title: P60 | 003 | TUMOUR

value: TRUE

tag: Sex

tag: smokingstatus

value: 3 mos


title: P60 | 005 | TUMOUR

status: Public on Aug 02 2024

type: protein

city: Brisbane

first: Habib

last: Sadeghirad

state: Queensland

address: 37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba

country: Australia

institute: The University of Queensland

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

molecule: protein

organism: Homo sapiens

source_name: HNSCC

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: tissue

value: HNSCC

tag: bestresponse

value: PD

tag: pathway

value: Nivolumab

tag: mortality

value: Y

tag: age

value: Male

value: Previous

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: TKO_Rep1

type: SRA

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

country: USA

institute: Washington University in St. Louis

description:
TKO_whole_lung_Rep1
Egln1 KO in Tie2+cells and FABP4-5 in all cells

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to mouse genome mm10 using STAR.
Reads were counted on the exons of mm10 genes using htseq.
Differential gene expression analysis was performed using edgeR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was harvested using Zymo Research Quick-RNA Miniprep Kits with DNase I digestion.
Novogene performed the library construction using NEB library kit.

value: lung

tag: genotype

value: Egln1Tie2Cre KO plus Fabp4-5 KO


title: GZLBM2022tissue027

type: genomic

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: Standard Illumina Protocol

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Lung adenocarcinoma

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded or fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

tag: disease state

value: Lung adenocarcinoma


title: Fgfr 1-3 knockout lens epithelial explants, 1 day in  differentiation media +24 hrs in culture media sample B

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

data_processing:
Raw reads were quality-analyzed using FastQC and MultiQC .
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cut adapt and trim galore with paramaters -q 20 --phred33 --length 20.
Trimmed sequence reads were mapped to GrCM39 using Hisat2 incorporating splice juncation from genecode GTF .
Gene counts were generated using Stringtie2.1.5
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: Normalized gene count matrix from DESeq2

source_name: Lens Epithelium

growth_protocol: Lens epitheliall explants were maintained in 35mm culture dish with pre-calibrated M-199 media supplemented with 1% antibiotic-antimycotic solution and 0.1% bovine serum albumin  diluted  to 50% concentration, with vitreous henceforth referred to as “differentiation medium (DM)”, for 1 day or 5 days or 10 days at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNEasy Mini Kit (Qiagen cat. 74104) following the manufacturer’s instructions.
RNA libraries were constructed by Novogene (Sacramento, CA, USA) using a TruSeq (Illumina) library prep kit.

value: Lens Epithelium

value: Fgfr 1-3 knockout in FVB/N background

tag: treatment


title: CKO_Rep3

description:
CKO_whole_lung_Rep3
Egln1 KO in Tie2+cells

value: Egln1Tie2Cre KO


title: GZLBM2022tissue026


title: GZLBM2022tissue025


title: Brain, Huntington's, no N-PPG, 11H

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 291 Campus Dr

institute: Stanford Medicine

description: library name: 11H

data_processing:
Per Genewiz standard data processing pipe, 2020
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA sent to Genewiz

value: Brain

tag: cell type

value: all brain

value: Huntington's

value: no N-PPG

tag: time

value: Day of demise


title: Brain, Huntington's, no N-PPG, 10H

description: library name: 10H


title: P60 | 001 | TUMOUR

value: HNSCC

value: PD

value: TRUE

tag: Sex

tag: smokingstatus

value: 3 mos


title: P60 | 002 | TUMOUR

tag: tissue

tag: bestresponse

value: Nivolumab

value: Y

value: Male

value: Previous


title: CKO_Rep1

description:
CKO_whole_lung_Rep1
Egln1 KO in Tie2+cells

value: lung


title: P21 | 014 | TME

value: SD

tag: pathway

tag: mortality

value: Never

value: NA mos

value: TME


title: GZLBM2022tissue024

value: Lung adenocarcinoma


title: Brain, Wildtype, N-PPG, 57

description: library name: 57

value: Brain

value: all brain

value: Wildtype

value: N-PPG


title: P21 | 012 | TME

value: HNSCC

tag: age

tag: pfs


title: GZLBM2022tissue023


title: Brain, Wildtype, N-PPG, 9WT

description: library name: 9WT

value: Day of demise


title: Brain, Huntington's, N-PPG, 13HT

description: library name: 13HT

value: Huntington's


title: P21 | 010 | TME

value: TRUE

value: Nivolumab

tag: countofloweprgene

tag: percentofloweprgene


title: Brain, Wildtype, N-PPG, 8WT

description: library name: 8WT


title: Brain, Huntington's, no N-PPG, 12H

description: library name: 12H

value: no N-PPG


title: GZLBM2022tissue022


title: GZLBM2022tissue021


title: WT_Rep1

description:
WT_whole_lung_Rep1
naive

value: WT


title: GZLBM2022tissue020


title: CKO_Rep2

description:
CKO_whole_lung_Rep2
Egln1 KO in Tie2+cells

value: lung

value: Egln1Tie2Cre KO


title: Brain, Wildtype, N-PPG, 7WT

description: library name: 7WT


title: Brain, Wildtype, N-PPG, 6WT

description: library name: 6WT


title: P21 | 009 | TME

value: SD

value: Y

value: Male

value: Never

tag: foi

tag: responsesintumour


title: P21 | 007 | TUMOUR

value: NA mos

tag: responsesintme

value: TUMOUR


title: Ext1f/f, Control 2

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed
Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package
Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: htseq output with gene counts for each sample

source_name: chondrocytes

growth_protocol: The isolated cells were embeded in 1.2% alginate beads and cultured in high glucose DMEM containing 10 % FBS fro 2 days. The cultures were then treated with 300 nM Palovaroten or the same volume of 100% ethanol in high glucose DMEM containing 2% charcoal-treated serum for 2 days.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini kit. An average of 700ng of total RNA was used for each sample as input for enrichment followed by library preparation.
Sample enrichment for mRNA was done using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep kit.

value: chondrocytes

tag: genotype

value: Ethanol


title: WT_Rep3

description:
WT_whole_lung_Rep3
naive


title: Ext1f/f, Control 3

tag: treatment


title: P21 | 011 | TME

value: HNSCC

value: TME


title: Brain, Wildtype, N-PPG, 5WT

description: library name: 5WT

value: Brain

tag: cell type

value: all brain

value: Wildtype

value: N-PPG

value: Day of demise


title: GZLBM2022tissue019

tag: disease state

value: Lung adenocarcinoma


title: Brain, Wildtype, no N-PPG, 4W

description: library name: 4W

value: no N-PPG

tag: time


title: Ext1f/f, Control 1


title: P21 | 004 | TUMOUR

value: SD

value: TRUE

value: Nivolumab

tag: Sex

tag: smokingstatus


title: P21 | 006 | TUMOUR

tag: tissue

tag: bestresponse

value: Y

value: Male

value: Never


title: P29 | 022 | TME

tag: pathway

tag: mortality

value: Female

value: Current

value: 9 mos


title: P21 | 003 | TUMOUR

value: HNSCC

tag: age

tag: pfs

value: NA mos

value: TUMOUR


title: Ext1f/f, Palovarotene 3

value: chondrocytes

value: Palovarotene 300 nM


title: GZLBM2022tissue017


title: Brain, Wildtype, no N-PPG, 3W

description: library name: 3W

value: Brain

value: all brain

value: Wildtype

value: Day of demise


title: WT_Rep2

description:
WT_whole_lung_Rep2
naive

value: lung

value: WT


title: P21 | 002 | TUMOUR

value: SD

value: TRUE

value: Nivolumab

value: Y

tag: countofloweprgene

tag: percentofloweprgene


title: GZLBM2022tissue016

value: Lung adenocarcinoma


title: Ext1f/f, Palovarotene 2


title: Ext1f/f, Palovarotene 1


title: Brain, Wildtype, no N-PPG, 1W

description: library name: 1W

value: no N-PPG


title: GZLBM2022tissue015


title: AggrecanCreER;Ext1f/f, Control 3

value: Ethanol


title: Brain, Wildtype, no N-PPG, 2W

description: library name: 2W


title: P21 | 001 | TUMOUR

value: HNSCC

value: Male

value: Never

value: NA mos

tag: foi

tag: responsesintumour


title: GZLBM2022tissue018


title: P20 | 011 | TME

value: PR

value: Female

value: Current

value: 11 mos

value: TME

tag: responsesintme


title: GZLBM2022tissue014


title: GZLBM2022tissue013


title: P20 | 010 | TME


title: AggrecanCreER;Ext1f/f, Control 2

value: chondrocytes

tag: genotype

tag: treatment


title: GZLBM2022tissue012

tag: disease state


title: GZLBM2022tissue011


title: Willd Type, time 10, replicate 1 [Ribosome profiling]

