title: HIV Positive with Cervical intraepithelial neoplasia [JCIN055]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN051]

status: Public on Nov 01 2024

type: genomic

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

country: USA

institute: Northwestern University

hyb_protocol: Bisulphite converted DNA was samplified, fragmented and hybridized to human infinium MethylationEPIC BeadChip (illumina) using standard illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing: ENmix package in R environment (v4.4.0)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: cervical tissue

label_protocol: Standard illumina Protocol

extract_protocol: DNA extraction was carried out on cervical tissue biopsies using QIAGEN QIAamp DNA Mini Kit

tag: participant id

tag: Sex

value: Female

tag: cancer stage

tag: colposcopy based dysplasia grade

tag: group

tag: tissue

value: cervical tissue

tag: hpv genotype

tag: age

tag: bmi

tag: site

value: JUTH


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN054]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN053]

value: CIN 2


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN082]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN059]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN062]

value: CIN 3


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN072]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN070]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN056]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN057]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN046]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN050]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN049]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN041]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN042]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN037]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN036]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN035]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN032]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN048]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN043]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN040]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN028]

value: CIN 1


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN039]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN027]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN033]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN026]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN058]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN024]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN030]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN031]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN029]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN014]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN015]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN013]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN012]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN025]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN011]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN010]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN023]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN022]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN021]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN047]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN008]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN017]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN018]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN020]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN006]


title: HIV negative Cervical Cancer from tumor tissue [JCACX138]

value: III


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN001]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX138]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN009]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN016]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN019]


title: HIV negative Cervical Cancer [JCACX134]

description: HIV negative Cervical Cancer


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN005]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN002]


title: HIV negative Cervical Cancer [JCACX139]

description: HIV negative Cervical Cancer

value: II


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN004]


title: HIV Positive Cervical Cancer [JCACX137]

description: HIV Positive Cervical Cancer


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN003]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX129]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX129]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX121]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX123]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX123]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX125]


title: HIV negative Cervical Cancer from tumor tissue [JCACX121]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX119]


title: HIV negative Cervical Cancer from tumor tissue [JCACX120]


title: HIV Positive with Cervical intraepithelial neoplasia [JCIN007]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX122]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX120]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX119]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX118]

value: I


title: HIV negative Cervical Cancer from tumor tissue [JCACX118]


title: HIV negative Cervical Cancer from tumor tissue [JCACX114]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX115]


title: HIV negative Cervical Cancer from tumor tissue [JCACX115]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX114]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX125]


title: HIV negative Cervical Cancer [JCACX113]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer from tumor tissue [JCACX122]


title: HIV Positive Cervical Cancer [JCACX128]

description: HIV Positive Cervical Cancer


title: HIV Positive Cervical Cancer from tumor tissue [JCACX112]


title: HIV negative Cervical Cancer from tumor tissue [JCACX110]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX112]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX107]


title: HIV negative Cervical Cancer from tumor tissue [JCACX111]


title: HIV negative Cervical Cancer from tumor tissue [JCACX105]


title: HIV negative Cervical Cancer from tumor tissue [JCACX107]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX116]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX111]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX106]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX103]


title: HIV negative Cervical Cancer from tumor tissue [JCACX109]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX109]


title: HIV negative Cervical Cancer [JCACX108]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from tumor tissue [JCACX106]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX105]


title: HIV negative Cervical Cancer from tumor tissue [JCACX116]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX101]


title: HIV negative Cervical Cancer from tumor tissue [JCACX104]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX103]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX104]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX102]


title: HIV negative Cervical Cancer from tumor tissue [JCACX099]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX099]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX098]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX110]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX100]


title: HIV negative Cervical Cancer from tumor tissue [JCACX100]


title: HIV negative Cervical Cancer from tumor tissue [JCACX095]

value: IV


title: HIV negative Cervical Cancer from tumor tissue [JCACX098]


title: HIV negative Cervical Cancer from tumor tissue [JCACX096]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX096]


title: HIV negative Cervical Cancer from tumor tissue [JCACX094]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX091]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX093]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX093]


title: HIV negative Cervical Cancer from tumor tissue [JCACX102]


title: HIV negative Cervical Cancer [JCACX092]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from tumor tissue [JCACX101]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX088]


title: HIV Positive Cervical Cancer [JCACX086]

description: HIV Positive Cervical Cancer


title: HIV Positive Cervical Cancer from tumor tissue [JCACX091]


title: HIV Positive Cervical Cancer [JCACX085]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from tumor tissue [JCACX088]


title: HIV negative Cervical Cancer from tumor tissue [JCACX090]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX090]


title: HIV negative Cervical Cancer from tumor tissue [JCACX083]


title: HIV negative Cervical Cancer from tumor tissue [JCACX084]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX084]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX083]


title: HIV negative Cervical Cancer [JCACX082]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX081]


title: HIV negative Cervical Cancer from tumor tissue [JCACX081]


title: HIV negative Cervical Cancer [JCACX097]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX095]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX094]


title: HIV negative Cervical Cancer from tumor tissue [JCACX080]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX080]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX079]


title: HIV negative Cervical Cancer from tumor tissue [JCACX077]


title: HIV Positive Cervical Cancer [JCACX078]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX077]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX076]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX076]


title: HIV negative Cervical Cancer from tumor tissue [JCACX075]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX075]


title: HIV negative Cervical Cancer from tumor tissue [JCACX074]


title: HIV negative Cervical Cancer [JCACX073]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX072]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX071]


title: HIV negative Cervical Cancer from tumor tissue [JCACX071]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX074]


title: HIV negative Cervical Cancer from tumor tissue [JCACX070]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX069]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX069]


title: HIV Positive Cervical Cancer [JCACX067]

description: HIV Positive Cervical Cancer


title: HIV Positive Cervical Cancer from tumor tissue [JCACX068]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX066]


title: HIV negative Cervical Cancer from tumor tissue [JCACX065]


title: HIV negative Cervical Cancer from tumor tissue [JCACX079]


title: HIV negative Cervical Cancer from tumor tissue [JCACX066]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX065]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX064]


title: HIV negative Cervical Cancer from tumor tissue [JCACX064]


title: HIV negative Cervical Cancer from tumor tissue [JCACX063]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX068]


title: HIV Positive Cervical Cancer [JCACX062]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX061]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX063]


title: HIV negative Cervical Cancer from tumor tissue [JCACX061]


title: HIV negative Cervical Cancer [JCACX059]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from tumor tissue [JCACX058]


title: HIV negative Cervical Cancer from tumor tissue [JCACX072]


title: HIV negative Cervical Cancer from tumor tissue [JCACX060]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX060]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX070]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX058]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX057]


title: HIV negative Cervical Cancer from tumor tissue [JCACX057]


title: HIV Positive Cervical Cancer [JCACX055]

description: HIV Positive Cervical Cancer


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX054]


title: HIV negative Cervical Cancer from tumor tissue [JCACX053]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX053]


title: HIV negative Cervical Cancer from tumor tissue [JCACX051]


title: HIV negative Cervical Cancer from tumor tissue [JCACX052]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX051]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX052]


title: HIV negative Cervical Cancer [JCACX048]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX047]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX046]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX044]


title: HIV negative Cervical Cancer from tumor tissue [JCACX044]


title: HIV negative Cervical Cancer [JCACX045]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer from tumor tissue [JCACX043]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX041]


title: HIV negative Cervical Cancer from tumor tissue [JCACX041]


title: HIV Positive Cervical Cancer [JCACX039]

description: HIV Positive Cervical Cancer


title: HIV Positive Cervical Cancer [JCACX056]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX036]


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX038]


title: HIV Positive Cervical Cancer from tumor tissue [JCACX038]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX035]


title: HIV negative Cervical Cancer from tumor tissue [JCACX036]


title: HIV negative Cervical Cancer from tumor tissue [JCACX035]


title: HIV negative Cervical Cancer from tumor tissue [JCACX033]


title: HIV negative Cervical Cancer [JCACX034]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer [JCACX032]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX033]


title: HIV negative Cervical Cancer from tumor tissue [JCACX031]


title: HIV negative Cervical Cancer from tumor tissue [JCACX029]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX031]


title: HIV Positive Cervical Cancer [JCACX028]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX029]


title: HIV negative Cervical Cancer from adjacent normal tissue [JCACX043]


title: HIV negative Cervical Cancer [JCACX026]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX027]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX042]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX025]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer [JCACX020]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer [JCACX021]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer [JCACX037]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer [JCACX023]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX024]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX019]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX022]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX018]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer from adjacent normal tissue [JCACX017]


title: HIV negative Cervical Cancer [JCACX012]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX013]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer [JCACX010]

description: HIV Positive Cervical Cancer


title: HIV negative Cervical Cancer [JCACX007]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX015]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX005]

description: HIV negative Cervical Cancer


title: HIV negative Cervical Cancer [JCACX001]

description: HIV negative Cervical Cancer


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with PBS control 4

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 5850 College St

department: Pathology

country: Canada

institute: Dalhousie University

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_NT_7

hyb_protocol: Purified genomic DNA samples to The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children (Toronto, ON, Canada). TCAG performed bisulfite conversion, hybridization, background subtraction, and normalization analysis.

scan_protocol: standard protocol

data_processing: Average Beta

label: Cy5 and Cy3

source_name: shRNA 1, PBS, 4

label_protocol: standard protocol

growth_protocol: MDA-MB-231 cells with control shRNA or MTHFD2 shRNA were expanded in DMEM supplemented with 10% FBS and 0.25 ug/mL puromycin. Two million cells were implanted into 8-9 week old NOD-SCID mice and tumours grew until humane endpoint (38 days).

extract_protocol: Genomic DNA was extracted using the PureLink Genomic DNA kit (Invitrogen).

treatment_protocol: Mice were treated with intraperitoneal injections of PBS control or 0.5mg/kg decitabine (based upon 25g mouse) in a 5 days on - 2 days off - 3 days on - 5 days off as used in patient treatment protocols.

tag: cancer type

value: breast

tag: subtype

value: triple-negative breast cancer

tag: cell line


title: HIV negative Cervical Cancer [JCACX016]

description: HIV negative Cervical Cancer


title: HIV Positive Cervical Cancer from tumor tissue [JCACX017]


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with PBS control 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_NT_11

source_name: shRNA 1, PBS, 1


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with PBS control 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_NT_2

source_name: shRNA 1, PBS, 2


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with decitabine 4

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_DAC_9

source_name: shRNA 1, decitabine, 4


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with decitabine 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_DAC_1

source_name: shRNA 1, decitabine, 1


title: HIV Positive Cervical Cancer from tumor tissue [JCACX054]


