s_L17


title: Blood samples 128110

description:
128110
200109370003_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP260BeadChip


title: heart_203s_L18


title: ChIP-seq-Clone21-CTCF-CRISPR-CTCF-rep1


title: heart_203s_L16


title: heart_203s_L14


title: heart_203s_L15


title: ChIP-seq-Clone25-Rad21-rep2


title: heart_203s_L13


title: ChIP-seq-Clone25-CTCF-rep2


title: heart_203s_L12


title: heart_203s_L11


title: ChIP-seq-Clone25-Rad21-rep1


title: ChIP-seq-Clone25-CTCF-rep1


title: heart_203s_L10


title: heart_203s_L19


title: Blood samples 129060

description:
129060
200109370003_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP255BeadChip


title: Blood samples 125099

description:
125099
200109370062_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP251BeadChip


title: Blood samples 1413M10

description:
1413M10
200109370003_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP253BeadChip


title: Blood samples 128161

description:
128161
200109370003_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP256BeadChip


title: Blood samples 1413M09

description:
1413M09
200109370003_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP252BeadChip


title: heart_203s_K8


title: heart_203s_L1


title: ChIP-seq-Clone21-Rad21-rep2


title: heart_203s_K5


title: heart_203s_K7


title: heart_203s_K23


title: ChIP-seq-Clone21-CTCF-rep2


title: ChIP-seq-Clone21-CTCF-rep1


title: Blood samples 128105

description:
128105
200109370062_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP249BeadChip


title: heart_203s_K4


title: ChIP-seq-Clone21-Rad21-rep1


title: heart_203s_K3


title: heart_203s_K24


title: Blood samples 123076

description:
123076
200109370062_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP250BeadChip


title: Blood samples 128107

description:
128107
200109370062_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP248BeadChip


title: heart_203s_K2


title: heart_203s_K18


title: Blood samples 127198

description:
127198
200109370062_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP246BeadChip


title: Blood samples 127195

description:
127195
200109370062_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP247BeadChip


title: heart_203s_K21


title: ChIP-seq-WT-Rad21-rep2


title: heart_203s_K9


title: ChIP-seq-WT-CTCF-rep1


title: heart_203s_K20


title: heart_203s_K12


title: heart_203s_K19


title: ChIP-seq-WT-CTCF-rep2


title: ChIP-seq-WT-2kb-CRISPR-H3K27Ac

description:
ChIP-seq
ChIP-insertions_or_edited_endo_bedgraphs.tar
ChIP_cpm_bw.tar

data_processing:
Raw sequencing reads were mapped to hg19 using Bowtie. SAM files were converted to BAM files using SAMtools. For transcription factor (or other targets with narrow peaks, such as CTCF and Rad21 here), MACS (Zhang et al., Genome Biol., 2008) was used for generating Wiggle and for peak calling. For histone marks (H3K27Ac), BAM files were converted to Wiggle using MACS and subsequently converted to bigWig. Subsequent peak calling was performed using Sicer (Xu et al., Methods Mol Biol., 2014). For the data tracks visualized in the figures, bamCoverage from Deeptools (Ramírez., Nucleic Acids Research, 2016) was used to generate counts-per-million (CPM)-normalized bigwig files from bam files. The CPM-normalized bigwig files were later converted to bedgraphs for insertion-proximal regions.
Basecalls using bcl2fastq2 v2.15.0.4, and parameters  --barcode-mismatches 1
Mapping to reference genome hg19 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 2615371906 --tsize 36 --bw 120 --mfold 12 --wig --space 1
For H3K27Ac (histone marks): peaks were called with Sicer V1.1 using parameters hg19 1 200 150 0.74 600 0.01
Genome_build: Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Supplementary_files_format_and_content: bw alignment files

