title: 181105L48_exp180712_MS63_SCGE-30nM-BE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H3K4me3 (Abcam #ab1012)


title: 181105L54_exp180712_MS63_SCGE-30nM-BE_anti-H3K79me2

status: Public on Nov 01 2023

type: SRA

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

description: Eluted H3K79me2 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

library_source: genomic

data_processing:
read alignment, ChIP-seq and gDNA data Bowtie (version 1.0.1)
read alignment, RNA-seq data STAR (version 2.5.3a
bigWig file generation custom code
Assembly: sacCer3
Supplementary files format and content: bigWig

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

growth_protocol:
S. pombe: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in Edinburgh Minimal Media (EMM).
C. Glabrata: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.
S. cerevisiae: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.

extract_protocol:
S. cerevisiae cultures were combined with spike-in cultures (C. glabrata or S. pombe) and immediately fixed  with formaldehyde at a final concentration of 1% for 15 minutes. Cells were then quenched with 0.125 M glycine (5 minutes), washed twice in cold PBS, pelleted, snap-frozen, and stored at −80 °C. Pellets were thawed and lysed in 300 µl FA lysis buffer (50 mM HEPES–KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) with ∼1 ml ceramic beads on a Fastprep-24 (MP Biomedicals). The entire lysate was then collected and adjusted to 1 ml before sonication with a 1/8” microtip on a Q500 sonicator (Qsonica) for 8-16 minutes (cycles of 10 seconds on and 20 seconds off). The sample tube was held suspended in a −20 °C 80% ethanol bath to prevent sample heating during sonication. Cell debris was then pelleted, and the supernatant was retained for ChIP or input. For each ChIP reaction, 20 µl Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA, incubate 40 minutes at room temperature), pre-bound with 5 µl of antibody in PBS (incubate 40 minutes at room temperature), and washed 2x with PBS before being incubated with supernatant (4°C overnight). Dynabeads were then washed (5 minutes per wash) 2x in FA lysis buffer and 3x in high-salt FA lysis buffer (50 mM Hepes-KOH pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) and DNA was then eluted in ChIP elution buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 1% SDS) at 65 °C for 20 minutes. 15 µl of input was mixed directly with 115 µl of ChIP elution buffer for input samples. Crosslinks were then reversed (65 °C, 5hr) before treatment with RNAse A (37 °C, 1 hour) and then Proteinase K (65 °C, 2 hours). DNA was then purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Indexed sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep kit (NEB Cat # E7645), pooled, and then sequenced by paired-end (2x150bp) Illumina sequencing.
spike-in normalised ChIP-seq

tag: sample

tag: cell type

value: yeast

tag: chip-antibody

value: anti-H3K79me2 (Abcam #ab3594)


title: 181105L46_exp180712_MS63_SCGE-0nM-BE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L45_exp180711_MS81_SCGE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L36_exp180712_MS63_SCGE-30nM-BE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H3K4me1 (Abcam #ab8895)


title: 181105L49_exp180711_MS01_SCGE_anti-H3K79me2

description: Eluted H3K79me2 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L43_exp180711_MS01_SCGE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L38_exp180711_MS80_SCGE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).

value: anti-H3K4me2 (Abcam #ab7766)


title: 181105L39_exp180711_MS81_SCGE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L42_exp180712_MS63_SCGE-30nM-BE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 181105L40_exp180712_MS63_SCGE-00nM-BE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L37_exp180711_MS01_SCGE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L41_exp180712_MS63_SCGE-10nM-BE_anti-H3K4me2

description: Eluted H3K4me2 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L34_exp180712_MS63_SCGE-00nM-BE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L35_exp180712_MS63_SCGE-10nM-BE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L32_exp180711_MS80_SCGE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L30_exp180712_MS63_SCGE-30nM-BE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H3K56ac (Millipore #07-677)


title: 181105L47_exp180712_MS63_SCGE-10nM-BE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L27_exp180711_MS81_SCGE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L44_exp180711_MS80_SCGE_anti-H3K4me3

description: Eluted H3K4me3 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L33_exp180711_MS81_SCGE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L26_exp180711_MS80_SCGE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L28_exp180712_MS63_SCGE-00nM-BE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L25_exp180711_MS01_SCGE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L24_exp180712_MS63_SCGE-30nM-BE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H4K9ac (Abcam #ab4441)


title: 181105L23_exp180712_MS63_SCGE-10nM-BE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L22_exp180712_MS63_SCGE-00nM-BE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L20_exp180711_MS80_SCGE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L18_exp180712_MS63_SCGE-30nM-BE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H4 (Abcam #ab10158)


title: 181105L21_exp180711_MS81_SCGE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L19_exp180711_MS01_SCGE_anti-H4K9ac

description: Eluted H4K9ac ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L31_exp180711_MS01_SCGE_anti-H3K4me1

description: Eluted H3K4me1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L17_exp180712_MS63_SCGE-10nM-BE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L12_exp180712_MS63_SCGE-30nM-BE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-H3 (Abcam #ab1791)


title: 181105L13_exp180711_MS01_SCGE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L08_exp180711_MS80_SCGE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L11_exp180712_MS63_SCGE-10nM-BE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L16_exp180712_MS63_SCGE-00nM-BE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L15_exp180711_MS81_SCGE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L14_exp180711_MS80_SCGE_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L29_exp180712_MS63_SCGE-10nM-BE_anti-H3K56ac

description: Eluted H3K56ac ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L07_exp180711_MS01_SCGE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 181105L06_exp180712_MS63_SCGE-30nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 181105L10_exp180712_MS63_SCGE-00nM-BE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L05_exp180712_MS63_SCGE-10nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 181105L04_exp180712_MS63_SCGE-00nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 181105L03_exp180711_MS81_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 181105L02_exp180711_MS80_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 181105L01_exp180711_MS01_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 211122L72_exp211102_MS205_RAPA-rep3_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L71_exp211102_MS05_SCGE-T07_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211122L70_exp211102_MS05_SCGE-T06_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.


title: 211122L68_exp211102_MS05_SCGE-T04_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211122L67_exp211102_MS05_SCGE-T03_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211122L66_exp211102_MS05_SCGE-T02_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211122L64_exp211102_MS205_SCGE-RAPA-rep2_anti-H4

value: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L65_exp211102_MS05_SCGE-T01_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211122L63_exp211028_MS64_SCGE-T07_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211122L62_exp211028_MS64_SCGE-T06_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 181105L09_exp180711_MS81_SCGE_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 211122L61_exp211028_MS64_SCGE-T05_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211122L60_exp211028_MS64_SCGE-T04_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211122L59_exp211028_MS64_SCGE-T03_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211122L54_exp211101_MS67_SCGE-T06_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211122L58_exp211028_MS64_SCGE-T02_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211122L56_exp211102_MS205_SCGE-RAPA-rep1_anti-H4


title: 211122L57_exp211028_MS64_SCGE-T01_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211122L53_exp211101_MS67_SCGE-T05_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211122L52_exp211101_MS67_SCGE-T04_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211122L50_exp211101_MS67_SCGE-T02_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211122L51_exp211101_MS67_SCGE-T03_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211122L69_exp211102_MS05_SCGE-T05_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211122L46_exp211102_MS05_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.