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with PBS control 4

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_NT_7

source_name: shRNA 2, PBS, 4


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with PBS control 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_NT_6

source_name: shRNA 1, PBS, 3


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with decitabine 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_DAC_4

source_name: shRNA 1, decitabine, 2


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 1 and treated with decitabine 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH68_DAC_11

source_name: shRNA 1, decitabine, 3


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with PBS control 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_NT_8

source_name: control shRNA, PBS, 3


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with decitabine 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_DAC_3

source_name: shRNA 2, decitabine, 3


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with decitabine 4

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_DAC_8

source_name: shRNA 2, decitabine, 4


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with decitabine 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_DAC_2

source_name: shRNA 2, decitabine, 2


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with PBS control 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_NT_1

source_name: shRNA 2, PBS, 1


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with PBS control 4

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_NT_9

source_name: control shRNA, PBS, 4


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with PBS control 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_NT_5

source_name: control shRNA, PBS, 2


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with PBS control 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_NT_2

source_name: control shRNA, PBS, 1


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with PBS control 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_NT_5

source_name: shRNA 2, PBS, 3


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with decitabine 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_DAC_10

source_name: shRNA 2, decitabine, 1


title: genomic DNA from MDA-MB-231 tumour with MTHFD2 shRNA 2 and treated with PBS control 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
MTH66_NT_3

source_name: shRNA 2, PBS, 2


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with decitabine 4

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_DAC_8

source_name: control shRNA, decitabine, 4


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with decitabine 3

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_DAC_6

source_name: control shRNA, decitabine, 3


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with decitabine 2

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_DAC_5

source_name: control shRNA, decitabine, 2


title: genomic DNA from MDA-MB-231 tumour with scramble control shRNA and treated with decitabine 1

description:
MDA-MB-231 tumor with or without MTHFD2 knockdown and/or decitabine treatment
GIPZ_DAC_2

source_name: control shRNA, decitabine, 1


title: Nalm6_H3K27ME3_R1

type: SRA

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
H3K27ME3_broadPeak.tar.gz
Nalm6_H3K27me3_pooled_FE.bw

library_source: genomic

data_processing:
Sequencing base calls were generated on the HiSeq 1500 instrument in the Advanced Genome Technologies Core Massively Parallel Sequencing Facility.
Fastq conversion and demultiplexing were done using bcl2fastq (Illumina, v1.8.4)
Adapters were cut by cutadapt (v1.11) and reads were trimmed for quality by FASTQ Trimmer (Galaxy utility)
Enriched regions (narrowPeak for H3K4me3 and broadPeak for H3K27me3) for each replicate were generated using MACS2 (Feng, et al.  Nat Protoc  2012) with a q-vale of 10e-5.
MACS2 bdgcmp FE -m FE was using to compare pooled treatment to input bedgraphs and then bedgraphs were converted to bigwig (UCSC bedGraphToBigWig)
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeaks - areas of enrichment; broadPeaks - broad areas of enrichment ; bigwigs - tracks of fold-enrichment of pooled pulldown over input samples

source_name: ATCC Cell Line

growth_protocol: Nalm6 and U937 cells were maintained in RPMI-1640 (Gibco), supplemented with 10% fetal bovine serum (FCS) (Peak Serum), 1% penicillin/streptomycin (Gibco), and 1% L-glutamine (Calsson Labs) in humidified air, at 37oC, with 5% CO2.

extract_protocol:
Nuclei extraction was performed using a protocol modified from Schjerven, et al (Schjerven, et al.  Nat Immunol.  2013). Isolated nuclei were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin with an average peak size of 500 bp.  A total of 10 ug of sheared chromatin was used for ChIP immunoprecipitation with 4 ug of H3K27me3 (Abcam, ab6002, lot GR218433-2 ) or 4 ug of H3K4me3 (Abcam, ab8580, lot GR273043-4 ) used at a ratio of 2.5:1 chromatin to antibody and incubated at 4°C overnight.  Immunoprecipitated complexes were isolated using magnetic protein A/G beads (Pierce, Ref# 88803, Lot TH272704A).  DNA fragments were isolated by uncross-linking the protein-DNA complex overnight at 67°C. The DNA was purified with a PCR Purification kit (Qiagen) and quantified using a Qubit fluorimeter (Life Technologies) prior to the library preparation.
Libraries were prepared using the NEBNext ChIPSeq Library Prep (New England Biolabs) for Illumina, and manufacturer’s instructions were followed. Libraries were sequenced at the Vermont Integrative Genomics Resource core facility, using the Illumina HiSeq2000, and 50bp single end sequencing reads were generated.

treatment_protocol: No prior treatment

tag: antibody

tag: cell type

value: Pre-B lymphoblast

tag: neoplasia type

value: acute lymphoblastic leukemia

tag: atcc id

value: ATCC CRL-3273


title: U937_H3K27ME3_R1

description:
H3K27ME3_broadPeak.tar.gz
U937_H3K27me3_pooled_FE.bw

value: myeloblast

value: histiocytic lymphoma

value: ATCC CRL-1593.2


title: U937_input_R1

value: input


title: CAPAN1, H3K27ac, input

city: Göttingen

first: Shiv

middle: K.

last: Singh

address: Robert-Koch-Straße 40

department: Gastroenterology, GI-Oncology and Endocrinology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Quality control using FastQC.
Alignment to hg38 using bowtie2.
Filtering of not properly aligned, low quality reads
Duplicate removal using PICARD
Peak calling using MACS2 callpeak with standard parameters.
Assembly: hg38
Supplementary files format and content: Peak file

source_name: cell line

extract_protocol:
Cells were fixed in 1% PFA in PBS for 20 min, after quencing and lysis, chromatin was sonicated on a Bioruptor Pico (Diagenode).
Libraries were constructed using Kapa Hyper Prep (KR0961) and double size-selected upon library preparation (Nucleomags, Macherey-Nagel), then multiplexed in 10 nM EB buffer.

value: cell line

tag: treatment

value: siCtrl/siJUNB


title: Nalm6_input_R1


title: Nalm6_H3K27ME3_R2


title: U937_H3K4ME3_R1

description:
H3K4ME3_narrowPeak.tar.gz
U937_H3K4me3_pooled_FE.bw


title: U937_H3K27ME3_R2


title: Nalm6_H3K4ME3_R1

description:
H3K4ME3_narrowPeak.tar.gz
Nalm6_H3K4me3_pooled_FE.bw


title: U937_H3K4ME3_R2


title: CAPAN1, siCtrl, H3K27ac, 2

value: siCtrl


title: CAPAN1, siJUNB, H3K27ac, 2

value: siJUNB


title: CAPAN1, siJUNB, H3K27ac, 1


title: Nalm6_H3K4ME3_R2


title: CAPAN1, HDAC1, input


title: CAPAN1, siCtrl, HDAC1, 1


title: CAPAN1, siJUNB, HDAC1, 3


title: PbSIP2_ChIP_2

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: text, Peak-calling

organism: Plasmodium berghei

source_name: ANKA

growth_protocol: PbSIP2::GFP was cultured for 16 h, and mature schizonts formed in the cultures were harvested by density gradient centrifugation using Iodixanol solution (Optiprep). The schizonts were then injected into mice and subjected to cultures again at 6 h post-injection (hpi). Parasites were then harvested for ChIP experiments at 24 hpi.

extract_protocol:
Parasite cultures were filtered with Plasmodipur to remove lymphocytes. The samples were then fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were lysed in SDS lysis buffer. The lysates were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power. After centrifugation of the sonicated lysates, the supernatants were subjected to immunoprecipitation with anti-GFP antibodies conjugated on Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),

tag: strain

value: ANKA

value: Schizont

tag: genotype


title: RTgill-W1 ctrl rep 12

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description:
cell lysate
e11.e11.ctrl.d06
rtgill.dmso.3.D06

library_source: transcriptomic

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files

molecule: total RNA

organism: Oncorhynchus mykiss

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

value: ctrl


title: PbSIP2_ChIP_1


title: CAPAN1, siJUNB, HDAC1, 1


title: CAPAN1, siCtrl, HDAC1, 2


title: CAPAN1, siCtrl, H3K27ac, 1


title: RTgill-W1 ctrl rep 10

description:
cell lysate
e11.e11.ctrl.b06
rtgill.dmso.3.B06


title: PbSIP2_input

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: text, Peak-calling
Library strategy: DIP-seq

extract_protocol:
Recombinant AP2 domains fused with MBP  was incubated with P. berghei ANKA genomic DNA fragments in binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol) for 30 min. The protein/DNA solution was further mixed with amylose resin and incubated for 30 min. After incubation, the resin was washed three times with binding/washing buffer, and bound protein-DNA complexes were eluted with 10 mM maltose solution.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),