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

country: Spain

institute: CRG

data_processing:
Basecalling with Illumina bcl2fastq version 2.17.1.14
Adaptor trimming with Skewer v0.2.2
Removal of rRNA/tRNA mapping reads with bowtie2 (parameters: --no-unal --mp 3 -L 10 -N 1 --local -D 10 -R 3)
STAR v2.5.3a mapping to Mus musculus Gencode version M14 (mm10) (with parameters: -parameters: --winAnchorMultimapNmax 100 --seedSearchStartLmax 15 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMatchNmin 10 –quantMode GeneCounts)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene obtained by STAR mapper’s –quantMode GeneCounts parameter (3rd column: forward stranded protocol)

source_name: Willd Type, time 10

growth_protocol: Embryoid bodies differentiation

extract_protocol:
The media was withdrawn and the cells washed with ice cold PBS supplemented with cycloheximide, scraped and pelleted. The cells were then lysed with lysis buffer (20mM Tris-HCl pH7,4, 150mM of NaCl, 5mM of MgCl2, 1mM DTT, 100 g/mL, 1% of Triton and 25U/mL of Turbo DNase I [AM 2238, Invitrogen] in RNase free water) with the help of glass beads by vortexing 5 seconds for 3 times. The lysate was then left 10 minutes on ice and consequently centrifuged at 10’000 rpm for 10 minutes.
To proceed we took an amount of RNA corresponding to 8-10 OD260nm. In order to digest the unprotected RNA, RNAse I (AM2294, Invitrogen) at a concentration of 100U/L was added and incubated at 25°C for 15 minutes. 10L of SUPERase In (AM 2694, Invitrogen) at 20U/L were added to stop RNase digestion and the sample loaded onto a sucrose cushion at 34% w/v in a polycarbonate ultracentrifuge tube (349622, Beckman Culture). The sample were then centrifuged at 70’000 rpm for 4 hours at +4°C. The supernatant was discarded and the pellet resuspended in the resuspension buffer of the Maxwell 16 LEV simplyRNA Cells Kit (AS1270, Promega). The RNA was then extracted according to the manufacturer instructions and resuspended in 40l of RNAse free water. In order to select the fragments of interest we pre-run a 15% TBE-Urea polyacrylamide gel (EC6885BOX, Invitrogen) at 200V for 15 minutes in TBE buffer. 5g of each sample were then mixed with the TBE-Urea sample buffer. The RNA was then denatured at 80°C for 90 seconds and loaded onto the gel and run at 200V for 65 minutes. The gel was then stained for 5 minutes with SYBR green (S32717, Invitrogen) and fragments between 28nt and 32nt excised. The bands were transferred into a RNase-free tube, resuspended in 360l of RNase free water and the RNA extracted by crushing the gel with a pestle. Then it was incubated at 70°C for 10 minutes in order to melt the gel. Once melted the sample was loaded into a spin column with filter made of 2 pieces of whatmann paper and centrifuged at max speed for 2 minutes. Consequently, the RNA was precipitated by adding 40L of 3M sodium acetate, 1L of glycoblue (00585590, Invitrogen) and 500L of isopropanol. The precipitation was performed either for 1 hour in dry ice or overnight at -80°C. Afterward the samples was centrifuged at 20’000g for 30 minutes at +4°C. The supernatant was discarded and the pellet washed with ethanol at 70% in RNase free water. It was then furtherly centrifuged at 20’000g for 2 minutes and then air dried for 10 minutes. Eventually, it was resuspended in 26L of RNase free water. The ribosomal RNA was then removed by making use of the Illumina Ribo-zero rRNA removal kit (20020596, Illumina) according to manufacturer’s instructions. The RNA left was then precipitated by adding 300L of isopropanol 20L of sodium acetate, 90L of H2O and precipitated for 1 hour in dry ice. Then it was centrifuged again at 20’000g for 30 minutes at +4°C, the supernatant discarded and the pellet washed with 500L of ethanol 70%, centrifuged again at 20’000g for 5 minutes at +4°C and the pellet was air-dried and resuspended in 10L of TRIS-HCl pH8 10mM. 33L of water were added and the samples were incubated at 80 °C for 90 seconds. In order to dephosphorylate the RNA, 5L of T4 PNK buffer, 1L of SUPERase IN and 1L of T4 PNK enzyme (M0202L, New England Biolabs) were added and the mix incubated at +37°C for 1 hour. The enzyme was then inactivated by rising the temperature at up to +70°C. The RNA was then precipitated and washed as previously stated and resuspended in 8,5L of RNase-free water. In order to add the linker, 1,5L of pre-adenylated linker were previously denaturated (0.5g/L) at +80 °C for 90 seconds and then cooled down at RT.  Then it was ligated by adding 2L of T4 RNA truncated ligase buffer, 6L of PEG 8000, 1L of SUPERase In (20U/L) and 1L of T4 RNA truncated ligase enzyme (200U/L, M024L, New England Biolabs), incubated for 2 hours and a half at RT. Then the RNA was precipitated and washed as previously described and resuspended in 10L of Tris-HCl pH8 10mM.  The samples were run on a 15% TBE gel as previously described, the RNA was excised, extracted and precipitated as previously described and resuspended in 10L of TRIS HCl pH 8 10 mM. In order to convert it to cDNA 2L of reverse transcription primer at 1.25M were added along with 4L of 5x first strand buffer, 1L of dNTPs mix (10 mM), 1L of 1M DTT, 1L of SUPERase In (20 U/L), 1L of Superscript III enzyme (200 U/L, 18080093, Invitrogen) and retro-transcribed at +50°C for 30 minutes. The cDNA was then precipitated and washed as previously described and resuspended in 10L of water. The cDNA was then electrophoretically run, excised and precipitated as previously described. The cDNA was circularized adding 2L of circ-ligase buffer, 1mM of ATP and 50mM of MnCl2 and 100 units of CircLigase I (CL4111K, Epicentre). The sample was then incubated 1 hour at +60°C in a thermal cycler and then heat-inactivate the enzyme for 10 min at +80°C and the rRNA depleted once again. After precipitation and wash the cDNA was resuspended in 5L of TRIS HCl pH8 10 mM and was PCR amplified in 100L volume containing 20L of Phusion HF buffer, 2l of dNTPs mix (10 mM), 0.5l of FW primer (100 M), 0.5l of RV barcoded primer (100 M) and 71L of RNase free water, 1l of Phusion polymerase (2 U/l, M05305, New England Biolabs). The PCR was performed with the following program: 1 cycle at 98°C for 30 sec, 14 cycles at 98°C for 10 sec, 65°C for 10 sec, +72°C for 5 sec. Eventually, the samples were run on an 8% (wt/vol) polyacrylamide non-denaturing gel for 40 min at 180V. The gel was then stained and a band at ~180nt was excised, extracted and purified as previously described. Then the libraries obtained were quality checked and sequenced

treatment_protocol: Cells were treated with cycloheximide (01810, Sigma Aldrich) at a concentration of 100 g/mL and were incubated for 15 minutes at 37°C.

tag: cell line background

tag: cell type

value: mouse embryonic stem cells

tag: knock-out

value: Wild Type

tag: time point


title: Willd Type, time 10, replicate 3 [Ribosome profiling]


title: AggrecanCreER;Ext1f/f, Palovarotene 2

value: Palovarotene 300 nM


title: Willd Type, time 0, replicate 3 [Ribosome profiling]

source_name: Willd Type, time 0


title: AggrecanCreER;Ext1f/f, Palovarotene 3


title: Willd Type, time 10, replicate 2 [Ribosome profiling]


title: Willd Type, time 0, replicate 2 [Ribosome profiling]


title: GZLBM2022tissue010


title: P20 | 008 | TME

tag: tissue

tag: bestresponse

value: TRUE

value: Nivolumab

value: Y

tag: Sex

tag: smokingstatus


title: P20 | 009 | TME

tag: pathway

tag: mortality

tag: age

tag: pfs


title: AggrecanCreER;Ext1f/f, Palovarotene 1


title: Willd Type, time 0, replicate 1 [Ribosome profiling]


title: P20 | 007 | TME

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: P20 | 006 | TUMOUR

tag: responsesintme

value: TUMOUR


title: GZLBM2022tissue008

tag: disease state

value: Lung adenocarcinoma


title: GZLBM2022tissue009


title: Sam68 KO, time 10, replicate 2 [Ribosome profiling]

source_name: Sam68 KO, time 10

tag: cell line background

tag: cell type


title: BMDMs, WT4_4h

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

source_name: bone marrow

growth_protocol: Bone marrow cells were isolated from the femurs and tibias of male WT and Nur77-KO mice aged 6-12 weeks. The cells were differentiated into macrophages by culturing them in RPMI 1640 medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 15% L929-conditioned medium, 1 mM sodium pyruvate, 1x MEM Non-Essential Amino Acids Solution, and 1x MEM Vitamin Solution for a period of 7 days. After the differentiation process, the cells were lifted, counted, and re-seeded at a density of 1 × 10^6 cells per ml.

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were stimulated with 100 ng/ml LPS for 0, 4 and 18h

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

tag: genotype

value: wt

tag: treatment

value: 4h 100 ng/ml LPS


title: AggrecanCreER;Ext1f/f, Control 1

value: Ethanol


title: GZLBM2022tissue007


title: BMDMs, WT4_0h

tag: tissue

value: untreated


title: P20 | 005 | TUMOUR

value: HNSCC

tag: bestresponse

value: PR

tag: Sex

value: Female

tag: smokingstatus

value: Current

value: 11 mos


title: Sam68 KO, time 10, replicate 1 [Ribosome profiling]

value: mouse embryonic stem cells

tag: knock-out

tag: time point


title: P20 | 003 | TUMOUR

value: TRUE

tag: pathway

tag: mortality

tag: age

tag: pfs

tag: countofloweprgene


title: GZLBM2022tissue006

tag: disease state


title: BMDMs, WT3_18h

value: 18h 100 ng/ml LPS


title: P65 | 012 | TME

value: CR

value: Nivolumab

value: Y

value: Male

value: Previous

value: NA mos

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: Sam68 KO, time 0, replicate 3 [Ribosome profiling]

source_name: Sam68 KO, time 0

tag: cell line background

tag: cell type


title: Sam68 KO, time 0, replicate 2 [Ribosome profiling]


title: GZLBM2022tissue005

value: Lung adenocarcinoma


title: P20 | 002 | TUMOUR

tag: tissue

tag: bestresponse

value: TUMOUR


title: Sam68 KO, time 10, replicate 3 [Ribosome profiling]


title: BMDMs, WT3_4h

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

tag: genotype

value: wt

tag: treatment

value: 4h 100 ng/ml LPS


title: P65 | 011 | TME

value: HNSCC

tag: pathway

tag: Sex

tag: smokingstatus


title: GZLBM2022tissue003


title: BMDMs, WT3_0h

value: untreated


title: GZLBM2022tissue004


title: BMDMs, WT2_18h


title: BMDMs, WT4_18h


title: Sam68 KO, time 0, replicate 1 [Ribosome profiling]

value: mouse embryonic stem cells

tag: knock-out

tag: time point


title: P65 | 010 | TME

value: TRUE

tag: mortality

tag: age

tag: pfs

tag: countofloweprgene


title: P65 | 009 | TME

value: CR

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme


title: GZLBM2022tissue002

tag: disease state


title: Quaking KO, time 10, replicate 3 [Ribosome profiling]

