title: Idiopathic Pulmonary Arterial Hypertension patient 2

city: Changsha

first: Yusi

last: Chen

state: Hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

description: Gene expression in idiopathic Pulmonary Arterial Hypertension blood

hyb_protocol: Cy3 labeled small RNAs were hybridized to Arraystar Human Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: After washing, the slides were scanned with Agilent Scanner G2505C

data_processing: Intensity data were extracted using Agilent Feature Extraction software. The probe signals passing P (Present) or M (Marginal) QC flags in a certain proportion were retained for further analysis

source_name: Peripheral Blood

label_protocol: For each sample, 100ng total RNAs were dephosphorylated to form a unified 3-OH end. 3-OH ended RNA were then denaturated by DMSO and enzymatically labeled with Cy3.

extract_protocol: total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis

treatment_protocol: The blood samples immediately were reserved at -80°C after being purified until further analysis


title: N50R1_2 lowN

status: Public on Jun 30 2023

type: RNA

city: Kiel

first: Meike

last: Kaehler

state: Schleswig-Holstein

address: Hospitalstraße 4

department: Institute of Experimental and Clinical Pharmacology

country: Germany

institute: University Hospital Schleswig-Holstein, Campus Kiel

description: Gene expression data from K-562 cells, resistant to 0.05 µM nilotinib, biological replicate 1.

hyb_protocol: 3.5 µg fragmented and labeled ssDNA were hybridized on HuGene 2.0 arrays for 16 h at 45 °C using the Affymetrix Hybridization Oven 640. The arrays were washed using the Fluidics Station 450 using the protocol FS450_0002.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were processed using the Transcriptome Analysis Console 4.0 (Thermo Fisher Scientific).

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: 100 ng RNA was used for each sample with the GeneChip WT PLUS Reagent Kit according to the manufacturer's recommendations.

growth_protocol: Cells were grown in RPMI 1640 + 10% v/v FCS + 1 % v/v Pen/Strep w/o imatinib or nilotinib.

extract_protocol: RNA was isolated using miRVana microRNA isolation Kit (Thermo Fisher Scientific) according to the manufacturer's recommendation from 3 million cells.

treatment_protocol: Resistant cells were generated by step-wise increase of imatinib concentration to 0.5 and 2 µM imatinib or 0.05 µM nilotinib.

tag: tki resistance

value: lowN

tag: treatment

value: resistant to 0.05 µM nilotinib


title: d2129n

type: SRA

city: Seoul

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

country: South Korea

institute: Sookmyung Women's university

description: The methylated fraction from TNBC

library_source: genomic

data_processing:
Paired-end 100bp sequence reads were aligned to the hg19 genome reference using bowtie.
The methylation abundance within region of interest (ROI) was estimated by MEDIPS R package with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed_Merged_Samples_averaged_read_counts_ROI_CDS.txt is a tab-delimited text file that contains the read counts of gene symbols located in CDS regions and processed_Merged_Samples_averaged_read_counts_ROI_PROMOTER.txt is a tab-delimited text file that contains the read counts of gene symbols located in promoter regions.

molecule: genomic DNA

source_name: human breast cancer adjacent normal tissue

extract_protocol:
Genomic DNA was isolated from normal breast and breast cancer samples with a Qiagen Puregene kit following the manufacturer's protocol. Approximately 1 µg genomic DNA was sheared to 200- to 400-bp fragments using a Covaris LE220 sonicator. The sonicated genomic DNA was immunoprecipitated with human MBD2 protein coupled with paramagnetic Dynabeads M-280 Streptavidin via a biotin linker using a MethylMiner Methylated DNA Enrichment Kit.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: gender

value: female

tag: methylated fraction

value: TNBC


title: d2195c_1

description: The methylated fraction from TNBC

source_name: human breast cancer tissue


title: N50R1_1 lowN


title: Healthy Control 3

country: China

description: Gene expression in healthy controls' blood

tag: tissue

value: plasma

value: male


title: S16

city: Huddinge

first: Christian

middle: Günter

last: Riedel

state: Stockholm

address: Blickagången 16 (Neo Building, 6th floor)

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Reads were mapped to 202,272 Ensembl transcript IDs using the Smallseq data analysis pipeline (Hagemann-Jensen et al., 2018), and to 4,121 transfer RNA fragments (tRF) using the MINTmap pipeline (Loher et al., 2017).
Only small RNA with read counts higher than 1 in more than 20% of samples were kept, resulting in a list of 4,767 small RNA.
Counts were rounded and data normalization and differential expression analysis was performed with the DESeq2 package (version 1.26.0) (Love et al. 2014). Small RNA levels were used as the dependent variable and chronological age as the explanatory variable. A local fit was used for estimating dispersions. Size factor normalized small RNA counts were obtained using the counts functions with arguments normalized = T.
After DESeq2 analysis, small RNA with unclear transcripts biotypes were removed from all analysis since they indicate potential degradation products (i.e. protein coding, lncRNA, processed transcript, retained intron, …). Transcript biotypes were defined using the biomaRt package (version 2.42.0) (Durinck et al. 2005). A total of 587 small RNA were kept after this filtering step, of which 276 were significantly associated with age at an FDR threshold of 0.2.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts_Smallseq_Ensembl.txt (raw counts)
Supplementary_files_format_and_content: raw_counts_MINTmap_tRF.txt (raw counts)
Supplementary_files_format_and_content: DESeq2_normalized_counts.xlsx (normalized counts)
Supplementary_files_format_and_content: DESeq2_small_RNA_association_with_age.xlsx (significance table)

source_name: plasma

extract_protocol:
Total RNA was extracted from plasma samples using the Qiagen miRNeasy Serum/Plasma Kit. Briefly, frozen plasma samples were thawed, vortexed and centrifuged for 16000 x g in 10 minutes and 50 µl was used for RNA extraction following the manufacturer’s protocol. Purified RNA was eluted in 50µl H2O and saved at -80C.
4 µl of purified RNA was used in a Small-seq protocol to construct the libraries (Hagemann-Jensen et al., 2018). Small RNA libraries were pooled and sequenced using an Illumina HiSeq 3000 platform for 100 bp single read.

tag: age

tag: disease state

value: healthy


title: Idiopathic Pulmonary Arterial Hypertension patient 1


title: 2R4_B highIM

description: Gene expression data from K-562 cells, resistant to 2 µM imatinib, biological replicate 4.

value: highIM

value: resistant to 2 µM imatinib


title: d2195n

description: The methylated fraction from TNBC


title: Healthy Control 2


title: Idiopathic Pulmonary Arterial Hypertension patient 3


title: 05R4_4 lowIM

description: Gene expression data from K-562 cells, resistant to 0.5 µM imatinib, biological replicate 4.

value: lowIM

value: resistant to 0.5 µM imatinib


title: d9984c

description: The methylated fraction from TNBC


title: Dunaliella tertiolecta, 2 d, 1.5 µM Fe, rep3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

country: USA

institute: UC Berkeley

data_processing:
Alignment to Dunaliella tertiolecta genome with the STAR aligner (v2.4.0j) with --alignIntronMax 5000.
FPKMs were calculated with cuffdiff (v2.0.2)  with --multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand.
Assembly: Dunaliella tertiolecta v1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: fasta file for genome assembly
Supplementary files format and content: gff3 file for annotations

molecule: polyA RNA

organism: Dunaliella tertiolecta

source_name: liquid culture

growth_protocol: Three days growth in liquid cultures grown on shaking platforms at 140 rpm at 24°C under constant light (100 µE m^-2 sec^-1).

extract_protocol:
TRI Reagent RNA exptraction plus TURBO DNase digestion.
Standard Illumina poly(A)-selected

treatment_protocol: Media supplemented with 1.5 µM iron or 0 µM iron.

value: liquid culture

tag: cell line

value: UTEX LB 999

tag: cell type

value: vegetative cells

tag: genotype

value: WT

tag: time

value: 2 d

value: 1.5 uM Fe


title: S13


title: d9984n

description: The methylated fraction from TNBC


title: S14


title: 2R4_A highIM


title: Healthy Control 1


title: 2R4_C highIM


title: Dunaliella tertiolecta, 2 d, 1.5µM Fe, rep1


title: S12


title: 05R4_2 lowIM


title: S15


title: 17_LV_mCherryNegative

first: Marena

middle: Isabelle

last: Trinidad

state: CA

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

data_processing:
Per the manufacturer's instructions, FASTQ files were analyzed using Cogent NGS Immune Profiler Software (Version 1.5), using a UMI-cutoff of 3.
Clonotypes were visualized using Cogent NGS Immune Viewer (Version 1.0) and a custom python script.
Supplementary files format and content: Processed data files are in csv format and contain detailed clonality results generated by Cogent NGS Immune Profiler.
Library strategy: TCR-seq

organism: Mus musculus

source_name: Spleen

extract_protocol:
Splenocytes from humanized mice were sorted into mCherry+ and mCherry- primary human T cells using an SH800S cell sorter (Sony Biotechnology). RNA was extracted from human primary T cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
TCR a/b libraries were prepared from each sample using the SMART-Seq Human TCR (with UMIs) kit (Takara Bio) according to the manufacturer’s instructions.

treatment_protocol: Following anesthesia induction with 2-3% isofluorane, 100 µl of Cas9-EDVs, lentivirus, or phosphate-buffered saline (PBS) was administered to humanized mice by retro-orbital injection.

