title: C16-TTR-SIG; healthy

tag: disease state

tag: treatment

tag: cdai

tag: time

tag: patient id

tag: affected area


title: HCA00102.E10

status: Public on Oct 22 2020

type: SRA

city: Solna

first: Vasilios

last: Zachariadis

address: Visionsgatan 4

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
https://github.com/EngeLab/DNTRseq
Genome_build: hg38
Supplementary_files_format_and_content: mRNA read counts summarized over genes; DNA read counts summarized over genomic bins

molecule: total RNA

organism: Homo sapiens

source_name: DNTR-seq mRNA

growth_protocol: HCT116 and A375 cells were cultured in DMEM medium supplemented with 10% FBS and 1% Penicillin/strepotomycin at 37°C, 5% CO2 and humidified atmosphere.

extract_protocol:
Individual live cells were FACS-sorted into 384-well plates with lysis buffer, snap-frozen and stored at -80 degrees C.
After splitting each cell, separate mRNA- (*R suffix) and DNA-libraries (*D suffix) were constructed. As comparison, a set of cells had mRNA libraries prepared with Smart-Seq2 (no suffix).
Barcoded libraries were sequenced paired-end (37bp x 2) on an Illumina NextSeq.

treatment_protocol: Cells were untreated, treated with etoposide (ETO) or X-ray at increasing concentrations and harvested at different timepoints.

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 35-T52-TTR-CIA-M

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

library_source: genomic

data_processing:
Sequences were trimmed to the first base with a quality score <3 and then paired.  Sequences with less than 300 and more than 600 nucleotides and paired reads with an expected error >3 were excluded from the analysis.
Processing of aw-reads was performed using IMNGS to operational taxonomic units of 97% sequence similarity
Following analyses were performed using R using edgeR
Supplementary_files_format_and_content: Comma-delimited text with the counts for each samples and OTUS

molecule: genomic DNA

source_name: biopsy

extract_protocol:
Biopsies were resuspended in 180 μl TET buffer and 20mg lysozyme. Samples were incubated for 1h at 37ºC and vortexed with 25 μl Proteinase K before incubating at 56ºC for 3h. Buffer B3  was added followed by a heat treatment. Two washing steps were performed before eluting DNA, concentrations and purity were checked using NanoDrop One (Thermo Fisher Scientific)
V3-V4 regions of the 16S rRNA gene were amplified using standard protocols  with forward and reverse primers 341F-785R. Following the manufacter’s protocol with a pooled samples in paired-end modus (PE275)
Paired sequencing on a MiSeq system (Illumina, San Diego, CA)

tag: Sex

value: FEMALE

value: NO

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ASCENDING COLON

tag: afected area

value: COLON

tag: involved

value: INVOLVED

tag: active area

value: ACTIVE

tag: transplant

value: Post

tag: surgery

tag: age diagnostic

tag: age sample


title: 33-T26-TTR-IH-M

value: MALE

tag: treatment

tag: cdai

value: ILEUM

tag: time

tag: patient id

value: HEALTHY

value: Pre


title: HCA00102.E12

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C15-TTR-CA; healthy

data_processing:
Quality filtering was performed using cutadapt v. 1.7.1
Reads were mapped against the human reference genome using the STAR aligner v.2.5.2a
Read counts per gene were obtained using RSEM program v.1.2.31 and the Ensembl gtf annotation file.
Following analyses were performed using R using edgeR
Genome_build: Ensembl gtf annotation file (release GRCh38.10)
Supplementary_files_format_and_content: Tab-delimited text with the counts for each sample

extract_protocol:
Tissue RNA was isolated by Rneasy Kit (Qiagen, Spain) according to the manufacturer's instructions. RNA were quantified by NanoDrop spectrophotometer (NanoDrop Technologies, USA). The purity and integrity of the total RNA was assessed via 2100 Bioanalyzer (Agilent, Germany). All RNA samples analyzed had a RNA Integrity Number ≥ 7.
Barcoded RNA sequencing libraries were prepared from 100 ng total RNA using Illumina’s TruSeq stranded mRNA kit according to the manufacturer’s instructions.
Libraries were subjected to paired-end sequencing (101 bp) on a HighSeq-4000 platform (Illumina, San Diego, CA).

tag: disease state

value: healthy

tag: Sex

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: C

tag: affected area

value: Baseline


title: HCA00102.E09


title: DR 32 hpf Rep2 [2-32-R]

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters --outSAMtype BAM Unsorted --outSAMunmapped Within
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using htseq -count (v0.6.1) and modelled using DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

organism: Danio rerio

source_name: dorsal retina_32 hpf

growth_protocol: zebrafish were harvested at appropriate time points (hpf), retinal regions dissected

extract_protocol:
RNA was extracted using Qiagen Rneasy FFPE kit and quantified
RNA-seq libraries were constructed using the SMARTer low input  kit using standard protocols

tag: hpf

tag: tissue

value: dorsal retina


title: 33-T26-TTR-CI-M

tag: treatment

tag: cdai

value: TRANSVERSE COLON

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.E08

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: DR 48 hpf Rep2 [2-48-R]

source_name: dorsal retina_48 hpf


title: 31-T52-TTR-IH-M

tag: Sex

value: FEMALE

value: YES

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id


title: DR 56 hpf Rep1 [1-56-R]

source_name: dorsal retina_56 hpf

tag: hpf

tag: tissue


title: C14-TTR-CA; healthy

tag: disease state

tag: treatment

value: NO

tag: cdai

value: ASCENDING COLON

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery


title: OF 56 hpf Rep1 [1-56-O]

source_name: optic fissure retina_56 hpf

value: optic fissure retina


title: 35-T106-TR-CH-M

tag: Sex

value: SIGMOID COLON

tag: afected area

value: COLON

tag: age diagnostic

tag: age sample


title: HCA00102.E07

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: C13-TTR-SIG; healthy

tag: disease state

value: MALE

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id


title: DR 48 hpf Rep1 [1-48-R]

tag: hpf

tag: tissue


title: C13-TTR-ILI; healthy

tag: Sex

tag: treatment

tag: cdai

value: ILEUM

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery


title: 31-T52-TTR-CIA-M

value: DESCENDING COLON

tag: afected area

value: INVOLVED

value: ACTIVE

value: Post

tag: age diagnostic

tag: age sample


title: OF 48 hpf Rep1 [1-48-O]