value: anti-Rpb1 (8wG16; Millipore # 05-952-I)


title: 211122L48_exp211102_MS205_SCGE-RAPA-rep3_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L49_exp211101_MS67_SCGE-T01_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 211122L47_exp211102_MS05_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211122L44_exp211102_MS05_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211122L42_exp211102_MS05_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211122L41_exp211102_MS05_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211122L40_exp211102_MS205_SCGE-RAPA-rep2_anti-Rpb1

value: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L39_exp211028_MS64_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211122L35_exp211028_MS64_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211122L36_exp211028_MS64_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211122L55_exp211101_MS67_SCGE-T07_anti-H4

description: Eluted H4 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 211122L33_exp211028_MS64_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211122L32_exp211102_MS205_SCGE-RAPA-rep1_anti-Rpb1


title: 211122L31_exp211101_MS67_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 211122L28_exp211101_MS67_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211122L45_exp211102_MS05_SCGE-T05_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211122L25_exp211101_MS67_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 211122L20_exp211102_MS05_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211122L23_exp211102_MS05_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211122L22_exp211102_MS05_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.


title: 211122L24_exp211102_MS205_SCGE-RAPA-rep3_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L38_exp211028_MS64_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 211122L17_exp211102_MS05_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211122L21_exp211102_MS05_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211122L13_exp211028_MS64_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211122L11_exp211028_MS64_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211122L19_exp211102_MS05_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211122L16_exp211102_MS205_SCGE-RAPA-rep2_input

value: Input ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L30_exp211101_MS67_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211122L10_exp211028_MS64_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211122L12_exp211028_MS64_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211122L29_exp211101_MS67_SCGE-T05_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211122L15_exp211028_MS64_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211122L09_exp211028_MS64_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211122L27_exp211101_MS67_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211122L26_exp211101_MS67_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211122L34_exp211028_MS64_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211122L08_exp211102_MS205_SCGE-RAPA-rep1_input


title: 211122L06_exp211101_MS67_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211122L07_exp211101_MS67_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 211122L04_exp211101_MS67_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211122L03_exp211101_MS67_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211122L18_exp211102_MS05_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211122L14_exp211028_MS64_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 211117L72_exp211025_MS205_SCGE-RAPA-rep3_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211122L01_exp211101_MS67_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 211122L02_exp211101_MS67_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211117L70_exp211026_MS05_SCGE-T06_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.


title: 211122L43_exp211102_MS05_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211117L68_exp211026_MS05_SCGE-T04_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211117L71_exp211026_MS05_SCGE-T07_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211117L66_exp211026_MS05_SCGE-T02_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211117L65_exp211026_MS05_SCGE-T01_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211117L64_exp211025_MS205_SCGE-RAPA-rep2_anti-H3

value: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211117L67_exp211026_MS05_SCGE-T03_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211117L62_exp211025_MS64_SCGE-T06_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 211117L61_exp211025_MS64_SCGE-T05_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211117L60_exp211025_MS64_SCGE-T04_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211117L63_exp211025_MS64_SCGE-T07_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211117L56_exp211025_MS205_SCGE-RAPA-rep1_anti-H3


title: 211117L57_exp211025_MS64_SCGE-T01_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211117L55_exp211021_MS67_SCGE-T07_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 211117L54_exp211021_MS67_SCGE-T06_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211117L58_exp211025_MS64_SCGE-T02_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211122L05_exp211101_MS67_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211117L52_exp211021_MS67_SCGE-T04_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211117L53_exp211021_MS67_SCGE-T05_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211117L50_exp211021_MS67_SCGE-T02_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211117L51_exp211021_MS67_SCGE-T03_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211117L48_exp211025_MS205_SCGE-RAPA-rep3_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211117L49_exp211021_MS67_SCGE-T01_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 211117L46_exp211026_MS05_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.


title: 211117L44_exp211026_MS05_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211117L69_exp211026_MS05_SCGE-T05_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211117L47_exp211026_MS05_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211117L43_exp211026_MS05_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211117L42_exp211026_MS05_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211117L45_exp211026_MS05_SCGE-T05_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211117L41_exp211026_MS05_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211117L59_exp211025_MS64_SCGE-T03_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211117L40_exp211025_MS205_SCGE-RAPA-rep2_anti-Rpb1


title: 211117L38_exp211025_MS64_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 211117L37_exp211025_MS64_SCGE-T05_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211117L35_exp211025_MS64_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211117L36_exp211025_MS64_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211117L34_exp211025_MS64_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211117L33_exp211025_MS64_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211117L30_exp211021_MS67_SCGE-T06_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211117L31_exp211021_MS67_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 211117L28_exp211021_MS67_SCGE-T04_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211117L29_exp211021_MS67_SCGE-T05_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211117L32_exp211025_MS205_SCGE-RAPA-rep1_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211117L27_exp211021_MS67_SCGE-T03_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211117L25_exp211021_MS67_SCGE-T01_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 211117L24_exp211025_MS205_SCGE-RAPA-rep3_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS205) and C. glabrata (MS99). MS205 was treated with rapamycin before collection.


title: 211117L23_exp211026_MS05_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 7.


title: 211122L37_exp211028_MS64_SCGE-T05_anti-Rpb1

value: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211117L26_exp211021_MS67_SCGE-T02_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211117L22_exp211026_MS05_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 6.


title: 211117L39_exp211025_MS64_SCGE-T07_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211117L15_exp211025_MS64_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 7.


title: 211117L21_exp211026_MS05_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 5.


title: 211117L18_exp211026_MS05_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 2.


title: 211117L16_exp211025_MS205_SCGE-RAPA-rep2_input


title: 211117L20_exp211026_MS05_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 4.


title: 211117L19_exp211026_MS05_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 3.


title: 211117L14_exp211025_MS64_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 6.


title: 211117L10_exp211025_MS64_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 2.


title: 211117L12_exp211025_MS64_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 4.


title: 211117L09_exp211025_MS64_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 1.


title: 211117L17_exp211026_MS05_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS05) and C. glabrata (MS99). MS05 was mock arrested and collected at timepoint 1.


title: 211117L08_exp211025_MS205_SCGE-RAPA-rep1_input


title: 211117L13_exp211025_MS64_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 5.


title: 211117L11_exp211025_MS64_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS64) and C. glabrata (MS99). MS64 was arrested in G1 and collected at timepoint 3.


title: 211117L05_exp211021_MS67_SCGE-T05_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 5.


title: 211117L03_exp211021_MS67_SCGE-T03_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 3.


title: 211117L04_exp211021_MS67_SCGE-T04_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 4.


title: 211117L06_exp211021_MS67_SCGE-T06_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 6.


title: 211117L02_exp211021_MS67_SCGE-T02_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 2.


title: 211117L01_exp211021_MS67_SCGE-T01_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 1.


title: 180723L16_exp180712_MS63_SCGE-30nM-BE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-Rpb1-S5P (3E8; Millipore #04-1572-1)


title: 180723L04_exp180712_MS63_SCGE-00nM-BE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180731L16_exp180711_MS80_SCGE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180731L04_exp180711_MS01_SCGE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180723L15_exp180712_MS63_SCGE-30nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.

value: anti-Rpb1-S2P (3E10; Millipore #04-1571-I)


title: 180723L09_exp180712_MS63_SCGE-10nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180723L03_exp180712_MS63_SCGE-00nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180731L15_exp180711_MS80_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180731L03_exp180711_MS01_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180723L08_exp180712_MS63_SCGE-10nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180723L14_exp180712_MS63_SCGE-30nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180723L10_exp180712_MS63_SCGE-10nM-BE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180731L14_exp180711_MS80_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180723L13_exp180712_MS63_SCGE-30nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180731L02_exp180711_MS01_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 211117L07_exp211021_MS67_SCGE-T07_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS67) and C. glabrata (MS99). MS67 was arrested in G1 and collected at timepoint 7.


title: 180723L07_exp180712_MS63_SCGE-10nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180723L02_exp180712_MS63_SCGE-00nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180731L10_exp180711_MS81_SCGE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180731L01_exp180711_MS01_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180731L13_exp180711_MS80_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180525L12_exp180222_MS81_SCGE_anti-Rpb1-S5P

value: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180529L11_exp180227_MS63_SCGE-10nM-BE_anti-Rpb1-S5P

value: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.