source_name: Quaking KO, time 10

tag: cell line background

tag: cell type

value: Quaking


title: BMDMs, WT2_4h

tag: tissue

tag: strain

tag: genotype

tag: treatment


title: BMDMs, WT2_0h


title: BMDMs, WT1_18h

value: 18h 100 ng/ml LPS


title: Quaking KO, time 10, replicate 2 [Ribosome profiling]

tag: knock-out


title: P65 | 007 | TME

tag: bestresponse

tag: pathway

value: Nivolumab

value: Y

tag: Sex

value: Male

tag: smokingstatus


title: P65 | 008 | TME

tag: mortality

tag: age

value: Previous

tag: pfs

value: NA mos

tag: countofloweprgene

value: TME


title: Quaking KO, time 10, replicate 1 [Ribosome profiling]

tag: time point


title: Quaking KO, time 0, replicate 2 [Ribosome profiling]

source_name: Quaking KO, time 0


title: P65 | 006 | TUMOUR

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: BMDMs, WT1_4h

tag: tissue

value: bone marrow

tag: strain

tag: cell type

value: bone marrow-derived macrophages


title: P65 | 005 | TUMOUR


title: P65 | 004 | TUMOUR


title: BMDMs, WT1_0h

tag: genotype

value: wt

tag: treatment


title: ARE-GFP replicate 3

type: RNA

city: Leuven

first: Johan

last: Van Weyenbergh

address: Herestraat 49

department: DMIT

country: Belgium

institute: KU Leuven

data_processing: Results were sequentially corrected for background (negative control probes), technical variation (positive control probes) and RNA content (housekeeping genes) using nSolver 4.0 (NanoString), followed by differential gene expression analysis and gene set enrichment analysis (based on GO-terms) using Omics Playground (BigOmics Analytics).

source_name: Neurospheroids

label_protocol: The RNA samples were used for nCounter (NanoString) analysis on a nCounter® MAX Analysis System. Briefly, RNA extracts were hybridized to ± 600 unique capture/reporter pairs (50bp each) targeting 585 immune transcripts and 15 housekeeping genes, as defined in the Human Immunology nCounter® panel, as well as six positive and eight negative control probes (all from NanoString).

extract_protocol: At 7 days post stimulation/infection, NSPHs for RNA extraction were washed with ice cold PBS, snap frozen in liquid nitrogen and stored at -80°C. RNA extraction was performed on 2 pooled NSPHs of each condition (in triplicate) using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer's protocol.

tag: sample type

value: ARE-GFP

tag: gene rlf

tag: cartridge id

tag: lane

tag: fov count

tag: fov counted

tag: binding density


title: BMDMs, Nur77-KO4_4h

value: cre

value: 4h 100 ng/ml LPS


title: ARE-GFP replicate 2


title: VZV replicate 3

value: VZV


title: BMDMs, Nur77-KO4_18h


title: Sam68 KO, time 10, replicate 2

description:
processed data file: SamD10_merged_crosslink_sites_annot.bed
SamD10_2_01808AAB_CACTGT

data_processing:
library strategy: iCLIP
Basecalling with Illumina bcl2fastq version 2.17.1.14
Adaptor trimming with Skewer v0.2.2
Removal of rRNA/tRNA mapping reads with bowtie2 (parameters: --no-unal --mp 3 -L 10 -N 1 --local -D 10 -R 3)
STAR v2.5.3a mapping to Mus musculus Gencode version M24 (mm10) (with parameters: --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --seedSearchStartLmax 15 --alignEndsType Extend5pOfRead1 --outReadsUnmapped Fastx --outSJfilterReads Unique --quantMode GeneCounts)
Reads de-duplication with umi_tools dedup (parameter –method=unique”)
Peak calling with PureCLIP v1.3.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: BED files: PureCLIP peaks, annotated

source_name: Sam68 KO_time 10

growth_protocol: Embryoid bodies differenation

extract_protocol:
The iCLIP2 protocol was carried out according to Buchbender et al., 2019. Briefly, cells were washed with 5 ml PBS and 6 ml of ice-cold PBS were added to cells growing in a 10cm plate. The plate was then placed on ice. The lid was removed and the cells were irradiated once with 150 mJ/cm2 in a UV-C crosslinker (CL 1000 Ultraviolet Crosslinker, UVP) at 254 nm. Cells were harvested by scraping and cell suspension was transferred in a microtube, spinned at 1,500 xg (4,000 rpm) for 1 min at 4°C. Snap frozen pellets were stored at -80°C until use. To prepare the immunoprecipitation, a volume of 100 µL of protein G Dynabeads per experiment was added to a microtube. Beads were washed twice with lysis buffer and resuspended in 100 µl of lysis buffer with 2 to 10 µg antibody per experiment. Bead-antibody conjugation occurred by rotating tubes at room temperature for 30-60 min (until lysate was ready). The beads were washed once with high-salt wash buffer, twice with lysis buffer and resuspended in 100 µL lysis buffer with added protease inhibitor. In parallel, cell pellets were resuspended in 1 ml lysis buffer supplemented with protease inhibitors
An optimized RNase I dilution in lysis buffer was prepared and added to the lysate together with 2 µl Turbo DNase. RNA was digested for 3 min shaking at +37°C and 1,100 rpm. After incubation the reaction was transferred to ice for 3 minutes and centrifuged at +4°C at full speed 21,100 xg (14,800 rpm) for 10 min and the supernatant transferred to a new 1.5 ml tube. A volume of 500 µl of lysate was loaded onto a Proteus mini clarification spin column and centrifuged at +4°C at 16,000 xg (12,900 rpm) for 1 min. The flow-through was moved to a new tube. The step was repeated with second half of the lysate. To carry out the immunoprecipitation, the beads were added to cell extracts and the sample were incubated on a rotating wheel for 2 hours at +4°C. Supernatant was discarded and the beads were washed twice with high-salt wash buffer and twice with PNK buffer in order to be resuspended in 1 ml PNK buffer. To promote RNA 3’ end dephosphorylation, the supernatant was carefully removed and the beads were resuspended in 20 µl of the following mix:8 µl water, 5 µl 4X ligation buffer 0.5 µl  RNase inhibitor, 1.5µl Pre-adenylated L3-App (20 µM) 4µl PEG400, 1µl  T4 RNA ligase. The samples were incubated overnight at +16°C in a thermomixer at 1,100 rpm and a volume of 500µl PNK buffer was added. Samples were washed twice with 1 ml high-salt wash buffer, twice with 1ml PNK buffer and left in 1 ml of the second wash. The samples were the loaded on a 4-12% NuPAGE Bis-Tris gel according to the manufacturer's instructions (Life Technologies) immerged in 1X MOPS running buffer. The run vas performed for 50 min at 180 V. Protein-RNA complexes were dry transferred from the gel to a nitrocellulose membrane and excised from the nitrocellulose membrane and the selected regions were cut in several pieces and placed into 1.5 ml tubes. A volume of 10µl proteinase K in 200µl PK buffer was added to the nitrocellulose pieces and the tubes were incubated in a thermomixer for 20 min at 37°C and 1,100rpm. Another 200µl of PK + urea buffer were added and the samples were incubate for further 20 min at +37°C and 1,100 rpm. The solution was collected and added together with 400µl phenol/chloroform to a 2 ml Phase Lock Gel Heavy tube. The tubes were then incubated for 5 min at +30°C shaking at 1,100rpm (do not vortex). In order to separate the phases the samples were spin for 5 min at 16,000 xg (12,900 rpm) at room temperature. The aqueous layer was transferred into a new tube and spin again for 1 min in order to be transferred again into a new tube. Precipitation was performed by adding 0.75µl GlycoBlue and 40µl 3M sodium acetate pH 5.5. After mixing 1ml 100% ethanol was added and the tubes were mixed by inverting several times and placed over night at -20°C. The tubes were centrifuged for 20 min at 21,100 xg (14,800 rpm) at +4°C in order to remove the supernatant and the pellet was washed with 0.9 ml of 80% ethanol, and centrifuged again for 5 min. After air-drying it for 3 min, the pellet was resuspended in 5µl water and transfer to a PCR tube in order to be retrotrascribed. Reverse transcription was promoted by adding the following reagents: 1µl primer RToligo (0.5 pmol/µl) and 1 µl dNTP mix 10 mM setting the temperature at +70°C for 5 min and +25°C hold until the RT mix (7µl water, 4µl of 5X RT buffer, 1 µl 0.1 M DTT, 0.5 µl RNase inhibitor, 0.5µl SuperScript III) was added. The following programme was used: +25°C for 5 min, +42°C  20 min, +50°C 40 min, +80°C 5 min, +4°C  hold. A volume of 1.65 µl 1 M NaOH was added and samples were incubated at 98°C for 20 min. Then 20 µl 1 M HEPES-NaOH pH 7.3 was added.  To clean up the samples from all the reagents, we used the MyONE clean-up. Briefly, a volume of 10μl MyONE Silane beads was considered per sample. Beads were magnetically attracted and washed with 500 μl RLT buffer and resuspended in 125 μl RLT buffer. A volume of 125 μl washed beads was added to each sample and mixed with an additional 150 μl of 100% ethanol.  After 5 min at room temperature, the sample were mixed once more by pipetting and incubated a second time for 5 min. Beads were magnetically attracted and the supernatant was discarded. Beads were resuspended in 1 ml 80% ethanol and transferred to a new tube. Again, beads were washed twice with 80% ethanol and incubated for 30 seconds at room temperature. The mix was briefly spin in a microcentrifuge and the supernatant was discarded. Beads were air-dried for 5 min at room temperature, resuspended in 5 μl water and incubate for 5 min at room temperature. The second adapter was added together with DMSO to the cDNA-bead solution and the mix was heated for 2 min at 75°C and immediately kept it on ice for >1 min:2 μl L##clip2.0 (10 µM), 1 μl 100% DMSO. The following ligation master-mix was prepared on ice: 0.3 µl water, 2.0 μl 10X NEB RNA ligase buffer (with DTT) , 0.2μl ATP, 100 mM, 9.0μl, 50% PEG 8000, 0.5 μl High conc. RNA Ligase. To ensure homogeneity, the ligation master-mix was mixed by vigorous stirring, pipetting and flicking. The mix was briefly centrifuged in a microcentrifuge. A volume of 12 µl of ligation master-mix was added to 8 µl sample-linker mix and mixed it thoroughly.  1 μl of RNA ligase was added to each sample (final volume: 21 µl), followed by stirring and the sample was incubated overnight at room temperature, shaking at 1,100 rpm.  Fresh MyONE Silane beads were added to the cDNA-bead mix. Therefore, 5μl of fresh MyONE Silane beads were magnetically attracted, discarding the supernatant and washed with 500μl of RLT buffer. Magnetic attraction was repeated and in order to resuspend the beads in 60µl RLT per sample. A volume of 60μl beads was added to the cDNA-bead slurry and mixed. Then 60μl of 100% ethanol were added and the solution was mixed by pipetting carefully. After 5 min at room temperature, the sample was mixed once more by pipetting and the 5 min incubation step was repeated a second time.   The beads were magnetically attracted and the supernatant was discarded. The beads were resuspended in 1 ml 80% ethanol and the mix was transferred to a new tube. This step was repeated other two times incubating the mix 30 seconds at room temperature in 80% ethanol. The mix was spin in a microcentrifuge and after the beads were magnetically attracted, the supernatant was discarded. After air-drying the beads for 5 min at room temperature, they were resuspended in 23μl of water and the mix was incubated for 5 min at room temperature. The beads were magnetically attracted and the eluate was added to the PCR mix of the next step. c-DNA was pre-amplified by adding the following PCR mix: 22.5 µl cDNA , 2.5 µl Primer mix of P5Solexa_s and P3Solexa_s, 10 µM each, 25.0 µl, 2X Phusion HF PCR Mast