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed as previously described (Hsiung, et al., Genes Dev., 2016), using the H3K27Ac antibody (Active Motif 39685), CTCF antibody (Millipore 07-729), and Rad21 antibody (abcam ab992). Briefly, ~20 million HAP1 cells were fixed in 1% formaldehyde in fresh culture medium at room temperature for 10 minutes, followed by quenching in 1M glycine for 5 minutes. Crosslinked cells were lysed for 10 minutes in 1mL cold Cell Lysis Buffer (10mM Tris pH 8.0, 10mM NaCl, and 0.2% NP-40/Igepal), supplied with Protease Inhibitors (Sigma-Aldrich P8340) and phenylmethylsulfonyl fluoride (PMSF). Nuclei were pelleted, resuspended in 1mL room temperature Nuclei Lysis Buffer (50mM Tris pH 8, 10mM EDTA, 1% SDS), with Protease Inhibitors and PMSF, and were incubated on ice for 20 minutes. The samples were sonicated at 100% amplitude, 30 seconds on/30 seconds off, for 45 minutes, in a bath sonicator (QSonica Q800R3). Sonicated materials were centrifuged, with the supernatant subsequently collected, and diluted with 4mL IP Dilution Buffer (20mM Tris pH 8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS), with Protease Inhibitors and PMSF. 50µL protein A/G agarose beads (Thermo Fisher 15918014, Thermo Fisher 15920010) and 50µg isotype-matched IgG control were added to sonicated chromatin to pre-clear it for >2 hours at 4°C. Beads were then spun down, with 200µL supernatant containing pre-cleared chromatin saved as “input” before immunoprecipitation. The remaining pre-cleared chromatin was split into equal volumes, each incubated with antibody or isotype-matched control (IgG) pre-bound protein A/G beads, and rotated overnight at 4°C. Chromatin-bound beads were washed on ice, once with IP Wash 1 (20mM Tris pH 8, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20mM Tris pH 8, 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.01% SDS), once with IP Wash 2 (10mM Tris pH 8, 1mM EDTA, 0.25M LiCl, 1% NP-40/Igepal, 1% sodium deoxycholate), and twice with TE. Beads were then moved to room temperature, and were eluted twice with a total volume of freshly prepared 200µL Elution Buffer (100mM NaHCO3, 1% SDS). Into each IP and input, 12µL 5M NaCl and 2µL RNase A (10mg/mL, Roche through Sigma 10109169001) were added, and samples were incubated at 65°C overnight. 3µL proteinase K (20mg/mL, Roche through Sigma 3115879) was then added, for an additional 2 hours at 65°C. DNA was column cleaned up using a QIAquick PCR Purification Kit (QIAGEN 28106). For ChIP-sequencing, library construction was performed using Illumina’s TruSeq ChIP sample preparation kit (Illumina IP-202-1012), followed by size selection using SPRIselect beads (Beckman Coulter, B23318). Libraries were quality checked, quantified prior to 1 x 75 bp sequencing on the Illumina NextSeq 500.


title: Blood samples 128084

description:
128084
200109370062_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP245BeadChip


title: ChIP-seq-WT-Rad21-rep1


title: Blood samples 127214

description:
127214
200109370062_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP242BeadChip


title: heart_203s_K17


title: Blood samples 128091

description:
128091
200109370003_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP254BeadChip


title: heart_203s_K22


title: Blood samples 122121

description:
122121
200109370062_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP244BeadChip


title: heart_203s_K15


title: Blood samples 122154

description:
122154
200109370062_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP243BeadChip


title: ChIP-seq-Clone21-CTCF-CRISPR-H3K27Ac


title: heart_203s_K1


title: heart_203s_K14


title: heart_203s_K16


title: heart_203s_K11


title: heart_203s_K13


title: heart_203s_K10


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#2-H3K27Ac


title: ChIP-seq-Clone21-TSS-CRISPR-H3K27Ac


title: ChIP-seq-Clone21-CTCF&TSS-CRISPR#1-H3K27Ac


title: Blood samples 127117

description:
127117
200109370002_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP239BeadChip


title: heart_203s_J6


title: Blood samples 1413M05

description:
1413M05
200109370062_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP240BeadChip


title: heart_203s_J8


title: heart_203s_J7


title: heart_203s_J5


title: Blood samples 1413M07

description:
1413M07
200109370062_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP241BeadChip


title: heart_203s_J4


title: Capture-C-Clone21-CTCF&TSS-CRISPR#1-2nd-rep2-seq

description:
Capture-C
Capture-C_chr2_13M_locus_FullSet.tar
Capture-C_chr6_75M_locus_FullSet.tar
Capture-C_DirectionalityIndex_InsertionLoci.tar

data_processing:
Library strategy: Capture-C
Two biological replicates for each cell line were performed. Raw reads were processed using published scripts (Davies, et al., Nat. Methods, 2016). Briefly, Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), a wrapper for FastQC and Cutadapt, was used to assess the quality and to trim adapter sequences of raw sequences. Trimmed reads were then merged or interleaved using FLASH. Once concatenated, the reads were in silico DpnII digested, aligned to hg19, and analyzed using CCanalyser3. Interactions were then normalized to total interactions. Bedgraph files from each individual replicate were merged.
Genome_build: hg19
Supplementary_files_format_and_content: For each locus with an insertion, and with a CRISPR editing, where applicable, each .tar has a collection of BedGraph files generated by combining the biological replicates of each sample