title: PbSIP2_DIP


title: RTgill-W1 ctrl rep 11

description:
cell lysate
e11.e11.ctrl.c06
rtgill.dmso.3.C06


title: RTgill-W1 ctrl rep 9

description:
cell lysate
e11.e11.ctrl.a06
rtgill.dmso.3.A06


title: RTgill-W1 ctrl rep 8

description:
cell lysate
e7.e7.ctrl.d05
rtgill.dmso.2.D05


title: RTgill-W1 ctrl rep 7

description:
cell lysate
e7.e7.ctrl.c05
rtgill.dmso.2.C05


title: RTgill-W1 ctrl rep 4

description:
cell lysate
e2.e2.ctrl.d04
rtgill.dmso.1.D04


title: RTgill-W1 ctrl rep 3

description:
cell lysate
e2.e2.ctrl.c04
rtgill.dmso.1.C04


title: RTgill-W1 ctrl rep 5

description:
cell lysate
e7.e7.ctrl.a05
rtgill.dmso.2.A05


title: CAPAN1, siJUNB, HDAC1, 2


title: RTgill-W1 site 74 rep 3 conc4

description:
cell lysate
e10.e10.74.d02
rtgill.74.3.D02


title: RTgill-W1 ctrl rep 6

description:
cell lysate
e7.e7.ctrl.b05
rtgill.dmso.2.B05


title: RTgill-W1 site 74 rep 3 conc7

description:
cell lysate
e10.e10.74.g02
rtgill.74.3.G02


title: RTgill-W1 site 74 rep 3 conc8

description:
cell lysate
e10.e10.74.h02
rtgill.74.3.H02


title: RTgill-W1 site 74 rep 3 conc2

description:
cell lysate
e10.e10.74.b02
rtgill.74.3.B02


title: RTgill-W1 site 74 rep 3 conc5

description:
cell lysate
e10.e10.74.e02
rtgill.74.3.E02


title: RTgill-W1 site 74 rep 2 conc7

description:
cell lysate
e6.e6.74.g02
rtgill.74.2.G02


title: RTgill-W1 site 74 rep 3 conc1

description:
cell lysate
e10.e10.74.a02
rtgill.74.3.A02


title: RTgill-W1 site 74 rep 2 conc8

description:
cell lysate
e6.e6.74.h02
rtgill.74.2.H02


title: RTgill-W1 site 74 rep 2 conc3

description:
cell lysate
e6.e6.74.c02
rtgill.74.2.C02


title: RTgill-W1 site 74 rep 2 conc4

description:
cell lysate
e6.e6.74.d02
rtgill.74.2.D02


title: RTgill-W1 site 74 rep 2 conc1

description:
cell lysate
e6.e6.74.a02
rtgill.74.2.A02


title: RTgill-W1 site 74 rep 1 conc7

description:
cell lysate
e1.e1.74.g02
rtgill.74.1.G02


title: RTgill-W1 site 74 rep 2 conc6

description:
cell lysate
e6.e6.74.f02
rtgill.74.2.F02


title: RTgill-W1 site 74 rep 2 conc5

description:
cell lysate
e6.e6.74.e02
rtgill.74.2.E02


title: RTgill-W1 site 74 rep 2 conc2

description:
cell lysate
e6.e6.74.b02
rtgill.74.2.B02


title: RTgill-W1 site 74 rep 1 conc3

description:
cell lysate
e1.e1.74.c02
rtgill.74.1.C02


title: RTgill-W1 site 74 rep 1 conc4

description:
cell lysate
e1.e1.74.d02
rtgill.74.1.D02


title: RTgill-W1 site 74 rep 1 conc5

description:
cell lysate
e1.e1.74.e02
rtgill.74.1.E02


title: RTgill-W1 ctrl rep 1

description:
cell lysate
e2.e2.ctrl.a04
rtgill.dmso.1.A04


title: RTgill-W1 ctrl rep 2

description:
cell lysate
e2.e2.ctrl.b04
rtgill.dmso.1.B04


title: RTgill-W1 site 74 rep 1 conc2

description:
cell lysate
e1.e1.74.b02
rtgill.74.1.B02


title: RTgill-W1 site 74 rep 3 conc6

description:
cell lysate
e10.e10.74.f02
rtgill.74.3.F02


title: RTgill-W1 site 74 rep 1 conc1

description:
cell lysate
e1.e1.74.a02
rtgill.74.1.A02


title: RTgill-W1 site 74 rep 3 conc3

description:
cell lysate
e10.e10.74.c02
rtgill.74.3.C02


title: RTgill-W1 site 49 rep 3 conc7

description:
cell lysate
e13.e13.49.g12
rtgill.49.3.G12


title: RTgill-W1 site 49 rep 3 conc3

description:
cell lysate
e13.e13.49.c12
rtgill.49.3.C12


title: RTgill-W1 site 49 rep 3 conc6

description:
cell lysate
e13.e13.49.f12
rtgill.49.3.F12


title: RTgill-W1 site 49 rep 3 conc4

description:
cell lysate
e13.e13.49.d12
rtgill.49.3.D12


title: RTgill-W1 site 49 rep 3 conc5

description:
cell lysate
e13.e13.49.e12
rtgill.49.3.E12


title: RTgill-W1 site 49 rep 3 conc1

description:
cell lysate
e13.e13.49.a12
rtgill.49.3.A12


title: RTgill-W1 site 49 rep 3 conc2

description:
cell lysate
e13.e13.49.b12
rtgill.49.3.B12


title: RTgill-W1 site 49 rep 3 conc8

description:
cell lysate
e13.e13.49.h12
rtgill.49.3.H12


title: RTgill-W1 site 49 rep 2 conc8

description:
cell lysate
e9.e9.49.h12
rtgill.49.2.H12


title: RTgill-W1 site 49 rep 2 conc7

description:
cell lysate
e9.e9.49.g12
rtgill.49.2.G12


title: RTgill-W1 site 49 rep 2 conc6

description:
cell lysate
e9.e9.49.f12
rtgill.49.2.F12


title: RTgill-W1 site 49 rep 2 conc5

description:
cell lysate
e9.e9.49.e12
rtgill.49.2.E12


title: RTgill-W1 site 74 rep 1 conc6

description:
cell lysate
e1.e1.74.f02
rtgill.74.1.F02


title: RTgill-W1 site 74 rep 1 conc8

description:
cell lysate
e1.e1.74.h02
rtgill.74.1.H02


title: RTgill-W1 site 49 rep 2 conc4

description:
cell lysate
e9.e9.49.d12
rtgill.49.2.D12


title: RTgill-W1 site 49 rep 1 conc8

description:
cell lysate
e4.e4.49.h12
rtgill.49.1.H12


title: RTgill-W1 site 49 rep 2 conc3

description:
cell lysate
e9.e9.49.c12
rtgill.49.2.C12


title: RTgill-W1 site 49 rep 2 conc2

description:
cell lysate
e9.e9.49.b12
rtgill.49.2.B12


title: RTgill-W1 site 49 rep 1 conc7

description:
cell lysate
e4.e4.49.g12
rtgill.49.1.G12


title: RTgill-W1 site 49 rep 1 conc5

description:
cell lysate
e4.e4.49.e12
rtgill.49.1.E12


title: RTgill-W1 site 49 rep 1 conc4

description:
cell lysate
e4.e4.49.d12
rtgill.49.1.D12


title: RTgill-W1 site 49 rep 1 conc3

description:
cell lysate
e4.e4.49.c12
rtgill.49.1.C12


title: RTgill-W1 site 49 rep 1 conc2

description:
cell lysate
e4.e4.49.b12
rtgill.49.1.B12


title: RTgill-W1 site 48 rep 3 conc8

description:
cell lysate
e10.e10.48.h03
rtgill.48.3.H03


title: RTgill-W1 site 49 rep 1 conc1

description:
cell lysate
e4.e4.49.a12
rtgill.49.1.A12


title: RTgill-W1 site 48 rep 3 conc6

description:
cell lysate
e10.e10.48.f03
rtgill.48.3.F03


title: RTgill-W1 site 48 rep 3 conc7

description:
cell lysate
e10.e10.48.g03
rtgill.48.3.G03


title: RTgill-W1 site 48 rep 3 conc5

description:
cell lysate
e10.e10.48.e03
rtgill.48.3.E03


title: RTgill-W1 site 48 rep 3 conc2

description:
cell lysate
e10.e10.48.b03
rtgill.48.3.B03


title: RTgill-W1 site 48 rep 3 conc1

description:
cell lysate
e10.e10.48.a03
rtgill.48.3.A03


title: RTgill-W1 site 48 rep 3 conc3

description:
cell lysate
e10.e10.48.c03
rtgill.48.3.C03


title: RTgill-W1 site 48 rep 3 conc4

description:
cell lysate
e10.e10.48.d03
rtgill.48.3.D03


title: RTgill-W1 site 48 rep 2 conc8

description:
cell lysate
e6.e6.48.h03
rtgill.48.2.H03


title: RTgill-W1 site 48 rep 2 conc7

description:
cell lysate
e6.e6.48.g03
rtgill.48.2.G03


title: RTgill-W1 site 48 rep 2 conc6

description:
cell lysate
e6.e6.48.f03
rtgill.48.2.F03


title: RTgill-W1 site 49 rep 2 conc1

description:
cell lysate
e9.e9.49.a12
rtgill.49.2.A12


title: RTgill-W1 site 48 rep 2 conc4

description:
cell lysate
e6.e6.48.d03
rtgill.48.2.D03


title: RTgill-W1 site 48 rep 2 conc3

description:
cell lysate
e6.e6.48.c03
rtgill.48.2.C03


title: RTgill-W1 site 48 rep 2 conc2

description:
cell lysate
e6.e6.48.b03
rtgill.48.2.B03


title: RTgill-W1 site 49 rep 1 conc6

description:
cell lysate
e4.e4.49.f12
rtgill.49.1.F12


title: RTgill-W1 site 48 rep 1 conc8

description:
cell lysate
e1.e1.48.h03
rtgill.48.1.H03


title: RTgill-W1 site 48 rep 2 conc1

description:
cell lysate
e6.e6.48.a03
rtgill.48.2.A03


title: RTgill-W1 site 48 rep 2 conc5

description:
cell lysate
e6.e6.48.e03
rtgill.48.2.E03


title: RTgill-W1 site 48 rep 1 conc5

description:
cell lysate
e1.e1.48.e03
rtgill.48.1.E03


title: RTgill-W1 site 48 rep 1 conc6

description:
cell lysate
e1.e1.48.f03
rtgill.48.1.F03


title: RTgill-W1 site 48 rep 1 conc7

description:
cell lysate
e1.e1.48.g03
rtgill.48.1.G03


title: RTgill-W1 site 48 rep 1 conc2

description:
cell lysate
e1.e1.48.b03
rtgill.48.1.B03


title: RTgill-W1 site 48 rep 1 conc3

description:
cell lysate
e1.e1.48.c03
rtgill.48.1.C03


title: RTgill-W1 site 30 rep 3 conc8

description:
cell lysate
e10.e10.30.h01
rtgill.30.3.H01


title: RTgill-W1 site 30 rep 3 conc7

description:
cell lysate
e10.e10.30.g01
rtgill.30.3.G01


title: RTgill-W1 site 30 rep 3 conc6

description:
cell lysate
e10.e10.30.f01
rtgill.30.3.F01


title: RTgill-W1 site 30 rep 3 conc4

description:
cell lysate
e10.e10.30.d01
rtgill.30.3.D01


title: RTgill-W1 site 30 rep 3 conc3

description:
cell lysate
e10.e10.30.c01
rtgill.30.3.C01


title: RTgill-W1 site 30 rep 3 conc2

description:
cell lysate
e10.e10.30.b01
rtgill.30.3.B01


title: RTgill-W1 site 30 rep 2 conc7

description:
cell lysate
e6.e6.30.g01
rtgill.30.2.G01


title: RTgill-W1 site 30 rep 2 conc8

description:
cell lysate
e6.e6.30.h01
rtgill.30.2.H01


title: RTgill-W1 site 30 rep 2 conc5

description:
cell lysate
e6.e6.30.e01
rtgill.30.2.E01


title: RTgill-W1 site 30 rep 3 conc1

description:
cell lysate
e10.e10.30.a01
rtgill.30.3.A01


title: RTgill-W1 site 30 rep 2 conc6

description:
cell lysate
e6.e6.30.f01
rtgill.30.2.F01


title: RTgill-W1 site 48 rep 1 conc4

description:
cell lysate
e1.e1.48.d03
rtgill.48.1.D03


title: RTgill-W1 site 30 rep 2 conc3

description:
cell lysate
e6.e6.30.c01
rtgill.30.2.C01


title: RTgill-W1 site 30 rep 1 conc8

description:
cell lysate
e1.e1.30.h01
rtgill.30.1.H01


title: RTgill-W1 site 30 rep 2 conc2

description:
cell lysate
e6.e6.30.b01
rtgill.30.2.B01


title: RTgill-W1 site 30 rep 2 conc4

description:
cell lysate
e6.e6.30.d01
rtgill.30.2.D01


title: RTgill-W1 site 30 rep 1 conc6

description:
cell lysate
e1.e1.30.f01
rtgill.30.1.F01


title: RTgill-W1 site 30 rep 2 conc1

description:
cell lysate
e6.e6.30.a01
rtgill.30.2.A01


title: RTgill-W1 site 48 rep 1 conc1

description:
cell lysate
e1.e1.48.a03
rtgill.48.1.A03


title: RTgill-W1 site 30 rep 1 conc7

description:
cell lysate
e1.e1.30.g01
rtgill.30.1.G01


title: RTgill-W1 site 30 rep 1 conc1

description:
cell lysate
e1.e1.30.a01
rtgill.30.1.A01


title: RTgill-W1 site 30 rep 1 conc2

description:
cell lysate
e1.e1.30.b01
rtgill.30.1.B01


title: RTgill-W1 site 30 rep 1 conc4

description:
cell lysate
e1.e1.30.d01
rtgill.30.1.D01


title: RTgill-W1 site 30 rep 1 conc5

description:
cell lysate
e1.e1.30.e01
rtgill.30.1.E01


title: RTgill-W1 site 20 rep 3 conc7

description:
cell lysate
e13.e13.20.g11
rtgill.20.3.G11


title: RTgill-W1 site 30 rep 3 conc5

description:
cell lysate
e10.e10.30.e01
rtgill.30.3.E01


title: RTgill-W1 site 20 rep 3 conc6

description:
cell lysate
e13.e13.20.f11
rtgill.20.3.F11


title: RTgill-W1 site 20 rep 3 conc3

description:
cell lysate
e13.e13.20.c11
rtgill.20.3.C11


title: RTgill-W1 site 20 rep 3 conc2

description:
cell lysate
e13.e13.20.b11
rtgill.20.3.B11


title: RTgill-W1 site 20 rep 3 conc1

description:
cell lysate
e13.e13.20.a11
rtgill.20.3.A11


title: RTgill-W1 site 20 rep 2 conc7

description:
cell lysate
e9.e9.20.g11
rtgill.20.2.G11


title: CTS2 miRNA (biol rep2)

