title: JN34

description: OTU genus read count

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: animal based_diet

tag: plant based_diet


title: JN36

status: Public on Jul 25 2024

type: SRA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: OTU genus read count

library_source: other

data_processing:
*library strategy: AmpliSeq
QIIME 2
Assembly: COBS, minHash and pp_sketch indices are available from: ftp.ebi.ac.uk/pub/databases/ENA2018-bacteria-661k
Supplementary files format and content: raw_count.txt

molecule: other

organism: Bacteria

source_name: faeces

extract_protocol:
microbial DNA extraction using QIAsymphony DSP Virus/Pathogen Midi Kit
16S metagenomics ION (ThermoFisher)

tag: tissue

value: faeces

tag: cohort

value: validation

tag: age

tag: bmi

value: Non smoker

value: No diabetes

tag: tumour risk_class

value: intermediate

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

value: Yes

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA


title: JN32

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: Appendectomy

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: animal based_diet

tag: plant based_diet


title: JN33

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: tumour risk_class

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class


title: JN31

description: OTU genus read count

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype


title: JN30

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Prostatectomy

value: Salvage

tag: fraction number

tag: dose/fraction

tag: animal based_diet

tag: plant based_diet


title: JN26

description: OTU genus read count

value: faeces

tag: smoke

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class


title: JN28

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: JN29

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: Non smoker

value: No diabetes

value: low

tag: prostatectomy

tag: appendectomy

tag: fraction number

tag: dose/fraction

tag: physical activity_status

value: undeclared


title: JN27

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

value: oligometastatic

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No prostatectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

value: active


title: JN23

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: prostatectomy

value: No appendectomy

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

value: Yes

value: sedentary

tag: molecule subtype

value: microbial DNA


title: JN22

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: fraction number

tag: dose/fraction


title: KG21

description: OTU genus read count

value: validation

tag: age

tag: bmi

tag: smoke

value: Non smoker

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: prostatectomy

value: Adjuvant

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status


title: JM79

description: OTU genus read count

tag: tissue

tag: cohort

value: Smoker

tag: diabetes

tag: tumour risk_class

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No prostatectomy

tag: appendectomy

value: VMAT

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: JM77

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: prostatectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity


title: JM76

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

value: Tx

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: appendectomy

tag: lymph node_irradiation

tag: mb risk_class

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: active


title: JM78

description: OTU genus read count

value: faeces

tag: age

tag: bmi

tag: smoke

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: intermediate

tag: prostatectomy

tag: rt technique

tag: rt intent

value: Radical

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: sedentary

tag: molecule subtype

value: microbial DNA


title: JM75

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: diabetes

tag: tumour risk_class

value: low

tag: appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: Yes


title: JM71

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: Non smoker

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

value: Prostatectomy

value: Appendectomy

value: Salvage

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status


title: JM72

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

value: Smoker

tag: diabetes

tag: clinical stage_at_diagnosis

value: No prostatectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: molecule subtype


title: JM70

description: OTU genus read count

value: faeces

tag: age

tag: bmi

tag: smoke

tag: tumour risk_class

value: high

tag: appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: No


title: JM69

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Radical

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: sedentary

value: microbial DNA


title: JM51

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: tumour risk_class

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: active

tag: molecule subtype


title: JM52

description: OTU genus read count

tag: tissue

tag: cohort

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

value: Oligometastatic

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: undeclared


title: JB91

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: No diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: appendectomy

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status


title: JN35

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes

tag: molecule subtype


title: JB86

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity


title: JB89

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: mb risk_class


title: JB85

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: VMAT

tag: semil vesicle_irradiation

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype


title: JN24

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: diabetes

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: probiotics use


title: JB87

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: Tx

value: Prostatectomy

value: Appendectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

value: No


title: JB84

description: OTU genus read count

tag: tissue

tag: cohort

tag: diabetes

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: Radical

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: sedentary

tag: molecule subtype

value: microbial DNA


title: JN25

description: OTU genus read count

value: discovery

tag: age

tag: bmi

tag: smoke

value: Non smoker

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: rt technique

tag: rt intent

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: probiotics use


title: JB83

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: diabetes

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

value: active


title: JB82

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: No prostatectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: lymph node_irradiation

tag: molecule subtype


title: JB63

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: diabetes

tag: tumour risk_class

value: high

tag: primary gps_at_diagnosis

value: VMAT

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status


title: JB81

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)


title: JM74

description: OTU genus read count

tag: tissue

tag: cohort

value: Smoker

tag: diabetes

tag: tumour risk_class

value: oligometastatic

tag: primary gps_at_diagnosis

tag: rt technique

tag: rt intent

value: Oligometastatic

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: molecule subtype


title: JB64

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

value: Salvage

tag: probiotics use

value: No

tag: physical activity_status

value: sedentary


title: JB60

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: secondary gps_at_diagnosis

