title: Msn2_570_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-570aaNterm Mnase::kanMX


title: Msn2_cGla_m4_Tail_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

status: Public on Nov 19 2023

type: SRA

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: RNA-seq

library_source: transcriptomic

data_processing:
demultiplexing with AdapterRemoval, --trim3p 0 21
identification of UMI with umi_tools extract, --bc-pattern=NNNNNNNNN
mapping the reads with bowtie2, -p8 --local --very-sensitive --trim-to 30 -x
sorting and indexing with samtools
deduplication of UMI with umi_tools dedup
calculation of coverage with bedtools coverage -counts -s -a
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: proceesed data files contain counts mapped with bedttols coverage in format of  (chromosome, chromosome location (start), chromosome location (stop), systemic name, number, strand, counts)

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose

extract_protocol:
RNA-seq: modified protocol of the nucleospin 96 RNA kit (Macherey-Nagel, Duren, Germany). Specifically, cell lysis was done in a 96 deep-well plate by adding 450 μl of lysis buffer containing 1 M sorbitol (Sigma-Aldrich), 100 mM EDTA, and 0.45 μl lyticase (10 IU/μl). The plate was incubated at 30°C for 30 minutes in order to break the cell wall and then centrifuged for 10 minutes at 2,500 rpm, and the supernatant was removed. From this point, extraction proceeded as in the protocol of nucleospin 96 RNA kit, only substituting β-mercaptoethanol with DTT 1M.
RNA libraries were created as described before (Chapal et al., 2019)

treatment_protocol: The cells were treated with H2O2 in final concentration of 0.3mM for 20 minutes in 30 degrees with constant shaking

tag: strain

tag: treatment

tag: genotype

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 C.glabrata Msn4 non-DBD Mnase::kanMX


title: Msn2_570_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dTAD_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-267aaNterm Mnase::kanMX


title: Msn2_dTAD_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_dTAD_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-267aaNterm Mnase::kanMX


title: Msn2_604_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-604aaNterm Mnase::kanMX


title: Msn2_604_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_520_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-520aaNterm Mnase::kanMX


title: Msn2_520_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_570_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-570aaNterm Mnase::kanMX


title: Msn2_604_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_520_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-520aaNterm Mnase::kanMX


title: Msn2_520_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_520_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_470_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-470aaNterm Mnase::kanMX


title: Msn2_570_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_470_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_470_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_470_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-470aaNterm Mnase::kanMX


title: Msn2_570_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_470_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_450_642_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-450-642 Mnase::kanMX


title: Msn2_450_642_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_420_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-420aaNterm Mnase::kanMX


title: Msn2_450_642_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-450-642 Mnase::kanMX


title: Msn2_420_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-420aaNterm Mnase::kanMX


title: Msn2_420_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_450_642_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_420_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_450_642_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_370_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-370aaNterm Mnase::kanMX


title: Msn2_370_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-370aaNterm Mnase::kanMX


title: Msn2_370_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_350_550_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-350-550 Mnase::kanMX


title: Msn2_350_550_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-350-550 Mnase::kanMX


title: Msn2_350_550_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_370_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_370_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_420_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_320_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2-delta-320aaNterm Mnase::kanMX


title: Msn2_320_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-320aaNterm Mnase::kanMX


title: Msn2_320_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_320_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_642_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-250-462 Mnase::kanMX


title: Msn2_250_550_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-250-550 Mnase::kanMX


title: Msn2_250_642_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_420_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_550_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_450_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-250-450 Mnase::kanMX


title: Msn2_250_550_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_350_550_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_320_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_200_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-200aaNterm Mnase::kanMX


title: Msn2_150_550_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-150-550 Mnase::kanMX


title: Msn2_150_450_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-150-450 Mnase::kanMX


title: Msn2_150_450_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_150_350_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2 -delta-150-350 Mnase::kanMX


title: Msn2_150_350_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_450_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2 -delta-250-450 Mnase::kanMX


title: Msn2_250_450_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_450_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_450_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_200_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2 -delta-200aaNterm Mnase::kanMX


title: Msn2_150_350_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-150-350 Mnase::kanMX


title: Msn2_200_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_200_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_200_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_135_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2 -delta-135aaNterm Mnase::kanMX


title: Msn2_150_550_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_135_dMsn4_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_135_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-135aaNterm Mnase::kanMX


title: Msn2_135_dMsn4_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_250_550_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_150_550_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_135_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2-Mnase (kanMX)


title: Msn2_150_350_dMsn4_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_5,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_6,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LIV_random1_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(LIV_random1)-Mnase (kanMX)


title: Msn2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LIV_deletion_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(LIV_deletion)-Mnase (kanMX)


title: LIV_random1_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LIV_deletion_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LIV_cluster2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(LIV_cluster2)-Mnase (kanMX)


title: LIV_cluster3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(LIV_cluster3)-Mnase (kanMX)


title: LIV_cluster3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LIV_cluster2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: LI_shift_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(LI_shift)-Mnase (kanMX)


title: LI_shift_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Left_positive_right_negative_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(Left_positive_right_negative)-Mnase (kanMX)


title: Msn2_150_350_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Left_positive_right_negative_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: L_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(L_to_A)-Mnase (kanMX)


title: Msn2_150_550_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: L_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: KR_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(KR_to_A)-Mnase (kanMX)


title: KR_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: G_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(G_to_A)-Mnase (kanMX)


title: FWY_shift_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_shift)-Mnase (kanMX)


title: FWY_to_A,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_to_A)-Mnase (kanMX)


title: FWY_random3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_random3)-Mnase (kanMX)


title: FWY_shift_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: FWY_deletion_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_deletion)-Mnase (kanMX)


title: FWY_cluster3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_cluster3)-Mnase (kanMX)


title: FWY_deletion_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: FWY_cluster3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: FWY_cluster2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(FWY_cluster2)-Mnase (kanMX)


title: ED_shift2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_shift2)-Mnase (kanMX)


title: ED_random3_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_random3)-Mnase (kanMX)


title: FWY_cluster2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_random1_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_random1)-Mnase (kanMX)


title: ED_deletion_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_deletion)-Mnase (kanMX)


title: ED_cluster2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_cluster2)-Mnase (kanMX)


title: ED_cluster2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_random1_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_random2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(ED_random2)-Mnase (kanMX)


title: E_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(E_nextto_N)-Mnase (kanMX)


title: dMsn2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2-delta-0


title: E_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: G_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: dMsn2_3,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_deletion_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: dMsn2_5,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: dMsn2_7,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_shift2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: dMsn2_4,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: dMsn2_8,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: DE_to_A_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(DE_to_A)-Mnase (kanMX)


title: ED_random3_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: D_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(D_nextto_N)-Mnase (kanMX)


title: D_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: A_nextto_N_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(A_nextto_N)-Mnase (kanMX)


title: DE_to_A_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: ED_random2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: A_nextto_N_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: charged_random_cluster_2_2,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(charged_random_cluster_2)-Mnase (kanMX)


title: charged_random_cluster_2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep5x4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt and picard
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome

molecule: genomic DNA

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 4 in SC medium with glucose