value: yeast


title: 180731L26_exp180711_MS81_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180529L12_exp180227_MS63_SCGE-30nM-BE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180529L10_exp180227_MS63_SCGE-00nM-BE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180731L25_exp180711_MS81_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180525L11_exp180222_MS80_SCGE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180525L10_exp180222_MS01_SCGE_anti-Rpb1-S5P

description: Eluted Rpb1-S5P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180525L08_exp180222_MS80_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180525L09_exp180222_MS81_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180529L07_exp180227_MS63_SCGE-00nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180529L08_exp180227_MS63_SCGE-10nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180529L09_exp180227_MS63_SCGE-30nM-BE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180529L05_exp180227_MS63_SCGE-10nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180525L07_exp180222_MS01_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180529L06_exp180227_MS63_SCGE-30nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180529L01_exp180227_MS63_SCGE-00nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180723L01_exp180712_MS63_SCGE-00nM-BE_input

value: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180529L02_exp180227_MS63_SCGE-10nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 10nM beta-estradiol.


title: 180529L04_exp180227_MS63_SCGE-00nM-BE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99).


title: 180525L01_exp180222_MS01_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180531L24_exp180524_MS01_SCGE-OD0.6_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.6.


title: 180525L06_exp180222_MS81_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180525L05_exp180222_MS80_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180531L21_exp180524_MS01_SCGE-OD0.3_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.3.


title: 180525L02_exp180222_MS80_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS80) and C. glabrata (MS99).


title: 180531L20_exp180524_MS01_SCGE-OD0.2_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.2.


title: 180525L04_exp180222_MS01_SCGE_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99).


title: 180531L23_exp180524_MS01_SCGE-OD0.5_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.5.


title: 180531L22_exp180524_MS01_SCGE-OD0.4_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.4.


title: 180531L19_exp180524_MS01_SCGE-OD0.1_anti-H3

description: Eluted H3 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.1.


title: 180531L18_exp180524_MS01_SCGE-OD0.6_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.6.


title: 180529L03_exp180227_MS63_SCGE-30nM-BE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS63) and C. glabrata (MS99). MS63 was cultured in the prescence of 30nM beta-estradiol.


title: 180531L17_exp180524_MS01_SCGE-OD0.5_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.5.


title: 180531L15_exp180524_MS01_SCGE-OD0.3_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.3.


title: 180531L12_exp180524_MS01_SCGE-OD0.6_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.6.


title: 180531L16_exp180524_MS01_SCGE-OD0.4_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.4.


title: 180531L11_exp180524_MS01_SCGE-OD0.5_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.5.


title: 180531L14_exp180524_MS01_SCGE-OD0.2_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.2.


title: 180531L13_exp180524_MS01_SCGE-OD0.1_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.1.


title: 180531L08_exp180524_MS01_SCGE-OD0.2_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.2.


title: 180531L10_exp180524_MS01_SCGE-OD0.4_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.4.


title: 180531L04_exp180524_MS01_SCGE-OD0.4_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.4.


title: 180531L02_exp180524_MS01_SCGE-OD0.2_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.2.


title: 180415LD04_exp180227_MS01-MS99_SCGE-ratio-1.00_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 1.00.


title: 180415LC04_exp180227_MS01-MS99_SCGE-ratio-0.50_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.50.


title: 180531L09_exp180524_MS01_SCGE-OD0.3_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.3.


title: 180415LB04_exp180227_MS01-MS99_SCGE-ratio-0.25_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.25.


title: 180531L07_exp180524_MS01_SCGE-OD0.1_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.1.


title: 180531L06_exp180524_MS01_SCGE-OD0.6_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.6.


title: 180531L05_exp180524_MS01_SCGE-OD0.5_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.5.


title: 180525L03_exp180222_MS81_SCGE_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: 180415LF01_exp180227_MS01-MS99_SCGE-ratio-4.00_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 4.00.


title: 180415LG01_exp180227_MS01-MS99_SCGE-ratio-16.0_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 16.0.


title: 180531L01_exp180524_MS01_SCGE-OD0.1_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.1.


title: 180415LE01_exp180227_MS01-MS99_SCGE-ratio-2.00_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 2.00.


title: 180415LG04_exp180227_MS01-MS99_SCGE-ratio-16.0_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 16.0.


title: 180415LC01_exp180227_MS01-MS99_SCGE-ratio-0.50_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.50.


title: 180415LB01_exp180227_MS01-MS99_SCGE-ratio-0.25_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.25.


title: 180415LF04_exp180227_MS01-MS99_SCGE-ratio-4.00_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 4.00.


title: 180415LG20_exp180227_MS01-MS99_SCGE-ratio-16.0_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 16.0.


title: 180415LA01_exp180227_MS01-MS99_SCGE-ratio-0.0625_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.625.


title: 180415LF20_exp180227_MS01-MS99_SCGE-ratio-4.00_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 4.00.


title: 180415LE04_exp180227_MS01-MS99_SCGE-ratio-2.00_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 2.00.


title: 180415LC20_exp180227_MS01-MS99_SCGE-ratio-0.50_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.50.


title: 180415LA20_exp180227_MS01-MS99_SCGE-ratio-0.0625_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.625.


title: 180415LD01_exp180227_MS01-MS99_SCGE-ratio-1.00_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 1.00.


title: 180415LG_exp180227_MS01-MS99_SCGE-ratio-16.0_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 16.0.


title: 180415LF_exp180227_MS01-MS99_SCGE-ratio-4.00_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 4.00.


title: 180531L03_exp180524_MS01_SCGE-OD0.3_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS01) and C. glabrata (MS99). MS01 was collecred at OD600=0.3.


title: 180415LE20_exp180227_MS01-MS99_SCGE-ratio-2.00_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 2.00.


title: 180415LD_exp180227_MS01-MS99_SCGE-ratio-1.00_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 1.00.


title: 180415LC_exp180227_MS01-MS99_SCGE-ratio-0.50_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.50.


title: 180415LD20_exp180227_MS01-MS99_SCGE-ratio-1.00_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 1.00.


title: 180731L27_exp180711_MS81_SCGE_anti-Rpb1-S2P

description: Eluted Rpb1-S2P ChIP DNA from a mixture S. cerevisiae (MS81) and C. glabrata (MS99).


title: CRC-RECOVERY-B

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

library_source: transcriptomic

data_processing:
The pipeline is built usingNextflow and processes data using the following steps: (1) FastQC (2) TrimGalore (3) Bowtie (4) SAMtools (5) edgeR (6) Bowtie (7) mirtop (8) miRTrace, and (9) MultiQC
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: colon adenocarcinoma

extract_protocol:
Total RNA from all samples was isolated using the miRNeasy RNA isolation mini kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared using SMARTer® smRNA-Seq Kit for Illumina® (Takara Bio) according to the manufacturer´s instructions using the bead based size selection.

tag: tissue

value: colon adenocarcinoma

tag: treatment

value: Recovery


title: 180415LA04_exp180227_MS01-MS99_SCGE-ratio-0.0625_anti-Rpb1

description: Eluted Rpb1 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.625.


title: 180415LE_exp180227_MS01-MS99_SCGE-ratio-2.00_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 2.00.


title: CRC-TGFB1-B


title: CRC-RECOVERY-A


title: 180415LA_exp180227_MS01-MS99_SCGE-ratio-0.0625_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.625.


title: 180415LB_exp180227_MS01-MS99_SCGE-ratio-0.25_anti-H3

description: Eluted H3 ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.25.