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

value: microbial DNA


title: JB59

description: OTU genus read count

tag: age

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

value: No prostatectomy

tag: rt technique

tag: rt intent

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: undeclared

tag: molecule subtype


title: JB62

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: validation

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: probiotics use

tag: physical activity_status


title: JB55

description: OTU genus read count

tag: age

tag: clinical stage_at_diagnosis

value: Tx

tag: tumour risk_class

tag: rt technique

value: VMAT

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

value: active


title: JB56

description: OTU genus read count

tag: tissue

tag: cohort

tag: bmi

tag: smoke

value: Smoker

value: low

tag: rt intent

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: molecule subtype


title: JB57

description: OTU genus read count

tag: age

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: probiotics use

value: No

tag: physical activity_status

value: sedentary


title: JB53

description: OTU genus read count

tag: tissue

tag: cohort

tag: bmi

tag: smoke

value: Non smoker

tag: tumour risk_class

value: Prostatectomy

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: semil vesicle_irradiation

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)


title: JB54

description: OTU genus read count

value: discovery

tag: age

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: lymph node_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

tag: molecule subtype

value: microbial DNA


title: JB52

description: OTU genus read count

tag: tissue

tag: cohort

tag: bmi

tag: smoke

tag: clinical stage_at_diagnosis

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: Radical

tag: probiotics use

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: JB49

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

value: Yes

tag: plant based_diet

tag: molecule subtype


title: JB88

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: bmi

tag: smoke

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: probiotics use

tag: physical activity_status


title: JB48

description: OTU genus read count

tag: age

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

value: No

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: JB47

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Diabetes

tag: clinical stage_at_diagnosis

value: oligometastatic

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: active

tag: molecule subtype


title: JB51

description: OTU genus read count

tag: tissue

tag: cohort

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

value: intermediate

value: Prostatectomy

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class


title: IW90

description: OTU genus read count

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: Salvage

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

value: microbial DNA


title: JB46

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: very low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No prostatectomy

value: Appendectomy

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

value: Yes

tag: physical activity_status

tag: molecule subtype


title: IW85

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: Diabetes

value: high

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW86

description: OTU genus read count

tag: tissue

tag: cohort

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: No appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: active

tag: molecule subtype


title: IW89

description: OTU genus read count

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW88

description: OTU genus read count

tag: tissue

tag: cohort

tag: psa at_diagnosis_(ng/ml)

value: Prostatectomy

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype

value: microbial DNA


title: IW84

description: OTU genus read count

value: faeces

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: very low

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1


title: IW87

description: OTU genus read count

tag: tissue

tag: cohort

value: Smoker

tag: psa at_diagnosis_(ng/ml)

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: IW91

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: Radical

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1


title: JB58

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: undeclared

tag: molecule subtype


title: IW79

description: OTU genus read count

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW78

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: psa at_diagnosis_(ng/ml)

value: No prostatectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

value: Yes

tag: plant based_diet

tag: physical activity_status

tag: logt0 tnfr1

tag: molecule subtype

value: microbial DNA


title: IW80

description: OTU genus read count

tag: tissue

tag: smoke

tag: diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW83

description: OTU genus read count

tag: cohort

tag: age

tag: bmi

tag: psa at_diagnosis_(ng/ml)

value: very low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: sedentary

tag: logt0 tnfr1

tag: molecule subtype


title: IW81

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: smoke

value: Smoker

tag: diabetes

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: Salvage

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use


title: IW82

description: OTU genus read count

tag: bmi

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW75

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

value: Tx

value: high

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: Oligometastatic

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype


title: JB50

description: OTU genus read count

tag: tissue

value: faeces

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: No prostatectomy

value: Appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

value: Yes


title: IW77

description: OTU genus read count

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Diabetes

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: mb risk_class

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

value: microbial DNA


title: JB61

description: OTU genus read count

tag: tissue

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: very low

value: No appendectomy

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype


title: IW32

description: OTU genus read count

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IW35

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype


title: IW33

description: OTU genus read count

tag: tissue

tag: cohort

tag: bmi

tag: smoke

tag: diabetes

value: low

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

value: Radical

tag: acute gi_toxicity

tag: mb risk_class

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IS87

description: OTU genus read count

value: discovery

tag: age

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: oligometastatic

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: Prostatectomy

value: Appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: molecule subtype