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out / igg control

tag: time point


title: Sam68 KO, time 10, replicate 3

description:
processed data file: SamD10_merged_crosslink_sites_annot.bed
SamD10_3_01809AAB_ATTGGC


title: P65 | 003 | TUMOUR

value: HNSCC

tag: bestresponse

value: CR

value: TRUE

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: VZV replicate 2

tag: sample type

tag: gene rlf

tag: cartridge id

tag: lane

tag: fov count


title: GZLBM2022tissue001

tag: disease state

value: Lung adenocarcinoma


title: Sendai replicate 3

value: Sendai

tag: fov counted

tag: binding density


title: Sam68 KO, time 10, replicate 1

description:
processed data file: SamD10_merged_crosslink_sites_annot.bed
SamD10_1_01807AAB_TGGTCA

tag: cell line background

tag: cell type

tag: knock-out / igg control

tag: time point


title: Quaking KO, time 0, replicate 3 [Ribosome profiling]

tag: knock-out

value: Quaking


title: P65 | 002 | TUMOUR

tag: tissue

tag: bestresponse

tag: pathway

value: Nivolumab

tag: mortality

value: Y

tag: age

tag: Sex

value: Male

tag: smokingstatus

value: Previous

tag: pfs

value: NA mos

tag: countofloweprgene

tag: responsesintme


title: BMDMs, Nur77-KO4_0h

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

tag: genotype

tag: treatment

value: untreated


title: BMDMs, Nur77-KO3_18h

tag: cell type

value: cre

value: 18h 100 ng/ml LPS


title: Sendai replicate 2

tag: sample type

tag: gene rlf

tag: cartridge id

tag: lane

tag: fov count

tag: fov counted

tag: binding density


title: P65 | 001 | TUMOUR

tag: tissue

tag: bestresponse

tag: pathway

tag: mortality

tag: age

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TUMOUR


title: CTR replicate 3

value: CTR


title: Sam68 KO, time 0, replicate 3

description:
processed data file: SamD0_merged_crosslink_sites_annot.bed
SamD0_3_01806AAB_GCCTAA

source_name: Sam68 KO_time 0

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out / igg control

tag: time point


title: BMDMs, Nur77-KO3_4h

tag: strain

tag: cell type

tag: genotype

tag: treatment

value: 4h 100 ng/ml LPS


title: P18 | 011 | TME

value: HNSCC

value: PD

value: TRUE

tag: Sex

value: Female

tag: smokingstatus

tag: pfs

value: 3 mos

tag: countofloweprgene

value: TME

tag: responsesintme


title: CTR replicate 2

tag: sample type

tag: gene rlf

tag: cartridge id

tag: lane

tag: fov count

tag: fov counted

tag: binding density


title: Quaking KO, time 0, replicate 1 [Ribosome profiling]

tag: cell line background

tag: knock-out

value: Quaking

tag: time point


title: P18 | 010 | TME

tag: tissue

tag: bestresponse

tag: pathway

value: Nivolumab

tag: mortality

value: Y

tag: age

value: Previous

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: VZV replicate 1

tag: sample type

value: VZV

tag: gene rlf


title: Quaking KO, time 10, replicate 2

description:
processed data file: QKI_D10_merged_crosslink_sites_annot.bed
QKI_D10_2_01814AAB_CACTGT

source_name: Quaking KO_time 10

tag: cell type

tag: knock-out / igg control


title: BMDMs, Nur77-KO3_0h

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

tag: genotype

value: cre

tag: treatment

value: untreated


title: BMDMs, Nur77-KO2_4h


title: Sam68 KO, time 0, replicate 1

description:
processed data file: SamD0_merged_crosslink_sites_annot.bed
SamD0_1_01804AAB_CGTGAT

tag: cell line background

value: mouse embryonic stem cells


title: P18 | 009 | TME

source_name: HNSCC

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: responsesintme


title: CTR replicate 1

value: CTR

tag: cartridge id

tag: lane

tag: fov count

tag: fov counted

tag: binding density


title: P18 | 008 | TME

tag: tissue

value: HNSCC

tag: bestresponse

tag: pathway

tag: mortality

tag: age

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: Sendai replicate 1

tag: sample type

value: Sendai

tag: gene rlf


title: Quaking KO, time 10, replicate 3

description:
processed data file: QKI_D10_merged_crosslink_sites_annot.bed
QKI_D10_3_01815AAB_ATTGGC

tag: cell line background

tag: cell type

tag: knock-out / igg control

tag: time point


title: Quaking KO, time 0, replicate 3

description:
processed data file: QKI_D0_merged_crosslink_sites_annot.bed
QKI_D0_3_01812AAB_GCCTAA

source_name: Quaking KO_time 0


title: RPM_10 week tumor_rep1

city: New York

first: Rodrigo

last: Romero

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering

description: RR1123 (10 week tumor)

data_processing:
FASTQ files were processed using the 10X Cell Ranger 6.1.2. Cell Ranger count was used to align reads to the GRCm38 (mm10) reference genome for snRNAseq samples and a modified version of GRCm38 (mm10) that includes the Myc-P2A-EGFP transgene sequences, given that organoids were infected with lentiviruses harboring its expression. We set “include introns=TRUE'' to accommodate the higher rate of intronic reads in snRNA. Finally, Cell Ranger count was used to generate feature-barcode matrices for subsequent bioinformatic analyses.
We first used CellBender to remove ambient RNA molecules from the raw count matrices with the parameter --expected-cells 5000 and --total-droplets-included 20000. These parameters were chosen by inspecting the barcode rank plot generated by Cell Ranger, following author recommendations. Defaults were used for all other parameters. All downstream processing of snRNA-seq data and scRNA-seq data, discussed in the section “Reclustering of the public scRNA-seq dataset”, were performed in Scanpy. We next removed low quality cells, unexpressed genes, and potential doublets from the CellBender output. We filtered to exclude i) genes detected in fewer than 3 cells, ii) cells with under 200 genes or 1000 UMIs, and iii) cells with a mitochondrial fraction above 10%. Mitochondrial and protein-coding ribosomal protein coding genes were also omitted from downstream analyses, as these are often a large source of spurious variance that can dominate clustering and confound deconvolution29. We used Scrublet to remove doublets. After Scrublet, 4,872 cells were retained for downstream analyses, with a median of 7055.5 UMIs per cell. Raw counts were normalized by log2 (X+1) transformation, where X = library size of each cell / 104.
We selected the top 3000 highly variable genes in each dataset using the Scanpy function pp.highly_variable_genes with raw counts as input, n_top_genes = 3000, flavor = ‘seurat_v3’ and span = 1. We applied PCA to these genes using the scanpy.tl.pca function with the arpack solver. We selected 30 PCs, which explain 40% of variance. For clustering, we used Phenograph63 with k = 30 and clustering_algo = 'leiden', which generated 19 clusters. Cell typing was performed using user-selected marker gene expression. To distinguish malignant cells from non-malignant cells, we performed copy number analysis inference using inferCNV (Trinity CTAT Project, https://github.com/broadinstitute/inferCNV). We used myeloid and endothelial cells determined based on marker expression as the normal cell reference. inferCNV showed a major CNV group of low CNV score containing two additional phenograph clusters, which were labeled as normal epithelial and mesenchymal cells. All other clusters show significant CNV changes, and were labeled as NE (neuroendocrine), EMT (epithelial-to-mesenchymal transition) and Tumor Luminal/Basal according to expression of marker genes, with each subtype containing 6, 4 and 5 cell states respectively.
Assembly: mm10/GRC38
Supplementary files format and content: barcodes.tsv.gz are processed cellranger barcodes
Supplementary files format and content: features.tsv.gz are processed cellranger features
Supplementary files format and content: matrix.mtx.gz are processed cellranger feature-barcode matrices

source_name: Prostate

growth_protocol: RPM (Rb1/Trp53 knockout; cMyc-overexpression) mouse prostate organoids were transplanted into immunocompetent C57BL/6 8-10 week old male mice (dorsal prostatic lobe). Primary and metastatic lymph node tumors were isolated from mice between 2-10 weeks post transplantation.