city: Guangzhou

first: Haoyu

last: Xie

state: Guangdong

address: 183 Zhongshan avenue west

country: China

institute: The Third Affiliated Hospital of Southern Medical University

data_processing:
The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke (v1.5.0). The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
After filtering, the clean tags were mapped to miRbase with Bowtie2 (v2.2.9). The miRDeep-P2 or miRDeep2 package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers following the protocol from Teemu Kivioja, et al., Nature Methods, 2012. The expression formula is: C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads count for all Sample.

source_name: cartilage

growth_protocol: Human primary chondrocytes were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from cells using TRIzol (Takara). Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).1.1 ug of total RNA was used for the construction of sequencing libraries.
MiRNA libraries were prepared for sequencing using standard Illumina protocols

value: cartilage

value: Primary cell

value: chondrocyte

value: WT

value: cyclic tensile strain loading (20%)


title: RTgill-W1 site 20 rep 2 conc5

description:
cell lysate
e9.e9.20.e11
rtgill.20.2.E11


title: RTgill-W1 site 20 rep 2 conc6

description:
cell lysate
e9.e9.20.f11
rtgill.20.2.F11


title: CTS1 miRNA (biol rep1)


title: RTgill-W1 site 20 rep 3 conc8

description:
cell lysate
e13.e13.20.h11
rtgill.20.3.H11


title: RTgill-W1 site 20 rep 2 conc8

description:
cell lysate
e9.e9.20.h11
rtgill.20.2.H11


title: NC1 miRNA (biol rep1)


title: RTgill-W1 site 20 rep 2 conc3

description:
cell lysate
e9.e9.20.c11
rtgill.20.2.C11


title: RTgill-W1 site 30 rep 1 conc3

description:
cell lysate
e1.e1.30.c01
rtgill.30.1.C01


title: CTS2 mRNA (biol rep2)

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all Sample.

extract_protocol:
Total RNA was isolated from cells using TRIzol (Takara). Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).1.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RTgill-W1 site 20 rep 2 conc1

description:
cell lysate
e9.e9.20.a11
rtgill.20.2.A11


title: RTgill-W1 site 20 rep 3 conc5

description:
cell lysate
e13.e13.20.e11
rtgill.20.3.E11


title: RTgill-W1 site 20 rep 1 conc8

description:
cell lysate
e4.e4.20.h11
rtgill.20.1.H11


title: CTS1 mRNA (biol rep1)


title: RTgill-W1 site 20 rep 1 conc6

description:
cell lysate
e4.e4.20.f11
rtgill.20.1.F11


title: NC2 mRNA (biol rep2)


title: RTgill-W1 site 20 rep 1 conc5

description:
cell lysate
e4.e4.20.e11
rtgill.20.1.E11


title: RTgill-W1 site 20 rep 3 conc4

description:
cell lysate
e13.e13.20.d11
rtgill.20.3.D11


title: Exe_KO_rep4

city: Beijing

first: Yiguo

last: Wang

address: Tsinghua University, Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
The RNA-seq data, consisting of 50-bp single-end reads from the DNBSEQ platform, underwent initial preprocessing, including the removal of adaptor sequences and quality assessment using the FastQC tool (v.0.12.1). Sequencing data were demultiplexed and subjected to primary analysis utilizing SOAPnuke (v.1.5.2)
The resulted high-quality reads were then mapped to the mouse reference genome (GRCm38.p6) using HISAT2 (v.2.2.1) 61. SAMtools (v.1.9) was employed to sort and index the alignment BAM files, while StringTie (v.2.1.4) was used for reads counting within gene ranges, utilizing mouse Ensembl mouse gene annotation v.102.38.
Alignment quality and statistics were assessed using SAMstat (v 1.5.2), revealing an alignment rate ranging from 92% to 95% for the samples in this study. Subsequently, the count vectors from all samples were consolidated into a table, which then underwent secondary analysis in R (v.4.3).
Quality control and sample consistency were assessed through principal-component analysis using the R package PCATools (v.2.14.0). The count table was further processed in the secondary statistical analysis using R scripts with DESeq2 (v.1.40.2)
A maximum likelihood estimate model with contrast tests was specifically employed in our analysis. This approach resulted in lists of genes ranked for differential expression, which were based on Wald test P values. The Benjamini-Hochberg-adjusted P Values were utilized to estimate the false discovery rate, providing a robust method for identifying significant gene expression changes. Differential expression was defined with a cutoff of log2 fold change (logFC) of +- 1 and a p-value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
Total RNA extraction was conducted using the GeneMark Total RNA Purification kit.
To assess RNA quality, a NanoDrop ND2000 spectrophotometer from Thermo Scientific was employed. Subsequently, 18 libraries were meticulously prepared by BGI Genomics, and all samples were sequenced on the DNBSEQ platform.

value: skeletal muscle

value: cFeimin MKO

value: after 90min running


title: NC2 miRNA (biol rep2)


title: RTgill-W1 site 20 rep 2 conc2

description:
cell lysate
e9.e9.20.b11
rtgill.20.2.B11


title: RTgill-W1 site 20 rep 1 conc7

description:
cell lysate
e4.e4.20.g11
rtgill.20.1.G11


title: NC1 mRNA (biol rep1)


title: Exe_KO_rep1


title: RTgill-W1 site 20 rep 1 conc4

description:
cell lysate
e4.e4.20.d11
rtgill.20.1.D11


title: Exe_KO_rep2


title: Exe_WT_rep5


title: RTgill-W1 site 20 rep 1 conc3

description:
cell lysate
e4.e4.20.c11
rtgill.20.1.C11


title: RTgill-W1 site 20 rep 1 conc2

description:
cell lysate
e4.e4.20.b11
rtgill.20.1.B11


title: RTgill-W1 site 20 rep 2 conc4

description:
cell lysate
e9.e9.20.d11
rtgill.20.2.D11


title: Exe_WT_rep4


title: Exe_WT_rep3


title: RTgill-W1 site 16 rep 3 conc8

description:
cell lysate
e12.e12.16.h09
rtgill.16.3.H09


title: Sed_KO_rep3

value: Sedentary


title: RTgill-W1 site 16 rep 3 conc7

description:
cell lysate
e12.e12.16.g09
rtgill.16.3.G09


title: Sed_KO_rep2


title: Sed_KO_rep1


title: RTgill-W1 site 16 rep 3 conc5

description:
cell lysate
e12.e12.16.e09
rtgill.16.3.E09


title: Sed_WT_rep3


title: RTgill-W1 site 16 rep 3 conc4

description:
cell lysate
e12.e12.16.d09
rtgill.16.3.D09


title: RTgill-W1 site 16 rep 3 conc1

description:
cell lysate
e12.e12.16.a09
rtgill.16.3.A09


title: RTgill-W1 site 16 rep 3 conc3

description:
cell lysate
e12.e12.16.c09
rtgill.16.3.C09


title: Sed_WT_rep1


title: TG_DSS2

city: Hangzhou

first: Haiting

state: Zhejiang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
SOAPnuke v1.5.2 software used for basecalling.
Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which  quality is lesser than 15 is greater than 50% in a read).
We use HISAT v2.0.4 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping  step.
We mapped clean reads to reference using Bowtie2 v2.2.5 (from Langmead B et al 2012), and then calculate gene expression  level with RSEM v1.2.12 (from Li B et al 2011), then got Fragments Per Kilobase of exon model per Million mapped fragments (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: intestinal tissue

extract_protocol:
Intestine were removed, flash frozen on dry ice, then purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic  beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.  The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.
RNA libraries were prepared for sequencing using BGISEQ-500 RNA-Seq Library Preparation Protocol

value: intestinal tissue

value: ITGB6-overexpressing transgenic mice

value: oral administration of 2.5percent DSS


title: RTgill-W1 site 16 rep 2 conc8

description:
cell lysate
e8.e8.16.h09
rtgill.16.2.H09


title: TG_DSS1


title: WT_DSS1

value: wild type


title: RTgill-W1 site 16 rep 3 conc2

description:
cell lysate
e12.e12.16.b09
rtgill.16.3.B09


title: RTgill-W1 site 16 rep 2 conc7

description:
cell lysate
e8.e8.16.g09
rtgill.16.2.G09


title: RTgill-W1 site 16 rep 2 conc6

description:
cell lysate
e8.e8.16.f09
rtgill.16.2.F09


title: TG_WTR2

value: untreated


title: RTgill-W1 site 16 rep 2 conc4

description:
cell lysate
e8.e8.16.d09
rtgill.16.2.D09


title: RTgill-W1 site 16 rep 2 conc5

description:
cell lysate
e8.e8.16.e09
rtgill.16.2.E09


title: RTgill-W1 site 20 rep 1 conc1

description:
cell lysate
e4.e4.20.a11
rtgill.20.1.A11


title: TG_WTR1


title: RTgill-W1 site 16 rep 2 conc3

description:
cell lysate
e8.e8.16.c09
rtgill.16.2.C09


title: WT_WTR3


title: RTgill-W1 site 16 rep 2 conc2

description:
cell lysate
e8.e8.16.b09
rtgill.16.2.B09


title: RTgill-W1 site 16 rep 3 conc6

description:
cell lysate
e12.e12.16.f09
rtgill.16.3.F09


title: Sed_WT_rep4


title: WT_WTR2


title: RTgill-W1 site 16 rep 2 conc1

description:
cell lysate
e8.e8.16.a09
rtgill.16.2.A09


title: WT_WTR1


title: RTgill-W1 site 16 rep 1 conc8

description:
cell lysate
e3.e3.16.h09
rtgill.16.1.H09


title: S106

city: Davis

first: Barbara

last: Blanco-Ulate

state: California

address: One Shields Ave

department: Plant Sciences

institute: University of California Davis

data_processing:
Quality and adapter trimming were done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Rhizopus stolonifer and each of the fruit hosts with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the Bowtie2 alignments using the script sam2counts.py v.0.91
Assembly: Rhizopus stolonifer BLUCD01v1, Solanum licopersicum build SL4.0 with ITAG 4.0 annotations, Vitis vinifera PN40024, Fragaria x ananassa Camarosa v1.0.a1, Prunus salicina Zhongli No. 6 v1.0
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-AZ, and transcript IDs being listed on column A
Supplementary files format and content: -