title: CRC-RECOVERY-C


title: CRC-TGFB1-C


title: CRC-CTR-C

value: vehicle control


title: CRC-TGFB1-A


title: Patient 20, Peritoneum metastasis

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

country: France

institute: INSERM

data_processing:
For each sample, FASTQ raw files were trimmed with Trimgalore then aligned to hg38 genome with STAR. MarkDuplicates (PicardTools) was used to remove PCR duplicates. Htseq-count (HTSeq) was used to quantify genes and counts were normalized in TPM (transcripts per kilobase per million).
Assembly: hg38

source_name: Peritoneum metastasis

extract_protocol:
After disruption and homogenization of the fresh frozen tumor samples, RNA was extracted using the Qiagen RNeasy Plus Mini kit. Paraffin embedded tissue block (FFPE) blocks were sectioned to prepare unstained sections (5μm thick) on glass slides for RNA extraction. For FFPE samples, after scraping the tumor tissue present on 15 slides with a razor blade, samples were de-paraffinized using the Qiagen Deparaffinization Solution and RNA was extracted using the Qiagen RNeasy FFPE kit. RNA yield and purity were measured photometrically with NanoDrop and Qubit Fluorometer. RNA quality was analyzed using the Fragment Analyzer System.
Total RNA libraries were prepared using Illumina stranded Total RNA prep ligation with ribo-zero plus kit starting with an input amount of 200 ng total RNA. Library size and quality were confirmed on Fragment Analyzer System. KAPA quantification kit for Illumina platforms was used to quantify libraries. Samples were pooled in equimolar fashion. Ten pb double indexed libraries were sequenced on a NextSeq 550 instrument using 74 base-length read chemistry in paired-end mode.

tag: individual

value: Patient 20

value: Peritoneum metastasis


title: CRC-CTR-A


title: CRC-CTR-B


title: Patient 20, Primary tumor

source_name: Primary tumor

value: Primary tumor


title: Patient 6, Primary tumor

value: Patient 6


title: Patient 14, Primary tumor

value: Patient 14


title: Patient 14, Skin metastasis

source_name: Skin metastasis

value: Skin metastasis


title: Patient 6, Liver metastasis

source_name: Liver metastasis

value: Liver metastasis


title: Patient 4, Primary tumor

value: Patient 4


title: Patient 16, Primary tumor

value: Patient 16


title: 180415LB20_exp180227_MS01-MS99_SCGE-ratio-0.25_input

description: Input ChIP DNA from  S. cerevisiae (MS01) and C. glabrata (MS99) cells mixed at a ratio of 0.25.


title: Patient 13, Primary tumor

value: Patient 13


title: Patient 12, Primary tumor

value: Patient 12


title: Patient 2, Primary tumor

value: Patient 2


title: Patient 18, Primary tumor

value: Patient 18


title: Patient 9, Primary tumor

value: Patient 9


title: Patient 7, Primary tumor

value: Patient 7


title: Patient 19, Primary tumor

value: Patient 19


title: Patient 13, Liver metastasis

data_processing:
For each patient, FASTQ raw files were trimmed with Trimgalore then aligned to hg38 genome with STAR. MarkDuplicates (PicardTools) was used to remove PCR duplicates. Htseq-count (HTSeq) was used to quantify genes and counts were normalized in TPM (transcripts per kilobase per million).
Genome_build: hg38
Supplementary_files_format_and_content: matrix_expression_TPM.csv


title: Patient 5, Lung metastasis

source_name: Lung metastasis

value: Lung metastasis

value: Patient 5


title: Patient 4, Liver metastasis


title: Patient 3, Peritoneum metastasis

value: Peritoneum metastasis

value: Patient 3


title: Patient 2, Liver metastasis


title: Patient 8, Liver metastasis

value: Patient 8


title: Patient 16 Lymph node metastasis

source_name: Lymph node metastasis

value: Lymph node metastasis


title: Patient 18, Lung metastasis


title: Patient 9, Liver metastasis


title: Patient 7, Liver metastasis


title: Patient 19, Liver metastasis


title: Patient 8, Primary tumor

value: Primary tumor


title: Patient 15, Liver metastasis

value: Liver metastasis

value: Patient 15


title: Patient 1, Liver metastasis

value: Patient 1


title: Patient 11, Liver metastasis

value: Patient 11


title: Patient 17, Liver metastasis

value: Patient 17


title: CHLA01 miR-211 3

city: St. Petersburg

first: Rudrmani

last: Pokhrel

state: United States

address: 600 Fifth Street S.

department: Oncology

institute: Johns Hopkins All Children’s Hospital

data_processing:
Demultiplexing:  bcl2fastq v2.20
Filtering and QC: FastP v0.20.1
Mapping to Genome: STAR v2.4.2a
Gene Count Matrix:  featureCounts v2.0.1
Differential Analysis: DESeq2 v1.34.0
Genome_build: Human 38 (GRCh38.p13)
Supplementary_files_format_and_content: CSV file of 2D matrix of gene count vs samples

source_name: Medulloblastoma cell line

growth_protocol: DAOY cells were cultured in DMEM supplemented with 10% FBS, 1% sodium pyruvate, 1% nonessential amino acids and 1% penicillin/streptomycin.  D425 cells were cultured in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin.  CHLA01 cells were cultured in DMEM/F12 with 10% FBS, 20 ng/mL EGF, 20 ng/mL bFGF, B-27 supplement and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was prepared from cell lines using a NucleoSpin RNA Mini kit (MACHEREY-NAGEL). The quality of RNA was determined with the Agilent 2100 Bioanalyzer Nano Assay (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Human medulloblastoma cell

tag: subgroup

value: Group 4

tag: genotype


title: CHLA01 V/O 3

value: control


title: CHLA01 V/O 1


title: Patient 10, Liver metastasis

value: Patient 10


title: Patient 12, Liver metastasis

value: Patient 12


title: CHLA01 miR-211 2


title: CHLA01 V/O 2


title: CHLA01 miR-211 1


title: D425 miR-211 3

value: Group 3


title: D425 miR-211 2


title: D425 V/O 3


title: D425 V/O 1


title: DAOY miR-211 3

value: DAOY

value: SHH


title: DAOY miR-211 1


title: D425 miR-211 1


title: DAOY V/O 1


title: DAOY V/O 2


title: D425 sh-HLX rep2

description:
count.csv
tpm_cell.csv

data_processing:
Demultiplexing:  bcl2fastq v2.20
Filtering and QC: FastP v0.20.1
Mapping to Genome: STAR v2.4.2a
Gene Count Matrix:  featureCounts v2.0.1
Differential Analysis: DESeq2 v1.34.0
Genome_build: Human 38 (GRCh38.p13)
Supplementary_files_format_and_content: count.csv (Raw gene counts file)
Supplementary_files_format_and_content: tpm_xeno.csv (TPM counts for xenograft samples)
Supplementary_files_format_and_content: tpm_cell.csv (TPM counts for cell-line samples)

growth_protocol: D425 cells were cultured in DMEM/F12 with 10% serum and 1% glutamate/penicillin/streptomycin. Intracranial xenografts were established by injecting D425 cells into the cerebellum of NOD-SCID mice (Jackson Laboratory). Cerebellar coordinates were -2 mm from lambda, +1 mm laterally, and 1.5 mm deep. After 14 days of injecting D425 cells into the cerebellum of NOD-SCID mice, intracranial D425 xenografts were treated with ASO-CTRL or ASO-lnc-HLX 2-7 once every 3 days for 24-36 days.