source_name: optic fissure retina_48 hpf


title: 31-T26-TTR-IH-M

tag: pcr

tag: sescd global

tag: sescd local

value: HEALTHY


title: HCA00102.E05

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 31-T26-TTR-CIA-M

tag: Sex

tag: treatment

tag: cdai

tag: exact location

tag: time

tag: patient id


title: HCA00102.E04


title: DR 32 hpf Rep1 [1-32-R]

tag: hpf

tag: tissue

value: dorsal retina


title: OF 32 hpf Rep1 [1-32-O]

source_name: optic fissure retina_32 hpf


title: 31-T106-TTR-IH-M

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: OF 32 hpf Rep2 [2-32-O]


title: C12-TTR-ILI; healthy

tag: disease state

value: healthy

tag: pcr

tag: sescd global

tag: sescd local

value: C

tag: affected area

value: Baseline


title: C12-TTR-SIG; healthy

tag: Sex

value: FEMALE

tag: treatment

tag: cdai

tag: exact location


title: HCA00102.E03

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: C14-TTR-ILI; healthy

value: NO

tag: time

tag: patient id

tag: involved

tag: active area

tag: transplant

tag: surgery


title: 31-S0-TTR-IH-M

tag: pcr

tag: sescd global

tag: sescd local

tag: afected area

tag: age diagnostic

tag: age sample


title: HCA00102.E02

tag: cell id

tag: treatment


title: 31-S0-TTR-CIA-M

tag: Sex

tag: cdai

tag: exact location


title: C12-TTR-CA; healthy

tag: disease state

value: ASCENDING COLON

tag: time

tag: affected area


title: C11-TTR-SIG; healthy

value: SIGMOID COLON

tag: patient id

tag: involved

tag: active area


title: 30-T52-TTR-IIA-M

tag: pcr

tag: transplant

tag: surgery


title: XEN_C

first: Mohamed

middle: I

last: Gatie

state: Ontario

address: 1151 Richmond street, Chemistry Building Room 003, Dock 11

department: Biology

country: Canada

institute: University of Western Ontario

data_processing:
Paired-end reads of 100bp were read through the BGISEQ-500 platform
Clean reads were mapped to reference genome using Bowtie2 (Langmead and Salzberg, 2012)
calculate gene expression levels with RSEM (Li and Dewey, 2011). Differentially expressed genes were detected with DEseq2 (Love et al., 2014)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Extraembryonic endoderm cell

growth_protocol: ES cells were maintained on 0.1% gelatin cultured in N2B27-2iLIF. XEN cells were maintained in RPMI1640 media supplemented with 15% FBS.

extract_protocol:
RNA was extracted using Qiagen Rneasy system
RNA libraries were prepared for sequencing using BGISEQ-500 platform

tag: strain

value: ICR

tag: tissue

value: embryonic


title: HCA00102.E06

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00102.C16

tag: cell id

value: malignant melanoma

tag: treatment


title: 30-T52-TTR-CH-M

tag: Sex

tag: cdai

tag: sescd global

tag: sescd local

tag: exact location

value: DESCENDING COLON

tag: afected area

value: COLON

tag: age diagnostic

tag: age sample


title: C11-TTR-ILI; healthy

tag: disease state

value: MALE

tag: pcr

value: ILEUM

tag: time

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: surgery


title: C11-TTR-CA; healthy

tag: Sex

tag: treatment

value: HEALTHY


title: HCA00102.E01

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: XEN_A

tag: strain

tag: tissue


title: 30-T26-TTR-IIA-M

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: afected area

value: INVOLVED

value: ACTIVE

value: Post

tag: age diagnostic

tag: age sample


title: HCA00102.C15


title: HCA00102.C14


title: C10-TTR-SIG; healthy

tag: disease state

value: healthy

tag: Sex

tag: time

value: C

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

value: Baseline

tag: surgery


title: ES_C

source_name: Embryonic stem cell

tag: strain

tag: tissue

tag: treatment


title: 30-T26-TTR-CH-M

value: FEMALE

value: NO

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local


title: ES_B


title: C10-TTR-ILI; healthy

tag: exact location

tag: age diagnostic

tag: age sample


title: HCA00102.C13

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 30-T106-TTR-IIA-M

tag: Sex

value: YES

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area

tag: transplant


title: C10-TTR-CA; healthy

tag: disease state

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

value: ASCENDING COLON

tag: affected area

tag: surgery


title: HCA00102.C12

tag: cell id

tag: cell type

tag: cell line


title: ES_A

tag: strain

tag: tissue

value: embryonic


title: C1-TTR-SIG; healthy

tag: Sex

tag: sescd local

tag: exact location

value: SIGMOID COLON

tag: time

tag: patient id

tag: age diagnostic

tag: age sample


title: 30-T106-TTR-CH-M

tag: treatment

tag: cdai

value: DESCENDING COLON

tag: afected area

tag: involved

tag: active area

tag: transplant


title: XEN_B

value: ICR


title: C1-TTR-CA; healthy

tag: disease state

tag: pcr

tag: sescd global

tag: affected area

tag: surgery


title: HCA00102.C10

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 29-T26-TTR-CIA-M

tag: Sex

tag: sescd local

tag: exact location

tag: time

tag: patient id

value: COLON

value: Pre

tag: age diagnostic

tag: age sample


title: 29-T26-TTR-CH-M

tag: treatment

tag: cdai

tag: afected area

tag: involved

value: HEALTHY

tag: active area

tag: transplant


title: 36-T26-TTR-IH; Crohn's disease

tag: disease state

value: Crohn's disease

value: MALE

tag: pcr

tag: sescd global

value: ILEUM

tag: affected area

tag: surgery


title: 30-S0-TTR-CH-M

tag: Sex

tag: sescd local


title: HCA00102.C08

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: 36-T26-TTR-CI; Crohn's disease