value: Spleen

value: T cell

value: Human peripheral blood mononuclear cell-engrafted NSG mice (745557)

value: Cas9-Lenti, mCherry Negative


title: 17_LV_mCherryPositive

value: Cas9-Lenti, mCherry Postive


title: Dunaliella tertiolecta, 2 d, 0 µM Fe, rep3

value: 0 uM Fe


title: S9

value: plasma

value: male

value: healthy


title: Dunaliella tertiolecta, 2 d, 0 µM Fe, rep2


title: S11


title: 14_LV_mCherryNegative


title: 05R4_1 lowIM

value: lowIM


title: Dunaliella tertiolecta, 2 d, 0 µM Fe, rep1


title: S7


title: 13_LV_mCherryPositive

value: Cas9-Lenti, mCherry Positve


title: Control_Myc_2

city: Spokane

first: Michelle

last: Pearson

state: WA

address: 3410 W Whistalks Way MS3280

department: Life Sciences

institute: Spokane Falls Community College

description: Non-drought with mycorrhizal fungus

data_processing:
Read quality was good and adapter sequences were not overrepresented, so no trimming occurred; quality assessed by FastQC v0.11.5 (Andrews, 2016)
Reads were pseudo-aligned with Kallisto v0.42.3 (Bray et al., 2016).
Data were analyzed using the sleuth package (Pimentel et al., 2017) in R 3.5.2 (R Core Team, 2019).
Genome_build: The transcriptomes for Daucus carota v2 and Rhizophagus irregularis 197198 v2 were merged; transcripts were aligned agained this merged transcriptome.
Supplementary_files_format_and_content: tsv files contain the read abundance quantified with Kallisto v0.42.3

organism:
Daucus carota
Rhizophagus irregularis

source_name: Fine roots of carrot

growth_protocol: Carrots (mycorrhizal and non-mycorrhizal) grew for 50 days prior to subjection to drought treatment. All plants received regular watering and nutrient addition using Enshi solution (a nutrient solution well-suited for carrots)

extract_protocol:
RNA extraction: PureLink RNA Mini Kit; removal of DNA contaminants: Turbo DNA-free kit (Life Technologies, Carlsbad, CA, USA)
Library preparation by Novogene LTD Co., Sacramento, CA, USA; secquenced on Illumina NovaSeq 6000

treatment_protocol: During the last 10 days of growth, carrots in the drought treatment group received water less frequently than controls, diminishing until sample collection. Nutrient inputs were the same for both control and drought groups.

tag: cultivar

value: Napoli

tag: infected with

value: Rhizophagus irregularis DAOM197198

tag: drought treatment status

value: non-drought

value: fine roots


title: 14_LV_mCherryPositive


title: 05R4_3 lowIM

value: resistant to 0.5 µM imatinib


title: 2R3_D highIM

description: Gene expression data from K-562 cells, resistant to 2 µM imatinib, biological replicate 3.

value: highIM

value: resistant to 2 µM imatinib


title: S10


title: Control_Myc_4

description: Non-drought with mycorrhizal fungus


title: 6_EDV_mCherryNegative

value: Spleen

value: T cell

value: Cas9-EDV, mCherry Negative


title: 2R3_C highIM


title: 13_LV_mCherryNegative

value: Human peripheral blood mononuclear cell-engrafted NSG mice (745557)

value: Cas9-Lenti, mCherry Negative


title: 2R3_B highIM


title: S8

value: plasma


title: Control_Myc_1

description: Non-drought with mycorrhizal fungus


title: 05R3_2 lowIM

description: Gene expression data from K-562 cells, resistant to 0.5 µM imatinib, biological replicate 3.


title: 6_EDV_mCherryPositive

value: Cas9-EDV, mCherry Positve


title: 2R3_A highIM


title: S4

value: male

value: healthy


title: 4_EDV_mCherryNegative


title: S5


title: 05R3_4 lowIM

value: lowIM


title: Drought_Myc_4

description: Drought with mycorrhizal fungus

value: Napoli

value: drought


title: Control_Myc_3

description: Non-drought with mycorrhizal fungus

value: Rhizophagus irregularis DAOM197198

value: non-drought


title: Drought_Myc_3

description: Drought with mycorrhizal fungus

value: fine roots


title: S3


title: Drought_Myc_2

description: Drought with mycorrhizal fungus


title: S6


title: 05R3_3 lowIM

value: resistant to 0.5 µM imatinib


title: 2_EDV_mCherryNegative


title: 05R3_1 lowIM


title: K562_4 TKI-sensitive

description: Gene expression data from treatment-naive K-562 cells

value: TKI-sensitive

value: treatment-naive


title: S2


title: S1


title: 2_EDV_mCherryPositive

value: Spleen

value: T cell


title: RNA-hht2b-aaspt6-rap080-s48

status: Public on Jun 29 2023

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq and adapter removal(internal barcode)
umiExtraction with UMI tools
adapter removal with cutadapt
alignment with bowtie2
UMI selection with umi-tools
gene coverage with bedtools
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.txt.gz file contains zipped table of names and readnumbers for 6701 ORFs in S. cerevisiae

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before addition of rapamycin samples were taken at indicated time points (0,10,..,90)

extract_protocol:
RNA Extraction with NucleoSpin 96 RNA(MN)
Libraries were constructed as described in Chapal(2019)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX

tag: sensor

tag: genotypeshort

tag: experiment

tag: timepoint


title: RNA-hht2b-aaspt6-rap090-s48


title: Drought_Myc_1

description: Drought with mycorrhizal fungus


title: RNA-hht2b-aaspt6-rap050-s48


title: RNA-hht2b-aaspt6-rap030-s48


title: RNA-hht2b-aaspt6-rap040-s48


title: RNA-hht2b-aaspt6-rap070-s48


title: K562_2 TKI-sensitive

tag: tki resistance

tag: treatment


title: RNA-hht2b-aaspt6-rap000-s48


title: RNA-hht2b-aaspt6-rap060-s48


title: K562_1 TKI-sensitive


title: RNA-hht2b-aaspt6-rap020-s48


title: RNA-hht2b-aaspt6-rap010-s48


title: 4_EDV_mCherryPositive

value: Human peripheral blood mononuclear cell-engrafted NSG mice (745557)


title: RNA-hht2b-aaspt16-rap070-s48

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: RNA-hht2b-aaspt16-rap060-s48


title: RNA-hht2b-aaspt16-rap050-s48


title: RNA-hht2b-aaspt16-rap090-s48


title: RNA-hht2b-aaspt16-rap020-s48


title: RNA-hht2b-aartt106-rap090-s48

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: RNA-hht2b-aaspt16-rap080-s48


title: RNA-hht2b-aaspt16-rap030-s48


title: RNA-hht2b-aaspt16-rap040-s48


title: RNA-hht2b-aaspt16-rap010-s48


title: RNA-hht2b-aaspt16-rap000-s48


title: RNA-hht2b-aartt106-rap070-s48


title: RNA-hht2b-aartt106-rap080-s48


title: RNA-hht2b-aartt106-rap050-s48


title: RNA-hht2b-aartt106-rap060-s48


title: K562_3 TKI-sensitive


title: RNA-hht2b-aartt106-rap010-s48


title: RNA-hht2b-aartt106-rap000-s48


title: RNA-hht2b-aartt106-rap040-s48


title: RNA-hht2b-aanofrb-rap040-s48

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12

value: aanofrb


title: RNA-hht2b-aanofrb-rap070-s48


title: RNA-hht2b-aartt106-rap020-s48


title: RNA-hht2b-aanofrb-rap090-s48


title: RNA-hht2b-aanofrb-rap060-s48


title: RNA-hht2b-aanofrb-rap050-s48


title: RNA-hht2b-aanofrb-rap020-s48


title: RNA-hht2b-aanofrb-rap010-s48


title: RNA-hht2b-aanofrb-rap000-s48


title: RNA-hht2b-aanofrb-rap080-s48


title: RNA-hht2b-aartt106-rap030-s48


title: spt16-hht2-aaspt6c-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt16-MNase  (insert has KANMX)

data_processing:
library strategy: Chromatin Endogenous Cleavage-sequencing (ChEC-seq)
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before addition of rapamycin samples were taken at indicated time points (0,30,60,90.120)

extract_protocol:
Phenol chlorofrom extraction
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. 2015

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt16-MNase  (insert has KANMX)

tag: mnase fusion

tag: spike-in

value: no


title: spt16-hht2-aaspt6a-async-x62

value: async


title: spt16-hht2-aaspt6b-async-x62


title: spt16-hht2-aaspt6a-rap060-x62


title: rtt106-hht2-aaspt6-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Rtt106-Mnase CRISPR (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Rtt106-Mnase CRISPR (insert has KANMX)


title: spt16-hht2-aaspt6b-rap060-x62


title: spt16-hht2-aaspt6c-async-x62


title: rtt106-hht2-aaspt6-async-x62


title: cac1-hht2-aaspt6-async-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Cac1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: cac1-hht2-aaspt6-rap060-x62


title: spt6-hht2-aaspt16b-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, SPT6-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, SPT6-MNase  (insert has KANMX)


title: spt6-hht2-aaspt16a-rap060-x62


title: cac1-hht2-aaino80-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Cac1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: spt6-hht2-aaspt16b-async-x62


title: cac1-hht2-aaspt6spt16-async-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , cac1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , cac1-MNase  (insert has KANMX)


title: cac1-hht2-aaspt16-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Cac1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: spt6-hht2-aaspt16a-async-x62


title: asf1-hht2-aaspt16c-async-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Asf1-MNase  (insert has KANMX)


title: cac1-hht2-aaino80-async-x62


title: asf1-hht2-aaspt16c-rap060-x62


title: cac1-hht2-aaspt16-async-x62


title: cac1-hht2-aaspt6spt16-rap060-x62


title: asf1-hht2-aaspt16b-async-x62


title: asf1-hht2-aaspt16a-async-x62


title: spt16-hht2-aachd1-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Spt16-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Spt16-MNase  (insert has KANMX)


title: asf1-hht2-aaspt16a-rap060-x62


title: cac1-hht2-aachd1-rap060-x62

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Cac1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: tbp-hht2-aaspt6a-rap060-x61L