title: IS83

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

value: microbial DNA


title: IS85

description: OTU genus read count

value: Smoker

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: active

tag: logt0 tgfb1

tag: polycytockinic risk_score

tag: molecule subtype


title: IS86

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa


title: IS82

description: OTU genus read count

tag: tissue

tag: cohort

value: validation

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: No prostatectomy

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: physical activity_status

value: undeclared

tag: molecule subtype


title: IS81

description: OTU genus read count

value: discovery

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: polycytockinic risk_score


title: IS80

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: very high

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: molecule subtype

value: microbial DNA


title: IS78

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1


title: IS67

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

value: active

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: IS50

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: molecule subtype


title: IS51

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Smoker

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

value: No appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: logt0 tgfb1


title: IS46

description: OTU genus read count

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: IS47

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

value: Prostatectomy

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 tgfb1


title: IW34

description: OTU genus read count

value: discovery

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: IS41

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes

tag: physical activity_status

tag: logt0 tgfb1


title: IS45

description: OTU genus read count

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: IS38

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

value: intermediate

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 tgfb1


title: IS48

description: OTU genus read count

tag: tissue

tag: cohort

value: Smoker

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: IS42

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: Prostatectomy

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

value: sedentary

tag: logt0 tgfb1


title: HU36

description: OTU genus read count

value: discovery

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

value: Radical

tag: acute gi_toxicity

tag: mb risk_class

value: No

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: molecule subtype


title: HU34

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HU39

description: OTU genus read count

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

value: oligometastatic

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: VMAT

tag: acute gi_toxicity

tag: mb risk_class

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: molecule subtype


title: IS39

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: smoke

tag: diabetes

value: No diabetes

tag: clinical stage_at_diagnosis

value: high

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: logt0 tnfa

value: microbial DNA


title: HU38

description: OTU genus read count

tag: tissue

tag: bmi

value: Smoker

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

tag: physical activity_status

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: polycytockinic risk_score

tag: molecule subtype


title: IS44

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: smoke

tag: diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

value: sedentary

tag: logt0 tnfa


title: IS40

description: OTU genus read count

tag: tissue

tag: cohort

tag: bmi

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

value: Radical

tag: acute gi_toxicity

tag: mb risk_class

tag: physical activity_status

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: polycytockinic risk_score

tag: molecule subtype


title: HU32

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: smoke

tag: diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: Yes


title: HU35

description: OTU genus read count

tag: bmi

value: Non smoker

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1


title: HJ42

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: smoke

tag: diabetes

value: Prostatectomy

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: HU33

description: OTU genus read count

tag: bmi

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

value: microbial DNA


title: HJ37

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

value: No appendectomy

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 tnfr1

tag: molecule subtype


title: HJ39

description: OTU genus read count

value: Smoker

value: Diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HU37

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: sedentary

tag: logt0 tnfr1

tag: molecule subtype


title: IS76

description: OTU genus read count

tag: tissue

tag: cohort

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: Radical

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HJ35

description: OTU genus read count

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: oligometastatic

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 tnfr1

tag: molecule subtype


title: HJ31

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: Non smoker

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

value: Yes

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HJ32

description: OTU genus read count

tag: tissue

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: Prostatectomy

tag: rt technique

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 tnfr1

tag: molecule subtype

value: microbial DNA


title: HeLa cells, sh-MePCE-3

city: Taipei

first: Chi-Kang

last: Tseng

address: No.1 Jen Ai road section 1

department: Graduate institute of microbiology

country: Taiwan

institute: National Taiwan university, College of Medicine

library_source: transcriptomic

data_processing:
The library samples were sequenced on the Novaseq X plus using RapidSeq-150 bp pair-end reads.
A 10-nt molecular barcode was used to remove PCR duplicates. After quality filtering, 4.7 to 6.1 million reads were analyzed per sample.
To pass the filter, a read required a minimum match of 20 nts to hTR reference sequence and 10 nts to the linker sequence.
For each filtered read, the most 3′ hTR reference coordinate between hTR:366–641 was identified by matching 20 nts closest to the 3′ end allowing for two mismatches not including the two most 3′ bases.
Assembly: hg38
Supplementary files format and content: excel file includes the raw counts

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: HeLa cells were maintained in DMEM (Gibco) supplemented with 10% heat-inactivated foetal bovine serum.

extract_protocol:
Total RNA was isolated from the pellets (1×107 cells) using Ambion TRIzol® Reagent according to the manufacturer’s instructions, followed by DNase I treatment at 37°C for 60 min.
Ligation reactions contained 2.0 µg total RNA, 1×T4 RNA ligase buffer, 5% PEG8000, 1 U T4 RNA ligase I, and 5 μM 3′ linker (CKOligo-666).
The ligation reaction mixture was incubated at 16°C for 18 hours and inactivated at 65°C for 15 minutes.
20 μl of reverse transcription reaction contained 1X ligation reactions, 1× SSIV buffer, 0.1 μM RT primer (CKOligo-667), 0.5 μM dNTPs, 5 mM DTT, RNase inhibitor, and SuperScript™ IV Reverse Transcriptase was incubated at 50°C for 10 minutes.
A total of 10 U E. coli RNase H was directly added into the reverse transcription reaction, followed by incubation at 37°C for 20 minutes and then heat-inactivation at 70°C for 15 minutes.
The first round PCR was performed with 0.5 μM CKOligo-667 and CKOligo-668 in 50 μl reactions containing 1× Phusion HF buffer, 0.2 mM dNTPs, and 0.02 U Phusion Hot Start II High Fidelity DNA polymerase. First-round PCR products were purified by PCR purification kit.
For the second-round PCR reactions, 5 μl of first-round PCR product was used as a template. 0.5 μM CKOligo-669 as the forward primer for all samples and reverse primers CKOligo-676 (sh-Luc), CKOligo-685 (sh-PARN), CKOligo-686 (sh-LARP7), and CKOligo-687 (sh-MePCE) were used. Amplicons were purified by PCR purification kit (TOOLS).

tag: tissue

value: cell line

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

value: MePCE knockdown


title: HJ29

description: OTU genus read count

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: No appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HeLa cells, sh-LARP7-3

