title: mCRC_034

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

value: IV

value: Right hemicolectomy

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: CIR

value: Not evaluated

value: KRAS, TP53

tag: genotype

value: intermediate


title: mCRC_033

status: Public on Jun 26 2022

type: RNA

city: BARCELONA

first: Leire

last: Pedrosa

state: Barcelona

address: Carrer del Villarroel 170

country: Spain

institute: IDIBAPS

hyb_protocol: Gene Expression RNA CodeSet Hybridization Protocol MAN-10056: Prepare Master Mix adding 70uL of Hybridization Buffer to the tube containing the 42uL of Reporter CodeSet. Add 8 μL of Master Mix to each well of a strip tube, Add 5 µL of sample to each tube containing Master Mix. Mix the Capture ProbeSet tube by inverting or flicking, and briefly spin down the contents. Add 2 μL of Capture ProbeSet to each tube. Cap the strip tubes tightly and mix. Spin briefly and immediately place the tubes in a pre-heated 65°C thermal cycler. Incubate hybridization reactions for 16 hours. Incubate at 4°C and read.

scan_protocol: nCounter Prep Station using nCounter Analysis System User Manual (MAN-C0035), nSolver software

data_processing: The raw data were analyzed with nSolver software. Only the samples that passed the control quality were normalized by nSolver, using default settings and taking into account the positive and negative probes and the housekeeping genes in the panel

molecule: total RNA

organism: Homo sapiens

source_name: tumour tissue

label_protocol: pathology of study (mCRC) and the order to RNA extraction

extract_protocol: High Pure FFPET RNA isolation kit, Roche

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

value: No

tag: extrahepatic metastasis

tag: cea

value: CAPECITABINA

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: NRAS

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: high


title: mCRC_040

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: left

value: Left hemicolectomy+Cytoreduction +HIPEC

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: BRAF

tag: genotype


title: mCRC_039

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

value: FOLFOX

tag: extrahepatic metastasis

tag: cea

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: CAP-BEV

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: mCRC_038

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: Yes

value: Left hemicolectomy

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: No

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: CIR

value: Not evaluated

value: Alive

value: BRAF, RAS

tag: genotype

value: intermediate


title: P80

type: genomic

city: Badalona

first: Manel

last: Esteller

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: Whole blood samples were obtained from 69 healthy children and adolescents collected during the pre-COVID-19 era (before December 2019)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting. Briefly, 600 ng of DNA of the studied samples was used to hybridize the BeadChip 850K microarray and scanned using HiScan SQ system (Illumina)

data_processing:
Raw signal intensity data were initially QC’d and preprocessed from resulting idat files in R statistical environment (v4.0.3) using minfi Bioconductor package (v1.36.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (probes with detection P value > 0.01 in at least 10% of samples were removed. If probe P value > 0.01 in less than 10% of samples, the Beta values of those probes in the failed samples were marked as NAs and later imputed using the median), cross-reacting probes, and probes that overlapped SNPs within ±1 bp of CpG sites, followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). All analyses were performed under R statistical environment (v4.0.3)
Minfi (v1.36.0) preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: High molecular weight DNA extracted from whole blood samples

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P87


title: P86

value: Male


title: P77


title: P84


title: P78


title: mCRC_037

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

value: left

tag: state at diagnosis

value: IV

tag: primary surgery

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX-CET

tag: response

value: Progression

tag: progression

tag: date of progression

tag: treatment at progression

value: FOLFIRI

tag: status

value: Dead

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: P76

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: P83


title: mCRC_027

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: XELOX

tag: metastasis

tag: liver metastasis

value: No

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

tag: genotype


title: P82

tag: tissue

value: whole blood

tag: group

tag: biological sex

tag: age (years)


title: mCRC_028

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Sigmoidectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: CIR

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

value: CAPOX

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification

value: intermediate


title: mCRC_032

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Transverse

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX

value: Estable

value: KRAS, PIK3CA

tag: genotype

value: high


title: P81

tag: tissue

tag: group

value: Control

tag: biological sex

tag: age (years)


title: mCRC_031

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: extrahepatic metastasis

tag: cea

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI-CET

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: FBXW7, PIK3CA

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: mCRC_030

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Sigmoidectomy

tag: date of surgery

value: No

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: CIR

value: Not evaluated

value: Alive

tag: genotype

value: low


title: mCRC_029

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: IV

value: Abdominal resection

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

value: RF

tag: status

tag: date of last follow up

tag: mutations

value: WT

tag: number of mutations

tag: mss

tag: gemcad classification

value: intermediate


title: P74

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P79

value: Female


title: mCRC_023

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFIRI

value: Parcial Response

value: PANI

value: Dead

value: BRAF

tag: genotype

value: MSS


title: P70

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: mCRC_021

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX-PANI

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

value: FOLFIRI-AFLI

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: P75

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Male

tag: age (years)


title: mCRC_026

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Sigmoidectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-CET

value: FOLFIRI-CETUXI

value: Alive

tag: genotype

value: MSI

value: low


title: P68

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: mCRC_025

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

value: Yes

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: KRAS, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: high


title: P66

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Male

tag: age (years)


title: mCRC_024

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

value: IV

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: Progression

value: IRI-BEV

tag: genotype

value: intermediate


title: P64

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: mCRC_022

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Sigmoidectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: CAPECIT

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX-BEV

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: KRAS, SMAD4

tag: number of mutations

tag: mss

value: MSI

tag: gemcad classification


title: P73

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P72


title: P62


title: mCRC_013

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-PAN

value: Parcial Response

value: Dead

value: FBXW7, TP53

tag: genotype

value: MSS

value: high


title: P71

tag: tissue

tag: group

tag: biological sex

tag: age (years)


title: mCRC_012

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

value: Yes

tag: surgery

tag: date of surgery

tag: adjuvancy

value: No

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: CIR

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

value: FOLFIRI

tag: status

value: Alive

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification

value: low


title: mCRC_020

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Rectosigmoidectomy

tag: date of surgery

value: FOLFOX

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFIRI-CETUXI

value: WT

tag: genotype


title: mCRC_019

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: PANI

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

value: BSC

tag: status

value: Dead

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: mCRC_011

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

tag: state at diagnosis

tag: primary surgery

tag: surgery

tag: date of surgery

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

tag: genotype


title: mCRC_018

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: IV

value: Yes

value: Left hemicolectomy

tag: adjuvancy

value: No

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI-PANI

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: P61

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: P69

value: Male


title: P67


title: P59


title: mCRC_017

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Sigma

tag: localization (right or left)

value: left

tag: state at diagnosis

value: I

tag: primary surgery

tag: surgery

value: Polipectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-PAN

value: Estable

tag: genotype

value: high


title: mCRC_016

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

tag: extrahepatic metastasis

tag: cea

value: FOLFOX

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: FBXW7, KRAS, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: intermediate


title: mCRC_015

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: Yes

tag: adjuvancy

tag: tipe of adjuvancy

value: CAPECIT

tag: metastasis

tag: liver metastasis

value: No

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

tag: genotype


title: P65

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P63

value: Female


title: P56


title: mCRC_008

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: left

tag: state at diagnosis

value: IV

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

tag: date of last follow up

tag: mutations

value: KRAS, TP53

tag: number of mutations

tag: mss

tag: gemcad classification

value: high


title: mCRC_009

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

tag: primary surgery

tag: surgery

value: Ileocecal resection

tag: date of surgery

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: CIR

value: Not evaluated

value: Alive

value: WT

tag: genotype


title: mCRC_014

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: III

value: Yes

value: Abdominal resection

tag: adjuvancy

tag: tipe of adjuvancy

value: CAPECIT

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: XELOX

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: KRAS, SMAD4, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: mCRC_006

tag: Sex

value: Female

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

value: No

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-BEV

value: Parcial Response

value: KRAS

tag: genotype

value: low


title: mCRC_010

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

tag: localization (right or left)

value: right

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: extrahepatic metastasis

tag: cea

value: FOLFOX

tag: response

tag: progression

tag: date of progression

tag: treatment at progression

value: IRI-PAN

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification

value: intermediate


title: P58

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: P60

description: Whole blood samples and clinical data from 43 patients with MIS-C were retrospectively collected between April 16th, 2020 and August 17th, 2021 from seven Hospitals in Spain. MIS-C was diagnosed based on the case definition provided by the World Health Organization

value: MIS-C


title: P57


title: mCRC_007

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

tag: primary surgery

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-PAN

value: FOLFIRI-PAN

value: Dead

tag: genotype

value: MSS


title: mCRC_005

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Transverse

tag: localization (right or left)

tag: state at diagnosis

value: IV

tag: primary surgery

tag: surgery

value: Right hemicolectomy

tag: date of surgery

value: No

tag: extrahepatic metastasis

tag: cea

value: CAPECITABINA

tag: response

value: Estable

tag: progression

tag: date of progression

tag: treatment at progression

value: PANI

tag: status

tag: date of last follow up

tag: mutations

tag: number of mutations

tag: mss

tag: gemcad classification


title: P55

tag: tissue

value: whole blood

tag: group

tag: biological sex

value: Female

tag: age (years)


title: F5_blue_sperm_flash_frozen

type: SRA

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

country: USA

institute: Auburn University

description: Illumina mRNA-seq

library_source: transcriptomic

data_processing:
FastQC (version 0.11.6) software was used for quality check.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic (version 0.39), and masked for low-complexity or low-quality sequence.
The ramaining high-quality clean reads were mapped to mus musculus whole genome using TopHat (version 2.1.1)
HTseq (version 1.0) was conducted to calculate the number of aligned reads of each gene overlapping its exons.
edgeR was used to calculate log2-fold change (log2FC), |log2FC| >2 and FDR < 0.05 was used as cutoff for generating DEGs.
Assembly: Ictalurus furcatus genome (GenBank assembly accession JAJOLW000000000)
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene in all samples

organism: Ictalurus furcatus

source_name: Ictalurus furcatus sperm

extract_protocol:
AllPrep DNA/RNA Kit (Qiagen, CA, USA)
The RNA integrity was evaluated with the LabChip GX Touch HT (PerkinElmer, MA, USA). The RNA library preparation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, MA, USA). Enriched RNAs were fragmented for 10 minutes at 94 °C. The first strand cDNA synthesis, second strand cDNA synthesis, end repair and adaptor ligation according to the manufacturer’s protocol. The library PCR amplification were performed with 16 cycle PCR. The RNA sequencing libraries were checked using the TapeStation 4200 D1000 ScreenTape (Agilent Technologies, CA, USA) and quantified by using Qubit 2.0 Fluorometer (Invitrogen, CA, USA).