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt15-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt15-MNase  (insert has KANMX)

value: tbp


title: tbp-hht2-aaspt6b-rap060-x61L


title: tbp-hht2-aaspt6b-async-x61L


title: spt16-hht2-aachd1-async-x62


title: tbp-hht2-aaino80b-async-x61L

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Spt15-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Spt15-MNase  (insert has KANMX)


title: tbp-hht2-aaspt6a-async-x61L


title: rtt106-hht2-aaspt6-rap060-x61


title: tbp-hht2-aaino80a-async-x61L


title: spt16-hht2-aaspt6-rap060-x61


title: rtt106-hht2-aaspt6-async-x61


title: spt16-hht2-aaspt6-async-x61


title: tbp-hht2-aaino80a-rap060-x61L


title: tbp-hht2-aaino80b-rap060-x61L


title: tbp-hht2-aaspt6b-async-x61


title: Dunaliella tertiolecta, 2 d, 1.5 µM Fe, rep2

tag: tissue

value: liquid culture

value: UTEX LB 999

value: vegetative cells

value: WT

value: 2 d

value: 1.5 uM Fe


title: asf1-hht2-aaspt6-rap060-x61

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: no


title: cac1-hht2-aaspt6-rap060-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: asf1-hht2-aaspt16b-rap060-x62


title: tbp-hht2-aaspt6a-rap060-x61


title: tbp-hht2-aaspt6a-async-x61

value: async


title: asf1-hht2-aaspt6-async-x61


title: cac1-hht2-aaspt6-async-x61


title: cac1-hht2-aachd1-async-x62


title: asf1-hht2-aaspt6spt16b-rap060-x61

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Asf1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Asf1-MNase  (insert has KANMX)


title: cac1-hht2-aaspt6spt16-async-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , cac1-MNase  (insert has KANMX)


title: cac1-hht2-aaspt6spt16-rap060-x61


title: asf1-hht2-aaspt6spt16b-async-x61


title: tbp-hht2-aaspt6b-rap060-x61


title: asf1-hht2-aaspt6spt16a-async-x61


title: spt6-hht2-aaspt16b-rap060-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, SPT6-MNase  (insert has KANMX)


title: spt6-hht2-aaspt16a-async-x61


title: tbp-hht2-aaino80b-rap060-x61


title: tbp-hht2-aaino80a-rap060-x61


title: spt6-hht2-aaspt16b-async-x61


title: spt6-hht2-aaspt16a-rap060-x61


title: cac1-hht2-aaino80-rap060-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: tbp-hht2-aaino80a-async-x61


title: asf1-hht2-aaino80a-rap060-x61

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Asf1-MNase  (insert has KANMX)


title: cac1-hht2-aaino80-async-x61


title: asf1-hht2-aaino80b-async-x61


title: cac1-hht2-aaspt16-rap060-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: asf1-hht2-aaino80a-async-x61


title: cac1-hht2-aaspt16-async-x61


title: asf1-hht2-aaspt16b-rap060-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, FACT-FRB::KANMX, Asf1-MNase  (insert has KANMX)


title: asf1-hht2-aaspt6spt16a-rap060-x61


title: asf1-hht2-aaspt16b-async-x61


title: asf1-hht2-aaspt16a-async-x61


title: asf1-hht2-aaspt16a-rap060-x61


title: spt6-hht2-aachd1b-async-x61

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, SPT6-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, SPT6-MNase  (insert has KANMX)


title: spt6-hht2-aachd1a-async-x61


title: spt6-hht2-aachd1a-rap060-x61


title: asf1-hht2-aaino80b-rap060-x61


title: spt16-hht2-aachd1b-async-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Spt16-MNase  (insert has KANMX)


title: asf1-hht2-aachd1b-async-x61

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Asf1-MNase  (insert has KANMX)


title: asf1-hht2-aachd1a-rap060-x61


title: spt6-hht2-aachd1b-rap060-x61


title: spt16-hht2-aachd1b-rap060-x61


title: cac1-hht2-aachd1-async-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX, Cac1-MNase  (insert has KANMX)


title: tbp-hht2-aaino80b-async-x61

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Spt15-MNase  (insert has KANMX)

value: tbp


title: asf1-hht2-aachd1a-async-x61


title: spt16-hht2-aachd1a-async-x61


title: spt16-hht2-aaspt6b-async-x58

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt16-MNase  (insert has KANMX)

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Spt16-MNase  (insert has KANMX)


title: asf1-hht2-aaspt6b-async-x58

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Asf1-MNase  (insert has KANMX)

value: no


title: cac1-hht2-aachd1-rap060-x61


title: asf1-hht2-aaspt6b-rap060-x58


title: spt16-hht2-aachd1a-rap060-x61


title: asf1-hht2-aachd1b-rap060-x61


title: asf1-hht2-aaspt6a-async-x58

value: async


title: reb1-hht2-aaspt6b-rap090-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Reb1-Nter-Mnase CRISPR

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Reb1-Nter-Mnase CRISPR


title: reb1-hht2-aaspt6b-rap030-x56


title: reb1-hht2-aaspt6a-rap060-x56


title: spt16-hht2-aaspt6b-rap060-x58


title: spt16-hht2-aaspt6a-rap060-x58


title: reb1-hht2-aaspt6a-async-x56


title: asf1-hht2-aaspt6a-rap060-x58


title: spt16-hht2-aaspt6a-async-x58


title: reb1-hht2-aaspt6b-rap060-x56


title: reb1-hht2-aaspt6b-async-x56


title: msn2-hht2-aaspt6a-rap030-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Msn2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Msn2-MNase


title: msn2-hht2-aaspt6a-rap060-x56


title: reb1-hht2-aaspt6spt16a-async-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Nter MNase-Reb1

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Nter MNase-Reb1


title: msn2-hht2-aaspt6spt16b-rap090-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Msn2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Msn2-MNase


title: reb1-hht2-aaspt6a-rap090-x56


title: reb1-hht2-aaspt16a-rap030-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt16-FRB::KANMX, Reb1-Nter-Mnase CRISPR

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt16-FRB::KANMX, Reb1-Nter-Mnase CRISPR


title: msn2-hht2-aaspt6spt16b-async-x56


title: reb1-hht2-aaspt16a-async-x56


title: reb1-hht2-aaspt16a-rap060-x56


title: reb1-hht2-aaspt6a-rap030-x56


title: msn2-hht2-aaspt6spt16a-rap090-x56


title: reb1-hht2-aaspt16a-rap090-x56


title: msn2-hht2-aaspt6a-async-x56


title: msn2-hht2-aaspt6spt16a-rap030-x56


title: reb1-hht2-aaspt6spt16b-rap090-x56


title: reb1-hht2-aaspt6spt16a-rap090-x56


title: msn2-hht2-aaspt16a-rap030-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Msn2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Msn2-MNase


title: reb1-hht2-aaspt6spt16b-rap030-x56


title: msn2-hht2-aaspt6spt16b-rap060-x56


title: reb1-hht2-aaspt6spt16b-rap060-x56


title: reb1-hht2-aaspt6spt16a-rap030-x56


title: reb1-hht2-aaspt6spt16a-rap060-x56


title: reb1-hht2-aaspt6spt16b-async-x56


title: reb1-hht2-aachd1a-rap060-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX,  Nter MNase-Reb1

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX,  Nter MNase-Reb1


title: reb1-hht2-aachd1a-rap090-x56


title: msn2-hht2-aaspt6a-rap090-x56


title: msn2-hht2-aaspt6spt16b-rap030-x56


title: msn2-hht2-aaspt6spt16a-rap060-x56


title: reb1-hht2-aachd1a-rap030-x56


title: msn2-hht2-aaspt16a-rap090-x56


title: msn2-hht2-aaspt16a-rap060-x56


title: msn2-hht2-aaspt6spt16a-async-x56


title: msn2-hht2-aaspt16a-async-x56


title: reb1-hht2-aachd1a-async-x56


title: reb1-h2b-aaino80b-rap090-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Nter MNase-Reb1

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Nter MNase-Reb1


title: reb1-h2b-aaino80b-rap030-x56


title: reb1-h2b-aaino80a-rap090-x56


title: reb1-h2b-aaino80b-rap060-x56


title: reb1-h2b-aaino80b-async-x56


title: reb1-h2b-aaino80a-async-x56


title: msn2-h2b-aaino80b-rap090-x56

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Msn2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX, Msn2-MNase


title: reb1-h2b-aaino80a-rap060-x56


title: msn2-h2b-aaino80b-rap060-x56


title: msn2-h2b-aaino80b-rap030-x56


title: msn2-h2b-aaino80b-async-x56


title: msn2-h2b-aaino80a-rap060-x56


title: msn2-h2b-aaino80a-rap030-x56


title: reb1-hht2-aaspt16b-rap090-x54

value: yes


title: reb1-hht2-aaspt16a-rap030-x54


title: reb1-hht2-aahir1b-rap090-x54

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Hir1-FRB::KANMX, Reb1-Nter-Mnase CRISPR

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Hir1-FRB::KANMX, Reb1-Nter-Mnase CRISPR


title: reb1-hht2-aaspt16b-rap060-x54


title: reb1-hht2-aaspt16a-async-x54


title: reb1-hht2-aaspt16a-rap090-x54


title: reb1-hht2-aaspt16b-async-x54


title: reb1-hht2-aaspt16b-rap030-x54


title: reb1-hht2-aahir1a-rap090-x54


title: reb1-hht2-aaspt16a-rap060-x54


title: reb1-h2b-aaino80a-rap030-x56


title: reb1-hht2-aahir1b-async-x54


title: reb1-hht2-aahir1b-rap060-x54


title: reb1-hht2-aahir1a-rap060-x54


title: reb1-hht2-aahir1a-async-x54


title: msn2-hht2-aaspt6b-rap060-x54


title: msn2-hht2-aaspt6b-rap090-x54


title: reb1-hht2-aahir1b-rap030-x54


title: msn2-hht2-aaspt6b-rap030-x54


title: msn2-hht2-aaspt6b-async-x54


title: msn2-h2b-aaino80a-rap090-x56


title: msn2-hht2-aaspt6a-rap090-x54


title: msn2-hht2-aaspt6a-rap030-x54


title: msn2-h2b-aaino80a-async-x56


title: msn2-hht2-aaspt6a-async-x54


title: msn2-hht2-aaspt16b-rap090-x54


title: msn2-hht2-aaspt16b-rap060-x54


title: msn2-hht2-aaspt16b-rap030-x54


title: msn2-hht2-aaspt16a-rap090-x54


title: msn2-hht2-aaspt16a-async-x54


title: msn2-hht2-aahir1a-rap090-x54

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX, Msn2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX, Msn2-MNase


title: msn2-hht2-aaspt16a-rap030-x54


title: msn2-hht2-aahir1b-rap090-x54


title: msn2-hht2-aahir1b-async-x54


title: msn2-hht2-aahir1b-rap030-x54


title: reb1-hht2-aahir1a-rap030-x54


title: sok2-hht2-aaspt6-rap120-m05

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Sok2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Sok2-MNase


title: msn2-hht2-aaspt16a-rap060-x54


title: sok2-hht2-aaspt6-rap090-m05


title: msn2-hht2-aahir1a-rap030-x54


title: msn2-hht2-aahir1a-rap060-x54


title: msn2-hht2-aaspt6a-rap060-x54


title: sok2-hht2-aaspt6-rap000-m05


title: sok2-hht2-aaspt16-rap120-m05

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Sok2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Sok2-MNase