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: LARP7 knockdown


title: HeLa cells, sh-PARN-3

value: PARN knockdown


title: HJ23

description: OTU genus read count

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: rt technique

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: active

tag: logt0 tnfr1

tag: molecule subtype


title: HJ20

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: No diabetes

tag: tumour risk_class

value: high

value: Prostatectomy

tag: appendectomy

value: Salvage

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfa

tag: polycytockinic risk_score


title: HeLa cells, sh-Luc-1

tag: tissue

value: cell line

tag: cell line

value: HeLa

tag: cell type

value: epithelial cell

tag: genotype

value: Luciferase knockdown


title: HU31

description: OTU genus read count

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 tnfr1

tag: molecule subtype

value: microbial DNA


title: Uninduced Rep1

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

country: USA

institute: University at Buffalo

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger mkfastq version 6.1.2
Cellranger count version 6.1.2
Assembly: TriTrypDB-46 T.Brucei TREU927 version 46
Supplementary files format and content: Tab separated values and matrix files

organism: Trypanosoma brucei

source_name: T. brucei 29-13

growth_protocol: SDM-79 medium supplemented with 10% fetal bovine serum and 10 U/ml of penicillin/streptomycin. Cells were maintained at a temperature of 27°C and in drug concentrations of 15 µg/mL neomycin, 50 µg/mL hygromycin, and 2.5 µg/mL phleomycin

extract_protocol:
cells were harvested 18 hours post-induction; 1x106 cells were then submitted for sc-RNAseq. An additional 5x105 cells were harvested and suspended in 4X SDS sample loading buffer for western blotting.
10X Genomics 3' scRNA-Sequencing version 2

treatment_protocol: RNAi was induced using 4 µg/ml doxycycline

tag: cell line

value: T. brucei 29-13

tag: genotype

value: RNAi construct against DRBD18

tag: treatment


title: HJ40

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: validation

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: No prostatectomy

tag: appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: active


title: Uninduced Rep2

description: 10x Genomics

tag: cell line

tag: genotype

tag: treatment


title: Induced Rep1

description: 10x Genomics

value: 4 µg/ml doxycycline


title: HJ04

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

value: Non smoker

value: No diabetes

value: intermediate

tag: prostatectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: No

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: HJ03

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: appendectomy

value: No appendectomy

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status


title: HJ02

description: OTU genus read count

tag: prostatectomy

value: Appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: WT, N24, siFoxo1, rep1

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Fastq files were analysed with a Nextflow 23.04.1.5866 /nf-core/rnaseq v3.10.1 pipeline.
Quality control was performed using fastQC (v0.11.9), and transcripts were mapped to the mm10 assembly mouse reference genome using Salmon (v1.9.0) as a pseudoaligner and STAR (v2.7.10a) as an aligner.
DESeq2 (v1.38.3) was used to generate normalised count tables and to perform differential expression analyses (FDR-adjusted p-value ≤ 0.05; H0: log2FC = 0)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include normalized counts for each Sample

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in DMEM high-glucose medium supplemented with 10% FBS, 2 mM L-Glutamine, 0.1 mM NEAA, 1 mM Sodium Pyruvate, 10 µg/ml penicillin-streptomycin , 55 µM β-mercaptoethanol, 10 ng/ml LIF and 2i (1.5 μM PD0325901 and 3 μM CHIR99021). mESCs were cultured at 37°C and 5%CO2.

extract_protocol:
RNA was extracted using the ExtractMe kit (Blirt, EM15) following the manufacturer's instructions.
200-500 ng of RNA were used as starting material for library preparation with the Lexogen 3' mRNA Seq Library Prep Kit. Libraries size was measured with the Agilent High Sensitivity DNA kit, and their qPCR-based quantification was performed with the KAPA Library Quantification kit.

treatment_protocol:
Rapamycin experiment: mESCs were plated on gelatin-coated plates in N2B27-2i + DMSO or N2B27-2i + 20 nM rapamycin. The following day, cells were washed with PBS and medium was exchanged to N2B27+DMSO or N2B27+ 20 nM rapamycin to induce differentiation for the indicated time.
RNAi experiment: mESCs were plated on gelatin-coated plates in N2B27-2i and transfected with FlexiTube siRNAs (Qiagen) using DharmaFECT 1 (Fisher Scientific, T-2001). The next day, cells were washed with PBS and medium was exchanged to either N2B27 without 2i to induce differentiation, or fresh N2B27-2i for the undifferentiated controls. Two siRNAs targeting FoxO1 (SI01005200, SI02694153) were used at a final concentration of 20 nM. As controls, siRNAs targeting GFP (siGFP) or scrambled siRNAs (siScr) were used.
MK-2206 experiment: mESCs were plated on gelatin-coated plates in N2B27-2i or N2B27-2i + 1 μM MK-2206. The following day, cells were washed with PBS and medium was exchanged to either N2B27 or N2B27+1 μM MK-2206 to induce differentiation for the indicated time, or to N2B27-2i or N2B27-2i+1 μM MK-2206 for the undifferentiated controls.