extract_protocol:
Capture-C was performed as previously described (Hughes et al., Nat. Genet., 2014; Huang et al., Genes Dev., 2017; Davies et al., Nat. Methods, 2016). Briefly, ~10 million cells HAP1 cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes, and then quenched in 1M glycine for 5 minutes, on an orbital shaker. Cells were then pelleted, washed with 1mL cold PBS, transferred to an Eppendorf tube, pelleted, resuspended in 1mL cold Cell Lysis Buffer (10mM Tris pH 8.0, 10mM NaCl, and 0.2% NP-40/Igepal), and incubated on ice for 10 minutes. Nuclei were then pelleted, washed once using NEBuffer™ DpnII, pelleted, and resuspended in 500µL NEBuffer™ DpnII. Samples were incubated in 0.3% SDS at 37°C, 950 rpm for 1 hour in a thermomixer, followed by the addition of a final concentration of 1.8% Triton X-100, for 1 hour at 37°C, 950 rpm. After adding 40µL water, 300U DpnII was added for in situ digestion at 37°C, overnight. An additional 300U DpnII was then added, and samples were incubated for 4 more hours at 37°C, followed by 20 minutes at 65°C, 950 rpm. Nuclei were pelleted, resuspended in a total volume of 1.2mL with 4000U T4 DNA Ligase (NEB), and incubated at 16°C for 4 hours and then at room temperature for 30 minutes. 20µL of 20mg/mL Proteinase K and 120µL of 10% SDS were added, and samples were incubated at 65°C overnight to reverse crosslinking. An additional 10µL proteinase K was added to each sample for 2 more hours at 55°C. 2µL DNase-free RNAase was added to each sample, followed by incubation at 37°C for 30 minutes. DNA was then extracted with phenol-chloroform. DNA was sonicated to 200-300bp in a bath sonicator (QSonica Q800R3), followed by beads clean-up. Sequencing libraries were subsequently prepared similarly as described in "Insertion-site-mapping” samples: End Repair, dA-Tailing, adaptor ligation, 6 cycles of indexing PCR, and 6 cycles of amplification using P5/P7. After sequencing library preparation, two rounds of target enrichment/capture were carried out using biotinylated hybridization oligos similarly as described in "Insertion-site-mapping” samples. Pulldown enrichment was confirmed using qPCR. Target enriched libraries were quality checked and quantified as in situ Hi-C samples prior to 2 x 75 bp sequencing on the Illumina NextSeq 500.
See "extract protocol"


title: Capture-C-Clone21-CTCF&TSS-CRISPR#1-2nd-rep1-seq


title: heart_203s_J24


title: heart_203s_J9


title: heart_203s_J3


title: Capture-C-Clone21-TSS-CRISPR-2nd-rep2-seq


title: heart_203s_J23


title: Capture-C-Clone21-TSS-CRISPR-2nd-rep1-seq


title: heart_203s_J22


title: Capture-C-Clone21-CTCF&TSS-CRISPR#1-1st-rep2-seq


title: Blood samples 127211

description:
127211
200109370002_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP238BeadChip


title: Blood samples 123118

description:
123118
200109370002_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP237BeadChip


title: heart_203s_J18


title: heart_203s_J19


title: Blood samples 128169

description:
128169
200109370002_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP236BeadChip


title: heart_203s_J21


title: heart_203s_J20


title: Blood samples 128076

description:
128076
200109370002_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP235BeadChip


title: Blood samples 126147

description:
126147
200109370002_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP234BeadChip


title: Capture-C-Clone21-CTCF&TSS-CRISPR#1-1st-rep1-seq


title: heart_203s_J17


title: Blood samples 127174

description:
127174
200109370002_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP233BeadChip


title: heart_203s_J16


title: heart_203s_J15


title: Capture-C-Clone21-TSS-CRISPR-1st-rep1-seq


title: Capture-C-Clone21-TSS-CRISPR-1st-rep2-seq


title: heart_203s_J14


title: heart_203s_J13


title: Hi-C-WT-2kb-CRISPR-rep2-2nd-seq

description:
Hi-C
wt_2kb_3_20000_iced.matrix
Hi-C_Matrices_2kb_endogenous_CRISPR_genotyped.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
wt_2kb_3.allValidPairs.hic