organism: Fragaria x ananassa

source_name: Strawberry

extract_protocol:
RNA was extracted from 1 g of ground tissue as described in Blanco-Ulate et al. (2013). Culture media-grown samples and resulting libraries were obtained from Petrasch et al. (2019) (GEO accession GSE122555).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

value: Strawberry

tag: agent

value: Rhizopus stolonifer

tag: time point

value: (hours_post_inoculation)  48


title: S107

tag: tissue


title: RTgill-W1 site 16 rep 1 conc6

description:
cell lysate
e3.e3.16.f09
rtgill.16.1.F09


title: WT_DSS2


title: S105


title: TG_WTR3


title: S104

value: (hours_post_inoculation)  24


title: RTgill-W1 site 16 rep 1 conc3

description:
cell lysate
e3.e3.16.c09
rtgill.16.1.C09


title: RTgill-W1 site 16 rep 1 conc5

description:
cell lysate
e3.e3.16.e09
rtgill.16.1.E09


title: S103


title: RTgill-W1 site 16 rep 1 conc4

description:
cell lysate
e3.e3.16.d09
rtgill.16.1.D09


title: S102


title: RTgill-W1 site 16 rep 1 conc2

description:
cell lysate
e3.e3.16.b09
rtgill.16.1.B09


title: S101

value: (hours_post_inoculation)  12


title: RTgill-W1 site 8 rep 3 conc8

description:
cell lysate
e11.e11.8.h04
rtgill.8.3.H04


title: S100


title: RTgill-W1 site 8 rep 3 conc7

description:
cell lysate
e11.e11.8.g04
rtgill.8.3.G04


title: S99

value: (hours_post_inoculation)  6


title: RTgill-W1 site 8 rep 3 conc6

description:
cell lysate
e11.e11.8.f04
rtgill.8.3.F04


title: RTgill-W1 site 8 rep 3 conc4

description:
cell lysate
e11.e11.8.d04
rtgill.8.3.D04


title: RTgill-W1 site 8 rep 3 conc3

description:
cell lysate
e11.e11.8.c04
rtgill.8.3.C04


title: S98


title: RTgill-W1 site 16 rep 1 conc7

description:
cell lysate
e3.e3.16.g09
rtgill.16.1.G09


title: BMDM 1mg_4

city: Shanghai

first: Yersen

last: Mulat

state: Shanghai

address: No. 650 Xin Songjiang Road

department: School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
HISAT2 (http://daehwankimlab.github.io/hisat2/)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: BMDM

growth_protocol: The cells were cultured in DMEM medium containing 10% FBS and 1% penicillin and streptomycin, and M-CSF was added. The culture medium was changed every 3, 5, and 7 days.

extract_protocol:
RNA was extracted using Trizol (Invitrogen, Cat# 15596026) reagent.
Libraries were prepared using the VAHTS Universal V5 RNA sequencing Library Prep Kit (Vazyme, China) following the manufacturer's protocol.

treatment_protocol: MD is derived from 8-week-old C57BL/6J male mice obtained under sterile conditions.Use DMSO to dissolve Bafilomycin A1 (MCE) and Bazedoxifene (MCE) to achieve a concentration of 5uM.