tag: treatment

tag: cdai

tag: exact location

value: TRANSVERSE COLON

tag: time

tag: patient id

value: INVOLVED

value: INACTIVE

value: Post

tag: age diagnostic

tag: age sample


title: 29-S0-TTR-CIA-M

value: FEMALE

value: NO

tag: pcr

tag: sescd global

value: ASCENDING COLON

tag: afected area

tag: involved

tag: active area

value: ACTIVE

tag: transplant

value: Baseline


title: HCA00102.C09

tag: cell id

tag: cell type

value: malignant melanoma


title: HCA00102.C11

tag: cell line

tag: time point


title: HCA00102.C07

tag: treatment

tag: cell count


title: 35-T52-TTR-CII; Crohn's disease

tag: disease state

tag: Sex

tag: cdai

tag: sescd local

tag: exact location

value: SIGMOID COLON

tag: affected area

value: COLON

tag: surgery


title: 35-T52-TTR-CIA; Crohn's disease

tag: pcr

tag: sescd global

tag: time

tag: patient id

tag: age diagnostic

tag: age sample


title: 28-T52-TTR-III-M

tag: afected area

tag: involved

tag: active area

tag: transplant


title: HCA00102.C06

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: HCA00102.C05


title: 35-T26-TTR-CIA; Crohn's disease

tag: disease state

tag: Sex

tag: cdai

tag: sescd local

tag: exact location

tag: affected area

tag: surgery


title: 28-T52-TTR-CII-M

tag: pcr

tag: sescd global

tag: time

tag: patient id

tag: afected area

tag: age diagnostic

tag: age sample


title: 28-T52-TTR-CH-M

tag: treatment

value: DESCENDING COLON

tag: involved

value: HEALTHY

tag: active area

tag: transplant


title: HCA00102.C04

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 28-T26-TTR-IIA-M

tag: Sex

tag: cdai

tag: sescd local

tag: exact location

tag: surgery


title: 35-T106-TR-CH; Crohn's disease

tag: disease state

value: Crohn's disease

value: YES

tag: pcr

tag: sescd global

tag: time

tag: patient id

tag: affected area


title: 35-T106-TR-CII; Crohn's disease

tag: treatment

tag: involved

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: 28-T26-TTR-CH-M

tag: Sex

tag: afected area


title: 33-T26-TTR-IH; Crohn's disease

value: MALE

tag: cdai

tag: sescd local

value: ILEUM

value: Pre


title: HCA00102.C02

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: 28-T26-TTR-CII-M

tag: pcr

tag: sescd global

tag: exact location

value: TRANSVERSE COLON

tag: time

tag: patient id

value: INVOLVED

value: INACTIVE

value: Post

tag: surgery


title: HCA00102.C03

tag: treatment


title: 33-T26-TTR-CI; Crohn's disease

tag: disease state

value: NO

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: HBP10-1

type: RNA

city: Stanford

first: Aida

last: Habtezion

state: CA

address: 291 Campus Drive

department: Medicine

country: USA

institute: Stanford University

description: Blood from healthy donors was subjected to processing delays that are commonly encountered in blood sample collection: 2hr RT, 5hr RT, 5hr 4C, and 15hr (ON) 4C.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Clariom D microarray

scan_protocol: Arrays were scanned on a GeneChip 3000 scanner

data_processing: Affymetrix chip, Experimental Quality Analyses, Probe summarization and Data Normalization were performed using the Transcriptome Analysis Software v4.0.2. Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST) algorithms to normalize CEL files. Subsequent processed data analysis was done using R (v3.5.1).

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using PAXgene Blood RNA tubes, following the manufacturer's instructions.

treatment_protocol: Samples were subjected to processing delays before starting RNA extraction and isolation.

tag: tissue

value: Whole blood

tag: age

tag: temperature

value: RT

tag: well

tag: Sex

value: Female

tag: race

value: White


title: HBP10-3


title: 28-T106-TTR-CII-M

value: FEMALE

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: afected area

value: COLON


title: HBP10-2


title: HCA00102.C01

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 31-T52-TTR-CIA; Crohn's disease

tag: disease state

value: Crohn's disease

value: DESCENDING COLON

tag: patient id

tag: affected area

tag: involved

tag: active area

value: ACTIVE

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HBP09-3

tag: tissue

tag: age

tag: temperature

tag: well

tag: Sex

value: Male

tag: race

value: Asian


title: HCA00102.A15

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: treatment

tag: time point


title: 31-T52-TTR-IH; Crohn's disease

tag: disease state

value: YES

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: time

tag: patient id

tag: affected area

tag: involved

value: HEALTHY


title: HCA00102.A16

tag: cell count


title: 28-T106-TTR-CH-M

tag: Sex

tag: afected area

tag: active area

tag: transplant

value: Post

tag: surgery

tag: age diagnostic

tag: age sample


title: HBP09-2

tag: tissue

tag: age

tag: temperature

tag: well

tag: race


title: HBP10-5


title: HBP10-4


title: HBP09-1


title: 28-S0-TTR-CIA-M

tag: treatment

value: NO

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: TRANSVERSE COLON

tag: time

value: INVOLVED

value: Baseline


title: 31-T26-TTR-IH; Crohn's disease

tag: disease state

tag: Sex

tag: patient id

tag: affected area

tag: involved

tag: active area


title: HCA00102.A14

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 31-T26-TTR-CIA; Crohn's disease