title: sok2-hht2-aaspt6-rap060-m05


title: sok2-hht2-aaspt16-rap090-m05


title: sok2-hht2-aaspt16-rap060-m05


title: sok2-hht2-aaspt16-rap000-m05


title: msn2-hht2-aaspt16-rap120-m05


title: msn2-hht2-aaspt16-rap090-m05


title: msn2-hht2-aaspt16b-async-x54


title: msn2-hht2-aahir1b-rap060-x54


title: sok2-hht2-aahir1-rap120-m05

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX, sok2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX, sok2-MNase


title: msn2-hht2-aaspt16-rap000-m05


title: sok2-hht2-aahir1-rap060-m05


title: msn2-hht2-aaspt16-rap060-m05


title: sok2-hht2-aahir1-rap090-m05


title: msn2-hht2-aahir1a-async-x54


title: msn2-hht2-aahir1b-rap000-m05


title: msn2-hht2-aahir1b-rap090-m05


title: msn2-hht2-aahir1b-rap120-m05


title: msn2-hht2-aahir1b-rap060-m05


title: msn2-hht2-aahir1-rap120-m05


title: sok2-hht2-aaspt6-rap120-m04


title: sok2-hht2-aaspt16-rap120-m04


title: sok2-hht2-aaspt6-rap060-m04


title: sok2-hht2-aaspt6-rap000-m04


title: sok2-hht2-aaspt6-rap090-m04


title: msn2-hht2-aahir1-rap060-m05


title: msn2-hht2-aahir1-rap090-m05


title: msn2-hht2-aaspt16-rap090-m04


title: sok2-hht2-aaspt16-rap000-m04


title: msn2-hht2-aaspt16-rap060-m04


title: msn2-hht2-aaspt16-rap000-m04


title: msn2-hht2-aahir1-rap000-m05


title: sok2-hht2-aaspt16-rap090-m04


title: msn2-hht2-aaspt16-rap120-m04


title: sok2-hht2-aahir1-rap090-m04


title: sok2-hht2-aahir1-rap060-m04


title: sok2-hht2-aahir1-rap000-m05


title: sok2-hht2-aahir1-rap000-m04


title: msn2-hht2-aahir1b-rap090-m04


title: msn2-hht2-aahir1b-rap060-m04


title: msn2-hht2-aahir1b-rap000-m04


title: msn2-hht2-aahir1b-rap120-m04


title: msn2-hht2-aahir1-rap120-m04


title: msn2-hht2-aahir1-rap060-m04


title: sok2-hht2-aaspt16-rap060-m04


title: sok2-hht2-aaspt6-rap120-m03


title: msn2-hht2-aahir1-rap000-m04


title: sok2-hht2-aaspt6-rap090-m03


title: sok2-hht2-aahir1-rap120-m04


title: sok2-hht2-aaspt6-rap000-m03


title: sok2-hht2-aaspt16-rap120-m03


title: sok2-hht2-aaspt16-rap090-m03


title: sok2-hht2-aaspt16-rap000-m03


title: sok2-hht2-aartt106-rap090-m02

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Rtt106-FRB::KANMX, sok2-Mnase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Rtt106-FRB::KANMX, sok2-Mnase


title: sok2-hht2-aartt106-rap000-m02


title: sok2-hht2-aartt106-rap060-m02


title: sok2-hht2-aartt106-rap120-m02


title: sok2-hht2-aaspt16-rap060-m03


title: msn2-hht2-aaspt6-rap120-m02


title: sok2-hht2-aaspt6-rap060-m02


title: sok2-hht2-aaspt16-rap120-m02


title: msn2-hht2-aaspt6-rap060-m02


title: msn2-hht2-aaspt6-rap090-m02


title: sok2-hht2-aaspt6-rap090-m02


title: msn2-hht2-aaspt6-control-m02

value: control


title: sok2-hht2-aaspt6-control-m02


title: msn2-hht2-aaspt6-rap000-m02


title: sok2-hht2-aaspt16-rap060-m02


title: sok2-hht2-aaspt16-rap090-m02


title: sok2-hht2-aaspt16-rap000-m02


title: sok2-hht2-aaspt16-control-m02


title: sok2-hht2-aaspt6-rap060-m03


title: msn2-hht2-aaspt16-rap120-m02


title: msn2-hht2-aaspt16-rap060-m02


title: msn2-hht2-aaspt16-rap090-m02


title: sok2-hht2-aaspt6-rap120-m02


title: sok2-hht2-aaspt6-rap000-m02


title: msn2-hht2-aaspt16-rap000-m02


title: sok2-hht2-aahir1-rap120-m02


title: msn2-hht2-aahir1-rap120-m02


title: sok2-hht2-aahir1-rap060-m02


title: sok2-hht2-aahir1-rap000-m02


title: yap1-hht2-aaspt6-rap090-m01

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Yap1-Mnase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt6-FRB::KANMX, Yap1-Mnase

value: no


title: msn2-hht2-aahir1-rap000-m02


title: yap1-hht2-aaspt6-rap120-m01


title: msn2-hht2-aahir1-rap090-m02


title: msn2-hht2-aahir1-rap060-m02


title: yap1-hht2-aaspt6-rap060-m01


title: yap1-hht2-aaspt6-rap000-m01


title: yap1-hht2-aaspt6-5aro80-m01


title: sok2-hht2-aaspt6-rap120-m01


title: yap1-hht2-aaspt6-25aro80-m01


title: yap1-hht2-aaspt16-rap000-m01

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt16-FRB::KANMX, Yap1-Mnase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-TevCleaveWT-MYC bar1 CRISPR, tor1-1*(Ser1971Ile), fpr1 CRISPR, RPL13A-2xFKB12, Spt16-FRB::KANMX, Yap1-Mnase


title: yap1-hht2-aaspt6-25cha4-m01


title: yap1-hht2-aaspt16-rap120-m01


title: yap1-hht2-aaspt16-rap060-m01


title: yap1-hht2-aaspt6-5cha4-m01


title: yap1-hht2-aaspt16-rap090-m01


title: sok2-hht2-aaspt6-rap090-m01


title: sok2-hht2-aahir1-rap090-m02


title: sok2-hht2-aaspt6-rap060-m01


title: msn2-hht2-aaspt6-control-m01

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Msn2-MNase


title: sok2-hht2-aaspt6-control-m01


title: sok2-hht2-aaspt6-5aro80-m01


title: sok2-hht2-aaspt6-25cha4-m01


title: sok2-hht2-aaspt6-25aro80-m01


title: sok2-hht2-aaspt6-rap000-m01


title: msn2-hht2-aahir1-rap090-m04


title: msn2-hht2-aaspt6-5cha4-m01


title: msn2-hht2-aaspt6-5aro80-m01


title: msn2-hht2-aaspt6-25cha4-m01


title: sok2-hht2-aaspt16-rap000-m01


title: sok2-hht2-aaspt16-rap090-m01


title: Spt6-none-wt-async-d

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Spt6-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Spt6-MNase-KANMX

value: wt

value: d

value: async


title: sok2-hht2-aaspt6-5cha4-m01


title: Spt6-none-wt-async-c

value: c


title: Rtt106-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Rtt106-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Rtt106-MNase-KANMX

value: b


title: sok2-hht2-aaspt16-rap060-m01


title: msn2-hht2-aaspt6-25aro80-m01

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Msn2-MNase


title: Ino80-none-wt-async-c

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Ino80-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Ino80-MNase-KANMX


title: Spt6-none-wt-async-e

value: e


title: Chd1-none-wt-async-c

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Chd1-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Chd1-MNase-KANMX


title: Spt6-none-wt-async-b


title: Sth1-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Sth1-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Sth1-MNase-KANMX


title: Sth1-none-wt-async-c


title: Snf2-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Snf2-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Snf2-MNase-KANMX


title: Ino80-none-wt-async-b


title: Vps75-none-wt-async-a

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Vps75-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Vps75-MNase-KANMX

value: a


title: Chd1-none-wt-async-b

value: no


title: Nap1-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Nap1-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Nap1-MNase-KANMX


title: Hir1-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Hir1-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Hir1-MNase-KANMX


title: Sth1-none-wt-async-a


title: Isw2-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Iswi2-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Iswi2-MNase-KANMX


title: Rlf2-none-wt-async-a

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Rlf2-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Rlf2-MNase-KANMX

value: wt


title: Asf1-none-wt-async-b

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0, Asf1-MNase-KANMX

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Asf1-MNase-KANMX

value: async


title: Ino80-none-wt-async-a


title: Snf2-none-wt-async-a


title: Hir1-none-wt-async-a


title: Nap1-none-wt-async-a


title: sok2-hht2-aaspt16-rap120-m01

description: MATa his3Δ1 leu2Δ0 LYS2 met15Δ0 ura3Δ0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Sok2-MNase

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Sok2-MNase


title: Rtt106-none-wt-async-a

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Rtt106-MNase-KANMX


title: Chd1-none-wt-async-a


title: Spt6-none-wt-async-a

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0, Spt6-MNase-KANMX


title: myc-hht2-aavps75-rap120-s45

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d -fs 1)
Assembly: combined S. cerevisiae (GCA_000146045.2) and C. glabrata () genome
Supplementary files format and content: *.out.txt.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata)

source_name: yeast cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha facor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail). Where indicated 10 ul of undiluted (HA,k9ac,k56ac) or 1:50 diluted (myc)  lysate of a C.Glabrata strain with myc-ha tagged H3 in  NP buffer were added to 110 ul of sample ( = 120 ul in total). SLIM-ChIP protocol was then continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

value: yeast cells

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Vps75-FRB::KANMX

tag: antibody

value: myc


title: myc-hht2-aavps75-rap090-s45


title: Asf1-none-wt-async-a


title: Vps75-none-wt-async-b

value: b


title: myc-hht2-aavps75-rap060-s45


title: myc-hht2-aavps75-rap020-s45


title: myc-hht2-aavps75-rap040-s45


title: myc-hht2-aavps75-rap000-s45


title: myc-hht2-aasth1-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Sth1-FRB::KANMX