data_processing:
Two replicates of each sample, WT, Clone 21 and Clone 25, underwent a pilot sequencing run, generating ~30 million raw reads for each replicate. Reads from each replicate were then mapped to hg19 using Bowtie 2. Detection and filtering of valid interaction pairs, assignment to restriction fragment and binning, and interaction matrix balancing with iterative correction and eigenvector decomposition (ICE) (Imakaev, et al., Nat. Methods, 2012) were all performed using the HiC-Pro pipeline (Servant, et al., Genome Biol. 2015). With each replicate of a given sample having highly reproducible metrics: >60% valid interaction pairs-raw read pairs ratio, <20% trans interaction, <8% dangling pairs, and contact ranges of interaction pairs, two replicates of the sample were subsequently pooled for further analysis. Deeper sequencing was subsequently performed to yield ~250 million raw reads for each sample, generating ~160 million valid interaction pairs per sample, after HiC-Pro processing. ICE balanced interaction matrices were binned at 20kb resolution, and used for downstream analyses, unless otherwise specified. Genome-wide Hi-C contacts Pearson correlations between two samples were calculated on non-empty bins shared between two samples.                             To generate heatmaps for each insertion site, ICE balanced matrices for the clone with the insertion, as well as for WT and the other clone without the insertion at this position, were extracted with the insertion bin in the middle and with 150 bins (3 million bps) on either side of it. These extracted matrices, adjusted for minor coverage differences, were plotted using lib5C (Gilgenast, et al., Cell Syst., 2019) in linear scale using color scheme “red8” from matplotlib (Hunter, et al., Computing in Science Engineering, 2007), highlighting a megabase-scale region centering around each insertion.                         Insulation score computations were implemented mechanistically similar to those in (Crane et al., Nature, 2015). Given an ICE balanced interaction matrix with the insertion bin at the center, averaged interactions within a sliding window of 10 bins by 10 bins (15 bins by 15 bins when the insert was at a pre-established boundary or at the endogenous boundary where the 2 kb test DNA was chosen), were recorded for each bin along the diagonal of interaction matrices. The insulation score for each diagonal bin was then normalized to all insulation scores across its nearby 240 bins (4.8 Mb chromosomal region), with the log2 ratio subsequently calculated. Positive log2 values indicate relatively enriched interactions, whereas negative log2 values suggest relatively depleted interactions, with local minima marking domain boundaries. Shared domain boundaries genome-wide among WT and insertion clones were identified similarly: averaged interactions within a sliding window of 10 bins by 10 bins, log2 after normalized to all scores chromosome-wide, and local minima determined, with a minimum domain size of 4 bins (80 kb).
Genome_build: hg19
Supplementary_files_format_and_content: hap1_wt_hic_20000_ord.bed: coordinates to bin # (each bin 20 kb) lookup table; hap1_wt/clone21/clone25_hic_20000_iced.matrix: genome-wide sparse matrix; hap1_wt_endo.matrix: extracted around the locus where the 2kb test DNA was derived from. Eigen_chr6.tar: eigenvalues of chr6, binned at 50 kb, where Clone 21 insertion site #4 resulting in a likely compartment change occurred.

extract_protocol: In situ Hi-C was performed as previously described (Rao et al., Cell, 2014; Nora et al., Cell, 2017; Huang et al., Genes Dev. 2017.). Briefly, ~10 million HAP1 cells, WT, Clone 21, Clone 25, and subsequent CRISPR-edited clones were crosslinked in 2% formaldehyde at room temperature for 10 minutes, and then quenched in 0.125M glycine for 5 minutes, on an orbital shaker. Cells were then transferred from a culture flask to a 15mL tube, pelleted, washed with 1mL cold PBS, transferred to an Eppendorf tube, pelleted, resuspended in 1mL cold Cell Lysis Buffer (10mM Tris pH 8.0, 10mM NaCl, and 0.2% NP-40/Igepal), and incubated on ice for 10 minutes. Nuclei were then pelleted, washed once using 800µL NEBuffer™ DpnII, pelleted, and resuspended in 500µL NEBuffer™ DpnII. A final concentration of 0.3% SDS was added, and samples were incubated at 37°C, 950 rpm for 1 hour in a thermomixer. A final concentration of 1.8% Triton X-100 was then added to each sample, which was subsequently incubated at 37°C, 950 rpm for 1 hour. 40µL nuclease-free water, as well as 300U DpnII (NEB R0543M), was added, and samples were digested at 37°C, at 950 rpm overnight in a thermomixer. Another 300U DpnII were added for an additional 4 hours of digestion with mixing. The samples were then incubated at 65°C, 950 rpm for 20 minutes. Nuclei were then pelleted, resuspended in 1X NEBuffer™ 2, with biotin-14-dATP, dTTP, dCTP and dGTP and DNA polymerase I, Large (Klenow) Fragment (NEB M0210), and incubated at 37°C, 950 rpm in a thermomixer for 90 minutes. Ligation reaction was subsequently carried out in a total volume of 1.2mL with 4000U T4 DNA Ligase (NEB) at 16°C for 4 hours, followed by 30 minutes at room temperature. 20µL of 20mg/mL Proteinase K and 120µL of 10% SDS were then added to each sample, followed by crosslinking reversal at 65°C overnight. An additional 10µL proteinase K was added to each sample, which was incubated at 55°C for 2 hours. 2µL DNase-free RNAase was added to each sample, followed by incubation at 37°C for 30 minutes. Phenol-chloroform extraction was performed to purify DNA. DNA was sonicated to 200-300bp in a bath sonicator (QSonica Q800R3), followed by beads clean-up. Biotinylated nucleotides-filled ligation junctions were pulled down with 50µL Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher 65001). Sequencing libraries were subsequently prepared: End Repair, dA-Tailing, adaptor ligation, followed by 6 cycles of indexing PCR. The quality and size (average 429 bp) of each library was evaluated using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems, KK4835). Libraries were then pooled and sequenced in paired-end mode on the NextSeq 500 to generate 2 x 75 bp reads using Illumina-supplied kits as appropriate.


