title: DNA methylation data of ccRCC tumor 46

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R06C01

source_name: ccRCC tumor 46

value: ccRCC tumor 46

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 45

status: Public on Jun 07 2024

type: genomic

city: Lyon

first: James

last: Mckay

address: 25 Av. Tony Garnier

country: France

institute: IARC - International Agency for Research on Cancer

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R05C01

hyb_protocol: The DNA (600 ng) of samples underwent pre-processing steps as follows: bisulfite-conversion, whole-genome amplification, fragmentation, and hybridization with complementary probes sequences on The Infinium MethylationEPIC BeadChip v1 using standard Illumina protocol.

scan_protocol: iScan system scanner (Ilumina) and probe intensities were obtained by GenomeStudio Software ((Ilumina)

data_processing:
The processing steps of probes were performed using the implemented functions in methylkey R package (https://github.com/IARCbioinfo/methylkey). Version 0.1.1.9000
tab-delimited file with a matrix of 121 samples as cols and 792,697 normalised (Funnorm) average beta values as rows. File named as 'MatrixProcessed.tsv',
Unmethylated and methylated signal intensities uploaded as 'rawdata2Geo.tsv' and unprocessed betas as 'betas2Geo.tsv'

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: ccRCC tumor 45

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable.

extract_protocol: DNA was isolated from tumor samples using the Flexigene DNA isolation kit from Qiagen as per manufacturer’s protocol and stored in aliquots at −20 °C.

treatment_protocol: Not applicable.

tag: tissue

value: ccRCC tumor 45

value: Male


title: patient 333

type: RNA

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

country: USA

institute: H Lee Moffitt Cancer Center

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

label: biotin

molecule: total RNA

source_name: macrodissected primary breast tumor

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 49

description:
clear clear renal carcinoma tumor, high-quality sample
206402350152_R01C01

source_name: ccRCC tumor 49

tag: tissue

value: ccRCC tumor 49

tag: age

tag: Sex

tag: batch


title: patient 338

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn


title: patient 329

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 339

tag: tissue

value: Partial breast irradiation

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 47

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R07C01

source_name: ccRCC tumor 47

value: ccRCC tumor 47

tag: age

tag: Sex

tag: batch


title: patient 347

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn


title: patient 332

value: ILC

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: D3D-BM-Tcm_3

type: SRA

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

country: China

institute: Shanghai Children's Medical Center

description:
batch3
counts_SI.txt

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCm38 whole genome using STAR 2.7.6a  with parameters  --runMode alignReads --runThreadN 5  --genomeLoad NoSharedMemory  --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
The gene expression level (TPM) was calculated according to the Sequencing depth and gene length, and remove batch effect by R package ComBat
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicated reads: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
scRNA-seq and scTCR-seq data processing: cellranger v6.1.2
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Total RNA was isolated using the TRIzol reagent; mRNA is reversely transcribed into cDNA using the Smart-seq2, and then amplified using KAPA HiFi DNA polymerase. The protocol from Jun Chen  et al., nature protocols, 2017.
DNA libraries were prepared for sequencing using TruePrep DNA Library Prep Kit V2 for Illumina(VazymeTD502)

treatment_protocol: CD8 cells were stained with antibodies CD44 and CD62L and sorted by flow cytometry.

tag: strain

tag: tissue

value: bone marrow

tag: treatment

value: 3 days post DNR chemotherapy of AF9 AML mice


title: D3D-BM-Tcm_2

description:
batch3
counts_SI.txt


title: DNA methylation data of ccRCC tumor 44

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R04C01

source_name: ccRCC tumor 44

value: ccRCC tumor 44

tag: age

tag: Sex

value: Female

tag: batch


title: patient 330

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 324

value: Positive

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 328

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Negative

value: White


title: patient 326

tag: pr status

tag: her2 status

value: External beam radiation

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: D3D-BM-Tcm_1

description:
batch3
counts_SI.txt

tag: strain

tag: treatment


title: DNA methylation data of ccRCC tumor 43

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R03C01

source_name: ccRCC tumor 43

value: ccRCC tumor 43

tag: age

tag: Sex

value: Male

tag: batch


title: DNA methylation data of ccRCC tumor 42

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R02C01

source_name: ccRCC tumor 42

value: ccRCC tumor 42


title: patient 327

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: D3D-BM-Teff_3

description:
batch3
counts_SI.txt

tag: tissue

value: bone marrow


title: DNA methylation data of ccRCC tumor 41

description:
clear clear renal carcinoma tumor, high-quality sample
206402350151_R01C01

source_name: ccRCC tumor 41

value: ccRCC tumor 41


title: DNA methylation data of ccRCC tumor 40

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R08C01

source_name: ccRCC tumor 40

value: ccRCC tumor 40


title: D3D-BM-Teff_2

description:
batch3
counts_SI.txt

value: 3 days post DNR chemotherapy of AF9 AML mice


title: patient 323

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: ILC

tag: er status

tag: pr status

tag: her2 status

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: D3D-BM-Teff_1

description:
batch3
counts_SI.txt

tag: strain

tag: treatment


title: DNA methylation data of ccRCC tumor 39

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R07C01

source_name: ccRCC tumor 39

value: ccRCC tumor 39

tag: age

tag: Sex

value: Female

tag: batch


title: D3D-SI-Tim_3

description:
batch3
counts_SI.txt

source_name: small intestine


title: DNA methylation data of ccRCC tumor 38

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R06C01

source_name: ccRCC tumor 38

value: ccRCC tumor 38


title: D3D-SI-Tim_2

description:
batch3
counts_SI.txt


title: DNA methylation data of ccRCC tumor 37

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R05C01

source_name: ccRCC tumor 37

value: ccRCC tumor 37


title: patient 325

value: Lumpectomy

value: Positive

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 319

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: locoregional recurrence

value: No

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 320

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: time to death or censor from date of diagnosis (years)


title: patient 316

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 321

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

tag: bioanalyzer rin (rna integrity number)


title: patient 317

tag: er status

tag: pr status

tag: her2 status

tag: locoregional recurrence

tag: death

value: Dead


title: patient 314

value: Mastectomy

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 36

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R04C01

source_name: ccRCC tumor 36

value: ccRCC tumor 36

tag: age

tag: Sex

tag: batch


title: D3D-SI-Tim_1

description:
batch3
counts_SI.txt

tag: strain

tag: tissue

value: bone marrow

tag: treatment

value: 3 days post DNR chemotherapy of AF9 AML mice


title: patient 318

tag: subject

tag: type of surgery

tag: histology

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: AF9-SI-Tim_3

description:
batch3
counts_SI.txt

value: AF9 AML mice


title: DNA methylation data of ccRCC tumor 35

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R03C01

source_name: ccRCC tumor 35

value: ccRCC tumor 35

value: Female


title: patient 312

value: Lumpectomy

value: ILC

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Unknown

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 313

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: Other

value: Yes

tag: type of radiotherapy

value: White

value: No


title: patient 310

value: macrodissected primary breast tumor

value: IDC

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 309

value: Mastectomy

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: bioanalyzer rin (rna integrity number)


title: AF9-SI-Tim_2

description:
batch3
counts_SI.txt

tag: strain

value: bone marrow

tag: treatment

value: AF9 AML mice


title: DNA methylation data of ccRCC tumor 34

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R02C01

source_name: ccRCC tumor 34

tag: tissue

value: ccRCC tumor 34

tag: age

tag: Sex

value: Male

tag: batch


title: DNA methylation data of ccRCC tumor 33

description:
clear clear renal carcinoma tumor, high-quality sample
206402350128_R01C01