tag: treatment

tag: cdai

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: HCA00102.A13


title: HBP08-5

tag: tissue

value: Whole blood

tag: age

tag: temperature

tag: well

tag: race

value: White


title: 28-S0-TTR-CH-M

tag: Sex

value: FEMALE

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

value: COLON

tag: involved

tag: active area


title: 27-T52-TTR-CIA-M

tag: treatment

tag: cdai

value: DESCENDING COLON

tag: transplant

tag: surgery

tag: age diagnostic


title: 31-T106-TTR-IH; Crohn's disease

tag: disease state

value: Crohn's disease

tag: affected area

tag: age sample


title: HBP08-3

tag: tissue

tag: age

tag: temperature

value: RT

tag: well

tag: Sex

value: Male

tag: race


title: HCA00102.A12

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 27-T26-TTR-CII-M

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: involved

tag: active area

value: INACTIVE

tag: transplant


title: HBP08-2

tag: tissue

tag: age

tag: temperature

tag: well

tag: Sex

tag: race


title: 31-S0-TTR-IH; Crohn's disease

tag: disease state

tag: treatment

tag: cdai

value: ILEUM

tag: affected area

tag: surgery

tag: age diagnostic

tag: age sample


title: 31-S0-TTR-CIA; Crohn's disease

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

value: ACTIVE


title: 27-S0-TTR-CII-M

tag: afected area

tag: involved

tag: active area

tag: transplant


title: 26-T52-TTR-CII-M

tag: Sex

value: Post


title: HCA00102.A11

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: HBP08-4

tag: tissue

tag: age

tag: temperature

tag: well

tag: race


title: HBP07-5

value: Female

value: Asian


title: HBP07-3


title: HBP08-1


title: 30-T52-TTR-IIA; Crohn's disease

tag: disease state

value: NO

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: affected area

value: INVOLVED

tag: surgery

tag: age diagnostic

tag: age sample


title: 26-T52-TTR-IH-M

tag: Sex

tag: treatment

tag: afected area

tag: involved

value: HEALTHY

tag: active area

tag: transplant


title: 30-T26-TTR-IIA; Crohn's disease

tag: disease state

tag: cdai


title: HCA00102.A07

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: HCA00102.A06


title: 30-T52-TTR-CH; Crohn's disease

value: FEMALE

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: affected area


title: HBP07-4

tag: tissue

value: Whole blood

tag: age

tag: temperature

tag: well

tag: Sex

tag: race


title: HCA00102.A10

tag: cell id

tag: cell type

tag: treatment


title: 26-T26-TTR-CII-M

tag: cdai

value: DESCENDING COLON

tag: afected area

value: COLON

tag: involved

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: 26-T26-TTR-IH-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id


title: 30-T26-TTR-CH; Crohn's disease

tag: disease state

value: Crohn's disease

tag: Sex

tag: affected area


title: 30-T106-TTR-IIA; Crohn's disease

tag: treatment

value: YES

tag: cdai


title: 26-T106-TTR-IH-M

tag: afected area

tag: involved


title: HBP07-2

tag: tissue

tag: age

tag: temperature

value: RT

tag: well

tag: race


title: HBP07-1


title: HCA00102.A08

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HBP06-5

value: White


title: HBP06-4


title: HBP09-4

value: Male


title: HCA00102.A05


title: 26-T106-TTR-CIA-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: active area

value: ACTIVE

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: 30-S0-TTR-CH; Crohn's disease

tag: disease state

tag: Sex

tag: treatment

tag: cdai

tag: affected area

tag: involved

value: Baseline


title: HCA00102.A09

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 30-T106-TTR-CH; Crohn's disease

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

value: Post


title: HCA00102.A04


title: HBP06-2

tag: tissue

tag: age

tag: temperature

tag: well

value: Female

tag: race


title: 29-T26-TTR-CIA; Crohn's disease

tag: disease state

tag: Sex

tag: treatment

value: NO

tag: cdai

value: ASCENDING COLON

tag: affected area

tag: involved

value: INVOLVED

tag: active area

tag: transplant

value: Pre

tag: surgery

tag: age diagnostic

tag: age sample


title: 29-T26-TTR-CH; Crohn's disease

value: FEMALE

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: SIGMOID COLON

tag: time

tag: patient id

value: HEALTHY


title: 23-T52-TTR-CH-M

tag: afected area

value: COLON


title: 26-S0-TTR-CIA-M

tag: Sex

value: DESCENDING COLON


title: HCA00102.A02

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 23-T52-TTR-CII-M

tag: cdai

tag: involved

tag: active area

value: INACTIVE

tag: transplant

tag: surgery


title: HCA00101.O08


title: 26-S0-TTR-IH-M

tag: pcr

tag: sescd global

tag: sescd local

value: ILEUM

tag: age diagnostic

tag: age sample


title: 23-T26-TTR-CII-M

tag: Sex

tag: exact location

tag: time

tag: patient id

tag: afected area


title: HCA00102.A03

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point


title: 28-T52-TTR-III; Crohn's disease

tag: disease state

value: Crohn's disease

tag: cdai

tag: affected area

tag: involved

tag: active area

tag: transplant


title: HBP06-3

tag: tissue

value: Whole blood

tag: age

tag: temperature

value: RT

tag: well

tag: race

value: White


title: HBP05-5

tag: Sex

value: Male

value: African


title: HBP05-4


title: HBP06-1

value: Female


title: 28-T52-TTR-CII; Crohn's disease

value: NO

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: TRANSVERSE COLON

tag: time

tag: patient id

value: INVOLVED

value: Post

tag: surgery

tag: age diagnostic

tag: age sample


title: HBP05-1


title: HCA00101.O07

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 28-T52-TTR-CH; Crohn's disease

tag: disease state

value: FEMALE

tag: cdai

tag: affected area

value: COLON

tag: involved

value: HEALTHY

tag: active area

tag: transplant


title: HBP05-2

tag: tissue

tag: age

tag: temperature

tag: well

tag: Sex

tag: race


title: 22-T52-TTR-CII-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

value: INACTIVE

tag: surgery

tag: age diagnostic

tag: age sample


title: 29-S0-TTR-CIA; Crohn's disease

tag: disease state

tag: treatment

tag: cdai

value: ASCENDING COLON

tag: affected area

tag: involved

tag: active area

value: ACTIVE

tag: transplant

value: Baseline


title: 22-T26-TTR-III-M

tag: Sex

tag: pcr

value: ILEUM


title: HCA00102.A01

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: HCA00101.O05


title: 22-T52-TTR-III-M

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: surgery


title: HBP04-4

tag: tissue

value: Whole blood

tag: age

tag: temperature

tag: well

tag: race

value: White


title: 22-T26-TTR-CII-M

tag: Sex

tag: treatment

tag: cdai

tag: pcr

value: RECTUM

tag: involved

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: HCA00101.O03

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 28-T26-TTR-CII; Crohn's disease