title: myc-hht2-aasth1-rap060-x52


title: myc-hht2-aasth1-rap020-x52


title: myc-hht2a-aaspt6spt16-rap090-x50

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double


title: myc-hht2a-aaspt6spt16-rap060-x50


title: myc-hht2-aasth1-rap040-x52


title: myc-hht2-aasth1-async-x52


title: myc-hht2-aaspt6spt16-rap090-x55


title: myc-hht2a-aaspt6spt16-rap040-x50


title: myc-hht2-aaspt6spt16-rap020-x55


title: myc-hht2-aaspt6spt16-async-x55


title: Isw2-none-wt-async-a

value: a

value: no


title: myc-hht2-aaspt6spt16-rap040-x55


title: myc-hht2a-aaspt6spt16-async-x50


title: myc-hht2-aaspt6cac1-async-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Cac1-FRB  (insert has KANMX)


title: myc-hht2-aaspt6cac1-rap060-x60


title: myc-hht2-aaspt6cac1-rap040-x60


title: myc-hht2-aaspt6-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX


title: myc-hht2-aaspt6-rap060-x55


title: myc-hht2-aaspt6-rap040-x55


title: myc-hht2-aaspt6-rap020-x55


title: myc-hht2-aaspt6wash-rap060-s44


title: myc-hht2-aaspt6wash-rap120-s44


title: myc-hht2a-aaspt6-async-x50


title: myc-hht2a-aaspt6-rap060-x50


title: myc-hht2-aaspt6wash-rap000-s44


title: myc-hht2-aaspt6-async-x55


title: myc-hht2-aaspt6wash-rap090-s44


title: myc-hht2-aaspt6wash-rap040-s44


title: myc-hht2a-aaspt6spt16-rap020-x50


title: myc-hht2-aaspt6spt16-rap060-x55


title: myc-hht2-aaspt6-rap090-s44


title: myc-hht2-aaspt6cac1-rap090-x60


title: myc-hht2-aaspt6-rap060-s44


title: myc-hht2-aaspt6-rap000-s44


title: myc-hht2b-aaspt6-rap120-s42


title: myc-hht2-aaspt6-rap120-s44


title: myc-hht2b-aaspt6-rap090-s42


title: myc-hht2-aaspt6-rap040-s44


title: myc-hht2-aaspt6cac1-rap020-x60


title: myc-hht2b-aaspt6-rap060-s42


title: myc-hht2b-aaspt6-rap020-s42


title: myc-hht2b-aaspt6-rap040-s42


title: myc-hht2-aaspt6-rap060-s42


title: myc-hht2-aaspt6-rap120-s42


title: myc-hht2b-aaspt6-rap000-s42


title: myc-hht2-aaspt6-rap090-s42


title: myc-hht2-aaspt6-rap040-s42


title: myc-hht2-aaspt6-rap020-s42


title: myc-hht2-aaspt6-rap000-s42


title: myc-hht2-aaspt16spt6cac1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Cac1-FRB


title: myc-hht2-aaspt16spt6cac1-rap020-x60


title: myc-hht2-aaspt6-rap000-s41


title: myc-hht2-aaspt6b-rap000-s41


title: myc-hht2-aaspt16spt6cac1-async-x60


title: myc-hht2-aaspt16spt6cac1-rap040-x60


title: myc-hht2-aaspt16cac1-rap060-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Cac1-FRB  (insert has KANMX)


title: myc-hht2-aaspt16cac1-rap040-x60


title: myc-hht2-aaspt16cac1-async-x60


title: myc-hht2-aaspt16-ypd120-x40

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: myc-hht2-aaspt16cac1-rap020-x60


title: myc-hht2a-aaspt16-rap060-x50


title: myc-hht2-aaspt16-ypd030-x40


title: myc-hht2a-aaspt16-async-x50


title: myc-hht2-aaspt16-rap120-x40


title: myc-hht2-aaspt16-rap120-s42


title: myc-hht2-aaspt16-rap030-x40


title: myc-hht2-aaspt16-async-x40


title: myc-hht2-aaspt16-rap090-s42


title: myc-hht2-aaspt16-rap040-s42


title: myc-hht2-aaspt16-rap060-s42


title: myc-hht2-aaspt16-rap020-s42


title: myc-hht2-aaspt16b-rap000-s41


title: myc-hht2-aaspt16-rap180-s41


title: myc-hht2-aaspt16-rap120-s41


title: myc-hht2-aaspt16spt6cac1-rap060-x60


title: myc-hht2-aaspt16-rap060-s41


title: myc-hht2-aaspt16cac1-rap090-x60


title: myc-hht2-aaspt16-rap040-s41


title: myc-hht2-aasnf2-rap020-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Snf2-FRB::KANMX


title: myc-hht2-aasnf2-rap090-x52


title: myc-hht2-aartt106-rap090-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: myc-hht2-aartt106-rap040-s45


title: myc-hht2-aartt106-rap060-s45


title: myc-hht2-aartt106-rap120-s45


title: myc-hht2-aaspt16-rap000-s42


title: myc-hht2a-aanofrb-async-x50

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12

value: aanofrb


title: myc-hht2-nofrb-rap120-s41

value: yeast cells


title: myc-hht2-aartt106-rap000-s45


title: myc-hht2a-aanofrb-rap060-x50


title: myc-hht2-aanap1-rap060-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Nap1-FRB::KANMX


title: myc-hht2-aasnf2-async-x52

value: myc


title: myc-hht2-aanap1-rap040-s45


title: myc-hht2-nofrb-rap000-s41


title: myc-hht2-aanap1-rap120-s45


title: myc-hht2-aaspt16-rap090-s41


title: myc-hht2-aaisw2-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, ISW2-FRB::KANMX


title: myc-hht2-aanap1-rap090-s45


title: myc-hht2-aasnf2-rap040-x52


title: myc-hht2-aanap1-rap000-s45


title: myc-hht2-aaisw2-rap060-x55


title: myc-hht2-aanap1-rap020-s45


title: myc-hht2-aasnf2-rap060-x52


title: myc-hht2-aaspt16-rap000-s41


title: myc-hht2-aaisw2-rap020-x55


title: myc-hht2-aaisw2-async-x55


title: myc-hht2-aaisw2-rap040-x55


title: myc-hht2-aaisw1-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, ISW1-FRB::KANMX


title: myc-hht2-aaisw1-rap060-x55


title: myc-hht2-aaisw1-rap040-x55


title: myc-hht2-aaisw1-async-x55


title: myc-hht2-aaino80-rap060-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX


title: myc-hht2-aaino80-rap040-x60


title: myc-hht2-aaino80-rap090-x60


title: myc-hht2-aaino80-async-x60


title: myc-hht2a-aahir1asf1rtt106-rap090-x50

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple


title: myc-hht2-aahir1-rap090-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX


title: myc-hht2-aaino80-rap020-x52


title: myc-hht2-aahir1-rap040-s45


title: myc-hht2-aahir1-rap120-s45


title: myc-hht2-aaino80-async-x52


title: myc-hht2-aaino80-rap090-x52


title: myc-hht2a-aahir1asf1rtt106-rap020-x50


title: myc-hht2-aaino80-rap060-x52


title: myc-hht2-aaino80-rap040-x52


title: myc-hht2-aahir1-rap020-s45


title: myc-hht2a-aahir1asf1rtt106-rap060-x50


title: myc-hht2-aaino80-rap020-x60


title: myc-hht2a-aahir1asf1rtt106-rap040-x50


title: myc-hht2-aahir1-rap000-s45


title: myc-hht2a-aahir1asf1rtt106-async-x50


title: myc-hht2-aahir1-rap060-s45


title: myc-hht2-aaisw1-rap020-x55


title: myc-hht2-aachz1-rap090-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chz1-FRB::KANMX


title: myc-hht2-aachz1-rap060-s45


title: myc-hht2-aachz1-rap020-s45


title: myc-hht2-aachz1-rap000-s45


title: myc-hht2-aachd1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX


title: myc-hht2-aachd1-rap060-x60


title: myc-hht2-aachd1-rap040-x60


title: myc-hht2-aachd1-rap020-x60


title: myc-hht2-aachd1-rap040-x55


title: myc-hht2-aacac1-rap090-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Cac1-FRB::KANMX


title: myc-hht2-aachd1-rap020-x55


title: myc-hht2-aachd1-async-x60


title: myc-hht2-aachd1-async-x55


title: myc-hht2-aacac1-rap000-s45


title: myc-hht2-aacac1-rap020-s45


title: myc-hht2-aacac1-rap040-s45


title: myc-hht2-aachz1-rap040-s45


title: myc-hht2-aacac1-rap120-s45


title: myc-hht2-aachd1-rap060-x55


title: myc-hht2-aaasf1-rap060-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Asf1-FRB::KANMX


title: myc-hht2-aaasf1-rap020-s45


title: myc-hht2-aaasf1-rap120-s45


title: myc-hht2-aa5-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , Spt6-FRB & spt16-FRB double


title: myc-hht2-aachz1-rap120-s45


title: myc-hht2-aaasf1-rap090-s45


title: myc-hht2-aaasf1-rap000-s45


title: myc-hht2-aaasf1-rap040-s45


title: myc-hht2-aa5-rap040-x55


title: myc-hht2-aa5-rap060-x55


title: myc-hht2-aa3spt6-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , spt6-FRB


title: myc-hht2-aa3spt6-rap060-x55


title: myc-hht2-aa3spt6-rap040-x55


title: myc-hht2-aa3spt6-rap020-x55


title: myc-hht2-aachd1-rap090-x55


title: myc-hht2-aacac1-rap060-s45


title: myc-hht2-aa3spt6b-rap090-x52


title: myc-hht2-aa3spt6b-rap020-x52


title: myc-hht2-aa3spt6-rap090-x52


title: myc-hht2-aa3spt16-rap040-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , spt16-FRB


title: myc-hht2-aa3spt6b-async-x52


title: myc-hht2-aa3spt16-rap060-x52


title: myc-hht2-aa3spt6b-rap060-x52


title: myc-hht2-aa5-rap020-x55


title: myc-hht2-aa3spt16-async-x52


title: myc-hht2-aa3spt6-async-x52


title: myc-hht2-aa3spt6-rap040-x52


title: myc-hht2-aa3spt6-rap060-x52


title: myc-hht2-aa5-async-x55


title: myc-h2b-aavps75-rap040-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Vps75-FRB::KANMX


title: myc-hht2-aa3spt6-rap020-x52


title: myc-hht2-aa3spt6b-rap040-x52


title: myc-hht2-aa3spt16-rap090-x52


title: myc-h2b-aavps75-rap120-s46


title: myc-hht2-aa3spt16-rap020-x52


title: myc-h2b-aavps75-rap060-s46


title: myc-h2b-aavps75-rap090-s46


title: myc-h2b-aavps75-rap020-s46


title: myc-h2b-aavps75-rap000-s46


title: myc-hht2-aa3spt6-async-x55


title: myc-h2b-aasth1-rap020-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Sth1-FRB::KANMX