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep5x4)-Mnase (kanMX)


title: 90p_10n_chargeratio_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(90p_10n_chargeratio)-Mnase (kanMX)


title: dMsn2_1,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: rep1x4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep1x4)-Mnase (kanMX)


title: rep3x4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep3x4)-Mnase (kanMX)


title: randomaa-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(randomaa)-Mnase (kanMX)


title: rep0x4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep0x4)-Mnase (kanMX)


title: P_is_placed_next_to_N_4, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(P_is_placed_next_to_N)-Mnase (kanMX)


title: raax4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(raax4)-Mnase (kanMX)


title: dMsn2_6,total RNA ,H2O2 0.3mM, 20min target O.D600 0.4

description: RNA-seq


title: Msn2_Scramble10_2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 Scrambled10aasregions Mnase::kanMX


title: P_is_placed_next_to_N_2, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Msn2_250_642_1-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-250-642 Mnase::kanMX


title: Msn2_Scramble10_1-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Msn2_250_550_2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-250-550 Mnase::kanMX


title: Msn2_150_450_1-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-150-450 Mnase::kanMX


title: Msn2_250_642_2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Msn2_150_550_1-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 -delta-150-550 Mnase::kanMX


title: Msn2_250_550_1-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Msn2_150_550_2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: rep8x4-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(rep8x4)-Mnase (kanMX)


title: Med15-Mnase, Msn2-T_nextto_N_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(T_nextto_N) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-S_nextto_N_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(S_nextto_N) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-S_nextto_N_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-PG_shift_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(PG_shift) Med15::Med15-Mnase (kanMX)


title: Msn2_150_450_2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-T_nextto_N_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-P_to_A_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(P_to_A) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-P_to_A_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-PG_shift_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-NQ_shift_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(NQ_shift) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_sMik_m2_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_sMik_m2_Tail) Med15::Med15-Mnase (kanMX)


title: raax2-Mnase, 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn2 ::Msn2(raax2)-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_sCerm4T_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_sCerm4T) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_sMik_m2_Tail_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_sCas_m4_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_sCas_m4_Tail) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_sCas_m4_Tail_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_kWal_m_Tail_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_kWal_m_Tail) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_kLac_m_Tail_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_kLac_m_Tail) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_ddMotAMotB_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_ddMotAMotB) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_ddMotAMotB_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_kLac_m_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_dTAD_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_dTAD) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_cGla_m2_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_cGla_m2_Tail) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_dTAD_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_dMotA_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_dMotA) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-NQ_shift_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_6 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_420_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_420) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_4 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_5 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_420_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_sCerm4T_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_cGla_m2_Tail_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_sKlu_m_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_sKlu_m_Tail) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_320_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_320) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_350_550_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_350_550) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_250_450_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_250_450) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_250_450_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_150_350_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_150_350) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_kWal_m_Tail_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_150_350_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_200_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_200) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_135_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(Msn2_135) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-Msn2_135_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_320_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_350_550_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-MotA_NLS_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(MotA_NLS) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-MotA_NLS_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-Msn2_3 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-MSN2_start_nls_3 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(MSN2_start_nls) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-MSN2_start_nls_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LI_shift_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LI_shift) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-MSN2_start_nls_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIV_deletion_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIV_deletion) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_to_Y_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_to_Y) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LI_shift_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_to_I_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_to_I) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to91_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to91) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_to_I_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_to_A_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_to_A) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to91_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_to71_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to71) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to51_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to51) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to51_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_to_A_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_to71_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_to31_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to31) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to11_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to11) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to31_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_to11_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_to111_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_to111) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_from81_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_from81) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_to111_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_from61_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_from61) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_from81_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_from41_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_from41) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_from61_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_from41_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIV_deletion_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_from101_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_from101) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_from21_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(LIVFWY_deletion_from21) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-LIVFWY_deletion_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-LIVFWY_deletion_from101_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-FWY_to_I_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(FWY_to_I) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-FWY_to_L_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(FWY_to_L) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-FWY_shift_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(FWY_shift) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-FWY_to_I_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-FWY_shift_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-FWY_to_L_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-DE_to_Q_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(DE_to_Q) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-DE_to_N_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(DE_to_N) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-FWY_random3_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(FWY_random3) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-DE_to_Q_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-DE_spread_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(DE_spread) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-DE_spread_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-DE_to_N_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-DEKR_to_Q_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(DEKR_to_Q) Med15::Med15-Mnase (kanMX)


title: T7- normal 2 (T7_NORM2 002)

city: Gainesville

first: Bryan

last: Alava

state: FL

country: USA

institute: University of Florida

description: NanoString Whole Transcriptome Atlas- mouse

data_processing:
raw sequencing data was aligned to Nanostring in sit hybridization probes.
transcript counts underwent standard NanoString quality control and normalization steps on the GeoMx DSP analysis suite
gene expression was analyzed using the GeoMx DSP analysis suite
Assembly: mm10
Supplementary files format and content: Q3 Normalized Processed Data- skm P301L-AAV8 study: excel file, normalized transcript expression in the 80 regions analyzed in this study
Library strategy: GeoMx spatial transcriptomics

organism: Mus musculus

source_name: Tibialis anterior 8micron flash frozen cross section

extract_protocol:
tibialis anterior muscles were embedded in OCT and cryosectioned into 8um cross sections
GeoMx spatial transcriptomics libraries were prepped following manufacturers protocols

tag: mouse id

tag: tissue

value: Tibialis anterior

tag: tissue region

value: normal

tag: cell type

value: Myofibers

value: WT

tag: Sex

value: female

value: tauopathy


title: T7- surrounding artery 2 (T7_SA2 002)

value: surrounding artery


title: T7- surrounding artery (T7_SA1 002)


title: T7- normal (T7_NORM1 002)


title: T7- central nuclei 2 (T7_CN2 002)

value: central nuclei


title: T7- nerve bundle  (T7_NB1 002)

value: nerve bundle


title: Med15-Mnase, Msn2-DEKR_to_Q_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: T7- central nuclei  (T7_CN1_FLAG)


title: Med15-Mnase, Msn2-90_chargedaa_to_N_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(90_chargedaa_to_N) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-90p_10n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(90p_10n_chargeratio) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-90p_10n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-FWY_random3_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: T14-surrounding artery (T14_SA1 002)

value: male


title: T14- normal (T14_NORM1 002)


title: T14-central nuclei  2 (T14_CN2 002)


title: Med15-Mnase, Msn2-80p_20n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(80p_20n_chargeratio) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-60p_40n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(60p_40n_chargeratio) Med15::Med15-Mnase (kanMX)


title: T14-nerve bundle  (T14_NB1 002)


title: Med15-Mnase, Msn2-70p_30n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(70p_30n_chargeratio) Med15::Med15-Mnase (kanMX)


title: T14-central nuclei  (T14_CN1 002)


title: Med15-Mnase, Msn2-60p_40n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-70p_30n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-50p_50n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(50p_50n_chargeratio) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-40p_60n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(40p_60n_chargeratio) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-50p_50n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: C40-normal (C40_NORM1)

value: Tibialis anterior

value: control


title: C40-surrounding artery (C40_SA1)

value: Myofibers


title: Med15-Mnase, Msn2-40p_60n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: C40-normal 2 (C40_NORM2)

value: normal

value: WT


title: C40-central nuclei  (C40_CN1)


title: C40-central nuclei 2 (C40_CN2)


title: C40-nerve bundle  (C40_NB1)


title: Med15-Mnase, Msn2-30p_70n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(30p_70n_chargeratio) Med15::Med15-Mnase (kanMX)


title: C3-surrounding artery 2 (C3_SA2)