tag: strain

value: D&B

value: sperm


title: mCRC_004

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: XELOX

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: CIR

value: Not evaluated

tag: genotype

value: low


title: Ly6G, IgG, monotherapy

city: Lebanon

first: Evelien

last: Schaafsma

state: New Hampshire

address: One Medical Drive

institute: Dartmouth

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Seurat objects for CD45+, AH1-specific CD8+ T cells, and Ly6G+ tumor infiltrating cells

organism: Mus musculus

source_name: Ly6G+ tumor infiltrating myeloid cells

growth_protocol: CT26 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine. These cells were purchased from the American Type Culture Collection (Product: ATCC CRL-2638). The experiments in this study used cells of lot number: 63226308. Tumor inoculations were performed intradermally (i.d.) into the flank with 10^5 cells per mouse.

extract_protocol:
Immune cells were isolated from tumors using the Miltenyi Tumor Dissociation Kit (Miltenyi Biotech, Bergish Gladbach, Germany) according to manufacturer’s directions. Where indicated, CD45 enrichment was performed using Miltenyi CD45 (TIL) kit according to directions, but with cells passed over 3 columns per sample for improved purity and viability. For scRNAseq experiments with AH1-specific T cells, or Ly6G+ myeloid cells, cells were first pre-enriched with Miltenyi CD45 (TIL) or Ly6G positive selection Microbeads according to manufacturer instructions. Cells were pre-stained with Fc-block and tetramer for 10 minutes at room temperature, and then antibodies were added without washing for a further 20 minutes. Cells were washed and then flow-sorted using FACS-ARIA II (BD Biosciences). Purity was validated by using subsequent flow cytometry. AH1-specific T cells were sorted as viability dye-, CD8+, CD4-, tet+, Dump (CD11c, CD19, F4/80, B220)-negative, singlet events. Ly6G+ myeloid cells were sorted as Ly6G+ CD11b+, CD45+ Ly6Cint, viability dye- singlet events.
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

treatment_protocol: For early intervention monotherapy experiments, mice were treated with either monoclonal hamster antibody (PIP; BioXCell, Lebanon, NH) or anti-VISTA (13F3; produced by Aragen Biosciences) at 300ug every 2 to 3 days for a maximum of 3 (MB49) or 6 (CT26) treatments. Treatment was initiated at a tumor volume of 1000mm3 (MB49; 7 days post-inoculation) or 40mm3 (CT26; 5-6 days post-tumor inoculation). For late intervention combination therapy experiments, mice were treated with isotype antibody or anti-VISTA at 300g, and anti-CTLA-4 (9H10; BioXCell) and anti-PD-1 (RMP1-14; BioXCell) at 200g per dose every 2 to 3 days for a maximum of 6 treatments. Treatment was initiated at a tumor volume of 600m3, generally at 14 days post-tumor inoculation.

tag: cell type

value: Ly6G+ cells

tag: tissue

value: Ly6G+ tumor infiltrating myeloid cells

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks old


title: AH1, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 1, combo therapy

description: 10x Genomics

source_name: Tetramer-sorted tumor infiltrating CD8+ T cells

value: AH1+ CD8+ T cells


title: P54

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: mCRC_001

tag: Sex

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Ascending

tag: localization (right or left)

value: right

tag: state at diagnosis

value: IV

tag: primary surgery

value: No

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

value: Yes

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: cea

value: FOLFOX

tag: response

value: Parcial Response

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Dead

tag: date of last follow up

tag: mutations

value: BRAF, TP53

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification

value: high


title: AH1, anti-PD-1+anti-CTLA4, combo therapy

description: 10x Genomics

tag: cell type

tag: tissue

value: Tetramer-sorted tumor infiltrating CD8+ T cells

tag: strain

value: BALB/c

tag: age


title: AH1, Untreated, combo therapy

description: 10x Genomics

value: AH1+ CD8+ T cells

value: 8-10 weeks old


title: mCRC_002

tag: Sex

value: Male

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Rectum

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

tag: surgery

value: Abdominal resection

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

tag: metastasis

tag: liver metastasis

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: metastatic lymph nodes

tag: metastasis in other

tag: number of affected organs

tag: ps

tag: ldh

tag: leukocytes

tag: pcr

tag: treatment

value: FOLFOX-BEV

value: FOLFIRI-AFLI

value: KRAS, TP53

tag: genotype

value: intermediate


title: C5_blue_sperm_cryo

description: Illumina mRNA-seq

tag: strain

value: D&B

tag: tissue

value: sperm


title: P53

value: whole blood

tag: group

value: Control

tag: biological sex

tag: age (years)


title: Ly6G, antiVISTA, monotherapy

description: 10x Genomics

tag: cell type

value: Ly6G+ cells

value: Ly6G+ tumor infiltrating myeloid cells

tag: age


title: AH1, anti-VISTA R, biol rep 1, monotherapy

description: 10x Genomics

value: AH1+ CD8+ T cells

value: Tetramer-sorted tumor infiltrating CD8+ T cells

value: BALB/c


title: P49

value: MIS-C

value: Female


title: P50


title: AH1, anti-VISTA NR, monotherapy

description: 10x Genomics

value: 8-10 weeks old


title: mMDSC, Male, Healthy, Biological replicate 1

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

library_source: genomic

data_processing:
Cutadapt v1.9.1 was used to remove paired-end adapter sequences and discard reads with a length less than 20bp from the raw FASTQs.
Trimmed and filtered reads were aligned to the mm10 genome assembly (retrieved from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips) using BWA-MEM v0.7.17-r1188 with default parameters in paired-end mode.
PCR duplicates were removed using SAMtools v1.10.
Peaks were detected with MACS v2.1.2 with --format=BAMPE.
DeepTools v3.2.0 was used to generate RPGC-normalized bigWig tracks with 50 bp bin sizes.
ATAC-Seq peaks called across all samples were filtered for significance (peaks with Benjamini-Hochberg corrected p-values (q-val) > 0.001 were excluded), combined together, overlapping peaks merged, and the resultant merged peak list was filtered to remove all peaks overlapping ENCODE blacklisted regions (mm10 blacklist file v2 downloaded from https://sites.google.com/site/anshulkundaje/projects/blacklists). Read depth for each merged peak region was determined using coverageBed from BEDTools v2.17.0, resulting in a read_counts.txt file for each sample.
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig
Supplementary files format and content: tab-delimited text files include read counts for the set of merged ATAC-seq peaks (peak IDs are given as genomic coordinates in the form chr_start_stop)

source_name: Monocytic myeloid-derived supressor cells

extract_protocol:
Cells were sorted from the bone marrow of sham-injected or GL261 cell-implanted male and female C57BL/6 mice. Cells were washed with cold PBS and counted on a Countess (Invitrogen). Pellets were resuspended in 1 ml of nuclei permeabilization buffer (PBS with 1 mM dithiothreitol, 5% bovine serum albumin, 0.2% IGEPAL-CA630 (Sigma Aldrich) and 1x cOmplete EDTA-free protease inhibitor (Roche)) and rotated for 10 min at 4°C as per the Ren et al. protocol (https://www.encodeproject.org/documents/4a2fc974-f021-4f85-ba7a-bd401fe682d1/). The nuclear suspension was filtered on a 30 µm CellTrics (Sysmex) and spun at 500 x g for 5 min at 4°C. The resulting pellet was resuspended in 50 µl tagmentation buffer (33 mM Tris-acetate pH 7.8, 66 mM potassium acetate, 11 mM magnesium acetate, and 16% N'N-dimethylformamide, in water). An aliquot of nuclear suspension was counted on a Countess. For each tagmentation reaction, 160,000 nuclei were mixed with 1 µl of Tagment DNA enzyme in a total of 20 µl and incubated for 30 min with 500 rpm at 37°C. Then 200 µl buffer PB (Qiagen) and 10 µl sodium acetate (3M, pH 5.2) were added, and the sample was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10 µl EB.
Fragments were amplified by PCR using indexed primers, then purified using the MinElute PCR purification kit with elution in 40 µl EB. Size selection was performed with PCRclean Dx beads (ALINE) by adding 160 µl EB to the 40 µl sample and adding 110 µl beads. After mixing and incubation for 5 min at room temperature, the tube was put on a magnetic stand and the supernatant transferred to a new tube, to which 190 µl beads was added. This suspension was mixed, incubated, and put on the magnetic stand, and this time the supernatant was discarded.  Beads were washed twice with 70% ethanol, then the DNA was eluted from the beads with 20 µl EB. The indexed libraries were sequenced on a NextSeq high-output flow cell, paired-end, 75 cycles.