source_name: ccRCC tumor 33

value: ccRCC tumor 33


title: AF9-O5D-Tn_3

description:
batch5
counts_BM.txt

value: 5 days post OXA chemotherapy of AF9 AML mice


title: patient 305

source_name: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: Positive

value: Negative

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: AF9-O5D-Tn_2

description:
batch5
counts_BM.txt


title: patient 307

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Yes

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: No

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 311

tag: tissue

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: pn

value: External beam radiation


title: patient 304

value: Mastectomy

value: IDC

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Hispanic, Asian & other

tag: locoregional recurrence

tag: death

value: Alive


title: patient 303

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: AA

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 31

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R07C01

source_name: ccRCC tumor 31

value: ccRCC tumor 31

tag: age

tag: Sex

value: Male

tag: batch


title: patient 308

tag: tissue

tag: subject

value: Lumpectomy

value: Other

value: Positive

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 302

tag: type of surgery

tag: histology

value: Negative

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: locoregional recurrence

tag: death


title: DNA methylation data of ccRCC tumor 30

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R06C01

source_name: ccRCC tumor 30

value: ccRCC tumor 30

tag: age

tag: Sex

tag: batch


title: patient 300

tag: tissue

tag: subject

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Yes

tag: age at diagnosis

value: White

value: No

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 29

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R05C01

source_name: ccRCC tumor 29

value: ccRCC tumor 29

value: Female


title: DNA methylation data of ccRCC tumor 32

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R08C01

source_name: ccRCC tumor 32

value: ccRCC tumor 32


title: AF9-SI-Tim_1

description:
batch3
counts_SI.txt

tag: strain

value: bone marrow

tag: treatment

value: AF9 AML mice


title: AF9-O5D-Teff_3

description:
batch5
counts_BM.txt

source_name: bone marrow

value: 5 days post OXA chemotherapy of AF9 AML mice


title: patient 298

value: macrodissected primary breast tumor

tag: type of surgery

value: Mastectomy

tag: histology

value: IDC

tag: pn

tag: ptnm

tag: radiotherapy

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Alive

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 306

tag: tissue

tag: subject

tag: er status

value: Positive

tag: pr status

value: Negative

tag: type of radiotherapy

value: Unknown

tag: locoregional recurrence

tag: death


title: patient 301

tag: type of surgery

value: ILC

tag: her2 status

tag: pt

tag: age at diagnosis

value: Yes

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: AF9-O5D-Teff_4

description:
batch5
counts_BM.txt

tag: strain

tag: treatment


title: patient 315

tag: histology

tag: pn

tag: ptnm

tag: radiotherapy

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: No


title: DNA methylation data of ccRCC tumor 28

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R04C01

source_name: ccRCC tumor 28

tag: tissue

value: ccRCC tumor 28

tag: age

tag: Sex

value: Male

tag: batch


title: AF9-O5D-Teff_2

description:
batch5
counts_BM.txt

value: bone marrow


title: patient 296

tag: subject

tag: type of surgery

value: Lumpectomy

tag: er status

tag: pr status

tag: her2 status

tag: type of radiotherapy

tag: locoregional recurrence

tag: death

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 294

value: macrodissected primary breast tumor

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 27

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R03C01

source_name: ccRCC tumor 27

tag: tissue

value: ccRCC tumor 27

tag: age

tag: Sex

tag: batch


title: patient 293

tag: subject

tag: type of surgery

value: Mastectomy

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: type of radiotherapy

tag: race

tag: chemotherapy


title: patient 295

tag: histology

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

tag: locoregional recurrence

tag: death

value: Alive

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: AF9-O5D-Teff_1

description:
batch5
counts_BM.txt

tag: strain

tag: tissue

tag: treatment

value: 5 days post OXA chemotherapy of AF9 AML mice


title: DNA methylation data of ccRCC tumor 26

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R02C01

source_name: ccRCC tumor 26

value: ccRCC tumor 26

tag: age

tag: Sex

tag: batch


title: patient 299

tag: subject

tag: type of surgery

tag: er status

value: Positive

tag: pr status

value: Negative

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 292

tag: histology

value: ILC

tag: pt

tag: pn

tag: ptnm

value: Yes

value: Partial breast irradiation

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 291

tag: tissue

tag: subject

tag: type of surgery

tag: er status

tag: pr status

value: White

value: No


title: patient 297

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: Dead


title: DNA methylation data of ccRCC tumor 25

description:
clear clear renal carcinoma tumor, high-quality sample
206402350127_R01C01

source_name: ccRCC tumor 25

value: ccRCC tumor 25

tag: age

tag: Sex

value: Male

tag: batch


title: AF9-O5D-Tcm_4

description:
batch5
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment


title: patient 290

value: macrodissected primary breast tumor

value: Mastectomy

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: AF9-O5D-Tcm_3

description:
batch5
counts_BM.txt

tag: tissue


title: DNA methylation data of ccRCC tumor 24

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R08C01

source_name: ccRCC tumor 24

value: ccRCC tumor 24

value: Female


title: AF9-O5D-Tcm_2

description:
batch5
counts_BM.txt

value: 5 days post OXA chemotherapy of AF9 AML mice


title: AF9-O5D-Tcm_1

description:
batch5
counts_BM.txt


title: patient 289

tag: subject

tag: type of surgery

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: Hispanic, Asian & other

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 23

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R07C01

source_name: ccRCC tumor 23

value: ccRCC tumor 23

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 22

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R06C01

source_name: ccRCC tumor 22

value: ccRCC tumor 22


title: patient 285

tag: histology

value: Positive

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death


title: patient 287

tag: tissue

tag: subject

tag: type of surgery

value: Lumpectomy

tag: er status

tag: pr status

tag: her2 status

value: No

value: Yes

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: AF9-D5D-Teff4_4

description:
batch5
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: 5 days post DNR chemotherapy of AF9 AML mice


title: DNA methylation data of ccRCC tumor 21

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R05C01

source_name: ccRCC tumor 21

value: ccRCC tumor 21

tag: age

tag: Sex

value: Female

tag: batch


title: patient 283

value: macrodissected primary breast tumor

tag: histology

value: IDC

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: bioanalyzer rin (rna integrity number)


title: patient 286

tag: tissue

tag: subject

tag: type of surgery

value: Mastectomy

tag: er status

tag: pr status

tag: her2 status

value: External beam radiation

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: AF9-D5D-Teff4_3

description:
batch5
counts_BM.txt

tag: strain

tag: treatment


title: patient 288

tag: histology

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 20

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R04C01

source_name: ccRCC tumor 20

tag: tissue

value: ccRCC tumor 20

tag: age

tag: Sex

value: Male

tag: batch


title: AF9-D5D-Teff4_2

description:
batch5
counts_BM.txt


title: patient 280

tag: subject

tag: type of surgery

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 284

tag: histology

value: Other

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: White

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 19

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R03C01

source_name: ccRCC tumor 19

tag: tissue

value: ccRCC tumor 19

tag: age

tag: Sex

tag: batch


title: patient 331

tag: subject

tag: type of surgery

value: Lumpectomy

tag: er status

tag: pr status

tag: her2 status

value: Yes

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

value: No

tag: time to death or censor from date of diagnosis (years)


title: patient 281

tag: histology

value: ILC

tag: pt

tag: pn

tag: ptnm

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 279

tag: tissue

value: macrodissected primary breast tumor

tag: radiotherapy

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 18

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R02C01

source_name: ccRCC tumor 18

value: ccRCC tumor 18

tag: age

tag: Sex

tag: batch


title: AF9-(BM)-Tim_3

description:
batch3
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: AF9 AML mice


title: DNA methylation data of ccRCC tumor 17

description:
clear clear renal carcinoma tumor, high-quality sample
206402350102_R01C01

source_name: ccRCC tumor 17

value: ccRCC tumor 17

value: Female


title: AF9-(BM)-Tim_2

description:
batch3
counts_BM.txt


title: DNA methylation data of ccRCC tumor 16

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R08C01

source_name: ccRCC tumor 16

value: ccRCC tumor 16


title: patient 275

source_name: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 272

tag: tissue

value: Other

value: Positive

value: Negative

tag: pn

tag: ptnm

tag: radiotherapy

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: AF9-D5D-Teff4_1

description:
batch5
counts_BM.txt

tag: strain

tag: treatment

value: 5 days post DNR chemotherapy of AF9 AML mice


title: patient 282

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: er status

tag: pr status

tag: her2 status

value: Yes

value: No

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 273

tag: tissue

value: macrodissected primary breast tumor

value: Lumpectomy

tag: pt

tag: pn

tag: ptnm

tag: type of radiotherapy

tag: age at diagnosis

tag: time to death or censor from date of diagnosis (years)


title: patient 276

tag: radiotherapy

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: AF9-(BM)-Tim_1

description:
batch3
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: AF9 AML mice


title: patient 277

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 271

tag: tissue

value: Mastectomy

tag: pt

tag: pn

tag: ptnm

tag: type of radiotherapy

tag: age at diagnosis

tag: time to death or censor from date of diagnosis (years)