value: surrounding artery

value: female


title: Med15-Mnase, Msn2-80p_20n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: Med15-Mnase, Msn2-20p_80n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(20p_80n_chargeratio) Med15::Med15-Mnase (kanMX)


title: C3-surrounding artery (C3_SA1)


title: C3-normal 2 (C3_NORM2)


title: Med15-Mnase, Msn2-10p_90n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ

value: MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0 Msn4-delta-0 Msn2::Msn2(10p_90n_chargeratio) Med15::Med15-Mnase (kanMX)


title: Med15-Mnase, Msn2-20p_80n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: C3-normal (C3_NORM1)


title: C3-central nuclei 2 (C3_CN2)

value: central nuclei


title: T30 - surrounding artery (T30_SA2 002)

value: tauopathy


title: ATAC-seq for cell grown in 3D normal media replicate 2

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: 3D growth

data_processing: ATAC-seq Peak Calling. Analysis of ATAC data was carried out as previously described (Ferrari et al., 2020) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie with aligning parameters of uniqueness (-S  m1  v2  t  q). p-values for the significance of ChIP-seq counts compared to input DNA were calculated as previously described (Pellegrini M. and Ferrari R, 2012) using a p-value threshold of 10-8 and a false discovery rate (FDR) < 1%. Bigwig for normalized tags (alltags) and -log10 poisson Pvalue (poissP) were generated as previously described (Pellegrini M. and Ferrari R, 2012).

organism: Homo sapiens

source_name: breast

growth_protocol:
2D growth of cells.T47D breast cancer cells were routinely grown in 10 cm dishese with RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin.
3D growth of cells. Prechilled p60 plates were coated with a thin layer of Matrigel (Corning Life Sciences) and then incubated for 20–30 min at 37ºC to allow polymerization without over drying. 200,00 cells trypsinized cells were resuspended and plated on-top of the Matrigel without disrupting the capsule. Culture was maintained for 10 days changing the medium every 2-3 days.  Spheroids extraction from 3D matrix: Dishes containing the spheroids grown for 10 days were rinsed twice with PBS followed by addition of 3 ml ice-cold PBS-EDTA. Matrigel including the 3D spheroids was carefully detached with a plastic scraper and left on ice for 30 min to allow complete depolymerization of the gel. The liquid solution was transferred to a conical tube, centrifuged for 5 min at 112 x g and rinsed twice with 0.5 volume of PBS-EDTA. The cell pellet was then ready for further processing.

extract_protocol: Library preparation for ATAC experiments were performed as described (Buenrostro et al., 2013) using nuclei obtained from 2D or 3D grown T47D cells.

treatment_protocol:
For the experiments with hormones, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.
For hormonal induction on the 3D spheroids, T47D cells were plated on top of phenol red-free Matrigel and after 7 days of culture medium was replaced by RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with 10 nM R5020 for different times at 37ºC.

value: breast

tag: cell line

value: Epithelial cancer metastatic

value: 3D culture normal media


title: C3-central nuclei  (C3_CN1)


title: T30 - normal 2 (T30_NORM2 002)


title: Med15-Mnase, Msn2-10p_90n_chargeratio_1 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: MM001, Evolved (Pool3), Lenti ATAC-seq

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
genome assembly: hg38 + EFS_randomSeqs.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against hg38 with EFS_evolvedSeqs.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.

growth_protocol: Ham's F10 nutrient mix, 10% fetal bovine serum, 1x penicillin/streptomcyin, cultured at 37°C and 5% CO2

extract_protocol: Transposed DNA was amplified for 10 cycles using i5- and i7-indexing primers.  Postamplification libraries were size selected at 200-1000 bp in length using Agencourt AmPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA high sensitivity kit.

treatment_protocol: Cells were lysed in cold ATAC resuspension buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2; 0.1 % NP40, 0.1% Tween20, 0.01% Digitonin) for 3 min. Isolated nuclei were incubated for 30 min at 37°C in transposition mix containing Tn5 transposase.

value: Patient-derived melanoma cell line 001


title: MM001, Repressed (Pool1), Lenti, ATAC-seq

data_processing:
genome assembly: hg38 + EFS_repressedSeqs.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against hg38 with EFS_repressedSeqs.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: ATAC-seq for cell grown in 2D normal media replicate 2

description: 2D growth


title: MM001, Random (Pool2), Lenti, ATAC-seq

data_processing:
genome assembly: hg38 + EFS_randomSeqs.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against hg38 with EFS_randomSeqs.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: T30 - normal (T30_NORM1 002)


title: Med15-Mnase, Msn2-30p_70n_chargeratio_2 , 30 sec CaCl pulse, target O.D.600-4

description: ChEC-SEQ


title: T30 - nerve bundle  (T30_NB1 002)

value: nerve bundle


title: MM001, 10 EFS, ATAC-seq

data_processing:
genome assembly: hg38 + EFS_10seqs.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against hg38 with 10_EFSseqs.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: MM001, Input, ChIP-seq

data_processing:
genome assembly: hg38
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against hg38. Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching and cell lysis, chromatin was sonicated used a Diagenode Bioruptor sonicator.
ChIP-seq libraries were prepared using the Illumina Truseq DNA sample preparation guide. 15 ng of DNA was used as starting material. Libraries were amplified using 18 cycles on the Thermocycler. Postamplification libraries were size selected at 300-500 bp in length using Agencourt AmPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA high sensitivity kit.


title: Hi-C for cell grown in 3D normal media

description: 3D growth

data_processing: We processed Hi-C data by using an in-house pipeline based on TADbit (12). First, the quality of the reads was checked with FastQC to discard problematic samples and detect systematic artifacts. Trimmomatic (8) with the recommended parameters for paired-end reads was used to remove adaptor sequences and poor-quality reads (ILLUMINACLIP:TruSeq3-PE.fa:2:30:12:1:true; LEADING:3; TRAILING:3; MAsXINFO:targetLength:0.999; and MINLEN:36). For mapping, a fragment-based strategy implemented in TADbit was used, which was similar to previously published protocols (13). Briefly, each side of the sequenced read was mapped in full length to the reference genome (GRCh38). After this step, if a read was not uniquely mapped, we assumed that the read was chimeric, owing to ligation of several DNA fragments. We next searched for ligation sites, discarding those reads in which no ligation site was found. The remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. These steps were repeated for each read in the input FASTQ files. Multiple fragments from a single uniquely mapped read resulted in a number of contacts identical to the number of possible pairs between the fragments. For example, if a single read was mapped through three fragments, a total of three contacts (all-versus-all) was represented in the final contact matrix. We used the TADbit filtering module to remove non-informative contacts and to create contact matrices. The different categories of filtered reads applied were: 1.Self-circle: reads coming from a single restriction enzyme (RE) fragment and pointing to the outside. 2.Dangling end: reads coming from a single RE fragment and pointing to the inside. 3.Error: reads coming from a single RE fragment and pointing in the same direction 4.Extra dangling end: reads coming from different RE fragments but that were sufficiently close and point to the inside; the distance threshold used was left to 500 bp (default), which was between percentiles 95 and 99 of average fragment lengths. 5.Duplicated: the combination of the start positions and directions of the reads was repeated, thus suggesting a PCR artifact; this filter removed only extra copies of the original pair. 6.Random breaks: the start position of one of the reads was too far from RE cutting site, possibly because of non-canonical enzymatic activity or random physical breaks; the threshold was set to 750 bp (default), >percentile 99.9. From the resulting contact matrices, low-quality bins (those presenting low contact numbers) were removed, as implemented in TADbit’s ‘filter columns’ routine. A single round of ICE normalization (14), also known as ‘vanilla’ normalization (16), was performed. That is, each cell in the Hi-C matrix was divided by the product of the interactions in its columns and the interactions in its row. Finally, all matrices were corrected to achieve an average content of one interaction per cell.