extract_protocol:
Total RNA was prepared from cell line and orthotopic xenograft using a Direct-zol RNA Miniprep kit (Zymo Research). The quality of RNA was determined with the Agilent 2100 Bioanalyzer Nano Assay (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human medulloblastoma cell line D425

tag: treatment period


title: DAOY V/O 3


title: D425 V/O 2


title: D425 sh-HLX rep3

description:
count.csv
tpm_cell.csv


title: DAOY miR-211 2


title: D425 sh-CTRL rep2

description:
count.csv
tpm_cell.csv


title: D425 sh-CTRL rep1

description:
count.csv
tpm_cell.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days ON + 12 days OFF, rep3

description:
count.csv
tpm_xeno.csv

source_name: Intracranial xenograft tumor cell

value: Intracranial xenograft tumor cell of human medulloblastoma cell line D425

value: ASO-lncHLX 2-7

value: 24 days ON + 12 days OFF


title: D425 sh-HLX rep1

description:
count.csv
tpm_cell.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days ON + 12 days OFF, rep1

description:
count.csv
tpm_xeno.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days, rep1

description:
count.csv
tpm_xeno.csv

value: 24 days


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days, rep3

description:
count.csv
tpm_xeno.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days ON + 12 days OFF, rep2

description:
count.csv
tpm_xeno.csv


title: D425 xenograft treated with ASO-CTRL rep3

description:
count.csv
tpm_xeno.csv

value: ASO-CTRL


title: D425 xenograft treated with ASO-CTRL rep1

description:
count.csv
tpm_xeno.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 36 days, rep2

description:
count.csv
tpm_xeno.csv

value: 36 days


title: D425 xenograft treated with ASO-lncHLX 2-7, 36 days, rep3

description:
count.csv
tpm_xeno.csv


title: D425 sh-CTRL rep3

description:
count.csv
tpm_cell.csv


title: D425 xenograft treated with ASO-lncHLX 2-7, 36 days, rep1

description:
count.csv
tpm_xeno.csv


title: D425 xenograft treated with ASO-CTRL rep2

description:
count.csv
tpm_xeno.csv


title: SHAM, replicate 2, small RNA-seq

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

description:
Norgen Biotek Small RNA Library
SV18506-0004_S6_R1_001.fastq.gz

data_processing:
Read sequences in fastq format were aligned to the mouse genome (Gencode version 22, mm10). miRBase version 22 was used as a reference for microRNA species.
Assembly: mm10
Supplementary files format and content: Text Document Read Counts

molecule: nuclear RNA

organism: Mus musculus

source_name: Plantaris Muscle

growth_protocol: Mice housed in a humidity- and temperature-controlled facility, maintained on a 14:10 hour light-dark cycle with food and water ad libitum. Three-month-old HSA-rtTA; TRE-H2B-GFP mice were administered doxycycline (0.5 mg/mL) in drinking water supplemented with 2% sucrose for 5 days.

extract_protocol:
Plantaris muscles were Dounce homogenized and subjected to Fluorescence-Activated Nuclei Sorting (FANS) for purification of myonuclei, followed by total RNA isolation
Norgen Biotek Small RNA Library Prep Kit (Cat. 63600) was used for library preparation

treatment_protocol: The synergist ablation surgery places a mechanical overload (MOV) on the plantaris muscle of the lower hind limb that induces a growth response associated with robust MuSC activation, proliferation and myofiber fusion. Mice were anesthetized (3% isoflurane with 1.5L of O2 per minute), placed in sternal recumbence, where a small incision was made on the dorsal aspect of the lower hind limb, with the distal portion of the gastrocnemius muscle tendon and approximately half of the soleus muscle carefully excised. No apparent damage was observed to the neural and/or vascular supply of the plantaris muscle following the surgery. At the designated time point post-surgery (72 h), mice were euthanized via CO2 inhalation followed by cervical dislocation with muscle collected and prepared accordingly for downstream analyses. The sham surgery consisted of performing the incision and carefully probing the plantaris tendon, without removing the tendon or muscle.

value: Myonuclei

value: Plantaris Muscle

tag: strain

value: HSA-rtTA; TRE-H2B-GFP

tag: age

value: 12 weeks

value: Sham


title: OVERLOAD, replicate 3, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0005_S7_R1_001.fastq.gz

value: Overload


title: OVERLOAD, replicate 4, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0007_S9_R1_001.fastq.gz


title: SHAM, replicate 3, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0006_S8_R1_001.fastq.gz


title: OVERLOAD, replicate 2, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0003_S5_R1_001.fastq.gz


title: OVERLOAD, replicate 1, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0002_S4_R1_001.fastq.gz


title: SHAM, replicate 1, small RNA-seq

description:
Norgen Biotek Small RNA Library
SV18506-0001_S3_R1_001.fastq.gz


title: GTKO, activated, beads 1:1 + p38i, rep19

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

data_processing:
Base calling was performed using Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The quality of reads was verified using FastQC 0.11.9 and MultiQC 1.13 software.
The reads were aligned against GRCm39 v106 reference downloaded from Ensembl using  STAR aligner (v.2.7.10a).
The results were quantified in R 4.2.1. using packages tximport 1.24.0 and GenomicAlignments 1.32.1.
Downstream analysis including normalization and differential gene expression analysis was performed using DESeq2 1.36.0.
Assembly: GRCm39 v106 (Ensembl)
Supplementary files format and content: raw counts for GTKO activation assay (replicates 6-9) in csv format
Supplementary files format and content: raw counts for p38i inhibition assay (replicates 17-19) in csv format

source_name: lymph nodes + spleen

growth_protocol: 1×106 CD8+ cells were FACS sorted from lymph nodes and spleen of OT-I Rag2KO ABIN1 WT or GTKO littermates per sample.

extract_protocol:
The RNA was isolated using RNA Clean & Concentrator-5 kit (Zymoresearch #R1014) according to the manufacturer's instruction. The quality of isolated RNA was validated by Agilent.
The cDNA libraries were prepared using KAPA mRNA Hyperprep Kit and then sequenced using NextSeq 500/550 High Output Kit v2.5 (75 cycles) according to the manufacturer's instructions. Separate sequencings were done for rep6-9 and rep17-19.

treatment_protocol: Non-activated controls had their RNA extracted directly without any further treatment. The remaining cells were activated with anti-CD3ε/CD28  beads at indicated beads to cell ratios for 16 hours prior to the RNA isolation, and inhibited samples were also additionally treated with p38 inhibitor for the whole activation period.

value: OT-I Rag2KO/KO C57Bl/6J

value: lymph nodes + spleen

value: CD8+ T cells

value: ABIN1 GTKO

value: 1:1 anti-CD3ε/CD28 beads to cell + p38i


title: pancreatic beta-cells, Adar-knockout, 7 days after tamoxifen injection, rep3

city: Jerusalem

first: agnes

last: klochendler

address: Hadassah Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description:
KO3_S7
normalized_counts.csv

data_processing:
Raw FASTQ quality was assessed using FastQC (version 0.11.8), and barcodes were preprocessed using UMI-tools versions 1.1.1 and 1.1.2 . Mate 2 reads were further trimmed to 60 bases using seqtk trimfq with -b 7. Fastq files were then uniquely aligned to reference genome using STAR (version 2.7.3a)  with parameters --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 600000 --outFilterMismatchNoverReadLmax 1 --outFilterMultimapNmax 1 and deduped using UMI-tools. Reads were counted with the htseq-count script version 2.0.1  and normalized using DeSeq2 version 1.28.1
Assembly: mm10
Supplementary files format and content: CSV matrix table file of normalized counts per gene for all samples

source_name: pancreas

extract_protocol:
7 days after tamoxifen injection, pancreatic islets were isolated, dissociated and Adar-mutant YFP-positive beta-cells were FACS-sorted
Libraries were generated as per  manufacturer’s instructions (SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara))

treatment_protocol: 1 month-old MipCreER; Adar floxed/floxed or floxed/+; R26R-EYFP mice were injected with tamoxifen (two 8mg doses of tamoxifen)

value: pancreas

value: pancreatic beta-cells

value: Adar KO


title: pancreatic beta-cells, Adar-heterozygotes, 7 days after tamoxifen injection, rep4