title: patient 269

tag: radiotherapy

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 15

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R07C01

source_name: ccRCC tumor 15

value: ccRCC tumor 15

tag: age

tag: Sex

value: Female

tag: batch


title: patient 268

tag: tissue

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

value: External beam radiation

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)


title: AF9-Teff_4

description:
batch5
counts_BM.txt

tag: strain

tag: treatment


title: patient 278

value: Positive

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)


title: DNA methylation data of ccRCC tumor 14

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R06C01

source_name: ccRCC tumor 14

tag: tissue

value: ccRCC tumor 14

tag: age

tag: Sex

value: Male

tag: batch


title: patient 266

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

value: No

value: White

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 267

value: macrodissected primary breast tumor

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Dead


title: AF9-Teff_3

description:
batch5
counts_BM.txt

source_name: bone marrow

tag: strain

tag: tissue

value: bone marrow

tag: treatment

value: AF9 AML mice


title: DNA methylation data of ccRCC tumor 13

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R05C01

source_name: ccRCC tumor 13

value: ccRCC tumor 13

tag: age

tag: Sex

tag: batch


title: DNA methylation data of ccRCC tumor 12

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R04C01

source_name: ccRCC tumor 12

value: ccRCC tumor 12


title: patient 270

tag: subject

tag: type of surgery

value: Mastectomy

tag: histology

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: time to death or censor from date of diagnosis (years)


title: patient 265

value: Lumpectomy

value: ILC

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: AF9-Teff_1

description:
batch5
counts_BM.txt

tag: strain

tag: tissue

tag: treatment


title: patient 322

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: chemotherapy


title: patient 264

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: No

value: Hispanic, Asian & other

tag: locoregional recurrence

tag: death

tag: time to death or censor from date of diagnosis (years)


title: patient 261

value: macrodissected primary breast tumor

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 11

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R03C01

source_name: ccRCC tumor 11

tag: tissue

value: ccRCC tumor 11

tag: age

tag: Sex

value: Female

tag: batch


title: patient 274

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: Yes

value: AA

tag: chemotherapy

value: Dead


title: AF9-(BM)-Tcm_3

description:
batch3
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: AF9 AML mice


title: AF9-(BM)-Tcm_2

description:
batch3
counts_BM.txt


title: DNA methylation data of ccRCC tumor 9

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R01C01

source_name: ccRCC tumor 9

value: ccRCC tumor 9


title: DNA methylation data of ccRCC tumor 8

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R08C01

source_name: ccRCC tumor 8

value: ccRCC tumor 8

value: Male


title: AF9-(BM)-Tcm_1

description:
batch3
counts_BM.txt


title: patient 260

value: Mastectomy

value: IDC

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: locoregional recurrence

tag: death

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: AF9-Teff_2

description:
batch5
counts_BM.txt

tag: tissue


title: WT-O5D-Tn_3

description:
batch4
counts_BM.txt

value: 5 days post OXA chemotherapy of C57 mice


title: patient 258

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: er status

value: Positive

tag: pr status

value: Negative

value: External beam radiation

value: No

tag: time to locoregional recurrence from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DNA methylation data of ccRCC tumor 10

description:
clear clear renal carcinoma tumor, high-quality sample
206402350066_R02C01

source_name: ccRCC tumor 10

value: ccRCC tumor 10

tag: age

tag: Sex

tag: batch


title: WT-O5D-Tn_2

description:
batch4
counts_BM.txt

tag: strain

tag: treatment


title: patient 255

value: macrodissected primary breast tumor

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy


title: DNA methylation data of ccRCC tumor 7

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R07C01

source_name: ccRCC tumor 7

tag: tissue

value: ccRCC tumor 7


title: patient 256

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

value: Yes

tag: locoregional recurrence

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 259

value: Other

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

value: Hispanic, Asian & other


title: patient 253

value: Mastectomy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: WT-O5D-Tn_1

description:
batch4
counts_BM.txt

tag: strain

tag: tissue

value: bone marrow

tag: treatment


title: DNA methylation data of ccRCC tumor 6

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R06C01

source_name: ccRCC tumor 6

value: ccRCC tumor 6

tag: age

tag: Sex

value: Male

tag: batch


title: patient 251

tag: subject

tag: type of surgery

tag: histology

value: IDC

tag: er status

tag: pr status

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 254

value: Positive

tag: her2 status

value: Negative

tag: pt

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 257

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: er status

value: No


title: DNA methylation data of ccRCC tumor 5

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R05C01

source_name: ccRCC tumor 5

value: ccRCC tumor 5

tag: age

tag: Sex

tag: batch


title: WT-O5D-Teff_3

description:
batch4
counts_BM.txt

tag: strain

tag: treatment

value: 5 days post OXA chemotherapy of C57 mice


title: DNA methylation data of ccRCC tumor 4

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R04C01

source_name: ccRCC tumor 4

value: ccRCC tumor 4


title: patient 252

value: macrodissected primary breast tumor

value: ILC

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

value: White

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 250

tag: tissue

tag: subject

tag: type of surgery

tag: histology

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: Yes


title: AF9-O5D-Tn_1

description:
batch5
counts_BM.txt

tag: strain

tag: treatment

value: 5 days post OXA chemotherapy of AF9 AML mice


title: DNA methylation data of ccRCC tumor 3

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R03C01

source_name: ccRCC tumor 3

value: ccRCC tumor 3

tag: age

tag: Sex

value: Female

tag: batch


title: WT-O5D-Teff_2

description:
batch4
counts_BM.txt

value: bone marrow


title: WT-O5D-Teff_1

description:
batch4
counts_BM.txt


title: DNA methylation data of ccRCC tumor 2

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R02C01

source_name: ccRCC tumor 2

value: ccRCC tumor 2

value: Male


title: patient 262

value: Mastectomy

value: IDC

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: locoregional recurrence

tag: death

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: WT-O5D-Tcm_3

description:
batch4
counts_BM.txt

tag: tissue


title: DNA methylation data of ccRCC tumor 1

description:
clear clear renal carcinoma tumor, high-quality sample
206402350014_R01C01

source_name: ccRCC tumor 1

value: ccRCC tumor 1


title: patient 248

source_name: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: Positive

value: Negative

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

value: No

tag: bioanalyzer rin (rna integrity number)


title: patient 243

value: macrodissected primary breast tumor

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: Dead


title: WT-O5D-Tcm_2

description:
batch4
counts_BM.txt

tag: strain

tag: treatment

value: 5 days post OXA chemotherapy of C57 mice


title: patient 263

tag: tissue

tag: subject

tag: ptnm

value: Yes

value: External beam radiation

value: White

tag: locoregional recurrence

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 246

tag: type of surgery

tag: histology

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race


title: patient 249

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: chemotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 247

tag: tissue

tag: subject

tag: ptnm

value: AA

tag: locoregional recurrence

tag: death


title: patient 241

tag: type of surgery

tag: histology

tag: radiotherapy

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 238

value: ILC

tag: er status

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race


title: patient 244

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: chemotherapy


title: patient 245

tag: tissue

tag: subject

tag: ptnm

tag: locoregional recurrence

tag: bioanalyzer rin (rna integrity number)


title: patient 240

tag: type of surgery

tag: histology

tag: radiotherapy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 242

tag: er status

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: time to death or censor from date of diagnosis (years)


title: WT-O5D-Tcm_1

description:
batch4
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: 5 days post DNR chemotherapy of C57 mice


title: WT-D5D-Tn_2

description:
batch4
counts_BM.txt

tag: tissue


title: WT-D5D-Tn_3

description:
batch4
counts_BM.txt


title: WT-D5D-Tn_1

description:
batch4
counts_BM.txt


title: EHEC yad deletion strain

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Ave.

department: Microbiology

institute: University of Virginia

description: Gene expression data from a yad deletion strain of EHEC

hyb_protocol: Samples were processed and scanned according to the Affymetrix Gene array protocols. Samples were hybridized to the E. coli 2.0 array chips.

scan_protocol: All protocols were done according to manufacturer's specifications (http://www.affymetrix.com/support/index.affx)

data_processing: The Affymetrix GeneChip Command Console Software (AGCC) was used to obtain the output from scanning a single replicate of the Affymetrix GeneChip E. coli Genome 2.0 array for each of the biological conditions, following the manufacturer’s instructions.