molecule: polyA RNA

extract_protocol:
Hi-C was performed as previously described (11) with the following modifications: (i) two million cells obtained from T47D cells cultured in 2D monolayer or as 3D spheroids were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1 NEB2 buffer; (iv) ligation was performed overnight at 24°C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300–400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 sec on and 60 sec off); (vi) DNA fragment-size selection was performed only after final library amplification
library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3 μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8–12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and lowcoverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n=2) of each biological replicate (n=2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate.


title: T13-nerve bundle  (T13_NB1 002)

value: Tibialis anterior


title: T13-central nuclei 3 (T13_CN3)


title: C3-nerve bundle  (C3_NB1)

value: control


title: T13-central nuclei  (T13_CN1 002)

value: Myofibers


title: DIPGXIII K27M Input

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Reads were aligned to the human genome (hg38) with Bowtie2 (v 2.4.2) using default parameters
Unmapped and duplicated reads were removed with SAMtools (v 1.10.0) and converted to wig files.
BigWig files were generated with Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1) and files were visualised in the UCSC browser
assembly: hg38
processed data files format and content: BigWig and Wig files of reads mapped to hg38 human genome

source_name: DIPGXIII

growth_protocol: Human patient derived glioma cells were cultured in complete media, consisting of human NeuroCult NS-A Proliferation media (Stemcell technologies) with 0.002% Heparin, 10 ng/ml bFGF, 20 ng/ml rhEGF, penicillin and streptomycin. BT245 cells were cultured in Neurobasal-A/DMEM/F12 media (Gibco ThermoFisher, cat no. 10888-022 and 11330-032) with NEAA, 2 mM Glutamax, penicillin/streptomycin, 10 mM Hepes, 1 mM sodium pyruvate, B27 supplement, 20 ng/ml rhEGF, 20 ng/ml bFGF, 0.002% Heparin, 10 ng/ml PDGF-AA, 10 ng/ml PDGF-BB.

extract_protocol:
5 million cells were fixed in growth media with 0.4% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was released by sequential lysis with cells lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% Igepal) and nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). Chromatin was sheared to ≈300 bp with 12 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and incubated overnight at 4 ᵒC with 5 μg H3.3 antibody (Abcam, Ab176840). Samples were immunoprecipitated with Protein A Agarose beads (Sigma-Aldrich, 05015979001) and washed sequentially with low salt (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), and LiCl buffers (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1% Igepal, 1% sodium deoxycholate). Chromatin was eluted with elution buffer (1% SDS, 100 mM NaHCO3), decrosslinked overnight at 65ᵒC, incubated with Proteinase K, phenol chloroform extracted and ethanol precipitated.
Ovation Ultralow System V2 using Nugen protocols M01379 v3.1. Denaturing and on-board clustering using 2pM of library pool containing 1% PhiX, Illumina protocol 15048776 v15 Apr 2020. 75 SR sequencing using Illumina NextSeq550 High output mode and v2.5 chemistry. Illumina Protocol 15069765 v06, Jul 2019.

value: DIPGXIII

value: human glioma

value: Input


title: MM099, 10 EFS, ATAC-seq

value: Patient-derived melanoma cell line 099


title: ATAC-seq for cell grown in 3D normal media replicate1

description: 3D growth


title: MM001, ZEB2, ChIP-seq


title: C30- surrounding artery (C30_SA1)

value: surrounding artery

value: WT

value: male


title: T30 - nerve bundle 2 (T30_NB2 002)

value: female


title: poly-A+ RNA-seq in normal media in 3D culture replicate 6

description: 3D growth

data_processing: Sequencing adapters and low-quality ends were trimmed from the reads using Trimmomatic, using the parameters values recommended (8) and elsewhere (https://goo.gl/VzoqQq) (trimmomatic PE raw_fastq trimmed_fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:12:1:true LEADING:3 TRAILING:3 MAsXINFO:50:0.999 MINLEN:36). The trimmed reads were aligned to GRCh38 (9) using STAR (10). First, the genome index files for STAR were generated with: star–runMode genomeGenerate–genomeDir GENOME_DIR–genomeFastaFiles genome_fasta– runThreadN slots–sjdbOverhang read_length–sjdbGTFfile sjdb–outFileNamePrefix GENOME_DIR/ Where genome_fasta is the FASTA file containing the GRCh38 sequence downloaded from the University of California Santa Cruz (UCSC) Genome Browser, excluding the random scaffolds and the alternative haplotypes; and sjdb is the GTF file with the GENCODE’s V24 annotation. Second, trimmed reads were aligned to the indexed genome with: star–genomeDir GENOME_DIR/–genomeLoad NoSharedMemory–runThreadN slots–outFilterType “BySJout”–outFilterMultimapNmax 20–alignSJoverhangMin 8–alignSJDBoverhangMin 1–outFilterMismatchNmax 999–outFilterMismatchNoverLmax 0.04–alignIntronMin 20– alignIntronMax 1000000–alignMatesGapMax 1000000–readFilesIn read1 read2– outSAMtype BAM SortedByCoordinate–outTmpDir TMP_DIR/–outFileNamePrefix ODIR1/$sample_id.–outWigType bedGraph–readFilesCommand zcat. Differences in gene expression were calculated by using a DESeq.R script for RNA analysis (available for download at Mendeley http://dx.doi.org/10.17632/mzjf96t3gc.5). Genes with fold change (FC) Å} 1.5 (p value < 0.05; FDR < 0.01) were considered as significantly regulated. Sitepro profiles were generated with the script, provided in the CEAS package

extract_protocol:
RNA-seq: RNA was isolated from cells cultured in 2D monolayer or as 3D spheroids with TRIzol reagent (Ambion), ethanol precipitated, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer and RNA subjected to Bioanalyzer for quality control.
Libraries were prepared using 1 μg of polyA+ RNA by PCR amplification of cDNA with bar-coded primers using the Illumina TruSeq kit at the CRG Genomic Facility. Libraries were sequenced using Illumina HIseq-2500 to obtain pairended (PE) 100-base-long reads.