extract_protocol:
A single 10-week RPM tumor was extracted from the mouse prostate, and EGFP signal was used to microdissect tumor tissue (Nikon, SMZ18). Tumor sample was sliced into ~5 mm x 5 mm pieces, dabbed on a kimwipe to remove moisture, and immediately flash frozen in liquid nitrogen. Tumor piece was loaded onto a Singulator 100 (S2 Genomics) cartridge supplemented with 3.5 μL of 1 M DTT (Sigma, 43816-10mL) and 87.5 units of Protector RNAse inhibitor (Sigma, 3335402001). Nuclei were isolated with standard-nuclei isolation protocol according to manufacturer recommendations. Nuclei suspension was cleaned with sucrose density gradient (Sigma, NUC201-1KT) in protein low-bind microcentrifuge tubes (Eppendorf, 0030108442) at 500g for 5 min. Nuclei were subsequently resuspended in nuclei wash buffer: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1 mM DTT, 1% BSA, 1 U/μL Protector RNAse inhibitor, strained through blue-capped 35 μm FACS tube, stained with 7-AAD, and flow sorted for 7-AAD+ population to obtain single nuclei suspension. Sorted nuclei were submitted to the Single Cell Analytics Innovation Lab (SAIL) at MSKCC. Nuclei were then validated for nuclear integrity under phase-contrast microscopy.
Nuclei were processed on a Chromium instrument (10X Genomics) following user guide manual for 3’ v3.1 snRNAseq. Nuclei were captured in droplets, emulsions were broken, and cDNA purified using Dynabeads (Thermo, 37012D) followed by PCR amplification per manual instruction. ~10,000 cells were targeted for each sample. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 - 28 cycles, i7 - 8 cycles, R2 - 90 cycles) at the Integrated Genomics Operation (MSKCC).

value: Prostate

tag: cell line

value: RPM RR112

value: Prostate epithelial

tag: genotype

value: Rb1/Trp53 KO; cMyc overexpressing (RPM)


title: BMDMs, Nur77-KO2_0h

tag: strain

tag: treatment


title: Quaking KO, time 0, replicate 2

description:
processed data file: QKI_D0_merged_crosslink_sites_annot.bed
QKI_D0_2_01811AAB_ACATCG

value: Quaking


title: Sam68 KO, time 0, replicate 2

description:
processed data file: SamD0_merged_crosslink_sites_annot.bed
SamD0_2_01805AAB_ACATCG


title: P18 | 004 | TUMOUR

tag: tissue

tag: bestresponse

value: PD

value: TRUE

value: Nivolumab

tag: Sex

value: Female

tag: smokingstatus

tag: pfs

value: 3 mos

tag: countofloweprgene

tag: responsesintme

value: TUMOUR


title: P18 | 005 | TUMOUR

tag: pathway

tag: mortality

value: Y

tag: age

value: Previous

tag: percentofloweprgene

tag: foi

tag: responsesintumour


title: fat body, mutant, replicate 4

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

institute: Indiana University

data_processing:
Quantification via Salmon 1.10.2
Normalization and analysis via DESeq2 1.42.0
Assembly: BDGP6.46
Supplementary files format and content: rlog-normalized counts from DESeq2

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Larvae were raised at 25C for 60 hrs on molasses agar plates with a smear of yeast in the center

extract_protocol:
RNA was extracted using a Qiagen RNeasy mini kit
Illumina Stranded mRNA prep, 96 index; Poly-A-selected total RNA prepared with TruSeq ligation for paired-end sequencing

value: fat body

value: ERR mutant


title: RPM_10 week lymph node met_rep2

description: RR1124 (10 week lymph node met) RR1128 (10 week lymph node met)

data_processing:
Cell type deconvolution using BayesPrism: We deconvolved Visium data from two replicates using the snRNA-seq data collected from the 10-week RPM tumor. We used BayesPrism to perform statistical deconvolution as it has been previously shown to yield accurate results for Visium data and outperformed other methods in multiple settings. More importantly, BayesPrism jointly imputes the posterior of cell type fraction and the cell type-specific gene expression profile in each Visium spot, enabling the cell type-specific gene count matrices by PrismSpot, as described below.
To increase signal to noise ratio for deconvolution, we selected marker genes that are differentially upregulated in each of the 19 cell types, which was defined as the 19 phenograph clusters in the snRNA-seq data. We then took the union of these marker genes and deconvolved over these genes. Specifically, we performed a  pairwise t-test using the findMarker function from the scran package70, provided in the wrapper function get.exp.stat from the BayesPrism package. As each cell type is compared against every other cell type, we need to summarize N-1 p-values and log2 fold change statistics for each cell type (N denotes number of total cell types). For each non-tumor cell types (4 in total), i.e., mesenchymal, myeloid, normal L/B (luminal/basal) and endothelial cells, we required both the maximum p value to be less than 0.01, and the minimum log2 fold change to be above 0.1, where the max and min were taken over every other cell type. For each tumor cell type (15 in total), i.e., NE, EMT and tumor L/B, we required the same threshold for p-value and log2 fold change, but the max and min were taken over every other non-tumor cell type. As a result, we avoided the comparison between tumor cell types when taking the max and min to retain the maximum number of tumor-specific genes for PrismSpot analysis. This was achieved by defining a coarse level cell type label, where 15 tumor cell types were grouped into a single tumor cell type and using it as the cell.type.labels argument, while setting the original 19 cell types as cell.state.labels in BayesPrism’s built-in function get.exp.stat. To speed up deconvolution we further excluded genes expressed in less than or equal to 3 spots. This yielded 5,125 genes in total used as the input for BayesPrism.
We defined each of the 19 cell states as individual cell types when constructing reference for deconvolution. We set pseudo.min to 0, the numerical lower bound for genes with zero count in a given cell type, to maximize the contrast between different cell types in the reference. All other parameters of BayesPrism were used as default. We performed the updated Gibbs sampling for a more robust correction of batch effects between the snRNA-seq and the FFPE Visium.
Benchmarking of BayesPrism. We benchmarked both the accuracy and robustness of the cell type fraction deconvolved by BayesPrism. A big challenge in the deconvolution field is the lack of ground truth for benchmarking. To estimate some ground truth of the cell type fractions from the Visium data we used 1) histology with H&E, and 2) a marker genes-based approach. The comparison with histologically defined NEPC regions showed strong concordance with the fraction of NEPC cells inferred by BayesPrism.  Additionally, we benchmarked the robustness of cell type fraction inferred by BayesPrism by assessing the concordance across 5 histologically defined regions between two technical replicates, which includes 3 neuroendocrine regions and 2 non-neuroendocrine regions. As tissues are slightly shifted between technical replicates, we manually adjusted the selected regions to achieve better spatial concordance on the x-y plane. For each region, we compute the average fractions for each cell type. We then computed both cell type-level and region-level Pearson’s correlation coefficients.
BayesPrism’s deconvolution infers cell type-specific gene expression matrices for each spot.  For the Hotspot analysis, we use spot specific tumor gene expression as the input. Specifically, to generate tumor-specific gene expression profiles, we summed up the posterior mean of cell type-specific gene expression, Z, across all tumor clusters (n=15) outputted by BayesPrism. As Hotspot models the raw count data using negative binomial distribution, we rounded up the posterior mean of Z.  An important step in Hotspot analysis is to define neighborhood structure over which the spatial co-expression is defined. In our Visium data, we have two adjacent slides, referred to as technical replicates. Each technical replicate contains tumor samples from two different mice, referred to as biological replicates. To leverage the full set of Visium data points to yield higher statistical power while accurately reflecting the neighborhood structure, we performed a single Hotspot analysis for all Visium spots while restricting neighborhoods to be only within each mouse and each technical replicate. We achieved this by shifting the coordinates of Visium data points for each tumor sample in each replicate by a large numeric number, e.g.,1000, such that coordinates have no overlap within the Kth (K=6, discussed below) nearest neighbor for Visium spots from different tumor samples. We excluded i) genes with zero count in all spots, and ii) spots containing fewer than 1000 genes or 1000 UMIs from downstream Hotspot analysis. We define n_neighbors=6 in the create_knn_graph in Hotspot to include only Visium spots that are adjacent to each other and disabled weighted_graph arguments to treat all adjacent spots and the self-spot equally. We selected genes with spatial autocorrelation FDR less than 0.01 and transcription factors within the top 500 autocorrelation Z score, followed by re-computing the pairwise local correlation between the top 500 transcription factors. To cluster transcription factors into modules, we used the “create_modules” function provided by the Hotspot package, with parameters min_gene_threshold=15, core_only=True, fdr_threshold=0.05, which performs a bottom-up clustering procedure by iteratively merging two genes/modules with the highest pairwise Z-score. We analyzed the Hotspot local correlation statistics over a more comprehensive gene set without pre-filtering genes based on autocorrelation to demonstrate the behavior of the statistics of different types of markers. We call the modules resulting from this combination of BayesPrism and Hotspot, PrismSpot.
Assembly: mm10/GRC38
Supplementary files format and content: .pdf file contains lowres tissue positions and tumor IDs
Supplementary files format and content: .tif files contain highres tumor slide scan
Supplementary files format and content: .cloupe are processed cloupe datafiles
Supplementary files format and content: barcodes.tsv.gz are processed spaceranger barcodes
Supplementary files format and content: features.tsv.gz are processed spaceranger features
Supplementary files format and content: matrix.mtx.gz are processed spaceranger feature-barcode matrices
Library strategy: Spatial Transcriptomics

source_name: periaortic lymph node met

extract_protocol:
We generated Visium data from two adjacent sections as technical replicates, with each slide containing RPM tumor tissues from at least two individual mice. Visium Spatial Gene Expression slides were prepared with FFPE sections by the Molecular Cytology Core at MSKCC. Tumor samples with a target RIN value > 0.5 were processed for spatial transcriptomics.
Probe pairs targeting the whole transcriptome were added to slide capture areas and allowed to hybridize overnight at 50°C. Bound pairs were ligated to one another, then released from the tissue by RNase treatment and permeabilization and captured by oligos bound to the slide. Probe extension and library preparation proceeded using the Visium Spatial for FFPE Gene Expression Kit, Mouse Transcriptome (10X Genomics, 1000337) according to the manufacturer’s protocol. After evaluation by real-time PCR, sequencing libraries were prepared with 11-14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 SP Reagent Kit (100 cycles) (Illumina). FASTQ files from sequencing (NovaSeq) were processed via spaceranger count (version 2.0.0) to align reads to the GRCm38 (mm10) reference genome and generate count matrices for subsequent bioinformatic analyses. An average of 74 million paired reads was generated per sample, corresponding to 37,000 reads per spot.