title: myc-h2b-aasth1-rap090-x52

value: yeast cells


title: myc-h2b-aasth1-rap060-x52


title: myc-h2b-aasth1-async-x52


title: myc-h2b-aasth1-rap040-x52


title: myc-h2b-aaspt6-rap090-s42

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX


title: myc-h2b-aaspt6-rap060-s42

value: myc


title: myc-h2b-aaspt6-rap020-s42


title: myc-h2b-aaspt6-rap040-s42


title: myc-h2b-aaspt6-rap060-s41


title: myc-h2b-aaspt6-rap120-s41


title: myc-h2b-aaspt6-rap090-s41


title: myc-h2b-aaspt6-rap180-s41


title: myc-h2b-aaspt16-rap120-x40

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: myc-h2b-aaspt16-ypd120-x40


title: myc-h2b-aaspt16-rap030-x40


title: myc-h2b-aaspt16-rap060-s42


title: myc-h2b-aaspt16-rap020-s42


title: myc-h2b-aaspt16-rap040-s42


title: myc-h2b-aaspt16-rap000-s42


title: myc-h2b-aaspt16b-rap000-s41


title: myc-h2b-aaspt16-rap120-s41


title: myc-h2b-aaspt16-ypd030-x40


title: myc-h2b-aaspt16-rap090-s41


title: myc-h2b-aaspt16-rap180-s41


title: myc-h2b-aaspt16-rap040-s41


title: myc-h2b-aaspt16-rap000-s41


title: myc-h2b-aaspt16-rap090-s42


title: myc-h2b-aasnf2-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Snf2-FRB::KANMX


title: myc-h2b-aasnf2-rap060-x52


title: myc-h2b-aaspt16-rap060-s41


title: myc-h2b-aaspt6-rap120-s42


title: myc-h2b-aaspt6-rap000-s42


title: myc-h2b-aaspt16-async-x40


title: myc-h2b-aasnf2-rap020-x52


title: myc-h2b-aasnf2-async-x52


title: myc-h2b-aartt106-rap060-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: myc-h2b-aasnf2-rap040-x52


title: myc-h2b-aartt106-rap000-s46


title: myc-h2b-aartt106-rap020-s46


title: myc-h2b-aartt106-rap040-s46


title: myc-h2b-nofrb-rap120-s41

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12

value: aanofrb


title: myc-h2b-aanap1-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Nap1-FRB::KANMX


title: myc-h2b-aanap1-rap120-s46


title: myc-h2b-aanap1-rap060-s46


title: myc-h2b-aanap1-rap040-s46


title: myc-h2b-aanap1-rap000-s46


title: myc-h2b-aaino80-rap060-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX


title: myc-h2b-aartt106-rap090-s46


title: myc-h2b-aanap1-rap020-s46


title: myc-h2b-aaino80-rap040-x52


title: myc-h2b-aaino80-rap020-x52


title: myc-h2b-aahir1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX


title: myc-h2b-nofrb-rap000-s41


title: myc-h2b-aahir1-rap040-s46


title: myc-h2b-aahir1-rap090-s46


title: myc-hht2-aartt106-rap020-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: myc-h2b-aahir1-rap020-s46


title: myc-h2b-aahir1-rap060-s46


title: myc-h2b-aahir1-rap000-s46


title: myc-h2b-aachz1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chz1-FRB::KANMX


title: myc-h2b-aartt106-rap120-s46


title: myc-h2b-aachz1-rap090-s46


title: myc-h2b-aachz1-rap060-s46


title: myc-h2b-aachz1-rap020-s46


title: myc-h2b-aachz1-rap000-s46


title: myc-h2b-aachz1-rap040-s46


title: myc-h2b-aaino80-rap090-x52


title: myc-h2b-aachd1-rap040-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX


title: myc-h2b-aachd1-rap090-x60


title: myc-h2b-aachd1-rap060-x60


title: myc-h2b-aachd1-async-x60


title: myc-h2b-aachd1-rap020-x60


title: myc-h2b-aacac1-rap090-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Cac1-FRB::KANMX


title: myc-h2b-aacac1-rap060-s46


title: myc-h2b-aacac1-rap000-s46


title: myc-h2b-aacac1-rap040-s46


title: myc-h2b-aaasf1-rap120-s46

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC, bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Asf1-FRB::KANMX


title: myc-h2b-aaasf1-rap060-s46


title: myc-h2b-aaasf1-rap040-s46


title: myc-h2b-aaasf1-rap090-s46


title: myc-h2b-aaasf1-rap020-s46


title: ha-hht2-aavps75-rap060-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Vps75-FRB::KANMX

value: ha


title: myc-h2b-aaasf1-rap000-s46

value: yeast cells


title: ha-hht2-aavps75-rap120-s45


title: ha-hht2-aavps75-rap020-s45


title: ha-hht2-aavps75-rap090-s45


title: ha-hht2-aavps75-rap040-s45


title: ha-hht2-aavps75-rap000-s45


title: ha-hht2-aasth1-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Sth1-FRB::KANMX


title: myc-h2b-aacac1-rap120-s46

value: myc


title: ha-hht2-aasth1-rap020-x52


title: ha-hht2-aasth1-async-x52


title: ha-hht2-aaspt6spt16-async-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double


title: ha-hht2a-aaspt6spt16-rap090-x50


title: ha-hht2a-aaspt6spt16-rap060-x50


title: ha-hht2-aaspt6spt16-rap090-x55


title: ha-hht2-aasth1-rap060-x52


title: ha-hht2-aasth1-rap040-x52


title: ha-hht2-aaspt6spt16-rap060-x55


title: ha-hht2-aaspt6spt16-rap020-x55


title: ha-hht2a-aaspt6spt16-rap040-x50


title: myc-h2b-aacac1-rap020-s46


title: ha-hht2a-aaspt6spt16-async-x50


title: ha-hht2-aaspt6cac1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX, Cac1-FRB  (insert has KANMX)


title: ha-hht2-aaspt6cac1-rap040-x60


title: ha-hht2-aaspt6cac1-rap060-x60


title: myc-h2b-aaino80-async-x52


title: ha-hht2-aaspt6-rap040-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB::KANMX


title: ha-hht2-aaspt6cac1-rap020-x60


title: ha-hht2-aaspt6-rap060-x55


title: ha-hht2-aaspt6cac1-async-x60


title: ha-hht2a-aaspt6-rap060-x50


title: ha-hht2-aaspt6-async-x55


title: ha-hht2-aaspt6-rap020-x55


title: ha-hht2-aaspt6spt16-rap040-x55


title: ha-hht2a-aaspt6-async-x50


title: ha-hht2-aaspt6wash-rap090-s44


title: ha-hht2-aaspt6-rap090-x55


title: ha-hht2-aaspt6wash-rap060-s44


title: ha-hht2a-aaspt6spt16-rap020-x50


title: ha-hht2-aaspt6-rap090-s44


title: ha-hht2-aaspt6wash-rap000-s44


title: ha-hht2-aaspt6-rap120-s44


title: ha-hht2b-aaspt6-rap090-s42


title: ha-hht2-aaspt6wash-rap040-s44


title: ha-hht2b-aaspt6-rap040-s42


title: ha-hht2b-aaspt6-rap020-s42


title: ha-hht2b-aaspt6-rap120-s42


title: ha-hht2b-aaspt6-rap000-s42


title: ha-hht2-aaspt6-rap040-s44


title: ha-hht2-aaspt6-rap060-s44


title: ha-hht2-aaspt6-rap090-s42


title: ha-hht2-aaspt6-rap120-s42


title: ha-hht2-aaspt6-rap040-s42


title: ha-hht2-aaspt6-rap000-s42


title: ha-hht2-aaspt16spt6cac1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt6-FRB & Spt16-FRB double , Cac1-FRB


title: ha-hht2-aaspt16spt6cac1-rap060-x60


title: ha-hht2-aaspt16spt6cac1-rap040-x60


title: ha-hht2-aaspt6wash-rap120-s44


title: ha-hht2-aaspt16spt6cac1-rap020-x60


title: ha-hht2-aaspt16cac1-rap060-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX, Cac1-FRB  (insert has KANMX)


title: ha-hht2-aaspt16spt6cac1-async-x60


title: ha-hht2-aaspt6-rap000-s44


title: ha-hht2b-aaspt6-rap060-s42


title: ha-hht2-aaspt16cac1-rap090-x60


title: ha-hht2-aaspt16cac1-rap020-x60


title: ha-hht2-aaspt16cac1-async-x60


title: ha-hht2-aaspt16-ypd120-x40

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Spt16-FRB::KANMX


title: ha-hht2-aaspt16-ypd000-s41


title: ha-hht2a-aaspt16-async-x50


title: ha-hht2a-aaspt16-rap060-x50


title: ha-hht2-aaspt16-rap120-x40


title: ha-hht2-aaspt16-rap030-x40


title: ha-hht2-aaspt16-ypd030-x40


title: ha-hht2-aaspt16-rap060-s42


title: ha-hht2-aaspt16-rap120-s42


title: ha-hht2-aaspt16-rap090-s42


title: ha-hht2-aaspt16-async-x40


title: ha-hht2-aaspt6-rap060-s42


title: ha-hht2-aaspt6-rap020-s42


title: ha-hht2-aaspt16-rap020-s42


title: ha-hht2-aaspt16-rap000-s42


title: ha-hht2-aaspt16-rap120-s41


title: ha-hht2-aaspt16-rap180-s41


title: ha-hht2-aaspt16-rap040-s41


title: ha-hht2-aaspt16cac1-rap040-x60


title: ha-hht2-aaspt16b-rap000-s41


title: ha-hht2-aaspt16-rap090-s41


title: ha-hht2-aaspt16-rap060-s41


title: ha-hht2-aasnf2-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Snf2-FRB::KANMX


title: ha-hht2-aasnf2-rap020-x52


title: ha-hht2-aasnf2-rap060-x52


title: ha-hht2-aasnf2-async-x52


title: ha-hht2-aasnf2-rap040-x52


title: ha-hht2-aartt106-rap120-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Rtt106-FRB::KANMX