title: Hi-C for cell grown in 2D normal media

description: 2D growth


title: C30- surrounding artery 2 (C30_SA2)


title: T13-surrounding artery (T13_SA1 002)

value: tauopathy


title: C30- normal (C30_NORM2)

value: normal


title: DIPGXIII K27KO Input


title: poly-A+ RNA-seq in normal media in 3D culture replicate 2

description: 3D growth

value: breast

value: Epithelial cancer metastatic


title: T13-normal (T13_NORM1 002)


title: poly-A+ RNA-seq in normal media in 3D culture replicate 5

description: 3D growth

value: 3D culture normal media


title: C30- central nuclei  (C30_CN2)

value: central nuclei


title: DIPGXIII K27KO H33ChIP L14

value: H3.3 ChIP (Abcam, Ab176840)


title: T13-central nuclei 2 (T13_CN2 002)

value: Tibialis anterior


title: C30- central nuclei  (C30_CN1)

value: Myofibers

value: control


title: BT245 K27M Input

value: human glioma


title: C30- normal (C30_NORM1)


title: C30- nerve bundle  (C30_NB2)

value: nerve bundle


title: ATAC-seq for cell grown in 2D normal media replicate1

description: 2D growth


title: DIPGXIII K27M H33ChIP L14

value: DIPGXIII


title: poly-A+ RNA-seq in normal media in 2D culture replicate 4

description: 2D growth

value: 2D culture nomal media


title: poly-A+ RNA-seq in normal media in 2D culture replicate 3

description: 2D growth


title: poly-A+ RNA-seq in normal media in 3D culture replicate 1

description: 3D growth


title: C30- nerve bundle  (C30_NB1)

value: WT


title: C2 - normal (C2_NORM1)


title: BT245 K27KO Input

value: Input


title: C2 - surrounding artery (C2_SA1)

value: surrounding artery

value: female


title: BT245 K27M H33ChIP L14


title: C2 - central nuclei  (C2_CN1)


title: BT245 K27KO H33ChIP L14


title: C2 - nerve bundle  (C2_NB2)


title: C2 - nerve bundle  (C2_NB1)


title: poly-A+ RNA-seq in normal media in 2D culture replicate 1

description: 2D growth


title: poly-A+ RNA-seq of T60 in 3D culture replicate 3

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 60min


title: T20 - surrounding artery (T20_SA2)

value: tauopathy


title: poly-A+ RNA-seq in normal media in 2D culture replicate 2

description: 2D growth

value: breast

value: Epithelial cancer metastatic


title: C2 - surrounding artery (C2_SA2)


title: poly-A+ RNA-seq of T60 in 3D culture replicate 2

description: 3D growth


title: CTFR-bESC-F7-102-5-5

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

country: China

institute: Inner Mongolia University

description: bovine embryonic stem cells cultured with CTFR+5μM MM-102

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
For each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: UCSC BT9
Supplementary files format and content: comma-separated values file includes raw counts for each sample

organism: Bos taurus

source_name: bovine embryonic stem cells

growth_protocol: In short, bovine ovaries were obtained from a local abattoir, and oocytes were cultured for 22–24 h after maturation and fertilized with frozen cattle sperm. Six hours after fertilization, the eggs were transferred to the embryonic culture medium. When the embryos had developed to the 8-cell stage at 48 h, MM-102, PD0325901 and CHIR99021 (2i), or MM-102 plus PD0325901 and CHIR99021 (3i), was added to the medium. The embryos were then cultured for 7–8 days to develop into blastocysts.The bovine blastocysts obtained via in vitro fertilization were removed from the zona pellucida and plated in 4-well plates, and mTeSR-E6 (05946, STEMCELL Technologies  , Vancouver,Canada) was added with 20 ng/mL FGF-2 (100-18B, STEMCELL Technologies, Vancouver,Canada), 2.5 μM IWR-1 (I0161, Sigma-Aldrich, Shanghai, ChinaUSA) and 0.1328 g/mL low fatty acid BSA (219989925, MP Biomedicals NZ, New Zealand, USA), and were incubated at 37 °C and 5% CO2. After 48–72 h, ICMs adhered to the feeder layer, and the medium was changed daily. Outgrowths (after 8–10 days in culture) were dissociated and passaged using TrypLE (12563011, Gibco, California, USA) and were reseeded in the presence of 10 μM Rho kinase (ROCK) inhibitor Y-27632 (SCM075, Sigma, Shanghai, ChinaGermany). The established bESC lines were grown in 12-well plates and were passaged every 5 days at a 1:4–1:6 split ratio. To increase cell survival, the ROCK inhibitor Y-27632 (10 μM) was added to the wells 1 h before passaging and was also added to the newly prepared wells containing MEFs treated with mitomycin and fresh culture medium during the first 24 h of cultivation.

extract_protocol:
Cells were collected by tryple-select enzyme  and the lyophilized cells were sent for sequencing. Transcriptome (RNA) sequencing was performed by Tianjin Nuohe Zhiyuan Biotechnology Co., LTD, Tianjin, China.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each samp

treatment_protocol: Bovine ovaries were obtained from a local abattoir, and oocytes were cultured for 22–24 h after maturation and fertilized with frozen cattle sperm. Six hours after fertilization, the eggs were transferred to the embryonic culture medium. When the embryos had developed to the 8-cell stage at 48 h, MM-102, PD0325901 and CHIR99021 (2i), or MM-102 plus PD0325901 and CHIR99021 (3i), was added to the medium. The embryos were then cultured for 7–8 days to develop into blastocysts.The bovine blastocysts obtained via in vitro fertilization were removed from the zona pellucida and plated in 4-well plates, and mTeSR-E6 (05946, STEMCELL Technologies  , Vancouver,Canada) was added with 20 ng/mL FGF-2 (100-18B, STEMCELL Technologies, Vancouver,Canada), 2.5 μM IWR-1 (I0161, Sigma-Aldrich, Shanghai, ChinaUSA) and 0.1328 g/mL low fatty acid BSA (219989925, MP Biomedicals NZ, New Zealand, USA), and were incubated at 37 °C and 5% CO2. After 48–72 h, ICMs adhered to the feeder layer, and the medium was changed daily. Outgrowths (after 8–10 days in culture) were dissociated and passaged using TrypLE (12563011, Gibco, California, USA) and were reseeded in the presence of 10 μM Rho kinase (ROCK) inhibitor Y-27632 (SCM075, Sigma, Shanghai, ChinaGermany). The established bESC lines were grown in 12-well plates and were passaged every 5 days at a 1:4–1:6 split ratio. To increase cell survival, the ROCK inhibitor Y-27632 (10 μM) was added to the wells 1 h before passaging and was also added to the newly prepared wells containing MEFs treated with mitomycin and fresh culture medium during the first 24 h of cultivation.

value: bovine embryonic stem cells

value: 5 uM of MM-102 to CTFR in long-term cultures


title: T20 - surrounding artery (T20_SA1 002)

value: Tibialis anterior


title: T20 - normal (T20_NORM2 002)

value: normal

value: Myofibers


title: T20 - nerve bundle  (T20_NB1 002)


title: CTFR-bESC-F7-102-5-4


title: poly-A+ RNA-seq of T0 in 3D culture replicate 3

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation


title: T20 - nerve bundle  (T20_NB2 002)

value: nerve bundle


title: C2 - normal (C2_NORM2)

value: control


title: T20 - central nuclei  (T20_CN1 002)

value: central nuclei


title: T20 - normal (T20_NORM1 002)

value: WT


title: T15 - surrounding artery (T15_SA3)

value: male


title: C2 - central nuclei  (C2_CN2)


title: CTFR-bESC-F7-102-5-3


title: CTFR-bESC-F7-102-50-4

description: bovine embryonic stem cells cultured with CTFR+50μM MM-102 for 7 days

value: bESCs were cultured for 7 days with the addition of 50 uM MM-102


title: CTFR-bESC-F7-102-50-5


title: T15 - surrounding artery 2 (T15_SA2)

value: surrounding artery


title: T15 - surrounding artery (T15_SA1)


title: poly-A+ RNA-seq of T0 in 3D culture replicate 1

description: 3D growth


title: T15 - normal (T15_NORM1)


title: CTFR-bESC-F7-102-50-3


title: T15 - nerve bundle 2 (T15_NB2)


title: T15 - central nuclei 3 (T15_CN3)