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: Foxo1 KD

tag: treatment

tag: timepoint


title: WT, N24, siCtrl, rep3

value: WT

value: siGFP


title: HJ01

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

value: Yes

tag: physical activity_status


title: HJ11

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

value: intermediate

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: WT, N24, siCtrl, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: timepoint


title: WT, N24, siFoxo1, rep2


title: HJ00

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: Tx

tag: tumour risk_class

value: high

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: No

tag: physical activity_status

value: sedentary


title: GJ88

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No appendectomy

value: VMAT

value: Salvage

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: HI99

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: Yes

tag: physical activity_status


title: Tsc2 KO, N24, Rapa, rep2

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: Tsc2 KO

tag: treatment

value: Rapamycin 20 nM

tag: timepoint


title: WT, N24, siCtrl, rep1

value: WT

value: siScr


title: HJ18

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: Appendectomy

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: No

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ86

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Oligometastatic

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

value: active

value: microbial DNA


title: GJ87

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: clinical stage_at_diagnosis

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: No prostatectomy

value: Radical

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: Pten KO, N24, Rapa, rep2

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: Pten KO

tag: treatment

value: Rapamycin 20 nM

tag: timepoint


title: HJ16

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status


title: GJ85

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: Prostatectomy

value: Salvage

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: No

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: Induced Rep2

description: 10x Genomics

tag: cell line

value: T. brucei 29-13

tag: genotype

value: RNAi construct against DRBD18

tag: treatment

value: 4 µg/ml doxycycline


title: GJ83

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

value: undeclared

value: microbial DNA


title: WT, N24, Rapa, rep2

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: WT

tag: treatment

value: Rapamycin 20 nM

tag: timepoint


title: GJ80

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: No prostatectomy

value: No appendectomy

value: Radical

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: WT, N24, DMSO, rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: DMSO

tag: timepoint


title: Tsc2 KO, N24, DMSO, rep2

value: Tsc2 KO


title: GJ79

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Adjuvant

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: No

tag: physical activity_status

value: active


title: Pten KO, N24, DMSO, rep2

tag: cell line

tag: cell type

value: embryonic stem cell

tag: genotype

value: Pten KO

tag: treatment

tag: timepoint


title: GJ75

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: VMAT

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: GJ77

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: Yes

tag: physical activity_status


title: Pten KO, N24, Rapa, rep1

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Rapamycin 20 nM

tag: timepoint


title: GJ74

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: low

value: Radical

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: WT, N24, Rapa, rep1

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

tag: timepoint


title: Tsc2 KO, N24, DMSO, rep1

value: Tsc2 KO

value: DMSO


title: GJ70

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: oligometastatic

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

value: No

tag: physical activity_status


title: GJ73

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

value: intermediate

value: VMAT

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: GJ66

description: OTU genus read count

tag: tissue

tag: cohort

value: Diabetes

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

value: undeclared


title: iSureHadCre_Postnatal HTO

city: Madrid

first: Rui

last: Benedito

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For alignment and quantification of gene expression the reference transcriptome was built using mouse genome GRCm38 and ensembl gene build version 98 (sep2019.archive.ensembl.org). The Cre, sv40pA, Tomato or WPRE transgenes sequences expressed in the samples were added to the reference
Single cell analysis was based on the Seurat R 50 package. Low quality cells were filtered out using the following criteria: total counts > 2000 and below 75000, genes detected > 500 and below, Mitochondrial transcripts content < 5%, Haemoglobin transcripts < 5%, Hashtag counts > 4 applying a 0.99 positive quantile threshold with the function HTODemux, where doublets were filtered out. Cells were de-multiplexed using the sample hashtag antibody signals (Biolegend). Counts were log-normalized and cells expressing normalized counts of Cdh5 ≤ 0.9 and WPRE ≤ 0.5 were removed to select Tomato+ expressing ECs for the analysis and remove minor contaminants.
Assembly: mm10
Supplementary files format and content: fasta file
Supplementary files format and content: gtf file
Supplementary files format and content: csv expression matrix
Supplementary files format and content: csv metadata

source_name: Heart

extract_protocol:
To isolate ECs for scRNAseq experiments, livers and hearts were dissected, minced, and digested for 30 min with pre-548 warmed (37C) dissociation buffer (2.5mg/ml collagenase I (Thermo Fisher 17100017 ), 2.5mg/ml dispase II (Thermo Fisher 17105041), 1ul/ml DNAse in PBS containing Ca2+ and Mg2+ (Gibco)). The digestion tube was agitated every 3-5 minutes in a water bath. At the end of the 30 minutes incubation, sample tubes were filled up to 15 ml with sorting buffer (PBS containing no Ca2+ or Mg2+ and supplemented with 10% FBS (Sigma, F7524)) and centrifuged (450g, 5 min, 4°C). The supernatant was aspirated, and cell pellets were resuspended in 2ml 1x RBC lysis buffer (BioLegend, 420301) and incubated for 5 min on ice. To each sample were added 6 ml of sorting buffer, and samples were then passed through a 70um filter. Live cells were counted in a Neubauer Chamber using trypan blue exclusion. Cells from each condition were collected in separate tubes, and cells were incubated for 30 min with horizontal rotation in 200ul antibody incubation buffer (PBS + 1% BSA) containing 1 μl CD31-APC and 1μl of hash tag oligo (HTO) conjugated antibodies (Biolegend). HTOs were used to label and distinguish the different samples when loaded on the same 10x genomics port, and in this way also guarantee the absence of batch effects. After the antibodies incubation, samples were transferred to 15 ml Falcon tubes, 1.4 ml sorting buffer was added, and samples were centrifuged (400g, 5min, 4°C). The supernatant was aspirated, pellets were resuspended in 1.5 ml sorting buffer and transferred to Eppendorf tubes, and the resulting suspensions were centrifuged (400g, 5min, 4°C). The resulting pellets were resuspended in 200 μl sorting buffer containing DAPI. Cells were sorted by FACS with an Aria Cell Sorter (BD Biosciences) using a 100um Nozzle 20 PSI and 16 32 0 or PURITY, Flow rate 1 - to preserve cell viability; ECs were identified as CD31+, MbTomato+ cells.
Single cell suspensions of freshly isolated ECs were resuspended in Cell Capture buffer to a final concentration of 800 to 1600 cells/μl. scRNA-seq libraries were prepared using the Chromium Single Cell 3´ Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Postnatal day 3 mice were induced with one dose of 40mg/kg 4-hydroxytamoxifen and tissues dissected and processed 3 days after.