tag: disease state

value: Crohn's disease

value: NO

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: affected area

tag: surgery


title: HBP05-3

tag: tissue

tag: age

tag: temperature

value: RT

tag: well

tag: Sex

value: Male

tag: race

value: African


title: 28-T26-TTR-CH; Crohn's disease

value: FEMALE

tag: treatment

tag: cdai

tag: pcr

value: DESCENDING COLON

tag: involved

tag: active area

tag: transplant

value: Post

tag: age diagnostic

tag: age sample


title: 22-T106-TTR-III-M

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: patient id

tag: afected area

value: INVOLVED

value: INACTIVE


title: 28-T106-TTR-CII; Crohn's disease

tag: disease state

value: TRANSVERSE COLON

tag: affected area

value: COLON

tag: surgery


title: 22-T106-TTR-CII-M

tag: Sex

tag: treatment


title: HCA00101.O04

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00101.O06

value: malignant melanoma


title: 28-T106-TTR-CH; Crohn's disease

tag: cdai

tag: pcr

tag: involved

value: HEALTHY

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: HCA00101.M08


title: HBP04-3

tag: tissue

value: Whole blood

tag: age

tag: temperature

tag: well

value: Female

tag: race


title: HBP04-2

tag: Sex

value: White


title: HCA00101.O02

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: treatment


title: 19-S0-TTR-IH-M

value: NO

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: time

tag: patient id

tag: afected area

value: Baseline

tag: surgery


title: 27-T52-TTR-CIA; Crohn's disease

tag: disease state

value: Crohn's disease

value: YES

tag: cdai

tag: pcr

tag: affected area

tag: involved

tag: active area

value: ACTIVE

tag: transplant

tag: age diagnostic

tag: age sample


title: HBP03-4

tag: tissue

tag: age

tag: temperature

tag: well

tag: Sex

value: Male

tag: race


title: HBP04-1

value: RT


title: HBP03-3


title: HCA00101.M05

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 22-S0-TTR-CIA-M

value: FEMALE

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: RECTUM

tag: time

tag: patient id

tag: afected area

tag: involved

value: INVOLVED

tag: surgery


title: HCA00101.M07

value: malignant melanoma


title: 21-S0-TTR-IH-M

tag: Sex

value: MALE

value: HEALTHY

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: HBP03-5

tag: tissue

value: Whole blood

tag: age

tag: temperature

tag: well

tag: race


title: HCA00101.M03

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 28-S0-TTR-CH; Crohn's disease

tag: disease state

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: DESCENDING COLON

tag: time

tag: patient id

tag: affected area

value: COLON

tag: involved

tag: surgery


title: 28-T26-TTR-IIA; Crohn's disease

tag: Sex

value: NO

tag: active area

tag: transplant

value: Post

tag: age diagnostic

tag: age sample


title: HCA00101.M06

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 21-S0-TTR-CI-M

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ASCENDING COLON

tag: afected area

value: Baseline


title: 19-S0-TTR-CH-M

tag: Sex

tag: time

tag: patient id

tag: involved

tag: surgery


title: HBP03-2

tag: tissue

tag: age

tag: temperature

tag: well

tag: race

value: White


title: HBP02-5


title: HCA00101.M02

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 26-T52-TTR-IH; Crohn's disease

tag: disease state

value: Crohn's disease

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: affected area

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: 18-T52-TTR-CII-M

tag: Sex

value: YES

value: TRANSVERSE COLON

tag: time

tag: patient id

tag: afected area

tag: involved

value: INACTIVE

tag: surgery


title: 19-S0-TTR-CI-M

value: FEMALE

tag: treatment

value: SIGMOID COLON

value: INVOLVED

value: ACTIVE


title: 27-T26-TTR-CII; Crohn's disease

tag: disease state

tag: cdai

value: DESCENDING COLON


title: HCA00101.M04

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 18-TM40-TTR-III-M

value: MALE

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: active area

tag: transplant


title: 27-S0-TTR-CII; Crohn's disease

tag: Sex

value: NO

tag: time

tag: patient id

tag: affected area

value: COLON

tag: age diagnostic

tag: age sample


title: 26-T52-TTR-CII; Crohn's disease

tag: disease state

tag: treatment

tag: cdai

tag: involved

value: Post

tag: surgery


title: HBP03-1

tag: tissue

value: Whole blood

tag: age

tag: temperature

value: RT

tag: well

value: Male

tag: race


title: 18-T26-TTR-CIA-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: afected area

tag: active area

tag: transplant


title: 18-T106-TTR-III-M

tag: Sex

tag: time

tag: patient id

tag: age diagnostic

tag: age sample


title: 18-S0-TTR-CI-M

tag: treatment

tag: cdai

value: RECTUM

tag: involved

value: Baseline

tag: surgery


title: HCA00101.K07

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 26-T106-TTR-IH; Crohn's disease

tag: disease state

value: Crohn's disease

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: affected area

value: HEALTHY


title: HCA00101.K06


title: 16-TM48-TTR-CII-M

tag: Sex

value: FEMALE

value: YES

value: ASCENDING COLON

tag: time

tag: patient id

tag: afected area

tag: active area

value: INACTIVE

tag: transplant

tag: age diagnostic


title: 26-T106-TTR-CIA; Crohn's disease

tag: treatment

tag: cdai

value: DESCENDING COLON

tag: involved

value: INVOLVED

value: ACTIVE

tag: surgery

tag: age sample


title: 26-S0-TTR-IH; Crohn's disease

tag: disease state

value: NO

tag: pcr


title: HCA00101.K04

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: HBP02-1

tag: tissue

value: Whole blood

tag: age

tag: temperature

value: RT

tag: well

tag: Sex

tag: race

value: White


title: HBP02-4

value: Male


title: HBP01-5

value: Female

value: Asian


title: HBP02-3


title: HBP02-2


title: HBP01-4


title: R6ST2R4: Inplanta_shoot_race6_rep4

city: MELBOURNE

first: Saidi

middle: Rahina

last: Achari

state: VICTORIA

address: 5 RING ROAD, BUNDOORA

department: Applied Systems Biology

country: Australia

institute: La Trobe University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the genome using Salmon 1.3.0 to create transcript abundance
Data normalisation was carried out using Sleuth v0.27.3 in R with default settings

organism: Fusarium oxysporum f. sp. pisi

source_name: in planta shoot, race6

extract_protocol:
TRNA extracted using Qiagen RNeasy mini kit and mRNA extracted using NEXTFLEX® Poly(A) Beads 2.0
NEXTFLEX® Rapid Directional RNA-Seq Library Prep Kit

tag: isolate


title: HCA00101.M01

tag: treatment


title: 26-T26-TTR-IH; Crohn's disease

value: Crohn's disease

tag: cdai

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: time

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

value: Post

tag: surgery

tag: age diagnostic


title: HCA00101.K08

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 26-S0-TTR-CIA; Crohn's disease