tag: Sex

value: Male

value: Sham-injected


title: P52


title: mCRC_003

tag: date of birth

tag: date of diagnosis

tag: age of diagnosis

tag: tumour localization

value: Descending

tag: localization (right or left)

value: left

tag: state at diagnosis

value: III

tag: primary surgery

value: Yes

tag: surgery

value: Left hemicolectomy

tag: date of surgery

tag: adjuvancy

tag: tipe of adjuvancy

value: FOLFOX

tag: metastasis

tag: liver metastasis

value: No

tag: number of liver metastasis

tag: extrahepatic metastasis

tag: lung metastasis

tag: peritoneal metastases

tag: metastatic lymph nodes

tag: cea

value: CIR

tag: response

value: Not evaluated

tag: progression

tag: date of progression

tag: treatment at progression

tag: status

value: Alive

tag: date of last follow up

tag: mutations

value: WT

tag: number of mutations

tag: mss

value: MSS

tag: gemcad classification


title: mMDSC, Male, Tumor, Biological replicate 2

tag: cell type

value: Monocytic myeloid-derived supressor cells

tag: Sex

tag: treatment


title: P51

tag: tissue

value: whole blood

tag: group

value: Control

tag: biological sex

value: Female

tag: age (years)


title: AH1, anti-PD-1+anti-CTLA4+anti-VISTA NR, combo therapy

description: 10x Genomics

value: AH1+ CD8+ T cells

value: Tetramer-sorted tumor infiltrating CD8+ T cells

tag: strain

value: BALB/c

tag: age

value: 8-10 weeks old


title: Ly6G, Untr, CP, CPV-NR, CPV-R, monotherapy

description: 10x Genomics

value: Ly6G+ cells

value: Ly6G+ tumor infiltrating myeloid cells


title: mMDSC, Male, Tumor, Biological replicate 1

value: Male


title: F3_blue_sperm_flash_frozen

description: Illumina mRNA-seq

value: D&B

value: sperm


title: P47

value: MIS-C


title: AH1, IgG, monotherapy

description: 10x Genomics


title: mMDSC, Female, Healthy, Biological replicate 2

value: Sham-injected


title: P46


title: P45


title: mMDSC, Male, Healthy, Biological replicate 2


title: AH1, anti-VISTA R, biol rep 2, monotherapy

description: 10x Genomics


title: mMDSC, Female, Tumor, Biological replicate 2


title: P48


title: CD45, anti-PD-1+anti-CTLA4, biol rep 2, combo therapy, exp 2

description: 10x Genomics

source_name: Tumor infiltrating leukocytes

value: CD45+ immune cells

value: Tumor infiltrating leukocytes


title: P44


title: CD45, anti-PD-1+anti-CTLA4, biol rep 1, combo therapy, exp 2

description: 10x Genomics


title: gMDSC, Male, Tumor, Biological replicate 1

source_name: Granulocytic myeloid-derived supressor cells


title: gMDSC, Male, Healthy, Biological replicate 2

value: Granulocytic myeloid-derived supressor cells


title: P42

value: whole blood


title: F2_blue_sperm_flash_frozen

description: Illumina mRNA-seq


title: RNA-seq LPS Cond parents rep3

city: Rishon Lezion

first: Tali

last: Rosenberg

address: Hamacabim

country: Israel

institute: ARO

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using Cutadapt. Resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome (galGal5.0, UCSD) according to Refseq annotations, using STAR.Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Read counts per gene were calculated using HTSeq-count, with the following parameters: 'htseq-count -s no --mode=union’. Normalization and differential expression analysis were performed using the DESeq2. Differentially expressed genes (DEG) were defined as genes that had a significant adjusted p value (padj) of less than 0.05 and at least 2-fold change. To elucidate gene alterations across all analyzed groups, the expression of all DEG was assessed. Respective heat maps were generated by custom R scripts and the Complexheatmap R package.
Assembly: galGal5
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Anterior preoptic hypothalamus

extract_protocol:
Total RNA was isolated with TriReagent.
15 ng of purified RNA was used for library preparation with the bulk MARS-seq method (Jaitin et al. 2014 Science.343:776-9).100bp single reads were sequenced on a Novaseq 6000 sequencing system. The output was ~25 million reads per sample.

treatment_protocol: Nonconditioned F1 chicks (day 10 posthatch) were subjected to Heat challenge (moved from 30°C environment to 36°C environment) or LPS  Challenge (LPS was injected into the third ventricle). Chicks were sacrificed 6 hours into each challenge and their APH dissected.  Unchallenged groups (t0) were used as controls. mRNA WAS extracted using Tri-Reagent. Total RNA was isolated from each sample and subjected to RNA-Seq.

value: whole tissue lysate

value: 6h LPS Cond parents

value: day 10 posthatch


title: RNA-seq LPS Cond parents rep1


title: C3_blue_sperm_cryo

description: Illumina mRNA-seq


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 2, combo therapy, exp 2

description: 10x Genomics


title: P40


title: mMDSC, Female, Tumor, Biological replicate 1

value: Monocytic myeloid-derived supressor cells

value: Female


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 1, combo therapy, exp 2

description: 10x Genomics

value: BALB/c

value: 8-10 weeks old


title: C2_blue_sperm_cryo

description: Illumina mRNA-seq


title: CD45, anti-PD-1+anti-CTLA4, biol rep 4, combo therapy, exp 2

description: 10x Genomics


title: gMDSC, Female, Tumor, Biological replicate 1


title: mMDSC, Female, Healthy, Biological replicate 1


title: RNA-seq LPS Cond parents rep2


title: CD45, anti-PD-1+anti-CTLA4, biol rep 3, combo therapy, exp 2

description: 10x Genomics


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA NR, biol rep 3, combo therapy, exp 2

description: 10x Genomics


title: gMDSC, Male, Tumor, Biological replicate 2


title: P38

value: Control


title: gMDSC, Female, Healthy, Biological replicate 2


title: P37

value: Male


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA NR, biol rep 2, combo therapy, exp 2

description: 10x Genomics


title: P43


title: RNA-seq LPS Non-Cond parents rep3

value: 6h LPS Non-Cond parents


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA NR, biol rep 1, combo therapy, exp 2

description: 10x Genomics


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 3, combo therapy, exp 2

description: 10x Genomics


title: RNA-seq LPS Non-Cond parents rep2


title: P36


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 2, combo therapy, exp 1

description: 10x Genomics


title: gMDSC, Male, Healthy, Biological replicate 1


title: RNA-seq LPS Non-Cond parents rep1


title: gMDSC, Female, Tumor, Biological replicate 2


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA NR, biol rep 2, combo therapy, exp 1

description: 10x Genomics


title: P39


title: RNA-seq Heat Cond parents rep3

value: 6h heat challenge Cond parents


title: P41

value: MIS-C


title: RNA-seq Heat Non-Cond parents rep3

value: 6h heat challenge Non-Cond parents


title: RNA-seq Heat Cond parents rep2


title: RNA-seq t0 Cond parents rep1

value: t0 Cond parents


title: P32


title: RNA-seq Heat Cond parents rep1


title: P35


title: gMDSC, Female, Healthy, Biological replicate 1

value: Sham-injected


title: RNA-seq t0 Non-Cond parents rep2

value: t0 Non-Cond parents


title: RNA-seq t0 Non-Cond parents rep3


title: RNA-seq Heat Non-Cond parents rep2


title: CD45, anti-PD-1+anti-CTLA4, biol rep 1, combo therapy, exp 1

description: 10x Genomics

value: CD45+ immune cells

value: Tumor infiltrating leukocytes


title: P33

value: whole blood


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA R, biol rep 1, combo therapy, exp 1

description: 10x Genomics


title: RNA-seq t0 Cond parents rep3

value: whole tissue lysate

value: day 10 posthatch


title: RNA-seq t0 Cond parents rep2


title: CD45, anti-PD-1+anti-CTLA4, biol rep 3, combo therapy, exp 1

description: 10x Genomics


title: P31


title: P30

value: Female


title: P34


title: RRBS_F1E_APH_rep4

data_processing:
Trimming of Illumina adapters, as well as quality trimming, were performed with Trim Galore
Reads were mapped to the chick genome (galGal5.0) using Bismark v. 0-22-3, bowtie mode. Next, methylation calls were extracted with Bismark, methylation extractor mode.
Differential methylation on a single CpGs site (DMS) was extracted and analyzed by edgeR, with the recommended cutoff of at least 8 reads in every sample before being considered in the analysis and FDR < 0.05. DMRs were extracted and  analyzed by metilene v. 0.2-8.
Genome_build: galGal5_0
Supplementary_files_format_and_content: Bedgraph files were generated using Bismark

source_name: APH

growth_protocol: We used 80 fertile Cobb strain broiler (Gallus gallus) eggs from one breeder flock of hens. The eggs were randomly divided into two incubation treatments: CTRL – eggs were incubated at 37.8°C and 56% relative humidity throughout the 21 days of the incubation period; EHC – eggs were incubated at 39.5°C and 65% relative humidity for 12 h/day on embryonic days 7 to 16

extract_protocol:
DNA was isolated by TRI Reagent.
Libraries were prepared using Zymo-Seq RRBS Library Kit (Zymo).

treatment_protocol: Hatched chicks were weighed, their sex was identified according to wing feathering, and they were tagged and randomly divided into 8 chicks per pen in climate-controlled rooms at 32°C under a 22/2 h cycle of artiﬁcial illumination with ad libitum access to food and water. On day 7 posthatch, the temperature was changed to 30°C and chicks were further divided into 5 chicks per pen.