description:
HET4_S4
normalized_counts.csv

value: Adar heterozygote


title: GTKO, activated, beads 1:1 + p38i, rep18


title: pancreatic beta-cells, Adar-knockout, 7 days after tamoxifen injection, rep2

description:
KO2_S6
normalized_counts.csv


title: pancreatic beta-cells, Adar-heterozygotes, 7 days after tamoxifen injection, rep2

description:
HET2_S2
normalized_counts.csv


title: pancreatic beta-cells, Adar-heterozygotes, 7 days after tamoxifen injection, rep3

description:
HET3_S3
normalized_counts.csv


title: pancreatic beta-cells, Adar-knockout, 7 days after tamoxifen injection, rep1

description:
KO1_S5
normalized_counts.csv


title: pancreatic beta-cells, Adar-knockout, 7 days after tamoxifen injection, rep4

description:
KO4_S8
normalized_counts.csv


title: pancreatic beta-cells, Adar-heterozygotes, 7 days after tamoxifen injection, rep1

description:
HET1_S1
normalized_counts.csv


title: GTKO, activated, beads 1:1, rep19

value: 1:1 anti-CD3ε/CD28 beads to cell


title: D425 xenograft treated with ASO-lncHLX 2-7, 24 days, rep2

description:
count.csv
tpm_xeno.csv

value: Intracranial xenograft tumor cell of human medulloblastoma cell line D425

value: ASO-lncHLX 2-7

value: 24 days


title: GTKO, activated, beads 1:1, rep17


title: GTKO, activated, beads 1:1, rep18


title: WT, activated, beads 1:1 + p38i, rep19

value: WT


title: WT, non-activated,  rep8


title: WT, activated, beads 1:1, rep18


title: WT, activated, beads 1:1, rep19


title: WT, activated, beads 1:1, rep17


title: WT, activated, beads 4:1,  rep8

value: 4:1 anti-CD3ε/CD28 beads to cell


title: WT, activated, beads 1:1,  rep8


title: WT, activated, beads 1:1,  rep6


title: GTKO, activated, beads 1:1 + p38i, rep17


title: WT, non-activated,  rep9


title: GTKO, activated, beads 1:1,  rep8


title: GTKO, activated, beads 4:1,  rep7


title: GTKO, activated, beads 1:1,  rep7


title: Ciaplatin, mRNA3

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

data_processing:
The adapter sequences in the raw data were trimmed using Cutadapt, and STAR was utilized for aligning paired-end (for total RNA) or single-end (for small RNA and Clipseq) sequences to the mouse genome (mm39) and quantification.
Assembly: mm39
Supplementary files format and content: tab delimited file for gene counts

source_name: Kidney

extract_protocol:
Total RNAs were extracted and then cleaned up with a quick RNA microprep kit (Zymo Research).
Library was constructed using QIAseq Stranded RNA Lib Kit

value: Kidney

value: cisplatin induced CKD


title: Control, mRNA2

value: control


title: WT, non-activated,  rep7

value: OT-I Rag2KO/KO C57Bl/6J

value: lymph nodes + spleen


title: Control, mRNA3


title: WT, activated, beads 4:1,  rep7

value: CD8+ T cells


title: WT, activated, beads 4:1,  rep6


title: GTKO, non-activated,  rep9

value: ABIN1 GTKO


title: WT, activated, beads 1:1 + p38i, rep18

value: 1:1 anti-CD3ε/CD28 beads to cell + p38i


title: Ciaplatin, miRNA3

extract_protocol:
Total RNAs including miRNAs were extracted and then cleaned up with a quick RNA microprep kit (Zymo Research).
Library was constructed using QIASeq miRNA library kit (Qiagen),


title: GTKO, activated, beads 4:1,  rep6


title: WT, activated, beads 1:1 + p38i, rep17


title: Control, miRNA2


title: Control, miRNA1


title: GTKO, non-activated,  rep7


title: GTKO, non-activated,  rep8


title: GTKO, activated, beads 1:1,  rep6


title: Ciaplatin, mRNA2


title: GTKO, activated, beads 4:1,  rep8


title: WT, activated, beads 1:1,  rep7


title: Ciaplatin, mRNA1


title: eCLIP, Background, Control 1

library_source: other

data_processing:
library strategy: eCLIP
The adapter sequences in the raw data were trimmed using Cutadapt, and STAR was utilized for aligning paired-end (for total RNA) or single-end (for small RNA and Clipseq) sequences to the mouse genome (mm39) and quantification.
Clipseq: PCR duplicates were removed for aligned reads (non-chimeric reads) using umi-tools, and Ago2 binding site peaks were identified using CLIPper. The clusters identified in the Ago2-immunoprecipitant are then normalized against a paired input sample.
Assembly: mm39
Supplementary files format and content: Clipseq: Bigwig peaks

molecule: other

extract_protocol:
Clipseq: snap-frozen kidneys in liquid nitrogen were pulverized using a mortar and pestle, UV-crosslinked, and lysed to immunoprecipitate miRNA-mRNA-argonaute2 (Ago2) complexes with anti-Ago2. The bound RNAs in the Ago2 immunoprecipitants were further trimmed with RNA exonuclease (RNase A) and then treated with T4 polynucleotide kinase (3’ phosphatase minus) to encourage ligation between miRNA and mRNA, and then T4 RNA ligase 1 was applied to the donor of ligase RNA with 5'phosphate and the 3’OH end of the RNA acceptor in the immunoprecipitants. The resultant chimeric reads were processed for highthroughput RNA sequencing.
We followed method described by Van Nostrand et al.


title: eCLIP, IP, Cisplatin 1


title: Ciaplatin, miRNA1


title: Control, miRNA3


title: Ciaplatin, miRNA2


title: eCLIP, Background, Cisplatin 2


title: eCLIP, Background, Cisplatin 1


title: eCLIP, Background, Control 3


title: eCLIP, Background, Control 2


title: eCLIP, Background, Cisplatin 3


title: eCLIP, IP, Control 2


title: eCLIP, IP, Control 1


title: Control, mRNA1


title: ChIPseq_input_CTCF_C21KO

city: Hong Kong

first: Lut Fei

last: Tam

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon

department: LIFS

country: Hong Kong

institute: HKUST

data_processing:
Reads were aligned against mouse reference genome mm10 (GRCm38) using Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
Assembly: mm10
Supplementary files format and content: BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

growth_protocol: ES cells were maintained in ES medium (DMEM with 15% certified FBS (Life Technologies), 20 mM HEPES, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.05 mM streptomycin, 1 U/ml Leukemia-inhibitory factor (LIF) and 2mM glutamine). Cells were passaged at 80% confluence. Setdb1 conditional KO ES cells were induced by the addition of 800 nM (Z)-4-Hydroxytamoxifen (4-OHT) (Abcam, 141943) for 4 days and harvested on day 6 post 4-OHT treatment.

extract_protocol:
Crosslinked cells were lysed and chromatin were sonicated. Histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were crosslinked using 1% formaldehyde for 10 minutes at room temperature then quenched with glycine.