tag: disease state

tag: Sex

value: FEMALE

tag: treatment

tag: cdai

tag: pcr

value: COLON

value: Baseline

tag: age sample


title: HCA00101.K02


title: 23-T52-TTR-CH; Crohn's disease

tag: sescd global

tag: sescd local

tag: exact location

value: ASCENDING COLON

tag: time

tag: patient id

tag: affected area

value: HEALTHY


title: HCA00101.K05

tag: cell id


title: HBP01-1

tag: tissue

tag: age

tag: temperature

tag: well

tag: race


title: 16-TM48-TTR-CH-M

tag: Sex

value: YES

value: RECTUM

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: surgery

value: NO

tag: age diagnostic


title: R6ST2R2: Inplanta_shoot_race6_rep2

tag: isolate


title: 16-TM36-TTR-IH-M

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

tag: age sample


title: 23-T52-TTR-CII; Crohn's disease

tag: disease state

value: SIGMOID COLON

tag: patient id

tag: affected area

value: INVOLVED

value: INACTIVE


title: 16-TM36-TTR-CH-M

tag: Sex

tag: afected area

tag: involved


title: 16-TM30-TTR-CIA-M

tag: active area

value: ACTIVE

tag: transplant

tag: surgery


title: R6ST2R3: Inplanta_shoot_race6_rep3

tag: isolate


title: HBP01-3

tag: tissue

value: Whole blood

tag: age

tag: temperature

value: RT

tag: well

value: Female

tag: race

value: Asian


title: 22-T52-TTR-III; Crohn's disease

value: Crohn's disease

tag: treatment

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: time

value: Post

tag: age diagnostic


title: 23-T26-TTR-CII; Crohn's disease

tag: disease state

tag: Sex

value: FEMALE

tag: patient id

tag: affected area

value: COLON

tag: involved

tag: active area

tag: age sample


title: HBP01-2

tag: tissue

tag: age

tag: temperature

tag: well


title: 16-TM30-TTR-CH-M

tag: treatment

tag: cdai

tag: pcr

tag: afected area

tag: transplant

tag: surgery


title: R6RT2R3: Inplanta_root_race6_rep3

source_name: in planta root, race6

tag: isolate


title: 16-TM36-TTR-CII-M

tag: Sex

tag: sescd global

tag: sescd local

tag: exact location

value: ASCENDING COLON

tag: time

tag: age diagnostic


title: R6RT2R2: Inplanta_root_race6_rep2


title: R6ST2R1: Inplanta_shoot_race6_rep1


title: HCA00101.I08

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: 22-T52-TTR-CII; Crohn's disease

tag: disease state

tag: treatment

tag: cdai

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: age sample


title: R6RT2R4: Inplanta_root_race6_rep4

tag: isolate


title: HCA00101.K03

value: colorectal carcinoma


title: HCA00101.I07


title: 22-T26-TTR-III; Crohn's disease

tag: Sex

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: ILEUM

tag: transplant

tag: surgery


title: 16-T52-TTR-IH-M

value: NO

tag: time

tag: afected area

value: HEALTHY

tag: age diagnostic


title: HCA00101.I06

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: R6RT2R1: Inplanta_root_race6_rep1

tag: isolate


title: HCA00101.I05


title: 22-T106-TTR-III; Crohn's disease

tag: disease state

tag: Sex

tag: cdai

tag: patient id

tag: affected area

tag: involved

value: INVOLVED

tag: active area

tag: age sample


title: 16-T52-TTR-CH-M

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: RECTUM

tag: time

tag: afected area

tag: transplant

tag: surgery


title: HCA00101.K01

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 16-T52-TTR-CII-M

tag: Sex

tag: cdai

tag: patient id

tag: involved

value: INACTIVE

tag: age diagnostic


title: 16-T26-TTR-CII-M

tag: pcr

tag: sescd global

tag: sescd local

tag: active area

tag: age sample


title: 6418FR4: Invitro_race 6_rep4

source_name: in vitro, race6

tag: isolate


title: 26-T26-TTR-CII; Crohn's disease

tag: disease state

tag: exact location

value: DESCENDING COLON

tag: time

tag: affected area

tag: transplant

tag: surgery


title: HCA00101.I04

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: HCA00101.I01


title: 6418FR3: Invitro_race 6_rep3


title: HCA00101.I03


title: 22-T26-TTR-CII; Crohn's disease

tag: Sex

tag: cdai

tag: pcr

tag: sescd global

tag: patient id

tag: involved

tag: age diagnostic


title: HCA00101.G08


title: 16-T106-TTR-CII-M

tag: sescd local

tag: exact location

tag: time

tag: afected area

tag: active area

tag: age sample


title: 22-T106-TTR-CII; Crohn's disease

tag: disease state

tag: affected area

tag: transplant

tag: surgery


title: 16-T26-TTR-IH-M

tag: Sex

tag: treatment


title: R5ST2R3: Inplanta_shoot_race5_rep3

source_name: in planta shoot, race5

tag: isolate


title: 6418FR2: Invitro_race 6_rep2


title: HCA00101.I02

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00101.G07


title: 16-S0-TTR-IH-M

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: patient id

tag: involved

value: Baseline

tag: age diagnostic


title: 22-S0-TTR-CIA; Crohn's disease

tag: disease state

tag: time

tag: affected area

tag: active area

value: ACTIVE

tag: transplant

tag: surgery

tag: age sample


title: HCA00101.G06

tag: cell id

tag: cell type

tag: cell line

tag: treatment

tag: time point


title: 16-T26-TTR-CH-M

tag: Sex

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: afected area


title: 21-S0-TTR-IH; Crohn's disease

tag: disease state

value: MALE

tag: exact location

tag: time

tag: patient id

tag: involved

tag: age diagnostic


title: 19-S0-TTR-IH; Crohn's disease

value: Crohn's disease

tag: affected area

tag: active area

tag: transplant

tag: surgery

tag: age sample


title: 16-S0-TTR-CI-M

tag: Sex

tag: treatment


title: R5ST2R4: Inplanta_shoot_race5_rep4

tag: isolate


title: 6418FR1: Invitro_race 6_rep1


title: 16-T106-TTR-CH-M

tag: cdai

tag: pcr

tag: sescd global

value: Post


title: 18-TM40-TTR-III; Crohn's disease

tag: disease state

value: YES

tag: sescd local


title: 19-S0-TTR-CH; Crohn's disease

value: FEMALE

tag: exact location

tag: time

value: COLON


title: 21-S0-TTR-CI; Crohn's disease

value: ASCENDING COLON

tag: patient id

tag: involved


title: 15-T26-TTR-CH-M

tag: afected area

value: Pre

tag: age diagnostic


title: HCA00101.G02

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: 18-T26-TTR-CIA; Crohn's disease