title: poly-A+ RNA-seq of T60 in 2D culture replicate 2

description: 2D growth

value: 2D cluture, charcolized serum + serum starvation + R5020 for 60min


title: poly-A+ RNA-seq of T60 in 2D culture replicate 3

description: 2D growth


title: T15 - central nuclei 2 (T15_CN2)

value: tauopathy


title: CTFR-bESC-102-4

description: bovine embryonic stem cells cultured with CTFR, MM-102 was added to embryo cultures

value: MM-102 was added to embryo cultures


title: T15 - central nuclei  (T15_CN1)


title: CTFR-bESC-102-3


title: poly-A+ RNA-seq of T60 in 2D culture replicate 1

description: 2D growth

value: breast

value: Epithelial cancer metastatic


title: C20 - surrounding artery 2 (C20_SA2)


title: C20 - surrounding artery (C20_SA1)


title: C20 - normal (C20_NORM2)


title: C20 - nerve bundle  (C20_NB2)


title: C20 - central nuclei 2 (C20_CN2)


title: poly-A+ RNA-seq of T0 in 2D culture replicate 2

description: 2D growth

value: 2D cluture, charcolized serum + serum starvation


title: CTFR-bESC-3i-4

description: bovine embryonic stem cells cultured with CTFR, MM-102 plus PD0325901 and CHIR99021were added to embryo cultures

value: bovine embryonic stem cells


title: CTFR-bESC-3i-5

value: MM-102 plus PD0325901 and CHIR99021were added to embryo cultures


title: C16 - surrounding artery (C16_SA1)

value: Tibialis anterior

value: Myofibers

value: female


title: poly-A+ RNA-seq of T0 in 2D culture replicate 1

description: 2D growth


title: CTFR-bESC-3i-3


title: ChIP-seq of PGR at T30 in 3D culture replicate 2

description: 3D growth

data_processing: Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of uniqueness (-S –m1 –v2 –t –q). p values for the significance of ChIP-seq counts compared to input DNA were calculated as described (Pellegrini and Ferrari, 2012) using a threshold of 10−8 and a false discovery rate (FDR) < 1%.

extract_protocol:
ChIP assays were performed as described (Strutt and Paro, 1999)
Single-end (SE) ChIP-seq libraries were constructed from 0,1-1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp of the human genome for each condition.

value: 3D cluture, charcolized serum + serum starvation + R5020 for 30min


title: C16 - normal (C16_NORM1)

value: normal

value: control


title: CTFR-bESC-3i-2

value: WT


title: C16 - normal  (C16_NORM2)


title: C16 - nerve bundle 2 (C16_NB2)

value: nerve bundle


title: CTFR-bESC-102-5


title: T15 - nerve bundle  (T15_NB1)

value: male


title: ChIP-seq of PGR at T0 in 3D culture replicate 2

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation


title: C16 - nerve bundle  (C16_NB1)


title: C16 - central nuclei  (C16_CN2)

value: central nuclei


title: CTFR-bESC-3i-1


title: ChIP-seq of PGR at T30 in 2D culture replicate 2

description: 2D growth


title: poly-A+ RNA-seq of T60 in 3D culture replicate 1

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 60min


title: poly-A+ RNA-seq of T0 in 2D culture replicate 3

description: 2D growth

value: breast


title: ChIP-seq of PGR at T30 in 2D culture after knock down with YAP1 siRNA (siYAP1)

description: 3D growth

value: Epithelial cancer metastatic

value: 2D cluture, charcolized serum + serum starvation + R5020 for 30min


title: CTFR-bESC-102-2

value: bovine embryonic stem cells

value: MM-102 was added to embryo cultures


title: CTFR-bESC-102-1


title: C20 - central nuclei  (C20_CN1)

value: Tibialis anterior


title: DO Fibroblast Cell Donor ID #8448, 0 uM MMAIII

city: Bar Harbor

first: Callan

last: O'Connor

state: Maine

address: 87 Pine Heath Rd

institute: The Jackson Laboratory

data_processing:
All samples were processed using the publically available GBRS pipeline (TheJacksonLaboratory/cs-nf-pipelines) aligned to the GRCm38 reference genome
Reads were first aligned to the 8 DO founder strain genomes using bowtie.
GBRS was then used to reconstruct each samples genotype
Total gene counts were estimated using EMASE
Assembly: GRCm38
Supplementary files format and content: comma separated values file includes expected counts for all samples together

source_name: primary tail tip fibroblast

growth_protocol: DO fibroblast cells were maintained in Advanced RPMI supplemented with RPMI 1640 media containing 1.0 % P/S, 1% Glutamax, 1.0 % non-essential amino acids, .0005% BME, and 10% fetal bovine serum (FBS) at 37C with 5% CO2 on a 60 mm tissue culture treated dish.

extract_protocol:
Treated and untreated samples were snap frozen on dry ice as cell pellets for 15 minutes. Samples were stored at -80°C prior to RNA isolation. RNA was extracted using a NucleoMag RNA Kit (Macherey Nagel) and purified with a KingFisher Flex system (ThermoFisher)
Library preparation was enriched for polyA containing mRNA using the KAPA mRNA HyperPrep Kit (Rocher Sequencing and Life Science) following manufacturer's protocol

treatment_protocol: Culture media with MMAIII (Toronto Research Chemicals) at 0.75 uM and standard media for untreated samples (0 uM) was administered for 24 hours in each 60 mm dish.

value: primary tail tip fibroblast

value: fibroblast

value: DO

value: 0 uM MMAIII

tag: time

value: 24 hr

value: M

tag: do generation


title: DO Fibroblast Cell Donor ID #8419, 0.75 uM MMAIII

value: 0.75 uM MMAIII

value: F


title: DO Fibroblast Cell Donor ID #8419, 0 uM MMAIII


title: DO Fibroblast Cell Donor ID #833, 0.75 uM MMAIII


title: DO Fibroblast Cell Donor ID #8448, 0.75 uM MMAIII


title: CTFR-bESC-F7-5

description: bovine embryonic stem cells cultured with CTFR

value: WT

value: CTFR


title: DO Fibroblast Cell Donor ID #833, 0 uM MMAIII


title: CTFR-bESC-F7-4


title: ChIP-seq of PGR at T0 in 2D culture replicate 2

description: 2D growth

value: 3D cluture, charcolized serum + serum starvation


title: CTFR-bESC-F7-102-5-2

value: 5 uM of MM-102 to CTFR in long-term cultures


title: ChIP-seq of PGR at T30 in 2D culture after knock down with scramble siRNA (siControl)

description: 2D growth

value: breast

value: Epithelial cancer metastatic


title: DO Fibroblast Cell Donor ID #8236, 0 uM MMAIII


title: DO Fibroblast Cell Donor ID #8207, 0.75 uM MMAIII


title: DO Fibroblast Cell Donor ID #8236, 0.75 uM MMAIII


title: DO Fibroblast Cell Donor ID #8207, 0 uM MMAIII


title: DO Fibroblast Cell Donor ID #5659, 0 uM MMAIII


title: input in normal media in 3D culture replicate 4

description: 2D growth

value: 3D culture normal media


title: CTFR-bESC-F7-102-5-1

value: bovine embryonic stem cells


title: ChIP-seq of PGR at T0 in 2D culture after knock down with scramble siRNA (siControl)

description: 2D growth

value: 2D cluture, charcolized serum + serum starvation


title: DO Fibroblast Cell Donor ID #5659, 0.75 uM MMAIII

value: primary tail tip fibroblast


title: DO Fibroblast Cell Donor ID #5398, 0.75 uM MMAIII

value: fibroblast


title: CTFR-bESC-F7-102-50-2

value: bESCs were cultured for 7 days with the addition of 50 uM MM-102


title: input in normal media in 3D culture replicate 3

description: 3D growth


title: DO Fibroblast Cell Donor ID #5398, 0 uM MMAIII

value: DO

value: 0 uM MMAIII


title: hos2-deleted mutant, YPGly, biol rep 3

city: Taipei

first: Wei-Han

last: Lin

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Raw reads were quality-trimmed using Trimmomatic v0.39.
The relative abundance of each gene in units of TPM for each sample was quantified using Salmon v1.9.0.
Tximport by default was used to convert the estimated transcript abundance files from Salmon to DESeq2 compatible dataset.
DESeq2 was used for the differential analysis of gene expression in R v4.0.4 with default settings.
Assembly: Saccharomyces cerevisiae W303 (GenBank: ALAV01000000)
Supplementary files format and content: Excel files from DESeq2 include log2 Fold Change of each transcript between mutant and wild-type samples.