title: ha-hht2-aartt106-rap090-s45


title: ha-hht2-aartt106-rap060-s45


title: ha-hht2-aartt106-rap040-s45


title: ha-hht2-aaspt16-rap040-s42


title: ha-hht2a-aanofrb-rap060-x50

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12

value: aanofrb


title: ha-hht2-nofrb-rap000-s41


title: ha-hht2-nofrb-rap120-s41


title: ha-hht2-aartt106-rap020-s45


title: ha-hht2a-aanofrb-async-x50


title: ha-hht2-aartt106-rap000-s45


title: ha-hht2-aanap1-rap060-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Nap1-FRB::KANMX


title: ha-hht2-aanap1-rap090-s45


title: ha-hht2-aanap1-rap020-s45


title: ha-hht2-aanap1-rap040-s45


title: ha-hht2-aaisw2-rap060-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, ISW2-FRB::KANMX


title: ha-hht2-aaisw2-rap040-x55


title: ha-hht2-aaisw1-rap040-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, ISW1-FRB::KANMX


title: ha-hht2-aaisw1-rap060-x55

value: ha


title: ha-hht2-aaisw1-rap020-x55

value: yeast cells


title: ha-hht2-aaisw2-rap020-x55


title: ha-hht2-aaisw1-rap090-x55


title: ha-hht2-aaisw1-async-x55


title: ha-hht2-aaino80-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Ino80-FRB::KANMX


title: ha-hht2-aaino80-rap060-x60


title: ha-hht2-aaino80-rap020-x60


title: ha-hht2-aaino80-rap040-x60


title: ha-hht2-aanap1-rap120-s45


title: ha-hht2-aaino80-async-x60


title: ha-hht2-aaino80-rap060-x52


title: ha-hht2-aaino80-rap040-x52


title: ha-hht2-aaino80-rap020-x52


title: ha-hht2-aaino80-async-x52


title: ha-hht2a-aahir1asf1rtt106-rap060-x50

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple


title: ha-hht2a-aahir1asf1rtt106-rap040-x50


title: ha-hht2a-aahir1asf1rtt106-rap020-x50


title: ha-hht2-aahir1-rap090-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB::KANMX


title: ha-hht2-aaisw2-rap090-x55


title: ha-hht2-aahir1-rap060-s45


title: ha-hht2-aaisw2-async-x55


title: ha-hht2-aanap1-rap000-s45


title: ha-hht2a-aahir1asf1rtt106-async-x50


title: ha-hht2-aahir1-rap040-s45


title: ha-hht2-aahir1-rap020-s45


title: ha-hht2-aahir1-rap000-s45


title: ha-hht2-aachz1-rap120-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chz1-FRB::KANMX


title: ha-hht2-aachz1-rap090-s45


title: ha-hht2-aachz1-rap020-s45


title: ha-hht2-aachz1-rap060-s45


title: ha-hht2-aaino80-rap090-x52


title: ha-hht2-aachz1-rap040-s45


title: ha-hht2-aahir1-rap120-s45


title: ha-hht2-aachz1-rap000-s45


title: ha-hht2-aachd1-rap090-x60

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Chd1-FRB::KANMX


title: ha-hht2a-aahir1asf1rtt106-rap090-x50


title: ha-hht2-aachd1-rap020-x60


title: ha-hht2-aachd1-rap060-x55


title: ha-hht2-aachd1-rap040-x55


title: ha-hht2-aachd1-rap040-x60


title: ha-hht2-aachd1-async-x55


title: ha-hht2-aachd1-rap060-x60


title: ha-hht2-aachd1-async-x60


title: ha-hht2-aachd1-rap020-x55


title: ha-hht2-aacac1-rap120-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Cac1-FRB::KANMX


title: 4CBS_CUT&Tag_ab4729

city: La Jolla

first: Yang

last: Xie

address: Rm.2071, 9500 Gilman Dr

department: Department of Cellular and Molecular Medicine

institute: UC San Diego

description:
Bulk CUT&Tag
YX823

data_processing:
All sequencing was carried out with our in-house Illumina Nextseq2000 sequencer. Adapter sequences were trimmed from paired-end reads using trim_galore with default parameters. Reads alignments were then performed using bowtie2. Duplicates were removed with Picard based on their mapped positions.
assembly: mm10
For Bulk CUT&Tag data, Bigwig files generated from de-duplicated alignment file is provided.

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESC) were maintained in feeder-free and serum-free 2i media (https://crem.bu.edu/wp-content/uploads/2022/01/2i-Media-Feeder-free-Serum-free.pdf) at 37 °C with 5% CO2.

extract_protocol:
To prepare nuclei, mESC were dissociated with Accutase (Innovative Cell Technologies, AT104), collected by centrifugation, washed twice with PBS (Gibco, 10010023) then resuspended in cold nuclei permeabilization buffer (10 mM Tris-HCl pH 7.4 (Sigma, T4661), 10 mM NaCl (Sigma, S7653), 3 mM MgCl2 (Sigma, 63069), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 0.1% IGEPAL CA630 (Sigma, I8896) and 0.02% Digitonin (Sigma, Cat#D141)) for 1 minute. Nuclei were counted using a BioRad TC20 cell counter with 0.4% Trypan Blue (Gibco, 15250061) staining. For each experiment, around 0.5 million nuclei were aliquoted, and centrifuged for 10 min at 1,000g, 4 °C before proceeding to Bulk CUT&Tag.
Tagmentated products are extracted using QIAGEN MiniElute after CUT&Tag, and directly amplified with indexed primers. Size selection using SPRI Beads is performed with amplified products to obtain the final sequencing library (150-800 bp)

value: embryonic stem cells

tag: cell line

value: F123-CASTx129 with Sox2 tags and 4 CTCF binding sites between Sox2 and its SE

tag: chip antibody


title: 4CBS_CUT&Tag_ab192985

description:
Bulk CUT&Tag
YX836v


title: ha-hht2-aacac1-rap090-s45

tag: genotype


title: ha-hht2-aacac1-rap040-s45


title: ha-hht2-aacac1-rap060-s45


title: FC_CUT&Tag_ab192985

description:
Bulk CUT&Tag
YX784

source_name: frontal cortex

growth_protocol: All animal work described in this manuscript has been approved and conducted under the oversight of the UC San Diego Institutional Animal Care and Use Committee. Male C57BL/6J mice were purchased from the Jackson Laboratory (#000664) at 12 weeks of age and housed in the barriered facility at UC San Diego in a 12-hour light/dark cycle in a temperature-controlled room, with ad libitum access to water and food, until euthanasia and tissue collection at 16 weeks of age. The frontal cortex and hippocampus were dissected, snap-frozen in liquid nitrogen, and stored at -80°C before proceeding to nuclei extraction.

extract_protocol:
Single-cell suspensions were prepared from frozen tissues by douncing in douncing buffer (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U µl−1 RNase OUT, 0.5 U µl−1 SUPERase Inhibitor). The cell suspension was then filtered through a 30-µm Cell-Tric (Sysmex) for debris removal, and spun down for 10 min at 300g, 4 °C. Cell pellets were washed once with douncing buffer, spun down again, and resuspended in cold nuclei permeabilization buffer for 10mins. Permeablized nuclei were pelleted by centrifuge for 10 min at 1,000g, 4 °C, and washed with sort buffer (1× PBS (Gibco, 10010023), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 1% BSA (Sigma, A1595)) once. After resuspension in sort buffer, nuclei are stained with 2 μM 7-AAD (Invitrogen, A1310) for 10mins on ice, and proceed to Fluorescence-activated cell sorting (FACS) with an SH800 cell sorter (Sony) for isolation of single nucleus. Nuclei are collected in collection buffer  (1× PBS (Gibco, 10010023), 5×Protease Inhibitor (Roche, 05056489001), 2.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 2.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 5% BSA (Sigma, A1595)) at 5 °C, then immediately proceed to centrifuge for 10 min at 750g, 4 °C. Nuclei were washed twice with sort buffer and counted on an RWD C100-pro fluorescence cell counter with DAPI staining to better estimate the nuclei number. For each histone modification, around 0.5 million sorted nuclei were aliquoted and proceeded to Bulk CUT&Tag experiments.
Tagmentated products are extracted using QIAGEN MiniElute after CUT&Tag, and directly amplified with indexed primers. Size selection using SPRI Beads is performed with amplified products to obtain the final sequencing library (150-800 bp)

value: frontal cortex


title: FC_CUT&Tag_ab4729

description:
Bulk CUT&Tag
YX817


title: 4CBS_Droplet_Paired-Tag_H3K27me3_RNA

description:
10XMultiome, gene expression
YX846

data_processing:
All sequencing was carried out with our in-house Illumina Nextseq2000 sequencer. Fastq files are demultiplexed using cellranger-arc v.2.0.0 (10x Genomics) with command `cellranger-arc mkfastq`; However, DNA and RNA data were preprocessed using cellranger-atac v.2.0.0 and cellranger v.6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei, we first filter the histone modality based on the per cell fragment number and fraction of reads in peaks (FRiP), then further select nuclei by pairing pass-filtered nuclei from both modalities.
assembly: mm10
For CUT&Tag data, processed data provided as a fragment file, each line represents a unique genomic DNA fragment captured by the assay. Valid cells information is provided as metadata in the supplementary file. Bigwig files generated from de-duplicated alignment file is also provided.
For RNA data, raw cell-by-features matrix is provided. Valid cells information is provided as metadata in the supplementary file.

molecule: nuclear RNA

extract_protocol:
To prepare nuclei, mESC were dissociated with Accutase (Innovative Cell Technologies, AT104), collected by centrifugation, washed twice with PBS (Gibco, 10010023) then resuspended in cold nuclei permeabilization buffer (10 mM Tris-HCl pH 7.4 (Sigma, T4661), 10 mM NaCl (Sigma, S7653), 3 mM MgCl2 (Sigma, 63069), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 0.1% IGEPAL CA630 (Sigma, I8896) and 0.02% Digitonin (Sigma, Cat#D141)) for 1 minute. Nuclei were counted using a BioRad TC20 cell counter with 0.4% Trypan Blue (Gibco, 15250061) staining. For each experiment, around 0.5 million nuclei were aliquoted, and centrifuged for 10 min at 1,000g, 4 °C before proceeding to Droplet Paired-Tag experiments.
Final DNA and RNA libraries amplification were performed according to the Chromium Single Cell ATAC Library kit manual, except that we used an increased number of amplification cycles (in total 12-13) for DNA (histone modality) library.