tag: Sex

tag: treatment

value: TRANSVERSE COLON

tag: affected area

tag: active area

tag: transplant

tag: surgery

value: NO

tag: age sample


title: R5ST2R2: Inplanta_shoot_race5_rep2

tag: isolate


title: 19-S0-TTR-CI; Crohn's disease

tag: disease state

tag: cdai

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

value: SIGMOID COLON

tag: time

tag: patient id

value: INVOLVED


title: HCA00101.G05

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: R5RT2R1: Inplanta_root_race5_rep1

source_name: in planta root, race5


title: R5ST2R1: Inplanta_shoot_race5_rep1


title: 15-T52-TTR-CII-M

tag: Sex

tag: treatment

tag: afected area

tag: involved

tag: active area

value: INACTIVE

tag: transplant

tag: age diagnostic


title: 14-TM48-TTR-CII-M

tag: cdai

tag: pcr

tag: sescd global

tag: surgery

tag: age sample


title: HCA00101.E08

tag: cell id


title: 18-S0-TTR-CI; Crohn's disease

tag: disease state

tag: sescd local

tag: exact location

value: RECTUM

tag: time

tag: patient id

tag: affected area

value: Baseline


title: HCA00101.G04

tag: cell type

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: R5RT2R4: Inplanta_root_race5_rep4

tag: isolate


title: 14-T52-TTR-III-M

tag: Sex

value: MALE

tag: cdai

tag: pcr

value: ILEUM

tag: afected area

tag: involved

tag: active area

tag: transplant

tag: age diagnostic


title: 15-T52-TTR-CH-M

tag: sescd global

tag: sescd local

tag: exact location

tag: time

value: HEALTHY

tag: surgery

tag: age sample


title: 6425FR3: Invitro_race 5_rep3

source_name: in vitro, race5


title: 16-TM48-TTR-CII; Crohn's disease

tag: disease state

value: Crohn's disease

tag: treatment

value: YES

tag: patient id

tag: affected area

value: Post


title: 28-S0-TTR-CIA; Crohn's disease

tag: Sex

value: FEMALE

tag: cdai

value: COLON

value: ACTIVE


title: R5RT2R3: Inplanta_root_race5_rep3

tag: isolate


title: 18-T52-TTR-CII; Crohn's disease

tag: pcr

value: TRANSVERSE COLON

tag: involved


title: HCA00101.G03

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: R5RT2R2: Inplanta_root_race5_rep2


title: 15-T26-TTR-CI-M

value: NO

tag: sescd global

tag: sescd local

tag: exact location

value: SIGMOID COLON

tag: time

tag: afected area

tag: active area

tag: transplant

value: Pre

tag: age diagnostic


title: 16-TM48-TTR-CH; Crohn's disease

tag: disease state

tag: Sex

tag: treatment

tag: cdai

tag: patient id

tag: affected area

tag: surgery

tag: age sample


title: 6425FR1: Invitro_race 5_rep1

tag: isolate


title: 14-TM48-TTR-III-M

tag: pcr

tag: sescd global

tag: involved

value: INVOLVED

value: INACTIVE


title: HCA00101.E05

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: HCA00101.G01


title: 16-TM36-TTR-CII; Crohn's disease

tag: disease state

tag: sescd local

tag: exact location

value: ASCENDING COLON

tag: time

tag: active area

tag: transplant

tag: age diagnostic


title: 6425FR4: Invitro_race 5_rep4


title: 14-T26-TTR-II-M

tag: Sex

value: MALE

tag: treatment

tag: cdai

value: ILEUM

tag: patient id

tag: afected area

tag: surgery

tag: age sample


title: HCA00101.E04

tag: cell id

tag: cell type

tag: cell line


title: 14-T26-TTR-CI-M

tag: pcr

tag: sescd global

tag: involved


title: 6425FR2: Invitro_race 5_rep2

tag: isolate


title: 18-T106-TTR-III; Crohn's disease

tag: disease state

value: Crohn's disease

tag: sescd local

tag: exact location

tag: time

tag: affected area

tag: active area


title: HCA00101.E07

tag: treatment

tag: time point

tag: cell count


title: 14-T52-TTR-CII-M

tag: Sex

tag: cdai

tag: patient id

tag: afected area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: 14-T106-TTR-III-M

tag: pcr

tag: sescd global

tag: involved


title: R2ST2R2: Inplanta_shoot_race2_rep2

source_name: in planta shoot, race2

tag: isolate


title: HCA00101.E06

tag: cell id

tag: cell type

tag: cell line


title: HCA00101.E02

tag: treatment

tag: time point


title: 16-TM36-TTR-IH; Crohn's disease

tag: disease state

tag: Sex

value: YES

tag: sescd local

tag: exact location

tag: time

tag: affected area

value: HEALTHY

tag: active area


title: 16-TM30-TTR-CH; Crohn's disease

value: FEMALE

tag: cdai

value: RECTUM

tag: patient id

tag: transplant

value: Post

tag: surgery

tag: age diagnostic

tag: age sample


title: R2ST2R1: Inplanta_shoot_race2_rep1

tag: isolate


title: R2ST2R4: Inplanta_shoot_race2_rep4


title: 16-TM36-TTR-CH; Crohn's disease

tag: pcr

tag: sescd global

value: COLON

tag: involved


title: R2ST2R3: Inplanta_shoot_race2_rep3


title: HCA00101.E03

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: treatment

tag: time point

tag: cell count


title: 14-T106-TTR-CII-M

tag: Sex

value: NO

tag: sescd local

tag: exact location

tag: time

tag: afected area

tag: active area


title: HCA00101.C08


title: HCA00101.C07


title: 13-TM48-TTR-CH-M

tag: cdai

tag: patient id

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: R2RT2R4: Inplanta_root_race2_rep4