organism: Saccharomyces cerevisiae W303

growth_protocol: Yeast cells were grown in 30 ml YPG at 28°C and harvested until the early-log phase.

extract_protocol:
Around 10 OD600 cells from cultures were harvested. Total RNA was extracted by the phenol-chloroform method and treated with the TURBO DNA-freeTM kit (Invitrogen).
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) following manufacturer's protocols.  2 μg of total RNA was used for the construction of sequencing libraries.

value: hos2 knockout

value: YPGly, 28C, log phase


title: hos2-deleted mutant, YPGly, biol rep 1


title: hos2-deleted mutant, YPGly, biol rep 2


title: poly-A+ RNA-seq of T0 in 3D culture replicate 2

description: 3D growth


title: Wild type, YPGly, biol rep 2

value: wild-type


title: ChIP-seq of PGR at T0 in 2D culture after knock down with YAP1 siRNA (siYAP1)

description: 3D growth


title: Wild type, YPGly, biol rep 3


title: ChIP-seq of PGR at T30 in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 30min


title: CTFR-bESC-F7-1

value: WT

value: CTFR


title: CTFR-bESC-F7-2


title: DO Fibroblast Cell Donor ID #5368, 0 uM MMAIII

value: 24 hr

value: M


title: DO Fibroblast Cell Donor ID #5328, 0.75 uM MMAIII

value: 0.75 uM MMAIII


title: ChIP-seq of PGR at T0 in 3D culture

description: 3D growth

value: breast

value: Epithelial cancer metastatic

value: 3D cluture, charcolized serum + serum starvation


title: Wild type, YPGly, biol rep 1


title: mES K27M H33Input R1

data_processing:
ChIP-seq of H3.3 and PML were aligned to the mouse genome (mm9) with Bowtie (v1.0.0) with default settings except (m -5).
Unmapped and duplicated reads were removed with SAMtools (v 1.10.0) and converted to wig files.
BigWig files were generated with Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1) and files were visualised in the UCSC browser
assembly: mm9
processed data files format and content: BigWig and Wig files of reads mapped to mm9 mouse genome

source_name: mES

growth_protocol: Mouse ES cells and derived cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 12% heat-inactivated foetal calf serum, 10^3 units/ml leukaemia inhibitory factor (Merck), 0.1 mM β-mercaptoethanol, non-essential amino acids, L-glutamine and penicillin/streptomycin. Cells were maintained in 37 °C incubator under 5% CO2.

extract_protocol:
5 million cells were fixed in growth media with 0.4% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was released by sequential lysis with cells lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% Igepal) and nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). Chromatin was sheared to ≈300 bp with 12 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and incubated overnight at 4 ᵒC with 5 μg H3.3 antibody (Abcam, Ab176840). Samples were immunoprecipitated with Protein A Agarose beads (Sigma-Aldrich, 05015979001) and washed sequentially with low salt (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), and LiCl buffers (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1% Igepal, 1% sodium deoxycholate). Chromatin was eluted with elution buffer (1% SDS, 100 mM NaHCO3), decrosslinked overnight at 65ᵒC, incubated with Proteinase K, phenol chloroform extracted and ethanol precipitated. For PML chromatin immunoprecipitation, cells were treated as above except that they were fixed with 2 mM EGS (Pierce 26103) for 45 min at room temperature in PBS. Formaldehyde was then added to 1% for 20 min and quenched with 125 mM glycine. Chromatin was sheared to under 500 bp with 20 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and lysates were immunoprecipitated with 10 μg PML antibody (Millipore, mab3738).
For the WT H3.3 R1 and H3.3 K27M H3.3 ChIP R1 samples: Ovation Ultralow System V2 using Nugen protocols M01379 v3.1. c-bot clustering using 200pM of library pool. Illumina Protocol 15006165 v02 Jan 2016. 75bp PE sequencing using Illumina HiSeq 3000. Illumina Protocol 15066493 Rev A, February 2015. For all other samples: Ovation Ultralow System V2 using Nugen protocols M01379 v3.1. Denaturing and on-board clustering using 2pM of library pool containing 1% PhiX, Illumina protocol 15048776 v15 Apr 2020. 75 SR sequencing using Illumina NextSeq550 High output mode and v2.5 chemistry. Illumina Protocol 15069765 v06, Jul 2019.

value: mES

value: mouse embryonic stem cells

value: Input


title: ChIP-seq of Pol2 in normal media in 3D culture replicate

description: 3D growth

value: 3D culture normal media


title: bovine fetal fibroblasts

description: bovine fetal fibroblasts

source_name: bovine fetal fibroblasts

value: bovine fetal fibroblasts

value: BFF


title: input in normal media in 3D culture replicate 2

description: 3D growth


title: CTFR-bESC-F7-102-50-1

value: bovine embryonic stem cells

value: bESCs were cultured for 7 days with the addition of 50 uM MM-102


title: DO Fibroblast Cell Donor ID #522, 0.75 uM MMAIII

value: primary tail tip fibroblast

value: fibroblast

value: DO

value: F


title: H3K4me1,CTFR-bESCs-F7-50,3

data_processing:
Illumina reads were first mapped to the UCSC bosTau9 reference using bwa-mem (version:0.7.17) with default parameters.
Next, Picard (http://broadinstitute.github.io/picard/, accessed on 12 June 2023, version 2.23.1) was used to mark up the PCR duplicates.
Then, we used macs2 (v2.2.7.1, -nomodel-broad-broad-cutoff 0.1-shift 0-gsize 2.7e9-keep-dup auto) to call the peaks.
H3K4me1 signals were normalized using the MA norm (version: 1.1.4) method for the quantitative comparison of ChIP-seq data, and the significant differential peaks were determined as log10(p-value) < 0 and M-value > 1. Subsequently, the differential peaks were annotated to UCSC bosTau9 using the R package ChIP seeker (version: 1.28.3) and TxDb.Btaurus.UCSC.bosTau9.refGene (version: 3.10.0).
Assembly: UCSC BT9
Supplementary files format and content: bigWig

extract_protocol:
Cells were collected by tryple-select enzyme  and the lyophilized cells were sent for sequencing. The sequencing was performed by Tianjin Nuohe Zhiyuan Biotechnology Co., LTD, Tianjin, China.
The Simple ChIP®Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (9005, Cell Signaling) was utilized to extract DNA fragments from the cells.