value: BMDM

value: Macrophage

value: WT

value: MD(1mg/ml) 6h


title: BMDM 1mg_3


title: BMDM 1mg_2


title: BMDM 1mg_1


title: RTgill-W1 site 8 rep 3 conc1

description:
cell lysate
e11.e11.8.a04
rtgill.8.3.A04


title: BMDM 50ug_3

value: MD(50ug/ml) 6h


title: RTgill-W1 site 8 rep 3 conc2

description:
cell lysate
e11.e11.8.b04
rtgill.8.3.B04


title: BMDM 50ug_4


title: BMDM 50ug_2


title: RTgill-W1 site 8 rep 2 conc7

description:
cell lysate
e7.e7.8.g04
rtgill.8.2.G04


title: RTgill-W1 site 8 rep 2 conc8

description:
cell lysate
e7.e7.8.h04
rtgill.8.2.H04


title: RTgill-W1 site 16 rep 1 conc1

description:
cell lysate
e3.e3.16.a09
rtgill.16.1.A09


title: RTgill-W1 site 8 rep 2 conc6

description:
cell lysate
e7.e7.8.f04
rtgill.8.2.F04


title: RTgill-W1 site 8 rep 2 conc5

description:
cell lysate
e7.e7.8.e04
rtgill.8.2.E04


title: BMDM con_2

value: Vehicle


title: BMDM con_4


title: BMDM 50ug_1


title: BMDM con_3


title: RTgill-W1 site 8 rep 2 conc3

description:
cell lysate
e7.e7.8.c04
rtgill.8.2.C04


title: RTgill-W1 site 8 rep 2 conc4

description:
cell lysate
e7.e7.8.d04
rtgill.8.2.D04


title: BMDM con_1


title: RTgill-W1 site 8 rep 2 conc2

description:
cell lysate
e7.e7.8.b04
rtgill.8.2.B04


title: RTgill-W1 site 8 rep 2 conc1

description:
cell lysate
e7.e7.8.a04
rtgill.8.2.A04


title: RTgill-W1 site 8 rep 3 conc5

description:
cell lysate
e11.e11.8.e04
rtgill.8.3.E04


title: BMDM MD72_3

value: MD(1mg/ml) 72h


title: BMDM MD72_4


title: RTgill-W1 site 8 rep 1 conc8

description:
cell lysate
e2.e2.8.h05
rtgill.8.1.H05


title: BMDM MD72_2


title: RTgill-W1 site 8 rep 1 conc5

description:
cell lysate
e2.e2.8.e05
rtgill.8.1.E05


title: RTgill-W1 site 8 rep 1 conc6

description:
cell lysate
e2.e2.8.f05
rtgill.8.1.F05


title: BMDM MD24_4

value: MD(1mg/ml) 24h


title: RTgill-W1 site 8 rep 1 conc7

description:
cell lysate
e2.e2.8.g05
rtgill.8.1.G05


title: BMDM MD72_1


title: BMDM MD24_3


title: BMDM MD24_2


title: RTgill-W1 site 8 rep 1 conc4

description:
cell lysate
e2.e2.8.d05
rtgill.8.1.D05


title: BMDM MD24_1


title: BMDM Baze_4

value: MD(1mg/ml)+Bazedoxifene(5uM) 24h


title: RTgill-W1 site 7 rep 3 conc8

description:
cell lysate
e12.e12.7.h07
rtgill.7.3.H07


title: BMDM Baze_3


title: RTgill-W1 site 8 rep 1 conc2

description:
cell lysate
e2.e2.8.b05
rtgill.8.1.B05


title: BMDM Baze_1


title: RTgill-W1 site 7 rep 3 conc6

description:
cell lysate
e12.e12.7.f07
rtgill.7.3.F07


title: BMDM Baf_4

value: MD(1mg/ml)+Bafilomycin A1(5uM) 24h


title: BMDM Baf_2


title: RTgill-W1 site 8 rep 1 conc1

description:
cell lysate
e2.e2.8.a05
rtgill.8.1.A05


title: RTgill-W1 site 7 rep 3 conc4

description:
cell lysate
e12.e12.7.d07
rtgill.7.3.D07


title: RTgill-W1 site 7 rep 3 conc3

description:
cell lysate
e12.e12.7.c07
rtgill.7.3.C07


title: BMDM Baze_2


title: RTgill-W1 site 7 rep 3 conc1

description:
cell lysate
e12.e12.7.a07
rtgill.7.3.A07


title: BMDM Baf_1


title: RTgill-W1 site 7 rep 3 conc2

description:
cell lysate
e12.e12.7.b07
rtgill.7.3.B07


title: BMDM M2_MD_3

value: IL4+MD(1mg/ml) 24h


title: BMDM M2_MD_4


title: RTgill-W1 site 8 rep 1 conc3

description:
cell lysate
e2.e2.8.c05
rtgill.8.1.C05


title: BMDM M2_MD_1


title: RTgill-W1 site 7 rep 2 conc8

description:
cell lysate
e8.e8.7.h07
rtgill.7.2.H07


title: RTgill-W1 site 7 rep 2 conc7

description:
cell lysate
e8.e8.7.g07
rtgill.7.2.G07


title: BMDM M2_MD_2


title: RTgill-W1 site 7 rep 2 conc6

description:
cell lysate
e8.e8.7.f07
rtgill.7.2.F07


title: RTgill-W1 site 7 rep 2 conc5

description:
cell lysate
e8.e8.7.e07
rtgill.7.2.E07


title: BMDM M2_3

value: IL4 24h


title: RTgill-W1 site 7 rep 3 conc7

description:
cell lysate
e12.e12.7.g07
rtgill.7.3.G07


title: RTgill-W1 site 7 rep 2 conc4

description:
cell lysate
e8.e8.7.d07
rtgill.7.2.D07


title: RTgill-W1 site 7 rep 3 conc5

description:
cell lysate
e12.e12.7.e07
rtgill.7.3.E07


title: BMDM M2_1


title: BMDM Baf_3


title: BMDM M2_2


title: RTgill-W1 site 7 rep 2 conc3

description:
cell lysate
e8.e8.7.c07
rtgill.7.2.C07


title: BMDM M1_MD_4

value: LPS+INFγ+MD(1mg/ml) 27h


title: RTgill-W1 site 7 rep 2 conc2

description:
cell lysate
e8.e8.7.b07
rtgill.7.2.B07


title: BMDM M1_MD_3

value: LPS+INFγ+MD(1mg/ml) 26h


title: RTgill-W1 site 7 rep 2 conc1

description:
cell lysate
e8.e8.7.a07
rtgill.7.2.A07


title: RTgill-W1 site 7 rep 1 conc8

description:
cell lysate
e3.e3.7.h07
rtgill.7.1.H07


title: BMDM M1_MD_2

value: LPS+INFγ+MD(1mg/ml) 25h


title: RTgill-W1 site 7 rep 1 conc7

description:
cell lysate
e3.e3.7.g07
rtgill.7.1.G07


title: BMDM M1_MD_1

value: LPS+INFγ+MD(1mg/ml) 24h


title: RTgill-W1 site 7 rep 1 conc6

description:
cell lysate
e3.e3.7.f07
rtgill.7.1.F07


title: RTgill-W1 site 7 rep 1 conc5

description:
cell lysate
e3.e3.7.e07
rtgill.7.1.E07


title: BMDM M1_4

value: LPS+INFγ 24h


title: BMDM M1_3

value: BMDM


title: RTgill-W1 site 7 rep 1 conc4

description:
cell lysate
e3.e3.7.d07
rtgill.7.1.D07


title: RTgill-W1 site 7 rep 1 conc3

description:
cell lysate
e3.e3.7.c07
rtgill.7.1.C07


title: BMDM M2_4

value: Macrophage


title: BMDM M1_2

value: WT


title: BMDM M1_1


title: RTgill-W1 site 7 rep 1 conc2

description:
cell lysate
e3.e3.7.b07
rtgill.7.1.B07


title: RTgill-W1 site 7 rep 1 conc1

description:
cell lysate
e3.e3.7.a07
rtgill.7.1.A07


title: BMDM Control_4


title: BMDM Control_3


title: RTgill-W1 site 5 rep 3 conc6

description:
cell lysate
e13.e13.5.f10
rtgill.5.3.F10


title: RTgill-W1 site 5 rep 3 conc4

description:
cell lysate
e13.e13.5.d10
rtgill.5.3.D10


title: RTgill-W1 site 5 rep 3 conc8

description:
cell lysate
e13.e13.5.h10
rtgill.5.3.H10


title: RTgill-W1 site 5 rep 3 conc7

description:
cell lysate
e13.e13.5.g10
rtgill.5.3.G10


title: BMDM Control_2


title: BMDM Control_1


title: RTgill-W1 site 5 rep 3 conc2

description:
cell lysate
e13.e13.5.b10
rtgill.5.3.B10


title: RTgill-W1 site 5 rep 3 conc3

description:
cell lysate
e13.e13.5.c10
rtgill.5.3.C10


title: RTgill-W1 site 5 rep 3 conc5

description:
cell lysate
e13.e13.5.e10
rtgill.5.3.E10


title: Renca, PBS, scTCR

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

description: 10x Genomics

data_processing:
Cellranger was used to align reads to the mouse reference transcriptome (mm10) and to generate cell-by-gene matrices for each sample library.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-Seq

source_name: Subcutaneous tumors

extract_protocol:
Tumors were dissociated by mincing in RPMI + 2% FBS, incubating with 0.1 mg/ml collagenase and DNase I for 30 min at 37ºC, filtering through a 70 μM filter to obtain a single cell suspension. They were then washed with RPMI + 10% FBS and resuspended in RPMI + 20% FBS. For sorting, cells were incubated for 30 min at 4ºC with fluorophore-conjugated antibodies using the following antibodies: anti-CD45 (clone 30-F11, BD Biosciences) and anti-CD3 (clone 17A2, BD Bioscience). Samples were sorted using a BD FACSAriaII into three populations: T cells (CD45+ CD3+); non-T immune cells (CD45+ CD3-); and tumor and stromal cells (CD45- CD3-). For live/dead staining, AmCyan Kit (Thermo Fisher Scientific) was used. Sorted cells for each subset were counted manually and then combined in a 2:1:1 ratio of T cells:non-T immune cells:tumor and stromal cells, with an equal contribution from each biologic replicate from an experimental condition. Ten thousand cells from each of the mixed sorted samples for each condition were loaded onto the 10x Genomics Chromium System.
Library preparation for scRNA-seq and scTCR-seq was performed using the 5’ Reagent Kit from 10x Genomics according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA) and passed quality control.

treatment_protocol: Renca cells were implanted subcutaneously in Balb/c mice, and after tumors formed, mice were treated for three cycles with PBS, DR-18, anti-CTLA-4, or DR-18 + anti-CTLA-4 (“Combo”) (n=3 mice/group), and 24 hours after the third treatment, tumors were collected.

value: Subcutaneous tumors

value: Renca

value: RCC

value: PBS


title: Renca, DR-18, scTCR

description: 10x Genomics


title: Renca, DR-18 + anti-CTLA-4, scTCR

description: 10x Genomics

value: DR-18 + anti-CTLA-4


title: Renca, anti-CTLA-4, scTCR

description: 10x Genomics


title: RTgill-W1 site 5 rep 3 conc1

description:
cell lysate
e13.e13.5.a10
rtgill.5.3.A10


title: Renca, DR-18, scRNA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger was used to align reads to the mouse reference transcriptome (mm10) and to generate cell-by-gene matrices for each sample library.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: Renca, DR-18 + anti-CTLA-4, scRNA

description: 10x Genomics


title: RTgill-W1 site 5 rep 2 conc7

description:
cell lysate
e9.e9.5.g10
rtgill.5.2.G10


title: RTgill-W1 site 5 rep 2 conc8

description:
cell lysate
e9.e9.5.h10
rtgill.5.2.H10


title: Renca, PBS, scRNA

description: 10x Genomics


title: RTgill-W1 site 5 rep 2 conc6

description:
cell lysate
e9.e9.5.f10
rtgill.5.2.F10


title: ventricle, 24 month,  scATAC, sample 2

city: Chapel Hill

first: Yiran

last: Song

state: NC

address: 111 Mason Farm Road

institute: The University of North Carolina

library_source: genomic single cell

data_processing:
Single-cell ATAC-seq: Sequencing reads from scATAC-seq experiments were processed using Cell Ranger ATAC (version 2.1.0). The cellranger-atac count pipeline was used with default parameters to align reads to the mouse reference genome (mm10, refdata-cellranger-arc-mm10-2020-A-2.0.0) and generate fragment files for each sample.
Assembly: mm10
Supplementary files format and content: scATAC: tab-separated barcode values file, matrix file and peaks bed

source_name: heart ventricle

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Male mouse hearts at 3 months of age, 12 months of age, and 24 months of age were collected for non-cardiomyocyte isolation. In accordance with UNC-Chapel Hill LARC guidelines, all animals were euthanized using CO2 and cervical dislocation. Hearts were perfused with Langendorff apparatus as described with minor modifications. Briefly, male mice of three ages groups were anesthetized with isoflurane (1%-2%), the heart was removed, retrograde perfusion was performed through an aortic cannulation, and continuous flow of 16-24 drops/min in a Langendorff apparatus. Both ventricles were digested with 1 mg/ml collagenase IaI for 10-15min, and the ventricle were further mechanically dissociated by pipetting. Then, the cell suspension was collected and filtered through a 100µm cell strainer. CMs were removed by centrifuging at 50g (200 rpm) for 3min, and nonCMs were enriched by centrifuge at 450g (2,000 rpm) for 5 min. The pelleted nonCMs were treated with 1ml red blood cell lysis buffer (Gibco) at room temperature (RT) and washed twice with wash buffer (4% FBS/PBS). Single live cells were FACS-sorted by 7-Amino Actinomycin D (7-AAD, R&D Systems), and Pacific Blue-conjugated Annexin V and SYTOX (Thermo) staining. Following sorting, cell concentration and viability of each sample were counted using automated cell counter (LUNA system, Logos biosytems) plus Acridine orange (AO)/ propidium iodide (PI) dual nuclear staining. Cell concentration was adjusted to 1x106 cells/ml for subsequent scRNA-seq via 10x Gemonics platform. Cells (50,000 per sample) for scATAC-seq were subjected to lysis for 3min and counted again with cell counter to determine the viability (lower than 5%) and concentration again.
Single-cell ATAC library preparation and sequencing: The single nuclei were processed for library preparation (Chromium Single Cell ATAC v1.0) following manufactural instructions from 10x Chromium. Sequencing was performed on Illumina NOVAseq-S1 platform.

value: heart ventricle

tag: time

value: 24 months

value: wild type


title: ventricle, 24 month,  scATAC, sample 1


title: RTgill-W1 site 5 rep 2 conc5

description:
cell lysate
e9.e9.5.e10
rtgill.5.2.E10


title: RTgill-W1 site 5 rep 2 conc3

description:
cell lysate
e9.e9.5.c10
rtgill.5.2.C10


title: ventricle, 3 month,  scATAC, sample 2

value: 3 months


title: Renca, anti-CTLA-4, scRNA

description: 10x Genomics


title: RTgill-W1 site 5 rep 2 conc2

description:
cell lysate
e9.e9.5.b10
rtgill.5.2.B10


title: RTgill-W1 site 5 rep 2 conc4

description:
cell lysate
e9.e9.5.d10
rtgill.5.2.D10


title: RTgill-W1 site 5 rep 2 conc1

description:
cell lysate
e9.e9.5.a10
rtgill.5.2.A10


title: ventricle, 3 month, scATAC, sample 1


title: RTgill-W1 site 5 rep 1 conc8

description:
cell lysate
e4.e4.5.h10
rtgill.5.1.H10


title: RTgill-W1 site 5 rep 1 conc7

description:
cell lysate
e4.e4.5.g10
rtgill.5.1.G10


title: Vil1Cre negative, Gsdmc1-4 fl/fl, Day 10 DSS colon, Hashtag counts

city: Boston

first: Ivan

last: Zanoni

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads
DSS_D10_GSDMC_WT_HT.csv

library_source: other

data_processing:
FASTQs, cell count matrices, and hashtag oligo counts were generated using cellranger v7.1.0 through cumulus tools (https://cumulus.readthedocs.io/en/stable/)
Cells were then broadly filtered based on Unique Molecular Identifiers (UMI) count (>500 & <6000), and percentage of mitochondrial genes (<75%). Finally, cells labeled as doublets by demultiplexing were removed
Downstream clustering analysis was performed using Seurat (v5.0.1) using scTransform normalization and corrected counts.
Remaining doublets were removed by inspection upon subclustering routines by identifying clusters expressing mutually exclusive cell type lineage markers
Assembly: mm10-2020-A
Supplementary files format and content: Cellranger output files: XXX.h5 contains the raw unfiltered cell count matrix
Supplementary files format and content: Cellranger output files: XXX.csv contains the hashtag oligo counts; feature_barcodes.xlsx contains the cellranger input and the streptavidin oligo sequences used for every sample
Supplementary files format and content: finalObject_allCells: final processed object, consisting of all samples merged and hashtag identity demultiplexed. This was the object used for the analysis presented in the paper
Supplementary files format and content: finalObject_epithelialCells: The final object subsetted to only include the epithelial cells.