tag: chip antibody

value: none (input)

value: Embryonic stem cell

value: Setdb1 KO


title: eCLIP, IP, Cisplatin 3


title: eCLIP, IP, Control 3


title: eCLIP, IP, Cisplatin 2


title: ChIPseq_input_H3K9me3_C31KO

extract_protocol:
Chromatin were extracted by lysing the cell and fragmented with MNase (Thermo Scientific™,  88216). The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using standard Illumina protocols


title: ChIPseq_CTCF_C21KO

value: CTCF (Active Motif, 61311)


title: ChIPseq_input_CTCF_C31KO


title: ChIPseq_CTCF_C31KO


title: ChIPseq_H3K9me3_C31KO


title: ChIPseq_H3K9me3_C21KO


title: ChIPseq_input_SMC3_WT_rep2

source_name: TT2 (C57BL/6/CBA F1)

value: TT2 (C57BL/6/CBA F1)


title: ChIPseq_SMC3_Setdb1KO_rep2

value: SMC3 (Abcam, 9263)


title: ChIPseq_input_CTCF_Setdb1KO_rep2


title: ChIPseq_input_H3K9me3_Setdb1KO_rep2


title: ChIPseq_input_H3K9me3_C21KO


title: ChIPseq_CTCF_Setdb1KO_rep2


title: ChIPseq_input_H3K9me3_WT_rep2


title: B4, blood, naïve

city: Brisbane

first: Jacky

last: Xie

state: QLD

address: The University of Queensland

country: Australia

institute: The University of Queensland

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), using a merged human and mice genome
Assembly: hg38, mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Blood

extract_protocol:
Blood was collected via cardiac puncture. Mice were then perfused with HBSS containing 0.2% heparin and the T8-T10 spinal cord was dissected into eppendorf tubes containing 500μl HBSS. Spinal cord was mechanically homogenised, incubated with papain enzymatic cocktail (L-glutamine-containing Leibovit's L-15 Medium with 0.1% papain and 0.1% DNAse I) for 20 minutes at 37°C on a shaker insubator, and filtered through a 40μm filter. 350μl blood was mixed 1:3 with 4mM EDTA and then incubated with red blood cell lysis buffer for 7 minutes at room temperature. Blood and cord samples were then stained with an anti-human CD45 APC-Cy7 antibody for 20 minutes on ice (in FACS buffer containing 0.5% BSA in 2mM EDTA with 1μg/μl mouse IgG for Fc-receptor blocking). huCD45+ were isolated from the spinal cord using anti-Cy7 magnetic beads for MACS sorting. Propidium iodide was added as a dead cell marker. Live huCD45+ were FACS sorted into eppendorf tubes containing 500μl ice cold PBS + 10% FBS.
Library was performed according to manufacturer's instructions (single cell 3' library and gel bead kit v3). Briefly, huCD45+ cells were resuspended in the mastermix and loaded together with partitioning oil and beads into the chip to generate the gel bead-in emulsion (GEM). The polyA RNA from every bead was reverse transcribed to cDNA. Denatured libraries of the pooled DNA were sequenced on an Illumina NextSeq-500. Read1 supplied the cell barcode and unique molecular identifier (UMI), i7 the sample index, and Read2 the 3' sequence of the transcript. All samples were processed in one sequencing run.

value: Blood

value: human CD45+

tag: Sex

value: male

value: 15 weeks


title: ChIPseq_input_CTCF_WT_rep2

value: WT


title: ChIPseq_H3K9me3_Setdb1KO_rep2


title: cd45_neg_8wk

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10X genomics

data_processing:
Raw sequencing data was pre-processed with CellRanger (v6.0.1, 10x Genomics) to demultiplex FASTQ reads, align reads to the mouse reference genome (mm10, v3.0.0 from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: mm10
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format

source_name: ankle

extract_protocol:
Joint tissue was digested for 1 hour at 37 ºC in RPMI containing 0.2 mg/ml liberase TL (Roche) and 1 unit/ml DNase (Thermo), inverting every 15 minutes. Cells were then filtered through a 40 µm filter and washed in PBS containing 2% FBS and 1 mM CaCl2. Live cells were obtained through magnetic sorting using the EasySep Dead Cell Removal (Annexin V) Kit (StemCell Technologies) per manufacturer’s instructions. Following dead cell removal, cells were washed in MACS buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ and CD45- cells separated using CD45 MicroBeads and a MiniMACS Separator per manufacturer’s instructions (Miltenyi Biotec).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ankle

tag: enrichment

tag: timepoint

value: week 8


title: cd45_pos_6wk

description: 10X genomics

value: week 6


title: ChIPseq_input_SMC3_Setdb1KO_rep2


title: cd45_neg_6wk

description: 10X genomics


title: cd45_neg_4wk

description: 10X genomics

value: week 4


title: cd45_neg_2wk

description: 10X genomics

value: week 2


title: B1, blood, sham, 7dpi

description: 10x Genomics

value: T9 laminectomy


title: ChIPseq_H3K9me3_WT_rep2


title: B2, blood, SCI, 7dpi

description: 10x Genomics

value: pooled male and female

value: T9 spinal cord injury


title: ChIPseq_SMC3_WT_rep2

value: Embryonic stem cell


title: cd45_pos_8wk

description: 10X genomics


title: Celastrol 3_4

city: Saskatoon

first: Andrew

last: Leask

state: Saskatchewan

address: 105 Wiggins

department: College of Dentistry

country: Canada

institute: University of Saskatchewan

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.3.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Skin tissue section, Celastrol

growth_protocol: 4 weeks old male C57BL/6 J mice were ordered from Jackson lab and the treatment was started from 6 weeks old.

extract_protocol:
NA
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression Reagents Kits for FFPE, User Guide CG000407, Rev C, 10x Genomics). Briefly,  after decrosslinking, probes were hybridized, ligated and released, followed by extention and cDNA library prep which included an indexed primer.
scRNA-seq

treatment_protocol: Phosphate buffered saline (PBS), group and bleomycin group were injected subcutaneously with 0.1 mL PBS and (0.1 units) bleomycin (Sigma, B5507), Celastrol groups were injected celastrol (Sigma, C0869) intraperitoneally with 1mg/kg every day for 21 days

value: Skin

value: Celastrol


title: ChIPseq_CTCF_WT_rep2

value: CTCF (Active Motif, 61311)

value: TT2 (C57BL/6/CBA F1)


title: cd45_pos_2wk

description: 10X genomics


title: Bleomycin 6_3

source_name: Skin tissue section, Bleomycin

value: Bleomycin


title: Celastrol 3

data_processing:
Partek Flow v10.0.22
fastq files were aligned to mm10 using Star 2.7.3a and annotated with Ensembl Transcripts release 102
Features were excluded if maximum reads <= 15.0
Reads were normalized using SESeq2 (poscounts)
Fold changes and p-values were caluclated using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including fold change and statistical significance value for each gene

source_name: Celastrol 21 days

extract_protocol:
The RNA was extracted using the TriZol extraction method.
Total RNA samples were processed using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (PN NR603) from Vazyme Biotech Co. Ltd.

treatment_protocol: Phosphate buffered saline (PBS), group and bleomycin group were injected subcutaneously with 0.1 mL PBS and (0.1 units) bleomycin (Sigma, B5507), Celastrol groups were injected celastrol (Sigma, C0869) intraperitoneally with either 1mg/kg or 2mg/kg every day for 21 days

value: Skin homogenate

value: male

value: C57 BL/6 J


title: Bleomycin 2_3


title: cd45_pos_0wk

description: 10X genomics

value: ankle

value: week 0


title: C2, cord, SCI, 7dpi

description: 10x Genomics

source_name: Spinal cord

value: Spinal cord

value: human CD45+

value: 15 weeks


title: cd45_neg_0wk

description: 10X genomics


title: PBS 2_4

source_name: Skin tissue section, PBS

value: PBS/ 0.1% DMSO


title: Bleomycin 2

source_name: Bleomycin 21 days


title: GL261-hCD19-luc ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 59

city: Boston

first: Catherine

middle: J.