value: WT


title: DO Fibroblast Cell Donor ID #5328, 0 uM MMAIII

value: 0 uM MMAIII

value: 24 hr

value: M


title: mES WT H33Input


title: mES K27M H33ChIP R1

value: H3.3 ChIP (Abcam, Ab176840)


title: H3K4me1,CTFR-bESCs-F7-50,2


title: DO Fibroblast Cell Donor ID #522, 0 uM MMAIII


title: input in normal media in 3D culture

description: 3D growth

value: breast

value: Epithelial cancer metastatic


title: CTFR-bESC-F7-3

value: CTFR


title: DO Fibroblast Cell Donor ID #5368, 0.75 uM MMAIII

value: 0.75 uM MMAIII


title: H3K4me1,CTFR-bESCs-F7-50,1


title: mES WT H33ChIP R1

value: mES

value: mouse embryonic stem cells


title: ChIP-seq of H3K27ac in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 30min


title: Kc, EFS-6, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-6.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-6.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.

organism: Drosophila melanogaster

source_name: Kc

growth_protocol: Drosophila flies were raised at 25°C on standard fly food.

treatment_protocol: Dissected central brains were lysed in cold ATAC resuspension buffer (10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2; 0.1 % NP40, 0.1% Tween20, 0.01% Digitonin) for 3 min. Isolated nuclei were incubated for 30 min at 37°C in transposition mix containing Tn5 transposase.

value: Kc

value: Drosophila embryonic cell line


title: H3K4me1,CTFR-bESCs-F7-5,3

value: bovine embryonic stem cells

value: 5 uM of MM-102 to CTFR in long-term cultures


title: H3K4me1,CTFR-bESCs-F7-5,2


title: ChIP-seq of H3K18ac in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation


title: DO Fibroblast Cell Donor ID #3625, 0 uM MMAIII

value: primary tail tip fibroblast

value: fibroblast

value: DO


title: Kc, EFS-5, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-5.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-5.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: DO Fibroblast Cell Donor ID #2358, 0.75 uM MMAIII

value: 24 hr

value: M


title: H3K4me1,CTFR-bESCs-F7-5,1

value: WT


title: ChIP-seq of CTCF in normal media in3D culture with Drosophila Spike-in + Truli

description: 3D growth

value: breast

value: Epithelial cancer metastatic

value: 3D culture normal media with Truli inhibitor + spikein


title: ChIP-seq of CTCF in normal media in 2D culture with Drosophila Spike-in + Truli replicate

description: 3D growth


title: DO Fibroblast Cell Donor ID #2358, 0 uM MMAIII

value: 0 uM MMAIII


title: Kc, EFS-4, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-4.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-4.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: Kc, EFS-3, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-3.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-3.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.


title: DO Fibroblast Cell Donor ID #12098, 0.75 uM MMAIII

value: 0.75 uM MMAIII

value: F


title: Kc, EFS-2, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-2.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-2.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.

value: Kc


title: H3K4me1,CTFR-bESCs-F7,2

value: CTFR


title: DO Fibroblast Cell Donor ID #12098, 0 uM MMAIII


title: H3K4me1,CTFR-bESCs-F7,1

value: bovine embryonic stem cells


title: Kc, EFS-1, ATAC-seq

data_processing:
genome assembly: dm6 + KC_EFS-1.fa
Demultiplexing of Illumina BCL files was performed with bcl2fastq 2.20. Reads were trimmed for adapters with TrimGalore 0.6.7. Reads were mapped with bwa-mem2 2.2.1 against dm6 with KC_EFS-1.fa added . Sorting , deduplicating and removing blacklisted regions from the BAM file were performed with SAMtools 1.16.1. A normalized bigWig file was generated with bamCoverage of deepTools 3.5.0.

value: Drosophila embryonic cell line


title: DO Fibroblast Cell Donor ID #3625, 0.75 uM MMAIII


title: H3K4me1,BFF,3

value: bovine fetal fibroblasts

value: BFF


title: H3K4me1,BFF,2


title: DO Fibroblast Cell Donor ID #12085, 0 uM MMAIII

value: primary tail tip fibroblast

value: fibroblast


title: ChIP-seq of CTCF in normal media in 3D culture control DMSO

description: 3D growth

value: 3D culture normal media with DMSO control


title: ChIP-seq of CTCF in normal media in 3D culture with Truli inhibitor

description: 3D growth

value: 3D culture normal media with Truli inhibitor


title: ChIP-seq of RAD21 at T30  in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 30min


title: DO Fibroblast Cell Donor ID #12014, 0.75 uM MMAIII

value: DO

value: 24 hr

value: M


title: DO Fibroblast Cell Donor ID #12014, 0 uM MMAIII

value: 0 uM MMAIII


title: H3K4me1,CTFR-bESCs-F7,Input,2

value: WT


title: H3K4me1,CTFR-bESCs-F7,3


title: H3K4me1,BFF,1


title: ChIP-seq of RAD21 at T0  in 3D culture

description: 3D growth

value: breast

value: Epithelial cancer metastatic

value: 3D cluture, charcolized serum + serum starvation


title: DO Fibroblast Cell Donor ID #11995, 0 uM MMAIII

value: F


title: ChIP-seq of CTCF in normal media in3D culture with Drosophila Spike-in replicate

description: 3D growth

value: 3D culture normal media + spikein


title: DO Fibroblast Cell Donor ID #11995, 0.75 uM MMAIII

value: 0.75 uM MMAIII


title: H3K4me1,BFF,Input,2

value: bovine fetal fibroblasts

value: BFF

value: CTFR


title: ChIP-seq of Pol2 at T30  in 3D culture

description: 3D growth


title: ChIP-seq of CTCF in normal media in3D culture with Drosophila Spike-in

description: 3D growth


title: IS-caput, Nell2 KO, rep2

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (FPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

source_name: IS-caput epididymis

extract_protocol:
RNA was harvested using RNeasy (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: IS-caput epididymis

tag: age

value: no treatment


title: IS-caput, Nell2 KO, rep3


title: H3K4me1,BFF,Input,1


title: ChIP-seq of H3K27ac at T30 in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation + R5020 for 30min


title: ChIP-seq of CTCF in normal media in 3D culture rep

description: 3D growth

value: 3D culture normal media


title: H3K4me1,CTFR-bESCs-F7-50,Input,2

value: bovine embryonic stem cells

value: bESCs were cultured for 7 days with the addition of 50 uM MM-102


title: ChIP-seq of H3K27ac at T0 in 3D culture

description: 3D growth


title: DO Fibroblast Cell Donor ID #12085, 0.75 uM MMAIII

value: primary tail tip fibroblast

value: fibroblast

value: DO

value: 24 hr


title: IS-caput, Nell2 KO, rep1


title: H3K4me1,CTFR-bESCs-F7-50,Input,1

value: WT


title: ChIP-seq of CTCF at T30 in 3D culture

description: 3D growth

value: breast

value: Epithelial cancer metastatic


title: H3K4me1,CTFR-bESCs-F7-5,Input,2

value: 5 uM of MM-102 to CTFR in long-term cultures


title: ChIP-seq of CTCF at T0 in 3D culture

description: 3D growth

value: 3D cluture, charcolized serum + serum starvation


title: IS-caput, WT, rep2

value: Wild-type


title: ChIP-seq of Pol2 at T0  in 3D culture

description: 3D growth


title: H3K4me1,CTFR-bESCs-F7-5,Input,1


title: H3K4me1,CTFR-bESCs-F7,Input,1

value: CTFR