value: periaortic lymph node met

tag: cell line

tag: cell type


title: fat body, mutant, replicate 2

tag: genotype


title: P18 | 006 | TUMOUR

value: HNSCC


title: fat body, mutant, replicate 1


title: RPM_10 week lymph node met_rep1


title: P18 | 003 | TUMOUR


title: Quaking KO, time 0, replicate 1

description:
processed data file: QKI_D0_merged_crosslink_sites_annot.bed
QKI_D0_1_01810AAB_CGTGAT

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out / igg control

tag: time point


title: BMDMs, Nur77-KO2_18h

tag: tissue

value: bone marrow

tag: strain

value: bone marrow-derived macrophages

value: cre

tag: treatment

value: 18h 100 ng/ml LPS


title: ARE-GFP replicate 1

tag: sample type

value: ARE-GFP

tag: gene rlf

tag: cartridge id

tag: lane

tag: fov count

tag: fov counted

tag: binding density


title: P18 | 007 | TME

tag: bestresponse

value: PD

value: TRUE

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: fat body, control, replicate 7

tag: tissue

tag: genotype

value: control heterozygote


title: P18 | 002 | TUMOUR

value: Nivolumab

value: Female

value: 3 mos

value: TUMOUR


title: RPM_10 week tumors_rep2

description: RR1123 (10 week tumor) RR1132 (10 week tumors)

value: Prostate

tag: cell line

value: RPM RR112

tag: cell type

value: Prostate epithelial

value: Rb1/Trp53 KO; cMyc overexpressing (RPM)


title: IgG, time 10, replicate 3

source_name: IgG_time 10

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out / igg control

value: IgG control

tag: time point


title: Quaking KO, time 10, replicate 1

description:
processed data file: QKI_D10_merged_crosslink_sites_annot.bed
QKI_D10_1_01813AAB_TGGTCA

value: Quaking


title: IgG, time 10, replicate 2


title: fat body, control, replicate 6

value: fat body


title: RPM_10 week tumors_rep1


title: P47 | 012 | TME

value: HNSCC

tag: bestresponse

tag: pathway

tag: mortality

value: Y

value: Male

value: Current


title: P18 | 001 | TUMOUR

value: PD

value: TRUE

tag: age

tag: Sex

tag: smokingstatus

value: Previous


title: RPM_4_&_6 weeks tumor_rep2

description: RR1109 (4 week tumor) RR1117 and RR1118 (6 week tumors)


title: whole animal, mutant, replicate 3

source_name: whole animal

value: whole animal

value: ERR mutant


title: IgG, time 0, replicate 3

source_name: IgG_time 0


title: whole animal, mutant, replicate 2


title: RPM_4_&_6 weeks tumor_rep1

value: Prostate


title: IgG, time 0, replicate 2


title: IgG, time 10, replicate 1


title: whole animal, mutant, replicate 1


title: IgG, time 0, replicate 1


title: RPM_2_&_3 weeks tumor_rep2

description: RR1104 (2 week tumor) RR1105 and RR1107 (3 week tumors)

value: RPM RR112


title: P47 | 011 | TME

value: Nivolumab

tag: pfs

value: 3 mos

tag: countofloweprgene

tag: percentofloweprgene

value: TME


title: P47 | 009 | TME

tag: foi

tag: responsesintumour

tag: responsesintme


title: RPM_2_&_3 weeks tumor_rep1

tag: tissue

tag: cell line

value: Prostate epithelial

tag: genotype

value: Rb1/Trp53 KO; cMyc overexpressing (RPM)


title: whole animal, control, replicate 1

value: control heterozygote


title: whole animal, control, replicate 3


title: RPM Tumor - Rep 9

first: Charles

middle: L

last: Sawyers

address: 417 E 68th Street, ZRC-661

department: Human Oncology and Pathogenesis

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Analysis of bulk RNA sequencing was performed at NYULMC HPC UltraViolet (formerly BigPurple) cluster using software provided in the Seq-N-Slide pipeline (ref; https://github.com/igordot/sns), through the rna-star followed by rna-star-groups-dge routes. Briefly, after quality control assessment with MultiQC (python/cpu/v2.7.15, PMID: 27312411) and sequencing adaptor trimming with Trimmomatic (v0.36, PMID: 24695404), reads were aligned to the mm10/GRCm38 mouse reference genome with a splice-aware (STAR v2.7.3a, PMID: 23104886) alignment, followed by featureCounts (subread/v1.6.3, PMID: 24227677) to generate the RNA counts table.
These were then normalized for gene length and sequencing depth, and tested for differential mRNA expression between RPM and PtPM groups using negative binomial generalized linear models implemented by the DESeq2 v1.40.1 (PMID: 25516281) R package (r/v4.1.2). RStudio v4.3.0 was used for additional downstream analyses and visualizations. Differential expression was assessed by principal component analysis (prcomp function from the stats v4.3.0 R package) or unsupervised hierarchical clustering (pheatmap v1.0.12 and ComplexHeatmap v2.16.0), and visualized by a volcano plot (EnhancedVolcano v1.18.0) and TPM expression heatmap illustrating genes of interest.
Differentially expressed genes (DEGs) identified were further analyzed for gene set enrichment analysis (GSEA) and pathway analysis with R packages: fgsea v1.26.0 and msigdbr v7.5.1. Moreover, DEGs from RPM and PtPM tumors were analyzed for enrichment of previously curated neuroendocrine signatures. For this, we used the java GSEA Desktop Application (v4.3.2) with the GSEAPreranked module using the variance-stabilized log fold changes as metric to rank the DGE gene list in a descending order.
Assembly: mm10

growth_protocol: PtPM (Pten/Trp53 knockout; cMyc-overexpression) and RPM (Rb1/Trp53 knockout; cMyc-overexpression) mouse prostate organoids were transplanted into immunocompetent C57BL/6 8-10 week old male mice (dorsal prostatic lobe). Tumors were isolated from mice between 4-10 weeks post transplantation.

extract_protocol:
Tumors were isolated from euthanized mice and validated for EGFP fluorescence under fluorescence stereomicroscope. Tumors were quickly placed within 250-500 μL of RLT buffer supplemented with B-mercaptoethanol into 2mL tube with ceramic beads (MP, 6910500). Tumor samples were lysed on a Fisher Bead Mill 24 using manufacturer recommended settings. Lysates were passed through a Qiashredder (Qiagen, 79656) and RNA isolated using the Qiagen RNeasy kit (Qiagen, 74106) with manufacturer recommended protocols. Organoids were dissociated as above and resuspended in 300 μL of RLT buffer supplemented with B-mercaptoethanol and spun through a Qiashredder. Qiagen RNeasy kit was performed to isolate RNA using manufacturer recommended protocols.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 8.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 SX Reagent Kit (Illumina). An average of 24 million paired reads was generated per sample. Ribosomal reads represented 0.4-1.5% of the total reads generated and the percent of mRNA bases averaged 86%.

treatment_protocol: Mice were not subjected to any treatment

value: RPM

tag: treatment


title: P47 | 010 | TME

value: HNSCC

value: Y


title: fat body, control, replicate 5

value: fat body


title: whole animal, control, replicate 2


title: RPM Tumor - Rep 8


title: RPM Tumor - Rep 7


title: P47 | 006 | TUMOUR

value: PD

value: Male

value: Current

value: TUMOUR


title: P47 | 008 | TME

value: TRUE


title: P47 | 007 | TME


title: P47 | 005 | TUMOUR


title: RPM Tumor - Rep 6

value: Prostate


title: input for p400b infection of IMR90

city: Parma

first: Giorgio

last: Dieci

address: Parco Area delle Scienze 23/A

department: Deparment of Life Sciences

country: Italy

institute: University of Parma

description:
IMR90_p400b_ChIP_Input
input control

library_source: genomic

data_processing:
ChIP-seq peak calling. Analysis of sequence data was carried out as previously described (Ferrari et al., 2014) with minor modifications. Reads were aligned to the hg38 human genome reference sequence (GRCh38) using Bowtie (Langmead et al., 2009) and aligning parameters of unique- ness (-S –m1 –v2 –t –q).
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: IMR90 primary human fetal lung fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37ºC in 5% CO2.

extract_protocol:
Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014).
Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp of the human genome for each condition.

treatment_protocol: Cells were infected with the dl1500 adenovirus-based mutant or mock-infected

tag: cell type

value: fetal lung fibroblasts

tag: chip antibody

value: normal

value: IMR90 infected with Ad400 minus adenovirus


title: RPM Tumor - Rep 5


title: PC3_Control

city: Madrid

first: Enrique

last: Perez Navarro

state: Madrid

address: Av. de Córdoba

department: Oncology Department

institute: Hospital 12 de Octubre

description: Gene expression data from whole blood samples from healthy patient

hyb_protocol: Complementary DNA (cDNA) was synthesized from 100 ng of each RNA sample using the WT PLUS Reagent Kit (Thermo Scientific, Newark, DE, USA) following the standard protocol. This cDNA was then amplified, fragmented, and labelled with biotin for hybridization.

scan_protocol: The hybridized array was scanned using the GeneChip Scanner 3000 (Affymetrix, Thermo Scientific, Newark, DE, USA).

data_processing: Gene microarray analyses were derived after a quality control, background correction, normalization, logarithmic conversion and remove batch effects processing using Transcriptome Analysis Console (TAC) Software (version 4.0.1, Thermo)

label: biotin

source_name: Healthy Patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Whole-blood samples collected in PAXgene RNA tubes were subjected to isolation and purification following the manufacturer’s prescribed protocol

treatment_protocol: The PREMIERE trial constituted a cohort of 98 mCRPC patients, all of whom had not received prior chemotherapy treatments   . These participants were recruited across 17 established hospitals within Spain. The selection criteria for patient inclusion incorporated individuals with histologically verified prostate adenocarcinoma, documented metastases, and tumour progression, alongside a serum testosterone level equal to or below 50 ng per decilitre, despite the continuation of androgen-deprivation therapy.