organism: Escherichia coli

source_name: enterohemorragic Escherichia coli O157:H7

growth_protocol: Strains were grown in DMEM tissue culture medium, statically at 37 degrees under a 5% CO2 atmosphere for 6 h.

extract_protocol: RNA was extracted using the Ambion RiboPure RNA extraction kit according to the manufacturer's specifications.

treatment_protocol: Not applicable

tag: genotype/variation

value: yad deletion strain of EHEC


title: H4K20R, His4rnull_rep2, anti-GFP

city: Chapel Hill

first: Robert

middle: J.

last: Duronio

state: NC

address: 250 Bell Tower Dr., Gen. Sci. Bldg. 3356, CB7100

institute: UNC Chapel Hill

library_source: genomic

data_processing:
Adapters were trimmed using bbduk
Reads were aligned to dm6 with bowtie2 and converted to bam format
Reads with quality score < 30 were removed via samtools and duplicates were removed
Bam files were converted to bed format with bedtools
bed files were scaled by values generated using yeast DNA spike-ins by Spike-in normalized Reads Per Million mapped reads in the negative Control (SRPMC) with bedtools genomeCoverage then converted to BigWig coverage files with ucsctools wigToBigWig
Peaks were called using the csaw package and edgeR. Aligned reads were binned into 150bp windows with a 50bp slide. Bins with a log(2) > 2 above background were retained. Windows were normalized for compositional bias and windows in enriched in GFP-L3mbt relative to Oregon-R were calculated using edgeR. Windows within 250bp were merged and windows with log(2)FC > 3 and FDR < 0.05 were called peaks
Assembly: dm6
Supplementary files format and content: GFP-L3mbt.vs.OregonR.peaks.bed bed file containing genomic coordinates of enriched regions in GFP-L3mbt relative to Oregon-R (l2fc > 3) using the csaw package and edgeR
Supplementary files format and content: GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw Spike-in normalized GFP genome coverage file in GFP-L3mbt. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: OregonR_spikeNorm_GFP_allReps_avg.bw Spike-in normalized GFP genome coverage file in Oregon-R. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: HWT_His4rnull_GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw Spike-in normalized GFP genome coverage file in HWT, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20R_His4rnull_GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw Spike-in normalized GFP genome coverage file in K20R, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: GFP-L3mbt_spikeNorm_GFP_rep1.bw Spike-in normalized GFP genome coverage file in GFP-L3mbt replicate 1
Supplementary files format and content: GFP-L3mbt_spikeNorm_GFP_rep2.bw Spike-in normalized GFP genome coverage file in GFP-L3mbt replicate 2
Supplementary files format and content: OregonR_spikeNorm_GFP_rep1.bw Spike-in normalized GFP genome coverage file in Oregon-R replicate 1
Supplementary files format and content: OregonR_spikeNorm_GFP_rep2.bw Spike-in normalized GFP genome coverage file in Oregon-R replicate 2
Supplementary files format and content: HWT_His4rnull_GFP-L3mbt_spikeNorm_GFP_rep1.bw Spike-in normalized GFP genome coverage file in HWT, His4rnull replicate 1
Supplementary files format and content: HWT_His4rnull_GFP-L3mbt_spikeNorm_GFP_rep2.bw Spike-in normalized GFP genome coverage file in HWT, His4rnull replicate 2
Supplementary files format and content: K20R_His4rnull_GFP-L3mbt_spikeNorm_GFP_rep1.bw Spike-in normalized GFP genome coverage file in K20R, His4rnull replicate 1
Supplementary files format and content: K20R_His4rnull_GFP-L3mbt_spikeNorm_GFP_rep2.bw Spike-in normalized GFP genome coverage file in K20R, His4rnull replicate 2
Library strategy: CUT&RUN

organism: Drosophila melanogaster

source_name: wing disc

growth_protocol: Animals were raised at 25C

extract_protocol:
20 wing imaginal discs were individually dissected in 1xPBS from 3rd instar wandering larvae. Following CUT&RUN protocol, DNA fragments in the supernatant (diffused out of the nucleus) were prepared and sequenced
DNA libraries were prepared using ThruPLEX DNA-seq Kit (Takara) and DNA Unique Duel Index Kit

value: wing disc

tag: Sex

value: female

tag: developmental stage

value: 3rd instar wandering

tag: genotype

value: deltaHisC; {12xK20R}, His4rnull, l3mbtGFP

tag: cut&run antibody

value: anti-GFP (Rockland 600-401-215)


title: HWT_His4rnull_rep2, anti-GFP

description: HWT_His4rnull_GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw

value: deltaHisC; {12xHWT}, His4rnull, l3mbtGFP


title: WT EHEC

description: Gene expression data from wild type EHEC

label_protocol: All protocols were done according to manufacturer's specifications (http://www.affymetrix.com/support/index.affx)

value: wild type EHEC


title: H4K20R, His4rnull_rep1, anti-GFP

description: K20R_His4rnull_GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw


title: patient 236

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

value: IDC

value: Negative

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: No

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: patient 239

tag: tissue

value: Mastectomy

tag: er status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White

value: Yes

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: EHEC yeh deletion strain

description: Gene expression data from a yeh deletion strain of EHEC

tag: genotype/variation

value: yeh deletion strain of EHEC


title: patient 229

tag: subject

tag: type of surgery

tag: histology

tag: pr status

tag: her2 status

tag: pt

value: External beam radiation


title: patient 228

value: Positive

tag: pn

tag: ptnm

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: bioanalyzer rin (rna integrity number)


title: WT-D5D-Teff_2

description:
batch4
counts_BM.txt

source_name: bone marrow

tag: strain

tag: tissue

value: bone marrow

tag: treatment

value: 5 days post DNR chemotherapy of C57 mice


title: patient 230

tag: er status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 237

tag: subject

tag: type of surgery

tag: histology

tag: pr status

tag: her2 status

tag: pt

tag: pn


title: patient 233

tag: tissue

tag: ptnm

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: bioanalyzer rin (rna integrity number)


title: HWT_His4rnull_rep1, anti-GFP

value: wing disc

tag: Sex

value: female

tag: developmental stage

value: 3rd instar wandering

tag: genotype

value: deltaHisC; {12xHWT}, His4rnull, l3mbtGFP

tag: cut&run antibody

value: anti-GFP (Rockland 600-401-215)


title: patient 226

value: macrodissected primary breast tumor

tag: subject

value: Lumpectomy

value: IDC

tag: er status

value: Negative

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 227

tag: tissue

tag: type of surgery

value: Mastectomy

tag: histology

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

tag: race

value: White

value: No

value: Alive


title: patient 235

tag: subject

value: Other

tag: er status

tag: chemotherapy

value: Yes

tag: locoregional recurrence

tag: bioanalyzer rin (rna integrity number)


title: patient 234

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death


title: patient 232

tag: tissue

tag: type of surgery

tag: histology

value: Positive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 231

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: Hispanic, Asian & other


title: WT-D5D-Teff_3

description:
batch4
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: 5 days post DNR chemotherapy of C57 mice


title: Oregon-R_rep2, anti-GFP

description:
GFP-L3mbt.vs.OregonR.peaks.bed
OregonR_spikeNorm_GFP_allReps_avg.bw

value: wing disc

tag: Sex

value: female

tag: developmental stage

value: 3rd instar wandering

tag: genotype

value: Oregon-R

tag: cut&run antibody


title: WT-D5D-Teff_1

description:
batch4
counts_BM.txt


title: patient 223

value: macrodissected primary breast tumor

tag: subject

tag: er status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: WT-D5D-Tcm_3

description:
batch4
counts_BM.txt

tag: strain

tag: tissue


title: patient 222

tag: type of surgery

value: Lumpectomy

tag: histology

value: IDC

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: External beam radiation

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: WT-D5D-Tcm_2

description:
batch4
counts_BM.txt

tag: treatment


title: GFP-L3mbt_rep2

description:
GFP-L3mbt.vs.OregonR.peaks.bed
GFP-L3mbt_spikeNorm_GFP_allReps_avg.bw

tag: Sex

tag: developmental stage

tag: genotype

tag: cut&run antibody

value: anti-GFP (Rockland 600-401-215)