tag: cell type

value: Endothelial cells

value: Liver

value: Heart

tag: strain

tag: genotype

value: Cdh5-CreERT2 + iHadSuRe-Cre

tag: age

tag: hto demultiplexing_conditions

value: BC305= iSureCre Heart

value: BC302= iSureCre Liver

value: BC306=Control Heart

value: BC303=Control Liver

value: BC301= iSureHadCre Heart

value: BC307= iSureHadCre Liver


title: WT, N24, DMSO, rep1

tag: cell line

value: embryonic stem cell

value: WT

tag: treatment

value: DMSO

tag: timepoint


title: iSureHadCre_Postnatal GEX

description: 10x Genomics

tag: tissue


title: GJ65

description: OTU genus read count

value: faeces

tag: cohort

value: discovery

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

value: No

tag: animal based_diet

value: Yes

tag: plant based_diet

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: GJ61

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

value: No prostatectomy

value: Appendectomy

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

value: undeclared

tag: logt0 tgfb1


title: GJ62

description: OTU genus read count

tag: tissue

value: Diabetes

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: dose/fraction

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ60

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

value: Prostatectomy

value: Salvage

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: acute gi_toxicity

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

tag: logt0 tgfb1


title: E1_hap_1_none_none_sg25_MYCsg25_cj_2

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

library_source: genomic

data_processing:
*library strategy: Targeted deep sequencing of an amplicon
Fastq files were analyzed with CRISPResso2 to yield an allele frequency table of repair outcomes for each sample.
Assembly: A custom reference was created for each amplicon which consisted of the two Cas9 cut sites for the amplicon being directly ligated together.
Supplementary files format and content: The processed data file is a csv file containing a merged allele frequency table for all the samples. It has every repair outcome, its frequency, and metadata, merged across all samples.

molecule: genomic DNA

growth_protocol: (C631) and Hap1 knockout cell lines (PRKDC-KO: HZGHC024034c011, LIG4-KO: HZGHC000759c014; POLQ-KO: HZGHC000647c003, Horizon Discovery) were maintained in IMDM supplemented with GlutaMAX and 10% FCS (Gibco). K562 cells (ATCC) were maintained in RPMI supplemented with 10% FCS. Cell lines were used as received without authentication. Cells regularly tested negative for mycoplasma contamination. The FTE5 organoid line was generated from phenotypically normal fresh surgical discards of a patient undergoing salpingectomy at Stanford University Hospital via Stanford University Hospital’s Tissue Procurement Shared Resource Facility. Isolation of fallopian tube epithelial cells followed previously established protocols. Isolated fallopian tube cells were resuspended in matrigel (R&D Systems: Basement Membrane Extract type 2 #3533-005-02) and plated in a 24 well plate as individual domes. Following solidification, organoid media supplemented with 10 uM Y-27632 (PeproTech: #1293823) was added to each well. After 2 days, Y-27632 was removed from the media and changed every 3-4 days. Organoids were passaged every 14 days by dissolving Matrigel and dissociating fallopian tube organoids to single cells using TrypLE (Invitrogen: #12604-012) at 37°C for 15 minutes inverting 2-3 times every 5 mins. TrypLE was quenched with FBS and removed following centrifugation for 3 minutes at 600g. The single cells were resuspended in matrigel and plated in a 24 well plate.

extract_protocol:
gDNA was isolated using DNeasy columns (QIAGEN) according to the manufacturer’s instructions, including a 10-min incubation at 56 °C during the proteinase K digestion step; DNA was eluted with 100 μl EB buffer.
20 cycles of primary PCR to amplify the region of interest was performed using ~200ng µL of genomic DNA in a 10 µL Platinum SuperFi II polymerase reaction (Thermo Fisher Scientific; for primers see Supplementary Data Set 1). Illumina adapters and indexing sequences were added via 15 cycles of secondary PCR with 1 µL of primary PCR product in a 10 µL Platinum SuperFi II polymerase reaction. The final amplicons were run on a TAE-agarose gel (0.7%); and the product band was excised and extracted using the Freeze and Squeeze Kit according to the manufacturer’s instructions (Bio-Rad). Gel-purified amplicons were quantified with a dsDNA HS Assay kit on a Qubit fluorometer (ThermoFisher Scientific). Then, amplicons were pooled and sequenced on the NextSeq 550 platform (Nextseq 500/550 Mid Output Kit v2.5, Illumina, for primers see Supplementary Data Set 1). DHFR CRISPR-C time course samples in Fig. 3D were reported previously described, and subsequently sequenced for this study