title: 4CBS_Droplet_Paired-Tag_H3K27ac_rep2_RNA

description:
10XMultiome, gene expression
YX845


title: ha-hht2-aaasf1-rap120-s45

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Asf1-FRB::KANMX


title: ha-hht2-aacac1-rap000-s45


title: ha-hht2-aacac1-rap020-s45


title: ha-hht2-aaasf1-rap090-s45


title: 4CBS_Droplet_Paired-Tag_H3K27ac_rep2_DNA

description:
10XMultiome, histone modification
YX843


title: 4CBS_Droplet_Paired-Tag_H3K27me3_DNA

description:
10XMultiome, histone modification
YX844


title: ha-hht2-aachd1-rap090-x55


title: ha-hht2-aaasf1-rap060-s45


title: ha-hht2-aaasf1-rap040-s45


title: FC_Droplet_Paired-Tag_H3K27me3_rep3_RNA

description:
10XMultiome, gene expression
YX842

data_processing:
All sequencing was carried out with our in-house Illumina Nextseq2000 sequencer. Fastq files are demultiplexed using cellranger-arc v.2.0.0 (10x Genomics) with command `cellranger-arc mkfastq`; However, DNA and RNA data were preprocessed using cellranger-atac v.2.0.0 and cellranger v.6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc. To select high-quality nuclei, we first filter the histone modality based on the per cell fragment number and fraction of reads in peaks (FRiP), then further select nuclei by pairing pass-filtered nuclei from both modalities.
assembly: mm10
For CUT&Tag data, processed data provided as a fragment file, each line represents a unique genomic DNA fragment captured by the assay. Valid cells information is provided as metadata in the supplementary file.
For RNA data, raw cell-by-features matrix is provided. Valid cells information is provided as metadata in the supplementary file.

extract_protocol:
Single-cell suspensions were prepared from frozen tissues by douncing in douncing buffer (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U µl−1 RNase OUT, 0.5 U µl−1 SUPERase Inhibitor). The cell suspension was then filtered through a 30-µm Cell-Tric (Sysmex) for debris removal, and spun down for 10 min at 300g, 4 °C. Cell pellets were washed once with douncing buffer, spun down again, and resuspended in cold nuclei permeabilization buffer for 10mins. Permeablized nuclei were pelleted by centrifuge for 10 min at 1,000g, 4 °C, and washed with sort buffer (1× PBS (Gibco, 10010023), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 1% BSA (Sigma, A1595)) once. After resuspension in sort buffer, nuclei are stained with 2 μM 7-AAD (Invitrogen, A1310) for 10mins on ice, and proceed to Fluorescence-activated cell sorting (FACS) with an SH800 cell sorter (Sony) for isolation of single nucleus. Nuclei are collected in collection buffer  (1× PBS (Gibco, 10010023), 5×Protease Inhibitor (Roche, 05056489001), 2.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 2.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 5% BSA (Sigma, A1595)) at 5 °C, then immediately proceed to centrifuge for 10 min at 750g, 4 °C. Nuclei were washed twice with sort buffer and counted on an RWD C100-pro fluorescence cell counter with DAPI staining to better estimate the nuclei number. For each histone modification, around 0.5 million sorted nuclei were aliquoted and proceeded to Paired-Tag experiments.
Final DNA and RNA libraries amplification were performed according to the Chromium Single Cell ATAC Library kit manual, except that we used an increased number of amplification cycles (in total 12-13) for DNA (histone modality) library.


title: FC_Droplet_Paired-Tag_H3K27ac_rep3_RNA

description:
10XMultiome, gene expression
YX841


title: FC_Droplet_Paired-Tag_H3K27me3_rep2_RNA

description:
10XMultiome, gene expression
YX840


title: ha-hht2-aaasf1-rap000-s45


title: ha-hht2-aa5-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , Spt6-FRB & spt16-FRB double


title: FC_Droplet_Paired-Tag_H3K27ac_rep2_RNA

description:
10XMultiome, gene expression
YX839


title: ha-hht2-aa5-rap020-x55


title: ha-hht2-aaasf1-rap020-s45


title: ha-hht2-aa5-rap040-x55


title: ha-hht2-aa5-rap060-x55


title: FC_Droplet_Paired-Tag_H3K27me3_rep2_DNA

description:
10XMultiome, histone modification
YX836


title: FC_Droplet_Paired-Tag_H3K27ac_rep3_DNA

description:
10XMultiome, histone modification
YX837


title: FC_Droplet_Paired-Tag_H3K27me3_rep3_DNA

description:
10XMultiome, histone modification
YX838


title: FC_Droplet_Paired-Tag_H3K27me3_rep1_RNA

description:
10XMultiome, gene expression
YX797


title: ha-hht2-aa3spt6-rap090-x55

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , spt6-FRB


title: ha-hht2-aa3spt6-rap060-x55


title: ha-hht2-aa5-async-x55


title: FC_Droplet_Paired-Tag_H3K27ac_rep1_DNA

description:
10XMultiome, histone modification
YX794


title: 4CBS_Droplet_Paired-Tag_H3K27ac_rep1_RNA

description:
10XMultiome, gene expression
YX737


title: ha-hht2-aa3spt6-rap040-x55


title: ha-hht2-aa3spt6-rap020-x55


title: ha-hht2-aa3spt6-async-x55


title: ha-hht2-aa3spt6b-rap090-x52


title: 4CBS_Droplet_Paired-Tag_H3K27ac_rep1_DNA

description:
10XMultiome, histone modification
YX735


title: DeltaLinker_3

city: Greenville

first: Kyle

last: Mansfield

state: NC

address: 600 Moye Blvd, MS622

department: Biochemistry and Molecular Biology

institute: East Carolina University, Brody School of Medicine

data_processing:
Sequences were basecalled using the high accuracy basecalling setting and default parameters for quality, barcode identification and trimming.
Passed reads were mapped using MinMap2 to Human Hg38 genome with the Oxford Nanopore read to reference mapping option enabled (minimap2 -x map-ont --q-occ-frac 0.01 -t 6 -a)
Reads were quantified using featureCounts and differential expression determined with DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file with normalized read counts for all genes in all samples/replicate

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated with TRIzol reagent (Ambion) according to manufacturer protocol.PolyA RNA was isolated total RNA using the Poly(A)Purist MAG Kit (Invitrogen) according to manufacturer protocol.
cDNA libraries were created with Nanopore Direct cDNA sequeuncing kit using  Native Barcoding according to manufacturer protocols

tag: cell type

value: Human Embryonic Kidney

value: Delta Linker


title: DeltaLinker_2


title: ha-hht2-aa3spt6b-rap040-x52


title: FC_Droplet_Paired-Tag_H3K27ac_rep2_DNA

description:
10XMultiome, histone modification
YX835


title: DeltaLinker_1


title: FC_Droplet_Paired-Tag_H3K27ac_rep1_RNA

description:
10XMultiome, gene expression
YX796


title: ha-hht2-aa3spt6b-rap020-x52


title: NtermRBD_3

value: N-term RBD


title: ha-hht2-aa3spt6b-async-x52

value: ha


title: ha-hht2-aa3spt6-rap090-x52

value: yeast cells


title: FC_Droplet_Paired-Tag_H3K27me3_rep1_DNA

description:
11XMultiome, histone modification
YX795


title: NtermRBD_1


title: ha-hht2-aa3spt6-rap060-x52


title: N184A_3


title: ha-hht2-aa3spt6-rap040-x52


title: N184A_2


title: ha-hht2-aa3spt6b-rap060-x52


title: ha-hht2-aa3spt6-rap020-x52


title: N184A_1


title: ha-hht2-aa3spt6-async-x52


title: NtermRBD_2


title: PP185_186AA_2


title: PP185_186AA_3


title: ha-hht2-aa3spt16-rap090-x52

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT2-GGS-HA-Fast-MYC bar1 , tor1-1*(Ser1971Ile), fpr1 , RPL13A-2xFKB12, Hir1-FRB, Rtt106 & Asf1-FRB triple , spt16-FRB


title: 129SVE background, Male, six week age, wild type [WT-M-06WK-2]

city: Cleveland

first: Julian

middle: E.

last: Stelzer

state: OH

address: 2109 Adelbert Rd.

department: Physiology and Biophysics

institute: Case Western Reserve University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Assembly: Mus musculus GRCm38
Supplementary files format and content: tab-delimited text include GFT format metadata and hit counts.

source_name: Left ventricle mid wall heart

extract_protocol:
Total RNA was extracted from Frozen Tissues samples using Qiagen RNeasy Plus Universal Mini Kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).

value: Left ventricle mid wall heart

tag: Sex

value: Male

tag: strain

value: 129SVE background

value: WT

tag: age

value: six week age


title: 129SVE background, Male, three week age, MLP KO [MLP-M-03WK-3]

value: MLP KO

value: three week age


title: 129SVE background, Male, three week age, wild type [WT-M-03WK-2]


title: 129SVE background, Male, six week age, wild type [WT-M-06WK-3]


title: 129SVE background, Male, six week age, wild type [WT-M-06WK-1]


title: 129SVE background, Male, three week age, MLP KO [MLP-M-03WK-2]


title: 129SVE background, Male, three week age, wild type [WT-M-03WK-3]


title: 129SVE background, Male, ten week age, MLP KO [MLP-M-10WK-3]

value: ten week age


title: 129SVE background, Male, six week age, MLP KO [MLP-M-06WK-3]


title: 129SVE background, Male, six week age, MLP KO [MLP-M-06WK-2]


title: 129SVE background, Male, ten week age, wild type [WT-M-10WK-1]


title: 129SVE background, Male, ten week age, MLP KO [MLP-M-10WK-2]


title: 129SVE background, Male, ten week age, wild type [WT-M-10WK-2]


title: 129SVE background, Male, ten week age, wild type [WT-M-10WK-3]


title: 129SVE background, Male, ten week age, MLP KO [MLP-M-10WK-1]


title: 129SVE background, Male, six week age, MLP KO [MLP-M-06WK-1]


title: ha-hht2-aa3spt16-rap060-x52

tag: sensor


title: 129SVE background, Male, three week age, MLP KO [MLP-M-03WK-1]


title: PP185_186AA_1


title: 129SVE background, Male, three week age, wild type [WT-M-03WK-1]


title: WildType_3

value: Wild Type