title: patient 225

tag: subject

value: Mastectomy

tag: er status

value: Negative

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: Oregon-R_rep1, anti-GFP

tag: tissue


title: WT-D5D-Tcm_1

description:
batch4
counts_BM.txt

tag: strain

tag: treatment


title: WT-Teff3_1

description:
batch4
counts_BM.txt

value: C57 mice


title: Set8rg_rep3

data_processing:
Adapters were trimmed using bbduk
Reads were aligned to dm6 with bowtie2 and converted to bam format
Reads with quality score < 5 were removed via samtools and duplicates were removed
Bam files were converted to bed format with bedtools
bed files were scaled by values generated using yeast DNA spike-ins by Spike-in normalized Reads Per Million mapped reads in the negative Control (SRPMC) with bedtools genomeCoverage then converted to BigWig coverage files with ucsctools wigToBigWig
Peaks were called using the csaw package and edgeR. Aligned reads were binned into 150bp windows with a 50bp slide. Bins with a log(2) > 2 above background were retained. Windows were normalized for compositional bias and windows in enriched in Oregon-R_K20me1 relative to Oregon-R_no_primary were calculated using edgeR. Windows within 1kb were merged and windows with log(2)FC > 1 and FDR < 0.05 were called peaks
Assembly: dm6
Supplementary files format and content: H4K20me1.vs.no_primary.peaks.bed bed file containing genomic coordinates of enriched regions in Oregon-R_K20me1 relative to Oregon-R_no_primary (l2fc > 1) using the csaw package and edgeR
Supplementary files format and content: OregonR_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: OregonR_spikeNorm_no_primary_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: HWT_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in HWT. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20A_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20R_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8null_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8null. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8wt_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: Set8rg_spikeNorm_K20me1_allReps_avg.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg. All replicates averaged using deeptools BigWigAverage with a 1bp bin size
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 1
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 2
Supplementary files format and content: OregonR_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R replicate 3
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 1
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 2
Supplementary files format and content: OregonR_spikeNorm_no_primary_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Oregon-R_no_primary replicate 3
Supplementary files format and content: HWT_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in HWT replicate 1
Supplementary files format and content: HWT_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in HWT replicate 2
Supplementary files format and content: K20A_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A replicate 1
Supplementary files format and content: K20A_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20A replicate 2
Supplementary files format and content: K20R_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 1
Supplementary files format and content: K20R_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 2
Supplementary files format and content: K20R_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R replicate 3
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 1
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 2
Supplementary files format and content: HWT_His4rnull_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in HWT, His4rnull replicate 3
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull replicate 1
Supplementary files format and content: K20R_His4rnull_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in H4K20R, His4rnull replicate 2
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 1
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 2
Supplementary files format and content: Set8null_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8null replicate 3
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 1
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 2
Supplementary files format and content: Set8wt_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8wt replicate 3
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep1.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 1
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep2.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 2
Supplementary files format and content: Set8rg_spikeNorm_K20me1_rep3.bw Spike-in normalized H4K20me1 genome coverage file in Set8rg replicate 3
Library strategy: CUT&RUN

tag: Sex

tag: developmental stage

value: yw;;{Set8rg}, Set820

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 224

tag: type of surgery

tag: histology

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: ptnm

value: Yes

value: Partial breast irradiation

value: White

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: GFP-L3mbt_rep1

value: wing disc

value: female

value: 3rd instar wandering

tag: genotype

tag: cut&run antibody


title: WT-Tcm2_3

description:
batch3
counts_BM.txt

value: bone marrow


title: patient 221

value: macrodissected primary breast tumor

tag: subject

value: Lumpectomy

value: IDC

tag: er status

value: Positive

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 220

tag: tissue

tag: type of surgery

value: Mastectomy

tag: histology

value: Negative

tag: pr status

tag: her2 status

tag: pt

tag: pn

value: External beam radiation

value: Alive


title: Set8rg_rep2

tag: Sex

tag: developmental stage

tag: genotype

value: yw;;{Set8rg}, Set820

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: WT-Tcm2_2

description:
batch3
counts_BM.txt

tag: strain

tag: treatment

value: C57 mice


title: Set8rg_rep1


title: patient 219

tag: subject

tag: er status

tag: ptnm

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: Yes

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: Set8wt_rep3

tag: tissue

value: wing disc

tag: Sex

value: female

value: yw;;{Set8wt}, Set820


title: patient 217

value: macrodissected primary breast tumor

tag: type of surgery

tag: histology

tag: pr status

tag: her2 status

tag: pt

tag: pn

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 218

tag: subject

tag: er status

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis


title: patient 214

tag: tissue

value: Lumpectomy

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 215

tag: type of surgery

tag: histology

value: IDC

tag: pr status

tag: her2 status

tag: pt

value: Dead


title: patient 212

tag: subject

value: ILC

value: Positive

tag: pn

value: Partial breast irradiation

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 216

tag: er status

value: Negative

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

value: Alive


title: Set8wt_rep2

tag: tissue

tag: Sex

tag: developmental stage

value: 3rd instar wandering

tag: genotype

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: Set8wt_rep1


title: Tassel, FM-S3, protoplasting, bulk RNA-seq, Replicate1

city: Wuhan

first: liang

last: dong

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

description:
PTFM-S3 Rep1
protoplast_raw_counts.txt

data_processing:
For bulk RNA-seq, the quality of raw sequencing data was controlled using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. For scRNA-seq, the adaptor sequence and the low-quality reads were filtered by fastp with the default parameters.
For bulk RNA-seq, clean data from all samples were mapped to the B73 AGPv4 reference genome using HISAT2 with default parameters. For scRNA-seq, the UMI-based clean data were mapped to the maize genome (B73 RefGen_v4) utilizing STAR mapping with customized parameters to obtain the UMI counts of each sample.
For bulk RNA-seq, we used featureCounts (v.1.6.3) to measure the abundance of RNA with the parameter (-p). “bamCoverage” in deeptools (v3.3.0) were used for bw files.
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files

molecule: polyA RNA

organism: Zea mays

source_name: Tassel FM-S3

growth_protocol: All samples were harvested from maize plants growing in the field

extract_protocol:
For bulk RNA-seq, RNA was extracted  using direct-zol RNA Miniprep (Zymo Research).For scRNA-seq, protoplasts were prepared as previously described (Satterlee et al., 2020). For each replicate, the freshly dissected FM-S2 or FM-S3 tissues from 15-20 ear or tassel were digested in protoplast lysis buffer for 2 hours at room temperature in the dark with gentle shaking. The mixture was then filtered twice through a 30 μm cell strainer (sysmex, 04-0042-2316) and the protoplasts were collected by horizontal centrifugation at 300 g for 3 min at room temperature. The supernatant was gently removed without disturbing the protoplast pellet. Next, the pellet was resuspended and washed two times using protoplast washing buffer (lysis buffer without enzyme) by the same centrifugation condition as before. After washing, the pellet was resuspended into 600 μl washing buffer and then filtered through the 30 μm cell strainer to remove adherent multicellular mass.
Bulk RNA-seq librarys were constructed using NEBNext Ultra Directional RNA Library Prep Kit or MGIEasy RNA Library Prep Kit according to the instructions. scRNA-seq librarys were constructed using BD Rhapsody™ Whole Transcriptome Analysis Amplification Kit.