value: Cobb

value: paternal EHC conditioned

value: APH


title: RRBS_F1E_APH_rep5


title: CD45, anti-PD-1+anti-CTLA4, biol rep 2, combo therapy, exp 1

description: 10x Genomics

value: BALB/c

value: 8-10 weeks old


title: RNA-seq Heat Non-Cond parents rep1


title: CD45, anti-PD-1+anti-CTLA4+anti-VISTA NR, biol rep 1, combo therapy, exp 1

description: 10x Genomics


title: P28

value: Male


title: CD45, Untreated, biol rep 2, combo therapy, exp 1

description: 10x Genomics


title: P26

value: MIS-C


title: RNA-seq t0 Non-Cond parents rep1


title: P25


title: P27


title: CD45, Untreated, biol rep 3, combo therapy, exp 1

description: 10x Genomics


title: SP2-R3

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

data_processing:
All reads were mapped to hg38 by nextflow-core pipeline to get the .bam file
BAM files were used as input in REDItool to quantify A-to-G base editing efficiency
Assembly: hg38
Supplementary files format and content: tab-delimited text files include AtoG editing efficiency

molecule: polyA RNA

growth_protocol: HEK293T (ATCC) cells were grown in Dulbecco’s modiﬁed Eagle’s medium (DMEM) (Sigma) with 10% fetal bovine serum (FBS)(ThermoFisher), 4% Glutamax (ThermoFisher), 1% Sodium Pyruvate (ThermoFisher) and penicillin-streptomycin (ThermoFisher). Incubator conditions were 37°C and 5% CO2.

extract_protocol:
HEK293T cells were harvested for RNA extraction using RNeasy Plus Mini Kit (Qiagene) or NucleoSpin RNA Plus Kit (Takara).
cDNA was generated from RNA via standard protocol of polyA selection for mRNA specie

treatment_protocol: For transfection, HEK293T cells were seeded in 12-well, 24-well or 96-well plates at the density of 1.5-2 million cells per plate one day prior to transfection. All transfection experiments were done with Lipo3000 (ThermoFisher) according to manufacturer’s instructions.

tag: cell line

value: immortalised cell line

tag: genotype

tag: treatment time


title: CD45, anti-VISTA R, biol rep 5, monotherapy, exp 2

description: 10x Genomics


title: P29


title: CD45, anti-VISTA R, biol rep 3, monotherapy, exp 2

description: 10x Genomics


title: RRBS_F1E_APH_rep3


title: CD45, anti-VISTA R, biol rep 4, monotherapy, exp 2

description: 10x Genomics


title: CD45, Untreated, biol rep 1, combo therapy, exp 1

description: 10x Genomics


title: CD45, anti-VISTA R, biol rep 2, monotherapy, exp 2

description: 10x Genomics


title: RRBS_F1E_APH_rep1


title: P21


title: CD45, anti-VISTA R, biol rep 1, monotherapy, exp 2

description: 10x Genomics


title: RRBS_F1E_APH_rep2


title: Plain_293T-R3


title: gCTRL-R3


title: P23


title: SP1-R3


title: P24


title: CD45, IgG, biol rep 2, monotherapy, exp 2

description: 10x Genomics


title: RRBS_F1C_APH_rep2

value: paternal non-conditioned


title: RRBS_F1C_APH_rep5


title: DF-R3


title: P22


title: P19


title: gTarget-R2


title: RRBS_F1C_APH_rep4


title: P18


title: CD45, IgG, monotherapy, exp 1

description: 10x Genomics


title: CD45, IgG, biol rep 3, monotherapy, exp 2

description: 10x Genomics


title: gCTRL-R2


title: RRBS_F1C_APH_rep3


title: SP2-R2


title: P20


title: CD45, IgG, biol rep 1, monotherapy, exp 2

description: 10x Genomics


title: RRBS_F1C_APH_rep1


title: DF-R2


title: Plain_293T-R2


title: CSR-1 sRIP rep 2 [SG0121_lib20]

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description: processed data file: sRIP_all_gene_rpkm_siRNAsuppression_revised.csv

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
siRNA RPKM values were calculated for all protein coding genes.
Assembly: WS190(ce6)
Supplementary files format and content: tab-delimited text file, rows are different genes, columns are different libraries.

organism: Caenorhabditis elegans

source_name: young adults

extract_protocol: Small RNAs were treated with phosphotase and then phosphorylated at the 5’ end by T4PNK and ATP, linker oligoes were added to both ends of sRNA, ligation products were gel purified, followed by RT-PCR

value: Cer3(red20), SF-HRDE-1, c-myc-CSR-1

tag: fragment inserted in cer3

tag: strain name

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs

tag: 5’ barcodes for srna or rna-seq

value: mixture of AGCG, CGTC, GTTA, TATG


title: P17


title: CD45, anti-VISTA R, monotherapy, exp 1

description: 10x Genomics

value: CD45+ immune cells

value: Tumor infiltrating leukocytes


title: HRDE-1 sRIP rep 2 [SG0121_lib19]


title: HRDE-1 sRIP rep 1 [SG0720_lib20]


title: SP1-R1


title: CD45, anti-VISTA NR, monotherapy, exp 1

description: 10x Genomics


title: P13

value: whole blood


title: SP1-R2


title: P12


title: P15


title: gTarget-R1


title: sRIP input, rep 2 [SG0121_lib12]


title: P16


title: SH-EP Neuroblastoma cells - H3K27me3 rep1

city: Boston

first: Rani

last: George

state: Massachusetts

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

data_processing:
Samples were aligned to the human genome (build hg19, GRCh37.75) with Bowtie2 (v3.4.3) with default parameters.
Next, non-duplicate reads that mapped to the reference chromosomes were retained using Samtools (v1.9) and MarkDuplicates (v2.1.1) from
Picard tools. Peaks were identified with MACS2 (2.1.1) for narrow peaks with the parameters ”--q 0.01--call-summits” and for broad peaks with the parameters ”--broad-cutoff 0.01”.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated that represent read counts scaled to reads per million/base pair (rpm/bp)
Supplementary_files_format_and_content: peak text files

source_name: SH-EP Neuroblastoma cells

growth_protocol: All cells were grown in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Invitrogen) and 1% penicillin/streptomycin (Life Technologies). SH-SY5Y cells resistant to the ALK inhibitor ceritinib (LDK378) were described previously (Debruyne et al., 2016) and were grown in complete RPMI-1640 in the presence of 1.5 µM ceritinib.

extract_protocol:
Soluble chromatin lysates were derived from sonicated nuclei and histone-DNA complexes were isolated with antibodies against H3K27ac, H3K4me3, and H3K27me3.
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries using the NEBNext Ultra II DNA Library Prep kit and the NEBNext Multiplex Oligos for Illumina (New England Biolabs) according to the manufacturer’s protocol. Libraries with distinct indices were multiplexed and run together on the Illumina NextSeq 500 (SY-415-1001, Illumina) for 75 base pairs.

value: SH-EP Neuroblastoma cells

value: Neuroblastoma cell line

tag: cell lineage

value: mesenchymal

tag: chip antibody


title: gCTRL-R1

tag: cell type


title: P11


title: SH-EP Neuroblastoma cells - input DNA (H3K27me3)


title: SI12R_uninjured

city: Fayetteville

first: Jeffrey

last: Wolchok

state: AR

address: 700 W. Research Blvd

department: Biomedical Engineering

institute: University of Arkansas

data_processing:
usegalaxy.org pipeline
Use RNA-STAR for Gapped-read mapper for RNA-seq data ( input 2 pair-end raw files per sample)
Use feature to measure gene expression in RNA-Seq experiments from BAM files ( generated from RNA-Star)
Use edgeR to perform differential expression of count data
Assembly: Rnor_6.0
Supplementary files format and content: tabular  files include normalized counted reads, per gene for each sample

organism: Rattus norvegicus

source_name: Rat TA, uninjured control

extract_protocol:
RNA extarction was are performed by comerical lab BGI
RNA libraries were constructed by comerical lab BGI

treatment_protocol: 100 ul PBS or IL-10 (200ng/injection)

value: Tibialis anterior muscle

tag: treatment

value: uninjured control


title: gTarget-R3


title: CSR-1 sRIP rep 1 [SG0720_lib22]


title: SP2-R1


title: SH-EP Neuroblastoma cells - H3K27me3 rep2


title: sRIP input, rep 1 [SG0720_lib30]


title: P10

tag: tissue


title: P14

tag: group


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - input DNA (H3K27me3)


title: Plain_293T-R1


title: SI6R_uninjured


title: P9

tag: biological sex

value: Female


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K27me3 rep1


title: P7

tag: age (years)


title: SH-SY5Y Neuroblastoma cells - H3K27me3 rep1

source_name: SH-SY5Y Neuroblastoma cells

value: SH-SY5Y Neuroblastoma cells

value: adrenergic


title: NBL-S Neuroblastoma cells rep2

data_processing:
Single-end RNA-seq samples with 40 base pair (bp) read lengths were mapped to the human genome (GRCh38) and ERCC spike-in sequences.
Reads were mapped to the genome using Bowtie2 (version 2.3.4.3) and default parameters.
Reads that overlapped with the genomic location for exonic regions were used to calculate gene counts with the FeatureCounts (Subread package of version 1.6.3) package.
Further, spike-in read counts were used for each sample to normalize the library sizes and used to perform differential expression analysis.
To compare the proportion of reads that mapped to a gene in each sample log2 normalized TPM values were also calculated.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include log2 normalized TPM values for each sample.

source_name: NBL-S Neuroblastoma cells

extract_protocol:
RNA-sequencing was performed on the following human NB cell lines: Kelly, NBL-S, CHP-212, SH-SY5Y, SH-SY5Y LDK-resistant and SH-EP. Biological duplicates (5 x 106 cells per replicate) were homogenized in 1 ml of TRIzol Reagent (Invitrogen) and purified using the mirVANA miRNA isolation kit (Ambion) following the manufacturer’s instructions. Total RNA was treated with DNA-freeTM DNase I (Ambion), spiked-in with ERCC RNA Spike-In Mix (Ambion) and analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies) for integrity.
Sequencing libraries were prepared using LP-KAPA mRNA Hyper Prep and sequenced using Illumina HiSeq for 40 bases.