title: heart_203s_J12


title: heart_203s_J11


title: heart_203s_J10


title: Blood samples 127197

description:
127197
200109370002_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP232BeadChip


title: Blood samples 125132

description:
125132
200109370002_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP231BeadChip


title: Blood samples 125136

description:
125136
200109370002_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP230BeadChip


title: Hi-C-WT-2kb-CRISPR-rep1-1st-seq


title: Hi-C-WT-2kb-CRISPR-rep1-2nd-seq


title: Hi-C-Clone21-CTCF&TSS-CRISPR#2-rep2-2nd-seq

description:
Hi-C
sc79-3-7_20000_iced.matrix
Hi-C_Matrices_CRISPR_Genotyped_Clone21Insertions.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
sc79-3-7.allValidPairs.hic


title: heart_203s_I5


title: heart_203s_I4


title: heart_203s_I6


title: heart_203s_I8


title: heart_203s_I3


title: heart_203s_I7


title: heart_203s_I9


title: heart_203s_I23


title: Hi-C-Clone21-CTCF&TSS-CRISPR#2-rep1-2nd-seq


title: Hi-C-WT-2kb-CRISPR-rep2-1st-seq


title: heart_203s_J1


title: heart_203s_I22


title: heart_203s_I21


title: Blood samples 127224

description:
127224
200109370002_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP229BeadChip


title: Blood samples 127194

description:
127194
200109370002_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP228BeadChip


title: Hi-C-Clone21-CTCF&TSS-CRISPR#2-rep1-1st-seq


title: Blood samples 1414139

description:
1414139
101035780058_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP227BeadChip


title: Blood samples 1414137

description:
1414137
101035780058_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP223BeadChip


title: Blood samples 1413156

description:
1413156
101035780058_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP222BeadChip


title: Blood samples 1413154

description:
1413154
101035780058_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP226BeadChip


title: Blood samples 1413153

description:
1413153
101035780058_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP224BeadChip


title: Blood samples 1414138

description:
1414138
101035780058_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP225BeadChip


title: heart_203s_I19


title: heart_203s_I17


title: heart_203s_I18


title: heart_203s_I14


title: heart_203s_I16


title: heart_203s_I13


title: heart_203s_I2


title: heart_203s_I12


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep1-2nd-seq

description:
Hi-C
sc79-2-3_20000_iced.matrix
Hi-C_Matrices_CRISPR_Genotyped_Clone21Insertions.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
sc79-2-3.allValidPairs.hic


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep2-3rd-seq


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep2-1st-seq


title: heart_203s_I1


title: heart_203s_I20


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep1-3rd-seq


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep2-2nd-seq


title: Blood samples 1414136

description:
1414136
101035780058_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP221BeadChip


title: Blood samples 1413155

description:
1413155
101035780058_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP220BeadChip


title: Hi-C-Clone21-CTCF&TSS-CRISPR#1-rep1-1st-seq


title: Blood samples 1413152

description:
1413152
101035780058_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP219BeadChip


title: heart_203s_H9


title: Blood samples 1413142

description:
1413142
101035780058_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP218BeadChip


title: heart_203s_H7


title: Blood samples 1413131

description:
1413131
101035780058_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP216BeadChip


title: heart_203s_I10


title: Blood samples 127237

description:
127237
101035780078_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP215BeadChip


title: heart_203s_H6


title: Blood samples 128072

description:
128072
101035780078_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP214BeadChip


title: Blood samples 1413151

description:
1413151
101035780058_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP217BeadChip


title: heart_203s_H4


title: Hi-C-Clone21-TSS-CRISPR-rep2-3rd-seq

description:
Hi-C
c21-2-13_20000_iced.matrix
Hi-C_Matrices_CRISPR_Genotyped_Clone21Insertions.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
c21-2-13.allValidPairs.hic


title: Hi-C-Clone21-TSS-CRISPR-rep2-2nd-seq


title: heart_203s_H3


title: heart_203s_H24


title: heart_203s_H8


title: heart_203s_H21


title: Hi-C-Clone21-TSS-CRISPR-rep1-3rd-seq


title: heart_203s_H23


title: heart_203s_H2


title: Hi-C-Clone21-TSS-CRISPR-rep1-1st-seq


title: Hi-C-Clone21-TSS-CRISPR-rep1-2nd-seq


title: heart_203s_H22


title: Blood samples 122061

description:
122061
101035780078_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP213BeadChip


title: heart_203s_H19


title: heart_203s_H5


title: heart_203s_H18


title: Hi-C-Clone21-TSS-CRISPR-rep2-1st-seq


title: Blood samples 122087

description:
122087
101035780078_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP212BeadChip


title: Blood samples 127235

description:
127235
101035780078_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP210BeadChip


title: heart_203s_H17


title: Blood samples 125038

description:
125038
101035780078_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP211BeadChip


title: Blood samples 125143

description:
125143
101035780078_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP209BeadChip


title: heart_203s_H16


title: heart_203s_H15


title: heart_203s_H20


title: Hi-C-Clone21-CTCF-CRISPR-rep2-2nd-seq

description:
Hi-C
sc79_20000_iced.matrix
Hi-C_Matrices_CRISPR_Genotyped_Clone21Insertions.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
sc79.allValidPairs.hic