value: Tassel FM-S3


title: Tassel, FM-S3, protoplasting, bulk RNA-seq, Replicate2

description:
PTFM-S3 Rep2
protoplast_raw_counts.txt


title: WT-Tcm2_1

description:
batch3
counts_BM.txt

tag: strain

value: bone marrow

tag: treatment

value: C57 mice


title: Set8null_rep3

description: Set8null_spikeNorm_K20me1_allReps_avg.bw

value: wing disc

value: female


title: Ear, FM-S3, protoplasting, bulk RNA-seq, Replicate2

description:
PFM-S3 Rep2
protoplast_raw_counts.txt

source_name: Ear FM-S3

value: Ear FM-S3


title: patient 209

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

tag: histology

tag: pr status

tag: her2 status

tag: pt

value: Yes

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: No

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: Ear, FM-S3, protoplasting, bulk RNA-seq, Replicate1

description:
PFM-S3 Rep1
protoplast_raw_counts.txt

tag: tissue


title: patient 210

value: IDC

tag: er status

value: Positive

tag: pn

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: Partial breast irradiation

tag: age at diagnosis

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 211

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: pr status

tag: her2 status

value: Negative

value: Alive


title: patient 207

tag: pt

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 213

tag: tissue

value: Mastectomy

tag: er status

tag: pn

tag: ptnm

tag: time to death or censor from date of diagnosis (years)


title: Set8null_rep2

tag: Sex

tag: developmental stage

value: 3rd instar wandering

tag: genotype

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 208

tag: subject

tag: type of surgery

tag: histology

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: locoregional recurrence

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 205

tag: tissue

tag: er status

tag: pr status

tag: her2 status

tag: pt

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 204

tag: subject

tag: type of surgery

tag: pn

tag: ptnm

tag: time to death or censor from date of diagnosis (years)


title: patient 203

tag: histology

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: locoregional recurrence


title: Ear, TS1, Mutant, bulk RNA-seq, Replicate3

description:
TS1 MU Rep3
TS1_raw_counts.txt

source_name: Ear TS1 Mutant

tag: tissue

value: Ear TS1 Mutant

tag: genotype

value: TS1 loss of funtion in B73


title: patient 201

value: macrodissected primary breast tumor

tag: er status

tag: pr status

tag: her2 status

tag: pt

value: AA

tag: death

tag: bioanalyzer rin (rna integrity number)


title: Set8null_rep1

value: wing disc

tag: Sex

value: female

tag: developmental stage

tag: cut&run antibody


title: Ear, TS1, Mutant, bulk RNA-seq, Replicate2

description:
TS1 MU Rep2
TS1_raw_counts.txt


title: patient 202

tag: subject

tag: type of surgery

tag: pn

tag: ptnm

value: No

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: Yes

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 200

tag: tissue

value: Lumpectomy

tag: histology

value: Other

tag: er status

value: Positive

tag: pr status

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

value: Hispanic, Asian & other

tag: locoregional recurrence


title: patient 199

tag: subject

value: IDC

value: Negative

tag: her2 status

tag: pt

value: External beam radiation

tag: death

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: Ear, TS1, Mutant, bulk RNA-seq, Replicate1

description:
TS1 MU Rep1
TS1_raw_counts.txt

value: Ear TS1 Mutant

tag: genotype


title: HWT_His4rnull_rep3

description: HWT_His4rnull_spikeNorm_K20me1_allReps_avg.bw

tag: Sex

tag: developmental stage

value: 3rd instar wandering

value: deltaHisC; {12xHWT}, His4rnull

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: H4K20R, His4rnull_rep2

description: K20R_His4rnull_spikeNorm_K20me1_allReps_avg.bw

tag: tissue

value: wing disc

value: deltaHisC; {12xK20R}, His4rnull


title: Ear, TS1, WT, bulk RNA-seq, Replicate3

description:
TS1 WT Rep3
TS1_raw_counts.txt

source_name: Ear TS1 WT

value: Ear TS1 WT

value: WT


title: Ear, TS1, WT, bulk RNA-seq, Replicate2

description:
TS1 WT Rep2
TS1_raw_counts.txt


title: HWT_His4rnull_rep2

value: female


title: Ear, TS1, WT, bulk RNA-seq, Replicate1

description:
TS1 WT Rep1
TS1_raw_counts.txt


title: patient 194

value: macrodissected primary breast tumor

tag: type of surgery

value: Mastectomy

tag: histology

tag: pn

tag: ptnm

value: No

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 198

tag: subject

value: IDC

tag: er status

value: Positive

tag: pr status

tag: her2 status

value: Negative

tag: pt

tag: radiotherapy

value: Yes

tag: type of radiotherapy

tag: age at diagnosis

value: AA

tag: locoregional recurrence


title: patient 192

tag: tissue

tag: type of surgery

tag: histology

tag: death

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: patient 195

tag: pn

tag: ptnm

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: patient 196

tag: subject

tag: er status

tag: pr status

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: HWT_His4rnull_rep1

value: wing disc

tag: Sex

tag: developmental stage

value: 3rd instar wandering

tag: genotype

value: deltaHisC; {12xHWT}, His4rnull

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 197

tag: tissue

tag: type of surgery

tag: histology

tag: her2 status

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: locoregional recurrence


title: Ear, SK1, Mutant, bulk RNA-seq, Replicate3

description:
SK1 MU Rep3
SK1_raw_counts.txt

source_name: Ear SK1 Mutant

value: Ear SK1 Mutant

value: SK1 loss of funtion in B73


title: K20R_rep3

value: female

value: deltaHisC; {12xK20R}


title: K20R_rep2


title: K20R_rep1


title: patient 190

value: macrodissected primary breast tumor

tag: subject

value: Mastectomy

tag: er status

tag: pn

tag: ptnm

value: No

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 189

tag: tissue

tag: type of surgery

value: IDC

value: Positive

tag: pr status

value: Negative

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: Ear, SK1, WT, bulk RNA-seq, Replicate2

description:
SK1 WT Rep2
SK1_raw_counts.txt

source_name: Ear SK1 WT

value: Ear SK1 WT

tag: genotype

value: WT


title: Ear, SK1, Mutant, bulk RNA-seq, Replicate2

description:
SK1 MU Rep2
SK1_raw_counts.txt


title: K20A_rep2

value: wing disc

tag: Sex

tag: developmental stage

value: deltaHisC; {12xK20A}

tag: cut&run antibody


title: patient 182

tag: subject

tag: histology

tag: er status

tag: her2 status

tag: pt

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

tag: locoregional recurrence

value: Alive


title: K20A_rep1

tag: tissue

value: 3rd instar wandering

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 186

tag: type of surgery

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis (dichotomized)

tag: race

value: AA

tag: chemotherapy

tag: death

value: Dead

tag: bioanalyzer rin (rna integrity number)


title: patient 183

value: macrodissected primary breast tumor

tag: subject

value: Mastectomy

tag: histology

tag: er status

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 188

tag: her2 status

tag: pt

tag: radiotherapy

value: No

tag: type of radiotherapy

tag: age at diagnosis

value: Hispanic, Asian & other


title: Ear, SK1, Mutant, bulk RNA-seq, Replicate1

description:
SK1 MU Rep1
SK1_raw_counts.txt

tag: tissue

value: Ear SK1 Mutant

tag: genotype

value: SK1 loss of funtion in B73


title: patient 180

tag: type of surgery

value: Lumpectomy

value: IDC

value: Negative

tag: pr status

tag: pn

tag: ptnm

value: Partial breast irradiation

tag: age at diagnosis (dichotomized)

value: White

tag: locoregional recurrence


title: patient 184

tag: subject

tag: histology

value: Positive

tag: race

tag: chemotherapy

tag: death

tag: bioanalyzer rin (rna integrity number)


title: HWT_rep2

value: wing disc

tag: Sex

value: female

tag: developmental stage

value: deltaHisC; {12xHWT}

tag: cut&run antibody


title: patient 185

tag: tissue

tag: er status

tag: her2 status

tag: pt

tag: radiotherapy

value: Yes

tag: type of radiotherapy

value: External beam radiation

tag: age at diagnosis

value: Alive

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 179

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

tag: histology

value: Other

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis (dichotomized)

tag: locoregional recurrence


title: patient 181

tag: tissue

value: Mastectomy

value: No

tag: race

tag: chemotherapy

tag: death

tag: bioanalyzer rin (rna integrity number)


title: Tassel, FM-S3, bulk RNA-seq, Replicate1

description:
TFM-S3 rep1
raw_counts.txt

value: Tassel FM-S3

tag: genotype


title: Ear, SK1, WT, bulk RNA-seq, Replicate1

description:
SK1 WT Rep1
SK1_raw_counts.txt

value: Ear SK1 WT

value: WT


title: HWT_rep1

tag: Sex

tag: developmental stage

value: 3rd instar wandering

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 187

tag: subject

value: IDC

tag: er status

tag: her2 status

value: Negative

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

value: Hispanic, Asian & other

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: Tassel, FM-S3, bulk RNA-seq, Replicate2

description:
TFM-S3 rep2
raw_counts.txt

tag: tissue


title: patient 177

tag: type of surgery

tag: histology

value: Positive

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis (dichotomized)