molecule: protein

source_name: Colon

extract_protocol:
After collecting the colons, the colonic content was squeezed out and the colons flushed with 1ml of ice-cold HBSS. The colons were first cut longitudinally and then into 0.5-1cm fragments. These fragments were washed three times with 30ml of ice-cold HBSS. After the final wash, the fragments were resuspended in 10ml of epithelial dissociation media (1X HBSS supplemented with 15 mM EDTA). Colonic fragments were shaken at 220 RPM and 37°C for 15 minutes and then placed on ice for 5 minutes. The colonic fragments were shaken vigorously 30 times, vortexed for 2 seconds, and then placed into 30 ml of ice-cold HBSS and gently inverted. Colonic fragments were then finely minced and incubated in 5 ml of pre-warmed tissue digestion media [tissue media (RPMI supplemented with 5% FBS, 10mM HEPES, 1mM Sodium Pyruvate, 5mM L-Glutamine, 1X NEAA, 1X Pen/Strep) supplemented with 100µg/ml Liberase™ TM Research Grade (Roche Life Science) and 100µg/ml DNase I (Sigma)] per 4 cm of colon tissue and incubated at 220 RPM, 37°C for 45 minutes. After digestion 50µl of 0.5M EDTA and 50µl of FBS were added to quench the reaction, gently swirled to mix, and pipetted 40 times using a wide bore P1000 pipet tip. This suspension was filtered through a 40µm cell strainer (Falcon). Cells were pelleted at 400xg for 10 minutes at 4°C. The pellet was resuspended in ACK buffer to lyse red blood cells and incubated on ice for 3 minutes. ACK was quenched using 20 ml of tissue base media and pelleted again at 400xg for 10 minutes at 4°C. The cells were resuspended in tissue media, counted and 2x106 cells were transferred to 5 ml FACS tubes (Falcon) for downstream analyses. In an effort to reduce technical batch effects, cells isolated from individual mice were labelled with unique oligos and pooled prior to loading the 10X controller.  Briefly, 2x106  cells were pelleted at 500xg for 5 minutes and incubated with 0.5 µg TruStain FcX (anti-mouse CD16/32) (Biolegend) in 50 µL of FACS buffer (PBS supplemented with 5% FBS, 2mM EDTA) for 10 minutes at 4°C. As commercially available hashtag antibodies target CD45 and MHC class I, we opted to reduce hashtag bias towards immune cells by utilizing a custom cocktail of antibodies with markers of major subsets. Following Fc receptor blockade, cells were stained with a cocktail of antibodies consisting of anti-CD45-biotin (clone 30-F11; 103104), anti-H-2K-biotin (clone 28-8-6, 114603), anti-CD31-biotin (clone IM7, 103004), anti-CD140a-biotin (clone APA5, 135910), anti-CD140b-biotin (clone APB5, 136010), anti-PDPN-biotin (clone 8.1.1, 127404) and, anti-EpCAM-biotin (clone G8.8, 118204), anti-CD31 (clone MEC13.3, 102504) (all Biolegend) resuspended at 0.5µg per antibody in 50µL of FACS buffer for 20 minutes at 4°C (Biolegend). Following antibody staining, cells from each individual animal were washed 3 times and incubated with a unique TotalSeqTm-B-0952, -B-0953, -B-0954 Streptavidin-PE (cat. # 405287, 405289, and 405291 respectively, all Biolegend) at 4°C for 20 minutes. Finally, cells were washed 3 times in 3mL of 1% BSA in PBS prior to resuspending the cells in 200µl 1% BSA in PBS. Cells were counted, and individual mice across the same condition were pooled at equal cellular ratios, for a total of 4 pools each representing one condition.
Libraries were constructed as outlined in the 10x Genomics guide for Dual-indexed 3' transcriptomics v3.1 with Feature Barcoding.

treatment_protocol: Mice were provided 2.5% DSS drinking water for 7 days and allowed to recover for 3 days prior to tissue harvesting

value: Colon

value: Dextran Sulfate Sodium (2.5%)

tag: timepoint

tag: disease state

value: day10 DSS

tag: library type

value: HTO

tag: hto

value: anti-CD45-biotin, anti-H-2K-biotin, anti-EpCAM-biotin,anti-CD31-biotin,anti-PDPN-biotin,anti-PDGFRA-biotin,anti-PDGFRB-biotin, TotalSeq™-B0952 PE Streptavidin,TotalSeq™-B0953 PE Streptavidin, TotalSeq™-B0954 PE Streptavidin


title: Vil1Cre positive, Gsdmc1-4 fl/fl, Day 10 DSS colon, Hashtag counts

description:
HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads
DSS_D10_GSDMC_KO.csv

value: Vil1(cre/+), Gsdmc1-4(fl/fl)


title: RTgill-W1 site 5 rep 1 conc6

description:
cell lysate
e4.e4.5.f10
rtgill.5.1.F10

tag: site


title: ventricle, 12 month,  scATAC, sample 2

value: 12 months


title: Vil1Cre positive, Gsdmc1-4 fl/fl, Day 10 DSS colon, Gene expression

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript
DSS_D10_GSDMC_KO.h5

molecule: polyA RNA

value: mRNA


title: RTgill-W1 site 5 rep 1 conc5

description:
cell lysate
e4.e4.5.e10
rtgill.5.1.E10

tag: cell line


title: RTgill-W1 site 5 rep 1 conc4

description:
cell lysate
e4.e4.5.d10
rtgill.5.1.D10


title: Vil1Cre negative, Gsdmc1-4 fl/fl, Day 10 DSS colon, Gene expression

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript
DSS_D10_GSDMC_WT.h5


title: Vil1Cre positive, Gsdmc1-4 fl/fl, Day 0 DSS colon, Hashtag counts

description:
HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads
DSS_D0_GSDMC_KO_HT.csv

value: naive


title: RTgill-W1 site 5 rep 1 conc3

description:
cell lysate
e4.e4.5.c10
rtgill.5.1.C10


title: Vil1Cre positive, Gsdmc1-4 fl/fl, Day 0 DSS colon, Gene expression

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript
DSS_D0_GSDMC_KO.h5


title: RTgill-W1 site 3 rep 3 conc8

description:
cell lysate
e11.e11.3.h05
rtgill.3.3.H05


title: ventricle, 12 month,  scATAC, sample 1


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterone treated cells replicate 6

city: Bethesda

first: Thomas

middle: A

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

description: RNA-SeqData_NormedCounts_Excel_v6.0.xlsx

data_processing:
Basecalling RTA 3.4.4 was used for Basecalling and Bcl2fastq 2.20 was used for demultiplexing allowing 1 mismatch. Sequences were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.  -p 8 -x ref_genome -U read1.fastq (ChIP reads). RNA reads were aligned using STAR 2.7.0f with default settings.
Trimmomatic was used for adapter trimming and quality control.
ChIP-Seq Peaks were called using HOMER program version 4.10.4 with findPeaks with following parameters; FDR<0.001, 5x fold enrichment over control, 5x fold enrichment over local background.
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: bigWig (ChIP-seq) and Excel file of normed counts (RNA-seq)

source_name: Mouse Colon Organoid

growth_protocol: Cell lines use typical growth protocols with DMEM 10% FBS. Organoids were established in Corning-Matrigel® and IntestiCult®. All cells were grown 24h on media with 10% charcoal stripped serum before hormone treatment.

extract_protocol:
Cells fixed in 1% Formaldehyde. Lysed, Sonicated, and ChIP'd with anti-GFP (10 μg, Abcam #AB290) or anti-GR (10ug Santa Cruz # sc-393232x. Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
ChIP-Seq libraries were made by TruSeq ChIP Library Prep Kit (IP-202-1012). RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep.
ChIP-seq was performed with Next-Seq (76bp single-end reads) and RNA-Seq was performed with NOVA-Seq (150bp stranded reads).

treatment_protocol: Aldosterone treatments were with 10 nano-molar. Corticosterone treatments were 100 nano-molar with treatment times as described in the paper.

value: Mouse Colon Organoid


title: RTgill-W1 site 3 rep 3 conc7

description:
cell lysate
e11.e11.3.g05
rtgill.3.3.G05


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterone treated cells replicate 2


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterone treated cells replicate 1


title: RTgill-W1 site 3 rep 3 conc3

description:
cell lysate
e11.e11.3.c05
rtgill.3.3.C05


title: RTgill-W1 site 3 rep 3 conc2

description:
cell lysate
e11.e11.3.b05
rtgill.3.3.B05


title: Vil1Cre negative, Gsdmc1-4 fl/fl, Day 0 DSS colon, Gene expression

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 contains transcript
DSS_D0_GSDMC_WT.h5


title: RTgill-W1 site 5 rep 1 conc1

description:
cell lysate
e4.e4.5.a10
rtgill.5.1.A10


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterone treated cells replicate 4


title: RTgill-W1 site 3 rep 3 conc1

description:
cell lysate
e11.e11.3.a05
rtgill.3.3.A05


title: RTgill-W1 site 3 rep 2 conc6

description:
cell lysate
e7.e7.3.f06
rtgill.3.2.F06


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate1


title: RTgill-W1 site 3 rep 2 conc7

description:
cell lysate
e7.e7.3.g06
rtgill.3.2.G06


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate 5


title: RTgill-W1 site 3 rep 3 conc6

description:
cell lysate
e11.e11.3.f05
rtgill.3.3.F05


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate 4


title: RTgill-W1 site 3 rep 2 conc3

description:
cell lysate
e7.e7.3.c06
rtgill.3.2.C06


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterone treated cells replicate 3


title: RTgill-W1 site 3 rep 3 conc5

description:
cell lysate
e11.e11.3.e05
rtgill.3.3.E05


title: RTgill-W1 site 3 rep 3 conc4

description:
cell lysate
e11.e11.3.d05
rtgill.3.3.D05


title: RTgill-W1 site 3 rep 1 conc8

description:
cell lysate
e2.e2.3.h06
rtgill.3.1.H06


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate 5


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate 4


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate 3


title: RTgill-W1 site 3 rep 1 conc6

description:
cell lysate
e2.e2.3.f06
rtgill.3.1.F06


title: RTgill-W1 site 3 rep 1 conc5

description:
cell lysate
e2.e2.3.e06
rtgill.3.1.E06


title: RTgill-W1 site 5 rep 1 conc2

description:
cell lysate
e4.e4.5.b10
rtgill.5.1.B10


title: Vil1Cre negative, Gsdmc1-4 fl/fl, Day 0 DSS colon, Hashtag counts

description:
HTO library: read1 file contains cell barcode and UMI; read2 file contains antibody derived Tag reads
DSS_D0_GSDMC_WT_HT.csv


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate 6


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate2


title: RTgill-W1 site 3 rep 2 conc4

description:
cell lysate
e7.e7.3.d06
rtgill.3.2.D06


title: OXA treatment_3

city: Hefei

first: MING

last: CHENG

address: 96 Jinzhai Road, Hefei City, Anhui Province

institute: University Of Science And Technology Of China

data_processing:
Reads were mapped to the mouse genome with STAR 2.5.3a. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor, www.bioconductor.org/) and then reads per kilobase of exon per million reads mapped (RPKM) were calculated. Genes showing differential expression between groups were identified using edgeR 3.12.1. Cutoffs of p = 0.05 and fold-change = 2 were used to judge the statistical significance of gene-expression differences.
Assembly: mm10
Supplementary files format and content: txt files include RPKM values for each sample

source_name: liver

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA)
Total RNA (2 μg) was employed for creation of a standard RNA-seq library using KC-Digital™ Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth. Wuhan, China) following manufacturer instructions.