value: NBL-S Neuroblastoma cells

tag: genomic mycn status

value: Non-amplified


title: P6

value: MIS-C


title: SI9R_uninjured


title: SH-EP Neuroblastoma cells - input DNA (H3K27ac)


title: SH-EP Neuroblastoma cells rep2


title: SI8R_uninjured


title: DF-R1

value: immortalised cell line


title: NBL-S Neuroblastoma cells rep1


title: SH-EP Neuroblastoma cells - H3K27ac rep2


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K27me3 rep2


title: CHP-212 Neuroblastoma cells rep2

source_name: CHP-212 Neuroblastoma cells

value: CHP-212 Neuroblastoma cells

value: Amplified


title: SH-SY5Y Neuroblastoma cells - input DNA (H3K27me3)


title: CHP-212 Neuroblastoma cells rep1


title: P8

value: Male


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - input DNA (H3K27ac)


title: SH-SY5Y Neuroblastoma cells - H3K27me3 rep2


title: SH-EP Neuroblastoma cells rep1


title: SI12L_PBS

source_name: Rat TA, PBS control

value: PBS control


title: P2

value: whole blood


title: SI2L_IL10

source_name: Rat TA, IL10 treated

value: IL10 treated


title: SI9L_PBS


title: SI1L_IL10


title: SH-SY5Y Neuroblastoma cells - input DNA (H3K27ac)

value: Neuroblastoma cell line


title: SI8L_PBS


title: P5

source_name: High molecular weight DNA extracted from whole blood samples


title: SH-SY5Y Neuroblastoma cells rep1


title: SI6L_PBS


title: P4


title: SH-EP Neuroblastoma cells - H3K27ac rep1

value: SH-EP Neuroblastoma cells

value: mesenchymal


title: Kelly Neuroblastoma cells rep2

source_name: Kelly Neuroblastoma cells

value: Kelly Neuroblastoma cells


title: SI4L_IL10

value: Tibialis anterior muscle


title: SI3L_IL10


title: K97E lamin A (mutant) transfected C1C12 cells (Biological replicate 1)

city: Kolkata

first: Kaushik

last: Sengupta

state: West Bengal

address: 1/AF Bidhannagar

department: Biophysics and Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

data_processing:
Hisat2 was used to align the fastqc checked fastq files with the reference.
Samtools was used to generate sorted BAM files.
Transcript assembly was carried out using StringTie
DESeq2 was used to generate differentially expressed genes and transcripts
Assembly: GRCm39.104
Supplementary files format and content: GTF file containing FPKM values generated from StringTie version 2.1.7

growth_protocol: C2C12 cells were cultured in ATCC formulated DMEM supplemented with 0.3% glucose, 10% FBS and 1% Penicillin-streptomycin. Cells were cultured using standard protocol and maintained at 37ᵒC and 5% CO2. Cells between 2nd and 3rd   passages were allowed to reach a confluency of 50-60% during transfection. 3µg of DNA was transfected with Lipofectamine 2000 at DNA: Lipo2k= 1:1.5 in serum and antibiotic free medium. Cells were further fixed or harvested post 24 hours of transfection.

extract_protocol:
Transfected cells were washed twice in ice cold PBS, trypsinized and transferred to a 15 mL conical tube and centrifuged for 2 min at 1000 rpm. The supernatant was discarded and the pellet was stored at -80ºC till further use.  RNA was isolated using Pure Link miniRNA isolation kit (Thermo Fisher Scientific, USA).
mRNA library preparation was performed using Kapa Hyperprep stranded library preparation kit (Roche,Switzerland) followed by sequencing on Novaseq 6000 (Illumina,Inc.,USA) using 2X100bp read length targeting 50 million paired-end reads.

value: Mouse myoblast cell line

value: K97E lamin A(mutant) transfected


title: SH-SY5Y-LDK-resistant Neuroblastoma cells  rep1


title: SH-SY5Y-LDK-resistant Neuroblastoma cells  rep2


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K27ac rep2


title: SH-SY5Y Neuroblastoma cells rep2

value: SH-SY5Y Neuroblastoma cells

value: adrenergic


title: Wild Type lamin A transfected C2C12 cells (Biological Replicate 2)

value: Wild type lamin A transfected


title: P1

value: MIS-C


title: SH-EP Neuroblastoma cells - input DNA (H3K4me3)


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K27ac rep1


title: R09_LK

city: Sydney

first: Ting

last: Zhang

state: NSW

address: 8 Macquarie Street

department: Save Sight Institute

country: Australia

institute: the University of Sydney

data_processing:
Real-Time Analysis (RTA) software (RTA3.4.4) used for basecalling.
Remove reads with adaptor contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
STAR software (v2.6.1d) is used to accomplish the mapping.
FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene.
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: primary retinal Müller cells

growth_protocol: the cells were cultured in DMEM (gibco, 10596) supplemented with 10%FBS and 1% penicillin-streptomycin

extract_protocol:
total RNA was extracted from treated huPMCs using GenEluteTM Single Cell RNA  Purification Kit (Sigma-Aldrich, RNB300). A total amount of 1 μg RNA per sample was used as  input material for the RNA sample preparations. Sequencing libraries were generated using  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the huPMCs were treated with either control siRNA or TKT siRNA for 72h before exposed to dim light （5 lux） or strong light （32k lux） for 4h

value: priamrily cultured retinal Muller cells, p3

value: strong light, TKT knockdwon

tag: donor id

value: donor 09


title: R09_DC

value: dim light, TKT control


title: P3

value: whole blood

value: Male


title: R09_LC

value: strong light, TKT control


title: SH-SY5Y Neuroblastoma cells - H3K27ac rep2

tag: cell line

value: Neuroblastoma cell line


title: SH-EP Neuroblastoma cells - H3K4me3 rep2

value: SH-EP Neuroblastoma cells

value: mesenchymal


title: SH-SY5Y Neuroblastoma cells - H3K27ac rep1


title: R09_DK

value: dim light, TKT knockdown


title: R04_DK

value: donor 04


title: Kelly Neuroblastoma cells rep1

value: Kelly Neuroblastoma cells

value: Amplified


title: K97E lamin A (mutant) transfected C1C12 cells (Biological replicate 2)

value: Mouse myoblast cell line

tag: genotype

value: K97E lamin A(mutant) transfected


title: SH-EP Neuroblastoma cells - H3K4me3 rep1


title: R04_DC


title: Wild Type lamin A transfected C2C12 cells (Biological Replicate 1)

value: Wild type lamin A transfected


title: 46T-a, exponential phase, biol rep 2

city: Busan

first: Soo Jae

last: Kwon

address: KIOST, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, KOREA

country: South Korea

institute: KIOST

data_processing:
The raw reads were assembled and aligned with the reference AWRP genome by using TopHat2 v2.0.13
The differential expression was analyzed by using the Cuffdiff v2.2.0
Assembly: ASM400639v2
Supplementary files format and content: mean values of FPKM obtained from two biological replicates

organism: Clostridium sp. AWRP

source_name: Prokaryotic cell

growth_protocol: The wild-type AWRP and acetated adapted strain were cultivated in a bioreactor containing basal medium with the gas substrate (20% CO2 and 80% H2)

extract_protocol:
RNA was extracted manually using RiboEX solution (GeneAll, Republic of Korea).
RNA libraries for RNA-seq were prepared using Truseq RNA sample prep (Illumina) according to manufacturer's protocols.

treatment_protocol:
The harvested culture was stabilized by mixing with 2 volumes of RNAProtect Bacteria reagent (Qiagen) and incubating at room temperature for 20 min
The stabilized cells were harvested and resuspended in 100 μL of the lysozyme solution (15 mg/mL in 30 mM Tris Cl and 1 mM EDTA) and 10 μL of the proteinase K solution (Qiagen)

value: Prokaryotic cell

tag: strain

value: Acetate-adapted strain

tag: growth phase

value: exponential phase


title: 46T-a, exponential phase, biol rep 1


title: 46T-a, stationary phase,  biol rep 1

value: stationary phase


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K4me3 rep1


title: 46T-a, stationary phase,  biol rep 2


title: Wild-type, stationary phase,  biol rep 2

value: AWRP

value: WT


title: R03_LC

value: priamrily cultured retinal Muller cells, p3

value: strong light, TKT control

value: donor 03


title: SH-SY5Y Neuroblastoma cells - H3K4me3 rep2

value: SH-SY5Y Neuroblastoma cells

value: Neuroblastoma cell line

value: adrenergic


title: R03_DK

value: dim light, TKT knockdown


title: SH-SY5Y Neuroblastoma cells - input DNA (H3K4me3)


title: Wild-type, exponential phase, biol rep 1


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - input DNA (H3K4me3)

value: mesenchymal


title: SH-SY5Y Neuroblastoma cells - H3K4me3 rep1


title: SH-SY5Y-LDK-resistant Neuroblastoma cells - H3K4me3 rep2


title: Input: shCtr9#5

status: Public on Jun 25 2022

city: Madison

first: Wei

last: Xu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

data_processing:
ChIP-seq reads were aligned to human genome (hg38, chromosomes 1 to 22 and X) by Bowtie (version 1.1.2) with command line options ‘--quiet -q -v 2 -a --best --strata -m 1 --phred33-quals -S’.  We removed reads that were unmapped or were PCR/optical duplicates and reads that did not pass platform/vendor quality controls.
ChIP-seq peaks were called by MACS (version 2.1.0.20151222) with a q-value cutoff of 0.05.  Narrow peaks were called for H3K4me3 and broad peaks were called for H3K27me3 and H3K36me3. Peaks that overlapped with ENCODE’s Blacklisted Regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were removed.
ChIP-seq signals were saved by MACS (version 2.1.0.20151222) as per million reads for fragment pileup profiles in bedGraph format and converted to bigWig format.
Genome_build: hg38
Supplementary_files_format_and_content: TSV files were generated based on ChIP-seq peaks called by MACS and R scripts to define a peak's genomic location type and nearby genes; bigWig files were generated based on ChIP-seq signal files in bedGraph format from MACS and were converted to bigWig format by UCSC's bedGraphToBigWig