tag: race

value: White

tag: chemotherapy

tag: locoregional recurrence


title: patient 174

tag: subject

tag: er status

tag: her2 status

value: Yes

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 176

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)


title: patient 175

tag: tissue

tag: type of surgery

value: Lumpectomy

tag: histology

tag: pr status

value: Partial breast irradiation

value: Alive

tag: time to death or censor from date of diagnosis (years)


title: patient 178

value: macrodissected primary breast tumor

value: Mastectomy

tag: pn

tag: ptnm

value: External beam radiation

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy


title: Oregon-R_no_primary_rep3

description:
H4K20me1.vs.no_primary.peaks.bed
OregonR_spikeNorm_no_primary_allReps_avg.bw

value: wing disc

tag: Sex

value: female

tag: developmental stage

tag: genotype

value: Oregon-R

tag: cut&run antibody


title: Ear, FM-S3, bulk RNA-seq, Replicate2

description:
FM-S3 rep2
raw_counts.txt

value: Ear FM-S3


title: patient 173

tag: subject

value: IDC

tag: er status

tag: her2 status

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: locoregional recurrence

value: No

tag: death

tag: bioanalyzer rin (rna integrity number)


title: Ear, FM-S3, bulk RNA-seq, Replicate1

description:
FM-S3 rep1
raw_counts.txt

tag: tissue


title: patient 172

tag: type of surgery

tag: histology

tag: pr status

value: Negative

tag: pn

tag: ptnm

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: Oregon-R_no_primary_rep2

tag: Sex

tag: developmental stage

value: 3rd instar wandering

tag: genotype

tag: cut&run antibody


title: Oregon-R_rep3

description:
H4K20me1.vs.no_primary.peaks.bed
OregonR_spikeNorm_K20me1_allReps_avg.bw

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: Tassel, FM-S2, bulk RNA-seq, Replicate1

description:
TFM-S2 rep1
raw_counts.txt

source_name: Tassel FM-S2

value: Tassel FM-S2


title: Ear, FM-S2, bulk RNA-seq, Replicate2

description:
FM-S2 rep2
raw_counts.txt

source_name: Ear FM-S2

value: Ear FM-S2


title: Oregon-R_rep2


title: Oregon-R_no_primary_rep1


title: Ear, FM-S2, bulk RNA-seq, Replicate1

description:
FM-S2 rep1
raw_counts.txt


title: patient 170

tag: subject

value: Other

tag: er status

value: Positive

tag: her2 status

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: race

value: White

tag: chemotherapy

value: Yes

tag: locoregional recurrence


title: Oregon-R_rep1

tag: tissue


title: patient 171

value: macrodissected primary breast tumor

tag: type of surgery

value: Lumpectomy

tag: histology

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: Tassel, FM-S1, bulk RNA-seq, Replicate3

description:
TFM-S1 rep3
raw_counts.txt

source_name: Tassel FM-S1

value: Tassel FM-S1

tag: genotype


title: Tassel, FM-S1, bulk RNA-seq, Replicate2

description:
TFM-S1 rep2
raw_counts.txt


title: patient 168

tag: subject

tag: er status

tag: her2 status

tag: pt

value: External beam radiation

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 167

tag: tissue

value: Mastectomy

tag: radiotherapy

tag: type of radiotherapy

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 164

tag: type of surgery

tag: histology

value: IDC

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis


title: patient 193

tag: subject

tag: er status

tag: age at diagnosis (dichotomized)

value: No

tag: death

tag: bioanalyzer rin (rna integrity number)


title: patient 206

tag: tissue

value: Negative

tag: her2 status

tag: pt

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 169

tag: radiotherapy

tag: type of radiotherapy

tag: race

tag: chemotherapy

tag: locoregional recurrence

value: Dead


title: DND41PHF6i_PHF6ActiveMotif61807_NA

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

data_processing:
trim_galore v0.6.3 remove adapter sequences
align quality reads using bwa mem v0.7.17 to a hybrid reference genome
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names
samtools -F 1804 -q 1 to define quality reads
fragments <2kb were isolated (awk) and normalized to 10M fragments using bedtools genomecov
peaks were called using MACS2 -f BEDPE and --keep-dup all
Assembly: GRCh37 & Escherichica coli genome r46 (Ensembl r46 ASM584v2)
Supplementary files format and content: normalized coverage bigwig files and peak calls in the narrowPeak format for the DOX treated sample
Library strategy: CUT&RUN

extract_protocol:
CUTANA kit
KAPA Hyperprep Library kit

treatment_protocol: Doxycycline treatment for induction of PHF6

tag: cell line

tag: cell type

value: T-ALL

tag: genotype

tag: treatment


title: DND41PHF6i_PHF6ActiveMotif61807_DOX

value: DOX


title: patient 163

tag: subject

tag: type of surgery

tag: histology

value: ILC

tag: er status

tag: pr status

tag: pn

tag: ptnm

tag: age at diagnosis

tag: age at diagnosis (dichotomized)


title: patient 166

tag: tissue

tag: her2 status

tag: pt

tag: radiotherapy

tag: type of radiotherapy

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: DND41PHF6i_IgG_DOX

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: patient 160

tag: subject

tag: type of surgery

tag: histology

tag: er status

tag: pr status

tag: pn

tag: race

tag: chemotherapy

tag: locoregional recurrence


title: patient 165

tag: tissue

tag: her2 status

tag: pt

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death


title: patient 161

tag: subject

tag: type of surgery

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Tassel, SM, bulk RNA-seq, Replicate3

description:
TSM rep3
raw_counts.txt

source_name: Tassel SM

value: Tassel SM

tag: genotype


title: DND41PHF6i_IgG_NA

tag: cell line

tag: cell type

tag: treatment


title: patient 158

tag: tissue

tag: histology

tag: er status

tag: pr status

tag: her2 status

tag: pn

tag: race

value: AA

tag: chemotherapy

tag: locoregional recurrence


title: Tassel, FM-S1, bulk RNA-seq, Replicate1

description:
TFM-S1 rep1
raw_counts.txt


title: patient 162

tag: subject

tag: type of surgery

tag: pt

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

value: White

tag: death


title: patient 156

tag: tissue

tag: histology

value: Yes

value: Unknown

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Tassel, SM, bulk RNA-seq, Replicate2

description:
TSM rep2
raw_counts.txt

tag: genotype


title: patient 155

value: macrodissected primary breast tumor

tag: er status

value: Positive

tag: pr status

tag: her2 status

tag: pn

tag: race

tag: chemotherapy


title: patient 159

tag: subject

tag: type of surgery

value: Lumpectomy

tag: pt

tag: ptnm

tag: radiotherapy

tag: locoregional recurrence

value: Alive


title: patient 154

tag: tissue

value: Mastectomy

tag: histology

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death


title: patient 191

value: IDC

tag: er status

tag: pr status

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: patient 152

tag: subject

tag: her2 status

tag: pn

value: External beam radiation

tag: race

tag: chemotherapy

value: No


title: patient 157

tag: type of surgery

value: Negative

tag: pt

tag: ptnm

tag: radiotherapy

tag: locoregional recurrence


title: Tassel, SM, bulk RNA-seq, Replicate1

description:
TSM rep1
raw_counts.txt

tag: tissue

tag: genotype


title: SPNORM8M-3093357_G401shPHF6_input_NA_1_PM

description: Input control for shPHF6

data_processing:
trim_galore v0.6.3 remove adapter sequences
align quality reads using bwa mem v0.7.17 to a hybrid reference genome
bamsormadup v2.0.87
samtools used to split bam file for hg19 and dm6 reads base on chromosome names
samtools -F 1024 -q 1 to define quality reads
estimate fragment size using spp R package
slopBed -r fragment size estimation determined by spp
Normalized using dm6 spike in scaling factor normalized to 8M reads
Assembly: hg19+dm6 (Gencode GRCh37 and Ensembl r97)
Supplementary files format and content: normalized coverage in the bigwig file format, macs2 narrow peaks

extract_protocol:
G401 cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum and 1% Glutamax (Gibco) at 37°C and 5% CO2.
In brief, cells were cross-linked directly on the plate using 1% paraformaldehyde for 10 min at room temperature and quenched with glycine. Nuclei were isolated using the Covaris TruCHIP kit and Chromatin extracts were sonicated for 8 min using a Covaris E220 focused ultrasonicator at a peak power of 140, a duty factor of 5 and 200 cycles per burst. Chromatin immunoprecipitation was carried overnight with antibodies bound to dynabeads. Chromatin was de-crosslinked, digested with RNase and Proteinase K and DNA was purified using a Qiagen DNA kit. For MNase ChIP, CST kit guidelines were followed. KAPA HyperPrep Kit (Kapa Biosystems, Cat# 7962363001).