last: Wu

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequencing data were aligned to the mm10 reference transcriptome with STAR (v2.7.7a)
Expression metrics for each gene were computed using RSEM (v1.3.3)
Differential expression analysis was performed using DESeq2 (v1.30.1), including genes with normalized transcript counts >10
Gene set enrichment analysis with the fgsea R package (v1.20.0) was performed across all genes pre-ranked by log10(p-value) * -(sign of the LFC)
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited output text files from RSEM include RPKM, TPM, and expected count values for each sample
Supplementary files format and content: Tab-delimited output text files from Salmon include TPM values for each sample

source_name: ex vivo tumor

extract_protocol:
RNA was harvested using RNeasy Plus Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers' protocols.

value: ex vivo tumor


title: GL261-hCD19-luc ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 58


title: GL261-hCD19-luc ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 57


title: GL261-hCD19-luc ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 60


title: GL261-hCD19-luc2 ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 91


title: Celastrol 1_4


title: cd45_pos_4wk

description: 10X genomics

value: week 4


title: Bleomycin 3


title: GL261-hCD19-luc2 ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 90


title: CT2A-hCD19-luc ex vivo tumor sorted for hCD19, Sample 70


title: PBS 3_4


title: GL261-hCD19-luc2 ex vivo tumor sorted for hCD19, Sample 84


title: PBS 3_3


title: GL261-hCD19-luc2 ex vivo tumor sorted for hCD19, Sample 83


title: ATACseq_WT

data_processing:
Reads with Phred score ≤20 were removed and adaptors were trimmed under paired-end mode default setting in trim_galore v0.4.3.
Reads were aligned to mouse reference genome mm10 (GRCm38) using Bowtie2 v2.3.3.1 (Langmead and Salzberg, 2012) with parameters -N 1 -L 25 -X 2000 --no-discordant --no-mixed.
Reads with more than one best alignment were removed. Duplicates were removed by Picard MarkDuplicates v2.9.0.
Duplicates were removed by Picard MarkDuplicates v2.9.0.
The alignments were then adjusted using MACS2 v2.1.0 (Zhang et al., 2008) with parameters --shift -75 --extsize 150 to make the start site of each read represent the center of the transposase binding (Buenrostro et al., 2013)
Normalization was done by applying S3norm (Xiang et al,. 2020) with default parameters to make the signal to noise ratio uniform.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by MAC2 v2.1.0 and UCSC utilites; Scores represent normalized RPM signal of piled up center adjusted alignments

source_name: Embryonic stem cell

extract_protocol:
Fresh cells were lysed in cold lysis buffer (10mM Tris-Cl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630, 1X PIC).
ATAC-seq libraries were prepared using Tn5 tagmentation (Vazyme) coupled with Illumina compatible indices according to manufacturer protocol.

value: Embryonic stem cell

value: WT


title: ATACseq_Setdb1KO

value: Setdb1 KO


title: Celastrol 5

value: Skin

value: Celastrol


title: PBS 2_3


title: ChIPseq_SMC3_Setdb1KO

data_processing:
Reads were aligned against mouse reference genome mm10 (GRCm38) using Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

value: SMC3 (Abcam, 9263)

value: TT2 (C57BL/6/CBA F1)


title: ChIPseq_SMC3_WT


title: ChIPseq_input_CTCF_WT


title: ChIPseq_input_CTCF_Setdb1KO


title: Celastrol 2

value: Skin homogenate

value: male


title: Bleomycin 4

value: C57 BL/6 J

value: Bleomycin


title: PBS 3

source_name: PBS 21 days

value: PBS


title: PBS 2


title: ChIPseq_H3K27ac_WT

value: H3K27ac (Active Motif, 39133)


title: GL261-hCD19-luc ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 61


title: ChIPseq_H3K9me3_WT


title: CT2A-hCD19-luc ex vivo tumor sorted for hCD19, Sample 71


title: CT2A-hCD19-luc ex vivo tumor sorted for hCD19, Sample 69


title: GL261-hCD19-luc2 ex vivo tumor cultured as a neurosphere and sorted for hCD19, Sample 89


title: GL261-hCD19-luc2 ex vivo tumor sorted for hCD19, Sample 82


title: GL261-hCD19-luc2 ex vivo tumor sorted for hCD19, Sample 81


title: BP11-Primary control (TNFR1-/+) CMFs-MS5

city: Los angeles

first: Xiangming

last: Ding

address: 4650 Sunset Blvd

institute: CHLA

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Primary control (TNFR1-/+) CMFs-MS

growth_protocol: Primary colonic myofibroblasts (CMFs) were isolated from the distal end of 16w old control (TNFR1+/-) and TNFR1-/- mice. The colon (1cm from the dentate line), cut horizontally, was stirred at 250 rpm in 5 mM EDTA/HBSS medium (without Ca++ and Mg++) at 37°C for 15 min and repeated for a total of 5 washes. Following two washes of ice-cold PBS, the tissue was digested in DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with, 0.31 mg/mL Dispase and 0.25mg/mL collagenase Type XI for up to 60 minutes at 250 rpm at 37°C, until the tissue appeared stringy. Digested tissue was treated with ACK lysis buffer (4.15 g NH4Cl, 0.5 g KHCO3, 18.6 mg Na2EDTA, 400 ml H2O, pH 7.2-7.4) for 5 min and then passed through a 100‐μm cell strainer into 6-well dishes of CMF-growth medium (DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with 10% FBS and 1X recombinant human insulin, human transferrin and sodium selenite (ITS) solution, and 20 ng/mL recombinant murine epidermal growth factor. After 24‐h incubation, non‐adherent cells were washed away. One week later, only myofibroblasts divided, and macrophages and epithelial cells had senesced after the first passage.

extract_protocol:
Control (TNFR1+/-) and TNFR1-/- primary CMFs (passage 6 - 8) were seeded at a density of 1x103 cells/50 µL of Matrigel into 24-well plates and were grown to 70% confluency. At D 5, CMFs were extracted from Matrigel after brief incubation at 4⁰C via centrifugation at 1200rpm for 5 min. Total RNA from primary CMFs was extracted with using the Ambion® PureLink® RNA Isolation Kit (Thermofisher Scientific, no. 12183025) according to the manufacturer’s protocol.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: RNA-Seq was performed on untreated control (TNFR1+/-) and TNFR1-/- primary CMFs.

tag: strain background

value: distal colon

value: control (TNFR1-/+)

tag: days post passage/cell type

value: d5/colonic myofibroblasts (CMFs)


title: BP12-Primary control (TNFR1-/+) CMFs-MS6


title: BP8-Primary control (TNFR1-/+) CMFs-MS2


title: ChIPseq_input_SMC3_WT

tag: cell type


title: ChIPseq_input_SMC3_Setdb1KO


title: BP5- Primary TNFR1-/- CMFs-MS5

source_name: Primary TNFR1-/- CMFs-MS


title: ChIPseq_CTCF_WT

data_processing:
Reads were aligned against mouse reference genome mm10 (GRCm38) using Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
Peaks for CTCF was called by MACS2 v2.1.0 with parameters --keep-dup all -g 2.43e9 -q 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

value: CTCF (Active Motif, 61311)


title: ChIPseq_input_H3K27ac_Setdb1KO

value: Embryonic stem cell


title: ChIPseq_input_H3K9me3_WT

value: WT


title: ChIPseq_H3K27ac_Setdb1KO

value: Setdb1 KO


title: ChIPseq_input_H3K27ac_WT


title: ChIPseq_CTCF_Setdb1KO


title: BP10-Primary control (TNFR1-/+) CMFs-MS4


title: ChIPseq_H3K9me3_Setdb1KO


title: ChIPseq_input_H3K9me3_Setdb1KO


title: BP9-Primary control (TNFR1-/+) CMFs-MS3


title: BP7-Primary control (TNFR1-/+) CMFs-MS1


title: BP4- Primary TNFR1-/- CMFs-MS4


title: BP3- Primary TNFR1-/- CMFs-MS3


title: BP2- Primary TNFR1-/- CMFs-MS2