treatment_protocol: Hap1 cells were trypsinized, quenched with IMDM (GlutaMAX, 10% FCS), counted and centrifuged at 300g for 5 min. Cells were washed once with PBS before resuspension in Neon Resuspension Buffer to 1.1 × 107 cells per mL for Hap1 cells and 2.67 × 107 cells per mL for K562 cells. Ribonucleoprotein (RNP) complexes were formed as follows: Cas9 (IDT) was diluted to 36 μM in Neon Resuspension Buffer. Equal volumes of diluted Cas9 and sgRNA (44 μM in TE, pH 8.0) were mixed and incubated at room temperature for 10–20 min. Left and right sgRNA RNPs were assembled separately. Then, 5.5 μl of each RNP, 5.5 22 μl of electroporation enhancer (10.8 μM; IDT) and 99 μl of cells were mixed and electroporated according to the manufacturer’s instructions using a 100-μl Neon pipet tip and electroporated with the Neon Transfection System (Thermo Fisher Scientific) using the following settings: Hap1 (1,575 V, 10 ms pulse width, 3 pulses); K562 (1,700 V, 20 ms, 1 pulse). Single-guide controls were prepared as above except 11 μl of the appropriate sgRNA was used. Volumes were scaled down for 10 uL electroporations. Cells were collected at the 24 hours post-electroporation as follows: cells were washed with 1 ml per well prewarmed PBS (Gibco), followed by the addition of 100 μl TrypLE Express (Thermo Fisher Scientific) and incubation at 37 °C for 5–10 min. TrypLE was quenched with 800 μl IMDM (GlutaMAX, 10% FCS) and the cell suspension was pelleted at 300 g for 5 min at 4 °C. The supernatant was discarded and the cell pellets were stored at −80 °C.  For experiments including inhibition of DDR proteins, after electroporation, cells were plated in media containing either AZD7648 (1 μM), SCR7 (1 μM,), Berzosertib (80 nM), KU-55933 (10 μM) Talazoparib (10 nM), or DMSO. Samples were harvested 24 hours after electroporation. All compounds were obtained from Selleck Chemicals. Final DMSO concentration in all wells was 0.2%. Final drug concentrations were selected based on effective doses for cell culture reported in the literature(50–54). For ecDNA generation vía CRISPR-C in FTE5 organoids, organoid media was supplemented with Y-27632 one day prior to electroporation. RNP complexes were made by incubating (per reaction) 10uL Opti-MEM (Gibco #31985062), 0.6ul 10ug/mL Cas9 (IDT #1081059), and 44umol sgRNA for each sgRNA and incubated at room temperature for 15 minutes before combining. FTE5 organoids were dissociated as above and 2x10^5 cells were resuspended 10ul Opti-MEM per reaction. Cells and RNP complexes were combined and 20ul was added per well of a Nucleocuvette strip (Lonza #NC0828118) and electroporated using a Lonza 4D Nucleofactor-x with protocol “Primary Cell P3 code CA137. Cells were collected from the cassette and resuspended in matrigel before plating in a 24 well plate and given organoid media containing Y-27632 for 3 days before removing. 3 reactions were performed per replicate. 24 hours post electroporation, organoids were dissociated as before and DNA was harvested from the organoids using a Qiagen DNAeasy Blood and Tissue kit (Qiagen #69506).

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg2, MYC sg5

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_1_none_none_sg26_MYCsg26_cj_2

value: MYC_sg2, MYC sg6


title: Tsc2 KO, N24, Rapa, rep1

tag: cell line

value: embryonic stem cell

tag: genotype

value: Tsc2 KO

tag: treatment

value: Rapamycin 20 nM

tag: timepoint


title: E1_hap_1_none_none_sg26_MYCsg26_cj_1


title: Pten KO, N24, DMSO, rep1

value: Pten KO

value: DMSO


title: E1_hap_1_none_none_sg25_MYCsg25_cj_1


title: E1_hap_1_none_none_sg16_MYCsg16_cj_2

value: MYC_sg1, MYC sg6


title: GJ54

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: low

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mean dose_to_the_rectum_(gy)

value: No

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: GJ46

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: prostatectomy

value: No prostatectomy

value: No appendectomy

value: Radical

tag: mb risk_class

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

value: undeclared

tag: logt0 tgfb1


title: E1_hap_1_none_none_sg24_MYCsg24_cj_1

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg2, MYC sg4

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_1_none_none_sg24_MYCsg24_cj_2


title: GJ48

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

value: high

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mean dose_to_the_rectum_(gy)

value: Yes

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ45

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: mb risk_class

tag: probiotics use

tag: physical activity_status

tag: logt0 tgfb1


title: GJ52

description: OTU genus read count

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mean dose_to_the_rectum_(gy)

tag: animal based_diet

tag: plant based_diet

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: E1_hap_1_none_none_sg15_MYCsg15_cj_2