tag: Stage

value: Control

value: Whole blood


title: input for dl1500 infection of IMR90

description:
IMR90_dl1500_ChIP_Input
input control

value: IMR90 infected with dl1500 adenovirus


title: PC5_Control


title: P47 | 004 | TUMOUR

tag: bestresponse

tag: pathway

value: Nivolumab

tag: mortality

value: 3 mos


title: RPM Tumor - Rep 4

value: RPM


title: PC4_Control


title: RPM Tumor - Rep 2


title: ChIP of BDP1 in dl312 infection of IMR90

description:
IMR90_dl312_ChIP_Bdp1
ChIP with Bdp1 antibody

value: IMR90 infected with dl312 adenovirus


title: ChIP of BDP1 in dl1500 infection of IMR90

description:
IMR90_dl1500_ChIP_Bdp1
ChIP with Bdp1 antibody


title: P47 | 003 | TUMOUR

value: HNSCC

value: Y

tag: age

tag: Sex

tag: smokingstatus


title: ChIP of BDP1 in p400b infection of IMR90

description:
IMR90_p400b_ChIP_Bdp1
ChIP with Bdp1 antibody


title: PtPM Tumor - Rep 11

value: PtPM


title: RPM Tumor - Rep 1


title: P1 | 016 | Full ROI

description:
hnscc_normalised_QC.csv
hnscc_WTA_QC.csv

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: hnscc_WTA_QC.csv: raw count data, hnscc_normalised_QC.csv: normalised count data
Library strategy: Spatial Transcriptomics

source_name: Head and neck

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Head and neck

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

value: PR

tag: date of_last_follow_up/_censored

value: NM

value: Male

tag: smoking status

value: Previous

tag: ecog performance

tag: pfs

value: 14 mos

tag: p16 status

value: Positive


title: PtPM Tumor - Rep 9

tag: tissue

value: Prostate

tag: genotype

tag: treatment


title: P47 | 002 | TUMOUR

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: bestresponse

value: PD

value: TRUE

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

value: Current

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme

value: TUMOUR


title: input for dl312 infection of IMR90

description:
IMR90_dl312_ChIP_input
input control

tag: cell line

tag: cell type

value: fetal lung fibroblasts

tag: chip antibody

value: normal


title: P73 | 001 | TME

tag: tissue

value: HNSCC

value: Nivolumab

value: Female

value: Unknown

tag: pfs

value: 3 mos

value: TME


title: P1 | 010 | Full ROI

value: Head and neck

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

value: PR

value: Y

tag: date of_last_follow_up/_censored

value: NM

value: Male

tag: smoking status

tag: ecog performance

tag: p16 status


title: P73 | 006 | TME

tag: tissue

tag: bestresponse

value: PD

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme


title: PC2_Control

tag: Stage

value: Control

value: Whole blood


title: PC1_Control


title: P107_Baseline

description: Gene expression data from whole blood samples from patients with mCRPC at Pre-treatment stage with enzalutamide

source_name: Patient with mCRPC at Pre-treatment stage

value: Pre-treatment


title: P109_Baseline


title: P106_Baseline


title: PtPM Tumor - Rep 8

value: Prostate

tag: genotype

value: PtPM

tag: treatment


title: P47 | 001 | TUMOUR

value: HNSCC

value: TRUE

value: Current

value: TUMOUR


title: P73 | 005 | Tumour

value: Nivolumab

value: Female

value: Unknown

value: 3 mos


title: PtPM Tumor - Rep 6


title: P1 | 008 | Full ROI

value: Head and neck

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

value: PR

value: Y

tag: date of_last_follow_up/_censored

tag: smoking status

value: Previous

tag: ecog performance

value: 14 mos

tag: p16 status

value: Positive


title: P1 | 004 | Full ROI

tag: tissue

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: mortality

value: NM

tag: age

tag: Sex

value: Male

tag: pfs


title: P1 | 003 | Full ROI

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: P1 | 009 | Full ROI

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

tag: date of_last_follow_up/_censored

tag: smoking status

tag: ecog performance

tag: p16 status


title: P73 | 003 | Tumour

tag: tissue

tag: bestresponse

value: PD

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme


title: PtPM Tumor - Rep 7

value: Prostate

tag: genotype

value: PtPM

tag: treatment


title: P1 | 006 | Full ROI

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

tag: date of_last_follow_up/_censored

tag: smoking status

tag: ecog performance


title: PtPM Tumor - Rep 5

tag: tissue

tag: genotype

tag: treatment


title: P73 | 002 | TME

value: HNSCC

tag: bestresponse

value: TRUE

tag: pathway

tag: mortality

tag: age

tag: Sex

tag: smokingstatus

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: PtPM Tumor - Rep 4


title: P73 | 004 | Tumour

value: Nivolumab

value: Female

value: TUMOUR


title: P108_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P73 | 002 | Tumour

value: Y

value: Unknown

value: 3 mos


title: PtPM Tumor - Rep 3


title: P73 | 001 | Tumour


title: P104_Baseline


title: PtPM Tumor - Rep 2


title: P1 | 002 | Full ROI

value: Head and neck

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: best response

value: PR

tag: date of_last_follow_up/_censored

tag: smoking status

value: Previous

tag: ecog performance

value: 14 mos

tag: p16 status

value: Positive


title: P102_Baseline

tag: Stage

tag: tissue


title: P103_Baseline


title: P1 | 001 | Full ROI

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: mortality

value: NM

tag: age

tag: Sex

value: Male

tag: pfs


title: P105_Baseline


title: P101_Baseline


title: P73 | 006 | Tumour

value: HNSCC

tag: bestresponse

value: PD

value: TRUE

tag: pathway

tag: smokingstatus

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme


title: P100_Baseline

tag: Stage

tag: tissue


title: PtPM Tumor - Rep 1

value: Prostate

tag: genotype

value: PtPM

tag: treatment


title: P747 | 001 | TME

value: TME


title: Gnao1-depleted Neuro2a #2

city: Fukuoka

first: Yasunari

last: Sakai

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pediatrics

country: Japan

institute: Kyushu University

data_processing:
illumina NovaSeq 6000 was used to sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with TranscriptId index (isoform level).

source_name: Neuro2a, siRNA-mediated silencing of Gnao1

growth_protocol: DMEM with 10%FCS at 37˚C under 5% CO2 and normoxic condition

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) , in accordance with the manufacturer’s instructions.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA kit (illumina).

treatment_protocol: Transfection in 6-well plate with 200 nM siRNA for 48-72 hr

tag: cell line

value: Neuro2a cell

tag: cell type

value: Neuroblastoma cell line (ATCC)

value: siRNA to Gnao1


title: HLBO on day 11 of culture after self-organization, scRNA-seq

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq demultiplexes raw base call (BCL) files were converted to FASTQ files by the bcl2fastq function, and Cell Ranger (10x Genomics) pipeline was used to align and quantify the sequencing reads, obtaining feature-barcode and raw UMI count matrix.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 1383D2 and 625-A4 iPSC line

growth_protocol: Inverted hanging cell culture insert with a multilayered gel-embedded cells were placed in Ultra-Low attachment 6 well plate and 2 mL of culture medium, which is a mixture of EGM and HCM containing dexamethasone (0.1 mM; Sigma-Aldrich), oncostatin M (10 ng/mL), hepatocyte growth factor (HGF) (20 ng/mL, PromoKine), SingleQuots (Lonza), SCF (50 ng/mL), IL-3 (10 ng/mL), TPO (50 ng/mL), Flt-3 ligand (10 ng/mL), IL-6 (10 ng/mL), IL-11 (5 ng/mL), IGF-1 (25 ng/mL) and EPO (2 Units/mL) was added for each well.

extract_protocol:
To dissociate into single cells, HLBOs attached to transwell membranes were harvested with a cell scraper and transferred to 2 mL tubes. The HLBOs were washed three times with HBSS without Ca2+ and Mg2+, then 500 μL of a dissociation solution containing 0.1 mg/mL Liberase TM (Roche) and 0.1 mg/mL DNase I (Sigma) diluted in DMEM/F12 medium was added. The mixture was incubated at 37°C for 30 minutes with shaking at 100 rpm. The HLBOs were physically dissociated by pipetting until no cell clumps were visible. The dissociated cells were then washed with 500 μL PBS containing 1% BSA and centrifuged at 300g for 5 minutes. The cell suspension was filtered through a 70 μm strainer, centrifuged again, and resuspended in PBS containing 1% BSA.
Cell counting was performed, and targeting 10,000 cells, the cell suspension was aliquoted and subjected to single-cell droplet formation using the 10x Chromium platform. The library preparation was performed using the NextGEM Single Cell 3’ v3.1 kit (10x Genomics) according to the manufacturer's instructions.

value: 1383D2 and 625-A4 iPSC line

value: human liver bud organoid (HLBO)

tag: time

value: day 11


title: Gnao1-depleted Neuro2a #3


title: P99_Baseline

value: Pre-treatment

value: Whole blood


title: HLBO on day 7 of culture after self-organization, scRNA-seq

value: day 7


title: P747 | 003 | TME

value: PR

tag: mortality

tag: age

tag: Sex


title: P747 | 004 | TME

tag: bestresponse

tag: pathway

tag: pfs


title: HLBO on day 3 of culture after self-organization, scRNA-seq

value: day 3


title: P747 | 003 | Tumour

value: HNSCC

tag: smokingstatus

tag: countofloweprgene

tag: percentofloweprgene

value: TUMOUR


title: Gnao1-depleted Neuro2a #1


title: NCI-H1299, NE, rep3

city: Dalian

first: jinxin

last: lu

state: Liaoning

address: lvshunkou district lvshun south goad west sector No.9

country: China

institute: Dalian Medical University

data_processing:
The RNA-seq data were mapped to the reference genome hg38 using the software Hisat2 v2.0.5 based on the default parameters.
The expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) estimated each gene expression levels by featureCounts (v1.5.0-p3).
Assembly: h38
Supplementary files format and content: tab-delimited text includes FPKM values for each Samples

growth_protocol: NCI-H1299 cells were cultured in RPMI-1640 medium (Gibco, C11875500BT) supplemented with 10% fetal bovine serum (Invitrogen Corp) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNAs were extracted according to TRIzol manufacturer's protocols.1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