treatment_protocol: G401 cells were infected with either control (shCTRL) or PHF6 (shPHF6) targeting shRNAs. 48hrs post infection, cells were selected with 1ug/mL puromycin for 72h and subsequently harvested.

tag: cell type

tag: shRNA


title: SPNORM8M-3093356_G401shctrl_input_NA_1_PM

description: Input control for shCTRL

value: shCTRL


title: patient 153

tag: histology

tag: er status

tag: pr status

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)


title: Tassel, SPM, bulk RNA-seq, Replicate3

description:
TSPM rep3
raw_counts.txt

source_name: Tassel SPM

value: Tassel SPM


title: Tassel, SPM, bulk RNA-seq, Replicate2

description:
TSPM rep2
raw_counts.txt


title: SPNORM8M-3093355_G401shPHF6_PHF6ActiveMotif61807_NA_3_PM

description: ChIP-Seq of PHF6 in shPHF6 rep3


title: SPNORM8M-3093354_G401shPHF6_PHF6ActiveMotif61807_NA_2_PM

description: ChIP-Seq of PHF6 in shPHF6 rep2


title: Tassel, SPM, bulk RNA-seq, Replicate1

description:
TSPM rep1
raw_counts.txt


title: Tassel, FM-S2, bulk RNA-seq, Replicate2

description:
TFM-S2 rep2
raw_counts.txt

value: Tassel FM-S2


title: SPNORM8M-3093353_G401shPHF6_PHF6ActiveMotif61807_NA_1_PM

description: ChIP-Seq of PHF6 in shPHF6 rep1


title: patient 151

tag: subject

tag: type of surgery

value: Other

tag: her2 status

tag: pn

tag: race

tag: chemotherapy

tag: time to death or censor from date of diagnosis (years)

tag: bioanalyzer rin (rna integrity number)


title: Tassel, IM, bulk RNA-seq, Replicate3

description:
TIM rep3
raw_counts.txt

source_name: Tassel IM

tag: tissue

value: Tassel IM

tag: genotype


title: SPNORM8M-3093352_G401shCTRL_PHF6ActiveMotif61807_NA_3_PM

description: ChIP-Seq of PHF6 in shCTRL rep3

tag: cell type

tag: shRNA


title: patient 149

tag: histology

value: ILC

tag: er status

tag: pr status

tag: pt

tag: ptnm

tag: radiotherapy

tag: type of radiotherapy

value: White

tag: locoregional recurrence


title: H4K20R, His4rnull_rep1

value: wing disc

tag: Sex

value: female

tag: developmental stage

value: 3rd instar wandering

value: deltaHisC; {12xK20R}, His4rnull

tag: cut&run antibody

value: anti-H4K20me1 (ThermoFisher MA5-18067)


title: patient 147

value: macrodissected primary breast tumor

tag: subject

tag: type of surgery

value: Lumpectomy

value: Positive

tag: her2 status

tag: pn

value: Yes

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

tag: chemotherapy

tag: death

value: Dead

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 148

tag: tissue

tag: histology

value: IDC

tag: er status

tag: pr status

value: Negative

tag: pt

tag: ptnm

tag: radiotherapy

value: External beam radiation

value: No

value: Alive

tag: bioanalyzer rin (rna integrity number)


title: patient 145

tag: subject

tag: type of surgery

value: Mastectomy

value: ILC

tag: her2 status

tag: type of radiotherapy

tag: locoregional recurrence


title: patient 146

tag: pn

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: race

value: AA

tag: chemotherapy


title: Tassel, IM, bulk RNA-seq, Replicate2

description:
TIM rep2
raw_counts.txt

tag: tissue

value: Tassel IM

tag: genotype


title: patient 150

tag: histology

tag: er status

tag: pr status

value: White

tag: death

tag: time to locoregional recurrence from date of diagnosis (years)

tag: time to death or censor from date of diagnosis (years)


title: patient 144

tag: subject

tag: type of surgery

tag: pt

tag: ptnm

tag: radiotherapy

tag: bioanalyzer rin (rna integrity number)


title: patient 143

tag: her2 status

tag: pn

tag: type of radiotherapy

tag: age at diagnosis

tag: age at diagnosis (dichotomized)

tag: locoregional recurrence


title: Tassel, IM, bulk RNA-seq, Replicate1

description:
TIM rep1
raw_counts.txt

tag: tissue

tag: genotype


title: patient 141

tag: histology

tag: er status

tag: pr status

tag: race

tag: chemotherapy

tag: death


title: SPNORM8M-3093350_G401shCTRL_PHF6ActiveMotif61807_NA_1_PM

description: ChIP-Seq of PHF6 in shCTRL rep1

tag: cell type

tag: shRNA

value: shCTRL


title: D1 Tonsil Protein

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

description:
D1_TNSL_Protein
D1TNSL_aligned_fiducials.jpg
D1TNSL_detected_tissue_image.jpg
D1TNSL_features.tsv.gz
D1TNSL_matrix.mtx.gz
D1TNSL_tissue_hires_image.png
D1TNSL_tissue_lowres_image.png
D1TNSL_tissue_positions.csv

library_source: other

data_processing:
*library strategy: spatial multi-omics
FASTQs were processed using 10X SpaceRanger v2.1.0
We filtered genes with minimum 10 cells within a spot
In the transcriptomics data, the gene expression counts are log-transformed, normalized by library size and scaling is performed using SCANPY package.
The top 3,000 highly variable genes (HVGs) are selected as input of PCA for dimension reduction.
In the protein data, the first k (number of proteins) principal components are retained and used as the input of the model.
The protein expresssion counts are normalized using CLR (Centered Log Ratio) and then scaling is performed using SCANPY package.
All principal components after PCA dimension reduction are used as the input of the model.
Assembly: GrCh38-2020-A
Supplementary files format and content: Each .h5ad file is a single-sample AnnData object
Supplementary files format and content: the SpaceRanger output files for each sample: isotype normalization factors for protein, aligned fiducials, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the features and matrix matrices from the filtered_feature_bc_matrix output folder

molecule: protein

source_name: Tonsil

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene and Protein Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking (CG000658, Rev A, 10x Genomics) protocol
Libraries were constructed according to the user guide for Visium CytAssist Spatial Gene and Protein Expression Reagent Kits (CG000494; Rev B; 10x Genomics).

value: Tonsil


title: Sin3a KO Treg, male, biol rep 3

city: Philadelphia

first: Lanette

middle: M

last: Christensen

state: PA

address: 3615 Civic Center Blvd.

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Hisat2 v2.0.5 and featureCounts v1.5.0-p3
Sequence reads were trimmed for adaptor sequence, reads containing N>10%, and reads in which more than 50% of the bases had a Qscore≤5.
Trimmed reads were aligned to the GRCm38/mm10 reference genome using Hisat2 v2.0.5.
Read counts and normalizations were performed using featureCounts v1.5.0-p3.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file containing gene counts for each sample
Supplementary files format and content: tab-delimited text file containing gene FPKM values for each sample

source_name: Secondary Lymphoid Organs

extract_protocol:
RNA was isolated from ex vivo CD25+FoxP3+ T-regulatory cells using standard TRIzol/chloroform extraction followed by the Zymo Research RNA Clean and Concentrator Kit. 0.35µg RNA was used for construction of each library.
RNA libraries were prepared by performing polyA enrichment using magnetic bead-linked polyT oligos followed by fragmentation and cDNA synthesis.

treatment_protocol: T-regulatory cells were collected from dissociated secondary lymphiod organs (spleens and lymph nodes). Following dissociation and red blood cell lysis, cells were enriched for CD4+CD25+ using magnetic bead isolation (Miltenyi) then purified by FACS sorting for CD25+FoxP3+ (FACSJazz).

value: Secondary Lymphoid Organs

value: CD25+FoxP3+ T-regulatory cells

tag: Sex

value: Male