source_name: breast cancer cell line: MCF7

growth_protocol: DMEM supplied with 10% FBS

extract_protocol:
Hao Z. et al., BMC Genomics, 2016
Applying Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies)  according to manufracturer's protocol(Hao Z. et al., BMC Genomics, 2016)

treatment_protocol: Dox: 500 ng/ml Doxycycline treatment for 7 days

value: breast cancer cell line

value: Input


title: Input: shCtr9#3


title: Wild-type, stationary phase,  biol rep 1


title: R04_LC

value: donor 04


title: R04_LK

value: strong light, TKT knockdwon


title: Wild-type, exponential phase, biol rep 2

value: Prokaryotic cell


title: Input: shControl

value: shControl


title: R03_LK


title: H3K36me3: shCtr9#5

value: H3K36me3 (Cell signaling Technology; Cat# 4909, RRID:AB_1950412)


title: R03_DC

value: dim light, TKT control


title: Input: + Dox

value: + Dox


title: H3K36me3: + Dox


title: Input: Vehicle

value: Vehicle


title: H3K36me3: shCtr9#3


title: H3K27me3: shCtr9#5

value: H3K27me3 (Cell signaling Technology; Cat# 9733, RRID:AB_916252)


title: H3K27me3: shCtr9#3


title: H3K27me3: shControl


title: H3K36me3: Vehicle


title: H3K27me3: Vehicle


title: H3K27me3: + Dox


title: H3K4me3: shCtr9#5

value: H3K4me3 (Cell signaling Technology; Cat# 9751, RRID:AB_2616028)


title: H3K4me3: shControl


title: H3K36me3: shControl


title: H3K4me3: + Dox


title: H3K4me3: shCtr9#3


title: H3K36me3_sdg26;aprf1_rep2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
Adapter and low-quality sequences were trimmed, and the clean reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.4.2) allowing one mismatch.
SICER (v2.0) was used to identify ChIP-enriched peaks between the WT type and four mutants.
Differentially expressed peaks in all mutants were identified based on the change of read counts (|log2FC| >=0.585 and P value<0.01) at peaks.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Unless otherwise specified, all plants used in this study were grown at 23℃ under long-day conditions with a 16 h light/8 h dark photoperiod.

extract_protocol:
A 2-g quantity of 10-day-old seedlings was harvested and ground into a fine powder in liquid nitrogen. The powder was suspended in 15 ml of Nuclear Extraction Buffer (NEB) (20 mM Tris-HCl [pH 7.5], 20 mM KCl, 2 mM EDTA [pH 8.0], 2.5 mM MgCl2, 25% glycerol, 250 mM sucrose, 5 mM DTT, 1% protease inhibitor cocktail, and 1 mM PMSF) and was then subjected to cross-linking with 1% formaldehyde (Sigma, F8775). The nuclei were washed in Nuclear Resuspension Buffer (NRBT) (20 mM Tris-HCl [pH 7.5], 2.5 mM MgCl2, 25% glycerol, and 0.2% Triton X-100) and then sonicated in Sonication Buffer (20 mM Tris-HCl [pH 8.0], 2 mM EDTA [pH 8.0], 0.2% NP-40, 1 mM PMSF, and 1% PPI). The sheared chromatin was diluted with Dilution Buffer (2 mM EDTA, 20 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM PSMF, and 1% protease inhibitor cocktail) and incubated with GBP (GFP-binding protein) coupled with  agarose beads (Cytvita, 17-096-01) or incubated with H3Ac antibody (Millipore, 06-599), H3K4me3 antibody (Abcam, ab8580), H3K27me3 antibody (Millipore, 07-449), and H3K36me3 antibody (Abcam, ab9050) coupled with Dynabeads Protein A (Invitrogen, 100–01D) at 4℃ overnight. The beads were washed 5 times with Wash Buffer (150 mM NaCl, 20 mM Tris-HCl [pH 8.0], 2 mM EDTA [pH 8.0], 0.1% Triton X-100, and 1 mM PMSF) and then with TE (10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH 8.0]). The bead-bound DNA-protein complexes were eluted from the beads and reverse cross-linked with NaCl and Proteinase K (Sigma, P4850). The chromatin DNA was extracted using Phenol/Chloroform/Isoamyl alcohol and was then subjected to qPCR or library construction.
Libraries were built for ChIP-seq (Illumina NovaSeq 6000; 150-bp paired-end sequencing)

treatment_protocol: The 10-day-old seedlings grown on MS plates were harvested and subjected to  ChIP analysis.

value: seedling

value: Abcam, ab9050


title: H3K36me3_ld_rep1


title: H3K36me3_fld_rep2


title: H3K36me3_sdg26;aprf1_rep1


title: H3K36me3_fld_rep1


title: H3K4me3: Vehicle


title: H3K27me3_sdg26;aprf1_rep2

value: Millipore, 07-449


title: H3K36me3_elf2/4_rep1


title: H3K36me3_Col-0_rep1

value: wild type


title: H3K36me3_Col-0_rep2


title: H3K27me3_ld_rep1


title: H3K27me3_sdg26;aprf1_rep1


title: H3K27me3_ld_rep2


title: H3K27me3_Col-0_rep1


title: H3K4me3_sdg26;aprf1_rep2

value: Millipore, 07-473


title: H3K27me3_fld_rep2


title: H3K4me3_ld_rep2


title: H3K4me3_ld_rep1


title: H3K4me3_fld_rep1


title: SciPlex Combo Library Well H12

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

data_processing:
First, data was demultiplexed by well. Cell barcode and UMI contained in Read1 were extracted, error corrected, and put into the header of each read.
Subsequently, reads were trimmed for polyA adaptors, mapped to the hg38 reference genome, and only transcripts mapping to the gencode annotated gene bodies were kept for further analysis
Reads were then deduplicated by UMI and assembled into a count matrix
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: sciPlex Combinations of Drugs

extract_protocol:
Resuspended cells were lsyed in a hypotonic buffer and fixed with a combination of DSP and 80% Methanol
Optimized sci-RNA-seq3 protocol was performed to make single cell sequencing libraries

treatment_protocol: Cells were treated with 2 drugs (or equivalent vehicle) at a concentration of 10uM at 24 hours post plating and then collected after 24 hours of treatment with compounds

value: Lung Adenocarcinoma

value: WT

value: Combinations of drugs at 10uM


title: H3K27me3_elf2/4_rep2


title: H3K27me3_elf2/4_rep1


title: H3K36me3_ld_rep2


title: H3K27me3_Col-0_rep2


title: H3K27me3_fld_rep1


title: SciPlex Combo Library Well H11


title: H3K4me3_sdg26;aprf1_rep1


title: H3K4me3_elf2/4_rep2


title: H3K36me3_elf2/4_rep2


title: H3K4me3_elf2/4_rep1


title: H3K4me3_fld_rep2


title: H3K4me3_Col-0_rep1


title: SciPlex Combo Library Well H06


title: H3K4me2_ld_rep2

value: Millipore, 07-030


title: SciPlex Combo Library Well H05


title: H3K4me2_fld_rep2


title: H3K4me3_Col-0_rep2


title: SciPlex Combo Library Well H10


title: H3K4me2_fld_rep1


title: H3K4me2_sdg26;aprf1_rep2


title: H3K4me2_ld_rep1


title: H3K4me2_sdg26;aprf1_rep1


title: SciPlex Combo Library Well H08


title: SciPlex Combo Library Well H03


title: H3K4me2_elf2/4_rep2


title: H3K4me2_elf2/4_rep1


title: SciPlex Combo Library Well H09


title: H3K4me2_Col-0_rep2


title: H3K4me2_Col-0_rep1


title: H3Ac_sdg26;aprf1_rep1

value: Millipore, 06-599


title: SciPlex Combo Library Well G10


title: SciPlex Combo Library Well G11


title: SciPlex Combo Library Well G12


title: SciPlex Combo Library Well H02


title: SciPlex Combo Library Well G08


title: H3Ac_ld_rep2


title: SciPlex Combo Library Well H07


title: SciPlex Combo Library Well G09


title: H3Ac_ld_rep1


title: SciPlex Combo Library Well H04


title: SciPlex Combo Library Well G05


title: SciPlex Combo Library Well H01


title: H3Ac_fld_rep1


title: H3Ac_elf2/4_rep2


title: SciPlex Combo Library Well G02


title: SciPlex Combo Library Well G03


title: SciPlex Combo Library Well G04


title: H3Ac_sdg26;aprf1_rep2


title: SciPlex Combo Library Well G06


title: SciPlex Combo Library Well G07


title: H3Ac_fld_rep2


title: H3Ac_Col-0_rep1


title: H3Ac_Col-0_rep2


title: SciPlex Combo Library Well F08


title: SciPlex Combo Library Well F10


title: SciPlex Combo Library Well F09


title: SciPlex Combo Library Well F11


title: SciPlex Combo Library Well F12


title: SciPlex Combo Library Well F07


title: KPCS530_48h_Hx

city: Zurich

first: Patrik

last: Simmler

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

description: Cultured in 1%O2 for 48 hours

data_processing:
The fastq data for the read pairs from the Illumina sequencer have been processed in abioinformatic workflow. First, the remains of the adapters and sub-standard quality reads have been trimmed with trimmomatic (v0.35).
For the pairs in which both reads have passed the trimming, they have been mapped to the mm10 mouse genome using STAR (v2.7.0a) and indexed BAM files obtained with samtools (v1.9).
The reads have been counted using featureCounts from subread package (v1.5.0) with the options for pairs of reads to be counted as RNA fragments. The counting used Ensembl v95 mouse genome annotation GTF file. The count vectors for all the samples have been combined into a count table. The table has been processed in the secondary (statistical) analysis with R scripts using edgeR (v3.24.3), in particular binomial generalized log-linear model with contrast tests. It resulted in lists of genes ranked for differential expression by p-value and used Benjamini-Hochberg adjusted p-value as the estimate of the false discovery rate.
Assembly: mm10
Supplementary files format and content: xls files include FPKM values for each sample

source_name: Organoids derived from pancreas duct cells

growth_protocol: Organoids were seeded as single cells at a density of 500 cells/μl GFR-Matrigel (Corning).