treatment_protocol: Cells were maintained in DMEM for 8–12 hours that was followed by RPMI-1640 supplemented with 2% FBS for 48 hours with PBS or NE (10 μM)

value: NE


title: P747 | 002 | Tumour

first: Habib

last: Sadeghirad

address: 37 Kent St, Woolloongabba, 37 Kent St, Woolloongabba

institute: The University of Queensland

value: TRUE

tag: foi

tag: responsesintumour

tag: responsesintme


title: Control Neuro2a #3

source_name: Neuro2a cell, control siRNA

tag: genotype

value: Control siRNA


title: Control Neuro2a #2


title: NCI-H1299, NE, rep1

tag: treatment


title: Control Neuro2a #1

tag: cell line


title: P94_Baseline

tag: Stage

tag: tissue


title: P747 | 004 | Tumour

tag: mortality


title: NCI-H1299, DMSO, rep3

value: Ctrl


title: P93_Baseline


title: P97_Baseline


title: P96_Baseline


title: P747 | 002 | TME

tag: age

value: TME


title: P98_Baseline


title: Pancreas, Young, Rep_2

city: Houston

first: Wenbo

last: Chen

address: 7000 Fannin Street

institute: The University of Texas Health Science Center at Houston

description: FFPE Spatial transcriptome sequencing

data_processing:
Images were manual aligned to remove air bubbles and debris using 10X Genomcis Loupe Browser.
Raw sequencing data were aligned to mm10 genome to gene expression count using 10X Genomics Space Ranger's default setting.
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image.
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordiantes specifying spots.
Supplementary files format and content: scalefactors_json.json: scalefactors in json format.
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue.
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue.
Supplementary files format and content: matrix.h5: gene expression count data in h5 format.
Library strategy: Spatial Transcriptomics

source_name: Pancreas

growth_protocol: Young (3 months) and aging (18 months) male mice were used.

extract_protocol:
Pancreatic formalin-fixed paraffin-embedded (FFPE) tissue sections were used.
Spatial transcriptomics sequencing libraries were prepared using 10xGenomics Visium Gene Expression Slides and Reagents kit according to manufacturer’s instruction.

treatment_protocol: All mice were treated with 5% alcohol liquid diet for two weeks and cerulein (50 ug/kg, ip, 3 hourly) injections for one day.

tag: strain

value: Pancreas

tag: Sex

value: Male

tag: developmental stage

value: Young

tag: condition

value: Acute Pancreatitis

value: Alcohol and cerulein


title: P747 | 005 | TME

city: Brisbane

tag: bestresponse

tag: pathway

tag: smokingstatus

tag: pfs


title: NCI-H1299, DMSO, rep2


title: Pancreas, Young, Rep_1

description: FFPE Spatial transcriptome sequencing


title: NCI-H1299, DMSO, rep1


title: TB_5, lumbar disc with bone and joint tuberculosis

city: Lanzhou City

first: Yapeng

last: Wang

address: 82 Cuiyingmen, Chengguan District

department: Department of Orthopaedics

institute: the Second Hospital & Clinical Medical School, Lanzhou Univeristy

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
The alternative splicing events (***-AS) and regulated alternative splicing events (***-RAS) between ***-OE and control samples were defined and quantified using the SUVA pipeline described previously . The frequency and proportion of reads of SUVA AS events (pSAR) were calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lumbar disc

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: Lumbar disc

value: male

tag: disease state


title: P747 | 005 | Tumour

tag: countofloweprgene

tag: percentofloweprgene

tag: foi

tag: responsesintumour

tag: responsesintme


title: Pancreas, Aging, Rep_1

description: FFPE Spatial transcriptome sequencing

tag: tissue

value: Aging

tag: treatment


title: NCI-H1299, NE, rep2

tag: cell line


title: P91_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P92_Baseline


title: P30 | 011 | Tumour

value: HNSCC

value: PD

value: Pembrolizumab

tag: mortality

value: Y

tag: age

tag: Sex

value: Previous

value: 1 mos


title: TB_4, lumbar disc with bone and joint tuberculosis


title: SC_39_4-WT(F726) with Unx + STZ

city: Stony Brook

first: Sandeep

middle: K

last: Mallipattu

state: New York

address: 101 Nicolls Rd

department: Medicine-Nephrology

institute: Stony Brook University

data_processing:
Illumina software used for basecalling
CellRanger used for raw processing
Seurat R-package
Signac R-package
Archr R-package
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files and arrow files

molecule: nuclear RNA

source_name: Kidney Cortex

extract_protocol:
A 2 mm3 section of tissue collected from perfused cortex stored at -80C was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 0.1% TritonX-100, 0.1% RNAse Inhibitor and 0.1% DAPI. The tissue was initially dissociated by pipetting up and down 10X with a p-1000 tip and then being passed through a 25G syringe 10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) and then passed through a 40 µm FlowMI filter before generating counts with hemocytometer. Nuclei were then diluted and prepared for snATA-seq with the 10X Chromium System according to the manufacturer’s instructions (10X Genomics)
ATAC libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: Kidney Cortex

tag: strain

value: FVB

tag: genotype

value: WT

value: Uninephrectomy + STZ


title: P747 | 006 | TME

source_name: HNSCC

tag: bestresponse

value: PR

value: TRUE

tag: pathway

tag: smokingstatus

value: TME


title: SC_39_3 WT(E410) with SHAM Unx + VEH

value: Sham Uninephrectomy + Vehicle


title: TB_3, lumbar disc with bone and joint tuberculosis

value: Lumbar disc

value: female

tag: disease state


title: P88_Baseline

value: Pre-treatment

value: Whole blood


title: P30 | 010 | TME

value: HNSCC

value: PD

value: Male

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: P87_Baseline


title: P30 | 009 | TME

value: Pembrolizumab

value: Y

value: Previous

tag: foi

tag: responsesintumour

tag: responsesintme


title: TB_2, lumbar disc with bone and joint tuberculosis

tag: tissue


title: 7d dermis WT  rep3

city: Beijing

first: Sha

last: Huang

address: 51 Fu Cheng Road

institute: PLA General Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: dermis

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: dermis

value: 6 weeks

value: wild type


title: Pancreas, Aging, Rep_2

description: FFPE Spatial transcriptome sequencing

value: Pancreas

tag: developmental stage

value: Aging

tag: condition

value: Acute Pancreatitis

tag: treatment

value: Alcohol and cerulein


title: SC_39_2-KLF6PODTA(F399) with Unx + STZ

value: Kidney Cortex

value: FVB

tag: age

value: KLF6 OEPODTA

value: Uninephrectomy + STZ


title: P30 | 005 | Tumour

value: HNSCC

value: TRUE

tag: mortality

tag: Sex

value: 1 mos

value: TUMOUR


title: P85_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P30 | 004 | Tumour

tag: bestresponse

value: PD

tag: pathway

value: Pembrolizumab

value: Y

value: Male

value: Previous


title: P30 | 001 | Tumour

tag: smokingstatus


title: 7d dermis WT  rep2

tag: strain

value: dermis

value: 6 weeks

tag: genotype

value: wild type


title: P30 | 003 | Tumour

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene


title: P86_Baseline


title: Ctrl_3, lumbar disc degeneration

value: Lumbar disc

value: female

tag: disease state

value: lumbar disc degeneration


title: P81_Baseline

tag: tissue


title: P84_Baseline


title: 0d dermis WT  rep3


title: Ctrl_5, lumbar disc degeneration

value: male


title: SC_39_1-KLF6PODTA(F353) with SHAM Unx + VEH

value: Kidney Cortex

value: FVB

value: KLF6 OEPODTA

value: Sham Uninephrectomy + Vehicle


title: Ctrl_4, lumbar disc degeneration


title: P30 | 003 | TME

value: HNSCC

value: TRUE

value: 1 mos

tag: foi

tag: responsesintumour

value: TME

tag: responsesintme


title: P95_Baseline

value: Pre-treatment

value: Whole blood


title: P75 | 001 | TME

value: PR

value: Nivolumab

value: N

tag: age

value: Female

value: Previous

value: 42 mos


title: J.gamma1 indisulam rep1

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: T-cell acute lymphoblastic leukemia

tag: treatment

value: 5uM indisulam


title: TB_1, lumbar disc with bone and joint tuberculosis

value: Lumbar disc

tag: Sex

value: male


title: 7d dermis WT  rep1

value: dermis

value: 6 weeks

value: wild type


title: P89_Baseline

tag: Stage


title: J.gamma1 DMSO rep2

value: DMSO


title: P80_Baseline


title: P76_Baseline


title: 0d dermis WT  rep2


title: 7d dermis Cthrc1-/-  rep1


title: J.gamma1 indisulam rep2


title: Ctrl_1, lumbar disc degeneration

value: lumbar disc degeneration


title: P83_Baseline

value: Pre-treatment


title: P78_Baseline

value: Whole blood


title: P77_Baseline


title: P75 | 004 | TUMOUR

value: HNSCC

tag: bestresponse

value: PR

value: TRUE

tag: pathway

tag: mortality

tag: smokingstatus

value: TUMOUR


title: 7d dermis Cthrc1-/-  rep3

tag: strain

tag: genotype


title: 0d dermis WT  rep1


title: P73_Baseline


title: 0d dermis Cthrc1-/-  rep3


title: P75 | 006 | TME

value: Nivolumab

value: N

value: Female

value: Previous

tag: pfs

tag: countofloweprgene

tag: percentofloweprgene

value: TME


title: Ctrl_2, lumbar disc degeneration

tag: tissue

value: Lumbar disc

value: male

tag: disease state


title: P90_Baseline


title: 7d dermis Cthrc1-/-  rep2

value: dermis

tag: age

value: 6 weeks


title: J.gamma1 DMSO rep1

tag: cell line

value: T-cell acute lymphoblastic leukemia

value: DMSO


title: P30 | 002 | TME

value: PD

value: Pembrolizumab

value: Y

value: Male

value: 1 mos

tag: foi

tag: responsesintumour

tag: responsesintme


title: P75 | 005 | TME

value: HNSCC

value: PR

value: TRUE

tag: Sex

value: 42 mos


title: P74_Baseline

tag: Stage

value: Pre-treatment

value: Whole blood


title: P75_Baseline