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg1, MYC sg5

tag: replicate

tag: amplicon name

tag: group


title: GJ69

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: physical activity_status

tag: logt0 tgfb1


title: E1_hap_1_none_none_sg16_MYCsg16_cj_1

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg1, MYC sg6

tag: replicate

tag: amplicon name

tag: group


title: GJ44

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: animal based_diet

tag: plant based_diet

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: E1_hap_1_none_none_sg15_MYCsg15_cj_1

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

tag: replicate

tag: amplicon name

tag: group


title: GJ43

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: physical activity_status

tag: logt0 tgfb1


title: E1_hap_1_none_none_sg14_MYCsg14_cj_2

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg1, MYC sg4

tag: replicate

tag: amplicon name

tag: group


title: GJ42

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ38

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

value: Adjuvant

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet

tag: physical activity_status

tag: logt0 tgfb1


title: GJ32

description: OTU genus read count

tag: tissue

tag: clinical stage_at_diagnosis

value: Tx

tag: prostatectomy

tag: appendectomy

value: Appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

value: active

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ33

description: OTU genus read count

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: tumour risk_class

value: intermediate

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

value: VMAT

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No


title: E1_hap_1_none_none_sg26_MYCsg26_sj_1

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg2, MYC sg6

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_1_none_none_sg25_MYCsg25_sj_2

value: MYC_sg2, MYC sg5


title: E1_hap_1_none_none_sg24_MYCsg24_sj_2

value: MYC_sg2, MYC sg4


title: E1_hap_1_none_none_sg25_MYCsg25_sj_1


title: GJ26

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: animal based_diet

tag: plant based_diet

value: Yes

tag: physical activity_status

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA


title: E1_hap_1_none_none_sg15_MYCsg15_sj_2

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg1, MYC sg5

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_1_none_none_sg15_MYCsg15_sj_1


title: E1_hap_1_none_none_sg16_MYCsg16_sj_1

value: MYC_sg1, MYC sg6


title: E1_hap_1_none_none_sg24_MYCsg24_sj_1


title: GJ22

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Non smoker

tag: diabetes

value: No diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: Prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Salvage

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

tag: animal based_diet

tag: plant based_diet


title: GJ36

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: high

value: VMAT

tag: physical activity_status

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: GJ23

description: OTU genus read count

tag: tissue

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet

value: active


title: GJ21

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: physical activity_status

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: E1_hap_5_none_none_none_DHFR_sj_3

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: DHFR_gL, DHFR_gR

tag: replicate

tag: amplicon name

value: DHFRsj

tag: group


title: GJ28

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

value: intermediate

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

value: microbial DNA


title: GJ24

description: OTU genus read count

tag: tissue

tag: cohort

tag: age

tag: bmi

tag: smoke

value: No diabetes

value: Tx

value: oligometastatic

value: Prostatectomy

value: Salvage

tag: probiotics use

tag: physical activity_status

value: sedentary

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype


title: E1_hap_5_none_none_none_DHFR_cj_3

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

tag: replicate

tag: amplicon name

value: DHFRcj

tag: group


title: GJ40

description: OTU genus read count

tag: tissue

value: faeces

tag: cohort

tag: age

tag: bmi

tag: smoke

tag: diabetes

tag: psa at_diagnosis_(ng/ml)

tag: clinical stage_at_diagnosis

tag: tumour risk_class

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

value: No prostatectomy

tag: appendectomy

tag: rt technique

value: VMAT

tag: rt intent

value: Radical

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

tag: fraction number

tag: dose/fraction

tag: acute gi_toxicity

tag: mb risk_class

tag: mean dose_to_the_rectum_(gy)

tag: probiotics use

value: No

tag: animal based_diet

tag: plant based_diet


title: E1_hap_1_none_none_sg14_MYCsg14_sj_2

tag: cell type

tag: day

tag: drug

tag: ko

tag: grna

value: MYC_sg1, MYC sg4

tag: replicate

tag: amplicon name

tag: group


title: E1_hap_1_none_none_sg16_MYCsg16_sj_2

value: MYC_sg1, MYC sg6


title: E1_hap_1_none_none_sg26_MYCsg26_sj_2

value: MYC_sg2, MYC sg6


title: E1_hap_1_none_none_sg14_MYCsg14_sj_1


title: E1_hap_5_none_none_none_DHFR_sj_2

value: DHFR_gL, DHFR_gR

value: DHFRsj


title: GJ30

description: OTU genus read count

tag: tissue

tag: cohort

value: discovery

tag: age

tag: bmi

tag: smoke

value: Smoker

tag: diabetes

value: Diabetes

tag: psa at_diagnosis_(ng/ml)

tag: primary gps_at_diagnosis

tag: secondary gps_at_diagnosis

tag: prostatectomy

tag: appendectomy

value: No appendectomy

tag: rt technique

tag: rt intent

tag: dose to_the_prostate_ptv_(gy)

tag: lymph node_irradiation

tag: semil vesicle_irradiation

value: Yes

tag: physical activity_status

value: undeclared

tag: logt0 ccl2

tag: logt0 pdgf_bb

tag: logt0 tgfb1

tag: logt0 tnfr1

tag: logt0 tnfa

tag: polycytockinic risk_score

tag: molecule subtype

value: microbial DNA