extract_protocol:
Organoids were harvested and RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel) according to the manufacturer’s instructions. For each organoid line, 2-3 wells of organoids from a 24 well plate were harvested in lysis buffer RA1 (RNA extraction kit, MN) supplemented with TCEP (Tris(2-carboxyethyl)phosphine hydrochloride).
For library preparation, the quantity and quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (1 μg) were ribosome depleted and then reverse-transcribed into double-stranded cDNA with Actinomycin added during first-strand synthesis. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters. The adapters contain the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 360 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. Cluster generation and sequencing involved application of the TruSeq SR Cluster Kit v4-cBot-HS or TruSeq PE Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) using 8 pM of pooled normalized libraries on the cBOT.

treatment_protocol: 48 hours after seeding, cells were exposed to 1% O2 in a hypoxia chamber or kept in a cell culture incubator at 21% O2 for additional 48 hours

value: KrasG12D, Trp53R172H

value: Sf3b1 heterozygous knockout

tag: condition

value: Hypoxia


title: KPCS520_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: H3Ac_elf2/4_rep1


title: KPC251_48h_Hx

description: Cultured in 1%O2 for 48 hours

value: Sf3b1 diploid


title: KPCS677_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: KPC305_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: KPC293_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: KPC625_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: KPCS398_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: SciPlex Combo Library Well F06


title: SciPlex Combo Library Well F05


title: SciPlex Combo Library Well F04


title: SciPlex Combo Library Well G01


title: KPCS520_Nx

description: Cultured in 21%O2

value: Normoxia


title: KPCS530_Nx

description: Cultured in 21%O2


title: SciPlex Combo Library Well F02


title: KPCS398_Nx

description: Cultured in 21%O2


title: SciPlex Combo Library Well E12


title: KPCS677_Nx

description: Cultured in 21%O2


title: SciPlex Combo Library Well F01


title: SciPlex Combo Library Well F03


title: SciPlex Combo Library Well E11


title: KPC571_48h_Hx

description: Cultured in 1%O2 for 48 hours


title: KPC305_Nx

description: Cultured in 21%O2


title: KPC571_Nx

description: Cultured in 21%O2


title: SciPlex Combo Library Well E09


title: SciPlex Combo Library Well E10


title: KPC251_Nx

description: Cultured in 21%O2


title: KPC625_Nx

description: Cultured in 21%O2


title: APP/PS1_AD4 [OAD4]

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

data_processing:
The sequenced reads from all replicates and samples were aligned to the mouse (mm10) reference genome with STAR.
The aligned reads were quantified to mRNA count table using HTSeq-count.
Low count genes were filtered out using the filterByExpr function from edgeR package. The count tables were normalized by taking log  counts per million using ‘cpm’ function available in edgeR package. The batch correction was performed using ‘ComBat’ function available in ‘sva’ Bioconductor package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include logCPM values for each Sample

source_name: brain endothelial cells

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen 74004).
Illumina HiSeq 4000 library preparation protocol.

value: brain endothelial cells

tag: time

value: 1 year old

tag: batch


title: APP/PS1_AD1 [OAD1]


title: Control 5 [OC5]


title: APP/PS1_AD5 [OAD5]


title: APP/PS1_AD2 [OAD2]


title: Control 4 [OC4]


title: SciPlex Combo Library Well E04


title: SciPlex Combo Library Well E03


title: SciPlex Combo Library Well E02


title: SciPlex Combo Library Well E08


title: APP/PS1_AD3 [OAD3]


title: SciPlex Combo Library Well E06


title: SciPlex Combo Library Well D10


title: SciPlex Combo Library Well E01


title: Control 1 [OC1]


title: SciPlex Combo Library Well D09


title: SciPlex Combo Library Well D08


title: Control 3 [OC3]


title: SciPlex Combo Library Well D11


title: Control 2 [OC2]


title: UPEC Thy 4

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq were aligned to mm10 using hisat2
Counts table was produced using Rsubread
Normalisation was carried out using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq 2 nomalised counts

source_name: bladder

growth_protocol: Mice were maintaind in SPF

extract_protocol:
Bladders were taken and RNA extracted using ambion RNA mini kit
Takara smarta high input

treatment_protocol: Mice were pretreate with either isotype control or anti thy 1.1 and subsequently given a UTI through infection with UPEC.

value: bladder

value: anti thy1.4

value: RAG KO

tag: disease state

value: UTI


title: UPEC Thy 5

value: anti thy1.5


title: SciPlex Combo Library Well D12

value: Lung Adenocarcinoma


title: SciPlex Combo Library Well E07

value: WT


title: KPC293_Nx

description: Cultured in 21%O2


title: SciPlex Combo Library Well D07

value: Combinations of drugs at 10uM


title: UPEC Thy 3

value: anti thy1.3


title: SciPlex Combo Library Well E05


title: UPEC ISO 4

value: isotype


title: UPEC Thy 2

value: anti thy1.2


title: UPEC ISO 3


title: SciPlex Combo Library Well D06


title: SciPlex Combo Library Well D02


title: P0 Vocal Fold Rep 2 [P0BioRep2TGACCA]

first: Christina

last: Kendziorski

address: 425, Henry Mall (2122 UWBC)

institute: UW-Madison

data_processing: Quality control on raw sequencing files was performed via FastQC v011.5(Andrews, 2010) using standard defaults. All samples appeared high quality based on available metrics and, in particular, passed our internal quality thresholds – 1) minimum per-base PHRED score of 5 and median per-base PHRED score of at least 20 and 2) modal per-sequence average PHRED score of at least 20 – and were used in downstream analysis. Sequenced reads were aligned to the GRCm39 reference genome, pre-indexed files accessed from the Bowtie2 repository, using Bowtie2 (v2.4.2), accessed by RSEM (v1.3.3) which was used quantify observed gene transcription levels, in units of expected counts from aligned reads(Langmead and Salzberg, 2012)(Li and Dewey, 2011). Expected counts were then normalized across samples by scaling observed expression using the method of Median-Ratio implemented in the EBSeq R package. Raw and normalized expression data were remapped to human ortholog gene symbols (HGNC format) using the mapping from the Molecular Signatures Database (Mouse_ENSEMBL_Gene_ID_Human_Orthologs_MSigDB.v7.3.chip),  53,647 Ensemble genes were mapped to 18,032 human orthologs in gene symbol notation (Daley and Vere-Jones, 2003)(Subramanian et al, 2005)(Mootha et al, 2003). All calculations were conducted in the R environment and with Bioconductor package management(R Core Team, 2013)(Gentleman et al, 2004).

source_name: P0 Vocal Fold

extract_protocol:
RNeasy Micro Kit 50 (Qiagen, Valencia, CA) was used for extraction of total RNA according to the manufacturer’s instructions. DNA digestion was performed using the DNase enzyme eliminator column- RNeasy MinElute spin columns. RNA concentration yield and integrity were evaluated using a Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), and samples that met the following three criteria were retained: a concentration of 1µg, an OD260−280 of 1.8–2.0 and an OD260:230 above two. Additionally, samples were evaluated for RNA integrity value (RIN) using the Agilent 2100 Bioanalyzer and RNA 6000 Pico kit (Agilent, Santa Clara, CA) according to the manufacturer’s instructions. Only samples with electropherograms exhibiting distinct 18S and 28S ribosomal RNA (rRNA) peaks and no evidence of degradation were retained.
Poly-A library preparation and RNA sequencing was performed by the DNA Sequencing facility at the University of Wisconsin-Madison Biotechnology Center per standard protocols. Briefly, first-strand cDNA using random hexamer-primed reverse transcription was generated, followed by second-strand cDNA synthesis using RNase MODULE and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of 350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. Sequencing of the prepared libraries was done on Illumina’s HiSeq 2000 and Illumina NovaSeq6000 2x150 S4 platforms with four RNA-Seq libraries per lane with a minimum depth of 2 × 100 bp paired-end reads by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.