value: liver

value: lymphocyte

tag: Stage

value: memory

value: OXA


title: RTgill-W1 site 3 rep 2 conc5

description:
cell lysate
e7.e7.3.e06
rtgill.3.2.E06


title: RTgill-W1 site 3 rep 1 conc1

description:
cell lysate
e2.e2.3.a06
rtgill.3.1.A06


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate 3


title: RTgill-W1 site 3 rep 2 conc2

description:
cell lysate
e7.e7.3.b06
rtgill.3.2.B06


title: OXA treatment_2

tag: cell type


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate2


title: control_2

value: naïve

value: solvent


title: RTgill-W1 site 2 rep 3 conc5

description:
cell lysate
e12.e12.2.e08
rtgill.2.3.E08


title: RTgill-W1 site 3 rep 2 conc1

description:
cell lysate
e7.e7.3.a06
rtgill.3.2.A06


title: RTgill-W1 site 3 rep 2 conc8

description:
cell lysate
e7.e7.3.h06
rtgill.3.2.H06


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of 10nM Aldosterontreated cells replicate1


title: GRKO_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate 2


title: RTgill-W1 site 3 rep 1 conc7

description:
cell lysate
e2.e2.3.g06
rtgill.3.1.G06


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate6


title: RTgill-W1 site 2 rep 3 conc2

description:
cell lysate
e12.e12.2.a08
rtgill.2.3.B08


title: RTgill-W1 site 2 rep 3 conc3

description:
cell lysate
e12.e12.2.c08
rtgill.2.3.C08


title: Bex4

city: Sendai

first: Tetsuya

last: Ikawa

state: Miyagi

address: 1-1 Seiryo, Aoba-ku

institute: Tohoku University

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.30.
Read quality was checked for each sample using FastQC v0.11.9. High-quality reads were imported into Hisat2 (v2.0.1) for alignment to reference genome.
HTSeq (v0.6.1) estimated gene and isoform from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor packeage (v.1.6.3).
Assembly: GRCm39.104
Supplementary files format and content: Microsoft excel file includes raw count for all samples

source_name: skin

growth_protocol: WT (C57BL/6J), 8week-old, female mice were used experiments. (n = 4 each group)

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen).  500ng of RNA was subjected to library construction. RNA was enriched by ribosomal RNA exclusion.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Ⅱ Directional RNA Library prep kit for Illumina.

treatment_protocol: T-cell lymphoma cells, EL4 (100 μl of 2 ×106 cells/ml) were subcutaneously injected into mice’s back skin on Day 0. For therapeutic experiments, 0.1mg bexarotene (Tokyo Chemical Industry, Tokyo, Japan) was intraperitoneally injected on Day 14, and the tumor was harvested on Day 16.

value: skin

value: WT

tag: age

tag: Sex

value: female

value: Bexarotene


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate5


title: RTgill-W1 site 2 rep 3 conc1

description:
cell lysate
e12.e12.2.b08
rtgill.2.3.A08

tag: treatment


title: RTgill-W1 site 2 rep 3 conc8

description:
cell lysate
e12.e12.2.h08
rtgill.2.3.H08


title: RTgill-W1 site 2 rep 2 conc8

description:
cell lysate
e8.e8.2.h08
rtgill.2.2.H08


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate4


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate3


title: NT3

tag: strain

value: Vehicle


title: RTgill-W1 site 3 rep 1 conc3

description:
cell lysate
e2.e2.3.c06
rtgill.3.1.C06


title: WT_Mouse_Colon_IEC_Organoid Total_RNA-Seq; 2 hour of vehicle treated cells replicate1


title: RTgill-W1 site 2 rep 2 conc6

description:
cell lysate
e8.e8.2.f08
rtgill.2.2.F08


title: RTgill-W1 site 3 rep 1 conc2

description:
cell lysate
e2.e2.3.b06
rtgill.3.1.B06


title: NT1

tag: genotype


title: RTgill-W1 site 2 rep 2 conc4

description:
cell lysate
e8.e8.2.d08
rtgill.2.2.D08


title: RTgill-W1 site 2 rep 2 conc5

description:
cell lysate
e8.e8.2.e08
rtgill.2.2.E08


title: tamoxifen treatment_3

data_processing:
Genome mapping is a key step in the analysis. We used Hisat2（version:2.0.4）to map the cleaned RNA-seq reads to the mouse mm10 genome with two mismatches, two gaps and one multihit allowed. After genome mapping, Stringtie（version:1.3.0）was used to quantify gene expression. The gene expression value was normalized by FPKM and adjusted by a geometric algorithm.
Assembly: mm10
Supplementary files format and content: txt files include RPKM values for each sample

extract_protocol:
The selected cells were processed for single-cell RNA extraction and reverse transcription within 1 h and were subjected to cDNA amplification and purification.
Single cells were gently transferred into lysis buffer, and reverse transcription was performed using a SMARTer Ultra Low RNA Kit (Clontech) directly in the cell lysate. Single-cell cDNA was amplified using an Advantage 2 PCR Kit (Clontech) according to the manufacturer’s protocol. After cDNA amplification, 50 μl of the sample was subjected to cDNA purification, whereas the remaining sample was kept for single-cell PCR experiments.

value: tamoxifen


title: OXA treatment_1


title: RTgill-W1 site 2 rep 3 conc7

description:
cell lysate
e12.e12.2.g08
rtgill.2.3.G08


title: tamoxifen treatment_2


title: Bex1


title: RTgill-W1 site 2 rep 2 conc1

description:
cell lysate
e8.e8.2.a08
rtgill.2.2.A08


title: RTgill-W1 site 2 rep 3 conc6

description:
cell lysate
e12.e12.2.f08
rtgill.2.3.F08


title: RTgill-W1 site 3 rep 1 conc4

description:
cell lysate
e2.e2.3.d06
rtgill.3.1.D06


title: control_3


title: control_1


title: RTgill-W1 site 2 rep 3 conc4

description:
cell lysate
e12.e12.2.d08
rtgill.2.3.D08


title: Bex3


title: Bex2


title: RTgill-W1 site 2 rep 2 conc7

description:
cell lysate
e8.e8.2.g08
rtgill.2.2.G08


title: NT4


title: oil_1

value: oil


title: NT2


title: treatment_3

source_name: lymphocyte


title: RTgill-W1 site 2 rep 2 conc3

description:
cell lysate
e8.e8.2.c08
rtgill.2.2.C08


title: treatment_1


title: RTgill-W1 site 2 rep 2 conc2

description:
cell lysate
e8.e8.2.b08
rtgill.2.2.B08


title: RTgill-W1 site 2 rep 1 conc3

description:
cell lysate
e3.e3.2.c08
rtgill.2.1.C08


title: RTgill-W1 site 2 rep 1 conc8

description:
cell lysate
e3.e3.2.h08
rtgill.2.1.H08


title: tamoxifen treatment_1


title: Rorafl/fl_3


title: oil_3


title: RTgill-W1 site 2 rep 1 conc6

description:
cell lysate
e3.e3.2.f08
rtgill.2.1.F08


title: RTgill-W1 site 2 rep 1 conc1

description:
cell lysate
e3.e3.2.a08
rtgill.2.1.A08


title: RTgill-W1 site 2 rep 1 conc7

description:
cell lysate
e3.e3.2.g08
rtgill.2.1.G08


title: treatment_2


title: Aging_Exos_skin, replicate 3, scRNAseq

city: Chaoyang District

first: Youkun

last: Bi

state: Beijing

address: NO.15, Datun Road

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Cellranger  (10X Genomics)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Skin tissues were incubated with a dissociation buffer composed of collagenase I (1 mg/mL), collagenase IV (1 mg/mL), dispase (1 mg/mL), and trypsin-EDTA (0.125%) at 37 °C for 1 h. Liver tissues were exposed to dissociation buffer containing collagenase IV (1 mg/mL) and incubated at 37 °C for 40 min. Digestion was terminated by adding cold high-glucose DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) (GIBCO). The dissociated cells were centrifuged at 1,000 rpm and 4 °C for 5 min, then resuspended in 15 mL red blood cell lysis buffer (BD Biosciences) at 37 °C for 5 min. Subsequently, these cells underwent another round of centrifugation at 1,000 rpm and 4 °C for 5 min, followed by two washes with cold PBS and resuspended in cold PBS containing 10% PBS. The cell suspension was filtered through a 40 μm strainer (BD Falcon), subjected to two PBS washes, centrifuged at 1,000 rpm and 4 °C for 5 min, and resuspended in cold PBS supplemented with 10% FBS.
The library was performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10ÍGenomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retro-transcripted to cDNA, which contains an Ilumina R1 primer sequence. Unique Molecular Identifier (UMI) and the 10ÍBarcode. The pooled barcode cDNA was then cleaned up with Silane DynaBead, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequence P5 and P7 sequences and a sample index were added.

value: hESC-Exos


title: RTgill-W1 site 2 rep 1 conc5

description:
cell lysate
e3.e3.2.e08
rtgill.2.1.E08

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files


title: Rorafl/fl_1


title: Aging_Exos_skin, replicate 1, scRNAseq


title: Rorafl/fl_2


title: oil_2


title: Aging_Exos_skin, replicate 2, scRNAseq


title: RTgill-W1 site 2 rep 1 conc2

description:
cell lysate
e3.e3.2.b08
rtgill.2.1.B08


title: RTgill-W1 site 2 rep 1 conc4

description:
cell lysate
e3.e3.2.d08
rtgill.2.1.D08


title: Aging_pbs_skin, replicate 2, scRNAseq

value: pbs


title: Aging_pbs_skin, replicate 1, scRNAseq


title: Aging_pbs_skin, replicate 3, scRNAseq


title: Aging_Exos_liver, replicate 3, scRNAseq


title: Aging_Exos_liver, replicate 1, scRNAseq


title: Aging_pbs_liver, replicate 3, scRNAseq


title: Aging_pbs_liver, replicate 2, scRNAseq


title: Aging_pbs_liver, replicate 1, scRNAseq


title: s18988 SwDI/TKO

city: Minneapolis

first: Ling

last: Li

email: lil@umn.edu, linglilab@umn.edu

state: MN

address: 2001 6th Street SE Rm 4-208

department: Department of Experimental and Clinical Pharmacology

institute: University of Minnesota

description: GEX

data_processing:
10x formated output files for GEX were generated using cellranger
Further analysis was performed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Mouse frontal lobe, brain

extract_protocol:
Nuclei from six mouse brain tissues (3 for each genotype) were isolated following the 10x Genomics Demonstrated Protocol (CG000375; Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing), with the following modifications: the NP40 Lysis Buffer was used at a 20X dilution, tissue dissociation was performed on the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, Bergisch Gladbach, North Rhine-Westphalia, Germany) using a modified version of the 4C_nuclei_1 program, and no nuclei permeabilization was performed.Isolated mouse nuclei were then subjected to droplet-based 3′ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3′ Reagent Kits v3.1 per the manufacturer’s protocol (10x Genomics).
Library was generated according to Chromium Single Cell 3ʹ v3 protocol (10x Genomics).

value: Mouse frontal lobe, brain

value: KO


title: s18687 SwDI/TWT

description: GEX


title: s18986 SwDI/TKO

description: GEX