title: heart_203s_H14


title: Blood samples 127188

description:
127188
101035780078_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP209BeadChip


title: Hi-C-Clone21-CTCF-CRISPR-rep2-1st-seq


title: Hi-C-Clone21-CTCF-CRISPR-rep1-3rd-seq


title: heart_203s_H13


title: Hi-C-Clone21-CTCF-CRISPR-rep1-2nd-seq


title: heart_203s_H12


title: heart_203s_H10


title: heart_203s_H11


title: heart_203s_G9


title: heart_203s_H1


title: Blood samples 122086

description:
122086
101035780078_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP208BeadChip


title: Hi-C-Clone21-CTCF-CRISPR-rep1-1st-seq


title: heart_203s_G8


title: Hi-C-Clone21-CTCF-CRISPR-rep2-3rd-seq


title: heart_203s_G7


title: Blood samples 123080

description:
123080
101035780078_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP207BeadChip


title: heart_203s_G6


title: heart_203s_G5


title: Blood samples 120008

description:
120008
101035780078_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP206BeadChip


title: heart_203s_G4


title: Blood samples 126175

description:
126175
200109370005_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP204BeadChip


title: heart_203s_G3


title: heart_203s_G24


title: Non-IPF patient 1445

city: St. Gallen

first: Florent

last: Baty

address: Rorschacherstrasse 95

department: Lung Center

country: Switzerland

institute: Cantonal Hospital St. Gallen

data_processing:
Primary analysis of sequencing data was conducted using RTA version 2.4.11 and bcl2fastq v2.20.0.422 (both from Illumina)
All analyses were done using the R statistical software, including packages from the Bioconductor such edgeR (v. 3.24.3)
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the human hg38 genome assembly with STAR with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax =10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Gene expression was quantified by the qCount function of the Bioconductor package QuasR as the number of reads that started within any annotated exon of a gene from the UCSC knownGenes annotation (downloaded on 2017-04-03). Read and alignment quality was evaluated using the qQCReport function of QuasR.
Genome_build: hg38
Supplementary_files_format_and_content: dataset2_hg38AnalysisSet_knownGene_geneLevel_counts.rds, dataset2_hg38AnalysisSet_knownGene_geneLevel_counts.csv

source_name: cultured epithelial cells

growth_protocol: DMEM supplemented with fetal bovine serum (10%), penicillin (20 U/l), streptomycin (20 μg/ml), amphotericin B (2.5 μg/ml) (37°C, 21% O2, 5% CO2)

extract_protocol:
MicroElute Total RNA Kit (Omega Bio-Tek, Norcross, GA)
TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina, San Diego, CA)

treatment_protocol: Epithelial cell-specific growth medium Cnt-17 (CELLnTEC Advanced Cell Systems AG, Bern, Switzerland)

tag: condition

value: control

value: Epithelial cells differentiated from mesenchymal stems cell-like cells


title: Non-IPF patient 1460


title: Non-IPF patient C1472


title: heart_203s_G22


title: heart_203s_G21


title: Non-IPF patient 1435


title: Non-IPF patient 1433


title: heart_203s_G19


title: heart_203s_G23


title: IPF patient 21

value: idiopathic pulmonary fibrosis (IPF)


title: Blood samples 129180

description:
129180
200109370005_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP201BeadChip


title: IPF patient 1434


title: Blood samples 126177

description:
126177
200109370005_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP202BeadChip


title: heart_203s_G18


title: heart_203s_G16


title: Blood samples 121102

description:
121102
101035780078_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP205BeadChip


title: Blood samples 129152

description:
129152
200109370005_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP203BeadChip


title: heart_203s_G15


title: heart_203s_G17


title: heart_203s_G14


title: Blood samples 129158

description:
129158
200109370005_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP198BeadChip


title: heart_203s_G13


title: heart_203s_G12


title: heart_203s_G11


title: heart_203s_G10


title: heart_203s_G2


title: heart_203s_G1


title: IPF patient 14


title: Blood samples 129157

description:
129157
200109370005_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP200BeadChip


title: Blood samples 129156

description:
129156
200109370005_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP196BeadChip


title: heart_203s_F9


title: Exp2Rep1Day56CloneK_WGS

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Low coverage genome sequencing for Exp2Rep1Day56CloneK

data_processing:
Library strategy: WGS
Barcode sequencing data was filtered to include only reads that match the expected WSx15 pattern. Error correction and further analysis was performed in R.
For single-cell RNA-seq, identification of cell barcodes, genome alignment and quantification of gene expression levels for each single cell was performed as described in detail in the publication using the splice-aware aligner STAR and the R.
Low-coverage WGS data was aligned to the human reference genome (hg19) using bwa mem. Alignments were coordinate sorted and putative PCR duplicates were removed using samtools. Read coverage in genomic bins of 50kb was calculated using igvtools count and visualized using the IGV browser.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files and bedgraph coverage files. For single-cell RNA-seq experiments, a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns), and an annotation file containing the associated lineage barcode is provided.