value: P0 Vocal Fold

value: Wild type FVB/N

tag: age


title: SciPlex Combo Library Well D05

tag: cell type


title: SciPlex Combo Library Well D04

tag: treatment


title: UPEC ISO 1

tag: tissue


title: SciPlex Combo Library Well D01


title: SciPlex Combo Library Well C12


title: E15.5 Vocal Fold Rep 1 [E155VFRep1ACAGTG]

source_name: E15.5 Vocal Fold

value: E15.5 Vocal Fold


title: SciPlex Combo Library Well C10


title: E15.5 Vocal Fold Rep 2 [E155VFRep2GCCAAT]


title: P0 Vocal Fold Rep 1 [P0BioRep1TTAGGC]


title: SciPlex Combo Library Well C09


title: SciPlex Combo Library Well D03


title: E15.5 Trachea Rep 1 [E155TracheaRep1CAGATC]

source_name: E15.5 Trachea

value: E15.5 Trachea


title: SciPlex Combo Library Well C11


title: 19WT (C57BL/6N) Bladder UPEC 72hrs

data_processing:
Fastq Files were aligned to the mm10 genome using HISAT2
Counts table was produced using Rsubread
Normalisation was perfomed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Deseq2 normalized counts matrix
Supplementary_files_format_and_content: raw counts matrix

source_name: Bladder

growth_protocol: Mice were maintained in SPF conditions prior to the experement

extract_protocol:
RNA was extracted from bladders using Ambion RNA mini kit
Libraries were produced using Illumina TruSeq mRNA

treatment_protocol: Mice were cathaterised and injected with either UPEC or PBS. After 24 or 72 hours mice were culled and the bladders placed into RNAlater

value: UPEC

tag: time point (hrs)


title: Adult Vocal Fold Rep 2 [AdultBioRep2CGATGT]

source_name: Adult Larynx

value: Adult Larynx

value: 6-8 week-old mice


title: 20WT (C57BL/6N) Bladder UPEC 72hrs


title: 17IL22R KO Bladder UPEC 72hrs

value: IL22R KO


title: 21IL22R KO Bladder UPEC 72hrs


title: SciPlex Combo Library Well C06


title: E15.5 Esophagus Rep 2 [E155EsophagusRep2TAGCTT]

source_name: E15.5 Esophgaus

value: E15.5 Esophgaus


title: E15.5 Esophagus Rep 1 [E155EsophagusRep1GATCAG]


title: UPEC ISO 2

value: bladder

value: RAG KO

value: UTI


title: Adult Vocal Fold Rep 1 [AdultBioRep1ATCACG]


title: SciPlex Combo Library Well C08

value: Lung Adenocarcinoma

value: WT


title: SciPlex Combo Library Well C07

value: Combinations of drugs at 10uM


title: A2780/CDDP_1

city: Nanjing

first: Daojuan

last: Wang

state: Jiangsu

address: Hankou Road, Gulou District

institute: Nanjing University

data_processing:
SOAPnuke software was used to filter reads, including removing reads with sequencing adapters to filter sequencing data, removing reads with a base quality less than 5, and removing reads with an unknown base ratio of more than 5%. The FASTQ format was used to store clean reads. HISAT2 was used to map clean reads to the reference genome, Bowtie2 was used to align clean reads to the reference coding genome, RSEM was used to calculate gene expression levels, and finally, differential expression analysis was performed by DESeq2.
Supplementary files format and content: TPM values for each sample

source_name: ovary

growth_protocol: A2780 and A2780/CDDP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA Miniprep kit reagent (Beyotime). The total RNA was used for the construction of sequencing libraries.
mRNA was purified by magnetic beads with Oligo(dT), and then the purified mRNA was fragmented using fragmentation buffer at the appropriate temperature. The first-strand cDNA was then generated by PCR in the First Strand reaction system, and the same operation was performed for the second-strand cDNA. The PCR product was purified with magnetic beads and incubated with A-Tailing Mix and RNA Index Adaptors to complete the repair process. cDNA fragments with adapters were amplified using PCR and purified using Ampure XP Beads. An Agilent 2100 Bioanalyzer was used to assess the quality and quantity of the library, followed by DSN processing. Finally, it was sequenced and analyzed on the BGI DNBSEQ platform (BGI-Shenzhen, China) protocols.

treatment_protocol: A2780/CDDP cells were treated with 1μg/ml cisplatin to maintain the drug-resistance

value: ovary

value: cancer cells

value: 1 μg/ml cisplatin


title: A2780/CDDP_3


title: 22IL22R KO Bladder UPEC 72hrs


title: CD69-Ly108+, WT, Biol rep 1 [LY_WT_1]

city: San Antonio

first: Nu

address: 7703 Floyd Curl Drive

institute: UTHSA

data_processing:
Data processing was performed by Novogene
Original image data file from Illumina is transformed to sequenced reads (Raw reads) by CASAVA base recognition
Raw reads of FASTQ format were firstly processed through fastp to obtain the clean reads
Paired-end clean reads were aligned to the reference genome (mm10) using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted using the Quick-RNA MiniPrep kit from Zymo Research
Libraray construction was performed by Novogene

value: spleen and lymph nodes

value: CD8 T cells

value: LCMV Clone 13 infection


title: SciPlex Combo Library Well C03


title: 18WT (C57BL/6N) Bladder UPEC 72hrs

value: UPEC


title: E15.5 Trachea Rep 2 [E155TracheaRep2ACTTGA]

value: E15.5 Trachea

value: Wild type FVB/N


title: SciPlex Combo Library Well C05


title: 12WT (C57BL/6N) Bladder PBS 72hrs

value: PBS


title: SciPlex Combo Library Well C04


title: 13WT (C57BL/6N) Bladder PBS 72hrs


title: SciPlex Combo Library Well C02


title: A2780_2


title: A2780_3


title: 16IL22R KO Bladder UPEC 72hrs

value: IL22R KO


title: A2780/CDDP_2


title: 11WT (C57BL/6N) Bladder PBS 72hrs


title: 15IL22R KO Bladder UPEC 72hrs


title: SciPlex Combo Library Well B12


title: A2780_1


title: 10IL22R KO Bladder UPEC 24hrs


title: CD69-Ly108+, WT, Biol rep 2 [LY_WT_2]


title: CD69-Ly108+, KO, Biol rep 2 [LY_KO_2]

value: Tgfbr2 f/f distal Lck-cre


title: CD69-Ly108+, KO, Biol rep 1 [LY_KO_1]


title: CD69+Ly108+, WT, Biol rep 1 [DP_WT_1]


title: 14IL22R KO Bladder UPEC 72hrs


title: CD69+Ly108+, WT, Biol rep 2 [DP_WT_2]


title: SciPlex Combo Library Well C01


title: Mouse_Cystic fluid,scRNA-seq

city: Guangzhou

first: Yilamujiang

last: Ainiwan

state: Guangdong

address: No. 1838, Guangzhou North Road

department: Neurosurgery

institute: Southern Medical University , Nanfang Hospital

description: 10x Genomics

data_processing:
Raw reads of mouse were aligned to the mouse genome (mm10) and raw reads of human were aligned to the human genome (hg38), cells were called and gene expression matrices were generated for each sample by the cellranger (v6.0.1) count function with default parameters.
Assembly: mm10 for the row reads of mouse , hg38 for the row reads of human
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: mouse hypothalamus

extract_protocol:
Mice were anesthetized 8 weeks after the operation. The hypothalamus of mice randomly selected from the cystic fluid group (1 case) and the sham operation group (1 case) were removed immediately under a light microscope for single-cell RNA sequencing. At the same time, a sample of fresh childhood ACP tumor tissue (with gliosis zone) immediately after collection during clinical surgery was also used for single-cell RNA sequencing.
The tissue was dissected out and flash frozen in liquid N2. Nuclei were isolated as followed by 10× Genomics demonstrate protocol (CG000375 • Rev A) .On the day of the experiment, frozen tissue was homogenized in NP40 Lysis Buffer with Protector RNAase Inhibitor (Sigma) and filtered through a 70μm strainer (falcon). Strained samples were centrifuged at 500 rcf × 5 min and pelleted nuclei were resuspended in wash buffer . Nuclei were strained again and recentrifuged at 500 rcf × 5 min. Washed nuclei were resuspended in wash buffer and stained nuclei underwent FACS sorting by 7-AAD (SML1633 sigma). Sorted nuclei were centrifuged at 500 rcf × 6 min and resuspended in wash buffer to obtain a concentration of 900 nuclei/μL. 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell G Chip (10× Genomics, 1000120), aiming for a recovery of 8000–9000 cells. The Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10× Genomics, 1000121) was used for single-cell barcoding, cDNA synthesis and library preparation, following manufacturer’s instructions according to the Single Cell 3′ Reagent Kits User Guide Version 3.1. Libraries were sequenced using the NovaSeq 6000 platform (Illumina) to a depth of approximately 300 million reads per library with 2×150 read length.

value: mouse hypothalamus

value: injected human ACP cystic fluid into the bilateral hypotalamus


title: 7WT (C57BL/6N) Bladder UPEC 24hrs


title: CD69+Ly108+, KO, Biol rep 2 [DP_KO_2]


title: SciPlex Combo Library Well B09

value: Lung Adenocarcinoma


title: Mouse_Sham,scRNA-seq

description: 10x Genomics

value: injected same amount of PBS into the bilateral hypotalamus


title: 9WT (C57BL/6N) Bladder UPEC 24hrs

value: WT


title: 8WT (C57BL/6N) Bladder UPEC 24hrs


title: CD69-Ly108-, WT, Biol rep 1 [DN_WT_1]


title: SciPlex Combo Library Well B11

value: Combinations of drugs at 10uM


title: E18.5 Trachea Rep 1 [18-5T1]

source_name: E18.5 Trachea

value: E18.5 Trachea


title: 6IL22R KO Bladder UPEC 24hrs


title: SciPlex Combo Library Well B07


title: SciPlex Combo Library Well B10


title: SciPlex Combo Library Well B08


title: CD69-Ly108-, KO, Biol rep 2 [DN_KO_2]


title: CD69-Ly108-, KO, Biol rep 1 [DN_KO_1]


title: CD69+Ly108+, KO, Biol rep 1 [DP_KO_1]


title: E18.5 Trachea Rep 2 [18-5T2]