source_name: GSC8 neurosphere culture

growth_protocol: Cells were maintained in stem cell-permissive, serum free, non-adherent spheroid cultures using Neurobasal medium (Gibco) supplemented with N2/B27 (Gibco), penicillin/streptomycin (Gibco), GlutaMAX (Gibco), recombinant human EGF (20 ng/mL, R & D systems), recombinant human FGF2 (20 ng/mL, R&D systems), and heparin (2000 ng/mL, Sigma). Cell dissociation was accomplished with trituration or Accutase (BD Bioscience) treatment.

extract_protocol:
For lineage barcode sequencing, genome DNA (gDNA) was prepared with a QIAmp DNA blood mini Kit (Qiagen). For single-cell transcriptome profiling, accutase-dissociated and filtered GSCs were counted and 10,000 single cells were loaded onto a Seq-Well nanowell array. For low-coverage WGS, gDNA was isolated using DNeasy Blood and Tissue Kit (Qiagen), and then quality and quantity of gDNA was determined by Nanodrop.
For lineage barcode sequencing, gDNA was amplified using primers bearing Illumina adaptor and index sequences. Single-cell transcriptome analysis was performed using the Seq-Well method. For low-coverage WGS, 50ng gDNA was used for tagmentation and sample preparation/amplification was performed using the Nextera DNA kit (Illumina) abd Nextera i7/i5 primers (Illumina).

treatment_protocol: Approximately 1x10E6 GSCs plated in stem cell permissive monolayer culture with laminin were infected with concentrated virus at an MOI of 10% for 24 hours prior to selection of barcode-incorporated GSCs using puromycin for 72 hours. Equivalent numbers (1x10E6) of stably-transduced barcoded cells were plated in replicates and treated with 1 μM dasatinib. Dissociation and passage of cells with renewal of compound-containing cell culture medium was performed at least weekly. Each replicate was passed and treated independently.

value: F


title: IPF patient H2


title: Blood samples 129196

description:
129196
200109370005_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP199BeadChip


title: Exp2Rep1Day56CloneJ_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneJ


title: heart_203s_F7


title: heart_203s_F6


title: Blood samples 129195

description:
129195
200109370005_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP197BeadChip


title: Blood samples 129181

description:
129181
200109370005_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP194BeadChip


title: IPF patient 15


title: Exp2Rep1Day56CloneI_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneI


title: heart_203s_F4


title: heart_203s_E17


title: heart_203s_F5


title: Exp2Rep1Day56CloneH_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneH


title: heart_203s_E16


title: heart_203s_E15


title: heart_203s_F8


title: heart_203s_I24


title: heart_203s_E14


title: Blood samples 129207

description:
129207
200109370004_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP192BeadChip


title: Blood samples 129191

description:
129191
200109370005_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP195BeadChip


title: Blood samples 129202

description:
129202
200109370005_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP193BeadChip


title: heart_203s_E13


title: Blood samples 129166

description:
129166
200109370004_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP191BeadChip


title: Blood samples 129205

description:
129205
200109370004_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP190BeadChip


title: Blood samples 129208

description:
129208
200109370004_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP188BeadChip


title: Exp2Rep1Day56CloneF_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneF


title: Exp2Rep1Day56CloneG_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneG


title: Hi-C-Clone21-CTCF&TSS-CRISPR#2-rep2-1st-seq

description:
Hi-C
sc79-3-7_20000_iced.matrix
Hi-C_Matrices_CRISPR_Genotyped_Clone21Insertions.tar
Hi-C_Eigen_Insertion_or_CRISPRed_Chromosomes
sc79-3-7.allValidPairs.hic


title: heart_203s_E11


title: heart_203s_E12


title: Exp2Rep1Day56CloneE_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneE


title: heart_203s_E10


title: heart_203s_D8


title: heart_203s_D9


title: heart_203s_D6


title: heart_203s_D7


title: Exp2Rep1Day56CloneC_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneC


title: Exp2Rep1Day56CloneD_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneD


title: heart_203s_D24


title: Exp2Rep1Day56CloneB_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneB


title: heart_203s_D22


title: heart_203s_D3


title: heart_203s_D5


title: Blood samples 129141

description:
129141
200109370004_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP189BeadChip


title: Blood samples 129169

description:
129169
200109370004_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP187BeadChip


title: Blood samples 129168

description:
129168
200109370004_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP185BeadChip


title: Exp2Rep1Day56CloneA_WGS

description: Low coverage genome sequencing for Exp2Rep1Day56CloneA


title: Blood samples 129145

description:
129145
200109370004_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP184BeadChip


title: Exp1Rep4Day70CloneK_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneK


title: Blood samples 129163

description:
129163
200109370004_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP186BeadChip


title: Exp1Rep4Day70CloneJ_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneJ


title: heart_203s_D20


title: heart_203s_D19


title: Blood samples 129131

description:
129131
200109370004_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP183BeadChip


title: heart_203s_D21


title: heart_203s_D4


title: Blood samples 129155

description:
129155
200109370004_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP182BeadChip


title: heart_203s_D2


title: heart_203s_D17


title: heart_203s_D18


title: heart_203s_D16


title: Exp1Rep4Day70CloneH_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneH


title: heart_203s_D23


title: heart_203s_D15


title: heart_203s_D14


title: Exp1Rep4Day70CloneE_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneE


title: Exp1Rep3Day70CloneF_WGS

description: Low coverage genome sequencing for Exp1Rep3Day70CloneF


title: heart_203s_D12


title: heart_203s_D13


title: heart_203s_D11


title: heart_203s_D10


title: Blood samples 129171

description:
129171
200109370004_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP181BeadChip


title: Exp1Rep3Day70CloneD_WGS

description: Low coverage genome sequencing for Exp1Rep3Day70CloneD


title: heart_203s_C8


title: heart_203s_D1


title: heart_203s_C9


title: Exp1Rep3Day70CloneC_WGS

description: Low coverage genome sequencing for Exp1Rep3Day70CloneC


title: Exp1Rep1Day70CloneB_WGS

description: Low coverage genome sequencing for Exp1Rep1Day70CloneB


title: heart_203s_C7


title: heart_203s_C6


title: Blood samples 1414053

description:
1414053
101035780076_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP180BeadChip


title: Blood samples 1414040

description:
1414040
101035780076_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP179BeadChip


title: Blood samples 1414052

description:
1414052
101035780076_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP178BeadChip


title: Blood samples 1414032

description:
1414032
101035780076_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP175BeadChip


title: Blood samples 1414051

description:
1414051
101035780076_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP176BeadChip


title: Exp1Rep1Day70CloneA_WGS

description: Low coverage genome sequencing for Exp1Rep1Day70CloneA


title: Blood samples 1414033

description:
1414033
101035780076_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP177BeadChip


title: heart_203s_C5


title: Blood samples 1414041

description:
1414041
101035780076_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP174BeadChip


title: heart_203s_C4


title: heart_203s_C24


title: Blood samples 1414018

description:
1414018
101035780076_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP173BeadChip


title: heart_203s_C23


title: heart_203s_C3


title: heart_203s_C22


title: Naive_WGS

description: Low coverage genome sequencing for Naive


title: Exp2Day28_SeqWell-Barcode

description: Single-cell transcriptome-based lineage barcode sequencing for Exp2Day28

data_processing:
Barcode sequencing data was filtered to include only reads that match the expected WSx15 pattern. Error correction and further analysis was performed in R.
For single-cell RNA-seq, identification of cell barcodes, genome alignment and quantification of gene expression levels for each single cell was performed as described in detail in the publication using the splice-aware aligner STAR and the R.
Low-coverage WGS data was aligned to the human reference genome (hg19) using bwa mem. Alignments were coordinate sorted and putative PCR duplicates were removed using samtools. Read coverage in genomic bins of 50kb was calculated using igvtools count and visualized using the IGV browser.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files and bedgraph coverage files. For single-cell RNA-seq experiments, a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns), and an annotation file containing the associated lineage barcode is provided.


title: heart_203s_C21


title: Blood samples 1413124

description:
1413124
101035780076_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP171BeadChip


title: Exp2Day28_SeqWell

description: Single-cell transcriptome analysis for Exp2Day28


title: Exp1Day28_SeqWell-Barcode

description: Single-cell transcriptome-based lineage barcode sequencing for Exp1Day28


title: heart_203s_C2


title: heart_203s_C20


title: Blood samples 1414089

description:
1414089
101035780076_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP170BeadChip


title: Blood samples 1414090

description:
1414090
101035780076_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP172BeadChip


title: Blood samples 128071

description:
128071
101035780048_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP168BeadChip


title: Exp2Rep6Day56

description: DNA-based lineage barcode sequencing for Exp2Rep6Day56

data_processing:
Library strategy: Amplicon-seq
Barcode sequencing data was filtered to include only reads that match the expected WSx15 pattern. Error correction and further analysis was performed in R.
For single-cell RNA-seq, identification of cell barcodes, genome alignment and quantification of gene expression levels for each single cell was performed as described in detail in the publication using the splice-aware aligner STAR and the R.
Low-coverage WGS data was aligned to the human reference genome (hg19) using bwa mem. Alignments were coordinate sorted and putative PCR duplicates were removed using samtools. Read coverage in genomic bins of 50kb was calculated using igvtools count and visualized using the IGV browser.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files and bedgraph coverage files. For single-cell RNA-seq experiments, a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns), and an annotation file containing the associated lineage barcode is provided.


title: Blood samples 1413117

description:
1413117
101035780076_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP169BeadChip


title: Exp1Day28_SeqWell

description: Single-cell transcriptome analysis for Exp1Day28