source_name: in planta root, race2

tag: isolate


title: 16-T52-TTR-CII; Crohn's disease

source_name: biopsy

tag: disease state

tag: pcr

tag: sescd global

tag: affected area

tag: involved


title: R2RT2R3: Inplanta_root_race2_rep3


title: 16-T52-TTR-IH; Crohn's disease

tag: Sex

tag: treatment

tag: sescd local


title: 13-TM48-TTR-CII-M

tag: exact location

tag: time

tag: afected area


title: R2RT2R2: Inplanta_root_race2_rep2


title: HCA00101.C05

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 16-TM30-TTR-CIA; Crohn's disease

tag: cdai

tag: patient id

tag: active area

value: ACTIVE

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: 16-T52-TTR-CH; Crohn's disease

tag: disease state

tag: Sex

tag: treatment

tag: pcr

tag: sescd global

tag: affected area

tag: involved


title: 13-TM36-TTR-III-M

tag: sescd local

tag: exact location

tag: time

tag: afected area


title: R2RT2R1: Inplanta_root_race2_rep1

tag: isolate


title: HCA00101.C06

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: HCA00101.E01


title: 16-T26-TTR-IH; Crohn's disease

tag: disease state

tag: cdai

tag: patient id

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic

tag: age sample


title: 6423FR4: Invitro_race 2_rep4

source_name: in vitro, race2


title: 13-TM36-TTR-CII-M

tag: Sex

tag: treatment

tag: pcr

tag: sescd global

tag: sescd local

tag: exact location

tag: involved


title: HCA00101.C04

tag: cell id

tag: cell type

tag: cell line

tag: time point


title: 13-TM48-TTR-IIA-M

tag: cdai

tag: time

tag: patient id

tag: afected area


title: 16-T26-TTR-CH; Crohn's disease

tag: disease state

tag: affected area

tag: active area

tag: transplant

tag: surgery

tag: age diagnostic


title: 13-TM36-TTR-CH-M

tag: Sex

tag: treatment

tag: pcr

tag: sescd global

tag: sescd local

tag: age sample


title: 16-T26-TTR-CII; Crohn's disease

tag: exact location

tag: involved


title: HCA00101.C03

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 13-T52-TTR-II-M

tag: cdai

tag: time

tag: patient id

tag: afected area

tag: active area


title: 6423FR2: Invitro_race 2_rep2

tag: isolate


title: 6423FR3: Invitro_race 2_rep3


title: 6423FR1: Invitro_race 2_rep1


title: 16-T106-TTR-CII; Crohn's disease

tag: disease state

tag: Sex

tag: treatment

tag: pcr

tag: affected area

tag: transplant

tag: surgery

tag: age diagnostic


title: 13-T106-TTR-III-M

tag: sescd global

tag: sescd local

tag: exact location

tag: involved

tag: age sample


title: HCA00101.C01

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 13-T52-TTR-CI-M

tag: Sex

tag: cdai

tag: time

tag: patient id

tag: afected area

tag: active area


title: R1ST2R4: Inplanta_shoot_race1_rep4

source_name: in planta shoot, race1

tag: isolate


title: HCA00101.C02

tag: treatment


title: 16-T106-TTR-CH; Crohn's disease

tag: disease state

tag: pcr

tag: sescd global

tag: sescd local

tag: affected area

tag: transplant

tag: surgery

tag: age diagnostic


title: HCA00101.A07

tag: cell id

tag: cell type

tag: cell line

tag: time point

tag: cell count


title: 13-T106-TTR-CH-M

tag: Sex

tag: cdai

tag: exact location

tag: time

tag: patient id

tag: afected area

tag: involved

tag: age sample


title: HCA00101.A08

tag: treatment


title: 16-S0-TTR-CI; Crohn's disease

tag: disease state

tag: pcr

tag: sescd global

tag: sescd local

tag: affected area

tag: active area

tag: transplant

value: Baseline


title: R1ST2R2: Inplanta_shoot_race1_rep2

tag: isolate


title: 13-T106-TTR-CII-M

tag: Sex

value: INVOLVED

tag: surgery

tag: age diagnostic


title: 15-T52-TTR-CII; Crohn's disease

tag: cdai

tag: exact location

value: SIGMOID COLON

tag: time

value: INACTIVE

value: Pre


title: HCA00101.A06

tag: cell id

tag: cell type

value: malignant melanoma

tag: cell line

tag: time point

tag: cell count


title: R1ST2R3: Inplanta_shoot_race1_rep3


title: HCA00101.A05

tag: treatment


title: R1ST2R1: Inplanta_shoot_race1_rep1


title: CASTAT5 spleen CD4+ T cells RNA-seq 3

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
Demultiplexing with Bcl2fastq2 were employed to generate the fastq file for each sample.
The RNAseq analysis was performed on Galaxy main server (usegalaxy.org). The raw reads were mapped to mouse genome mm10 using HISTAT2 (Galaxy Version 2.1.0) with default settings.
Reads mapped to annotated features were counted using featureCounts (Galaxy v1.6.3).
The DEseq2 v1.18.1 implemented in Galaxy (v2.11.40.2) was used to normalize the raw accounts and identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: DEseq2 output files including differential analysis results and normalized count table as well as raw count files generated by featureCounts

source_name: FACS_sorted CD4 T cells

growth_protocol: CD4 T cells were purified from 6.5-TCR Tg mouse splenocytes and stimulated with mouse CD3/CD28 activation Dynabeads in the presence of hrIL2 overnight. Cells were harvested and transduced twice in two consecutive days with retroviral supernatant. Cells were harvested 24 hours after the second transduction.

extract_protocol:
Total RNA was isolated from FACS-sorted donor CD4+ T cells using TRIzol reagent.
100 ng of total RNA was used for RNAseq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide. The RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequently sequenced on a HiSeq3000 (Illumina) sequencer with 50bp single-end cycling.

treatment_protocol: A20HA Tumor cells were subcutaneously injected to the right flank of mice. When tumor sizes reached the desired sizes, mice were randomly assigned into groups to receive the specified treatments. Cyclophosphamide (CTX) was i.p. injected to mice at 150 mg/kg one day before T cell transfer. For adoptive CD4 T-cell transfer, in vitro cultured T cells were harvested and injected into each recipient via tail vein (10^5 cells/mouse).

tag: cell surface marker

tag: genotype/variation

value: Stat5a (H229R & S711F) mutant

tag: strain

value: Balb/c


title: CASTAT5 spleen CD4+ T cells RNA-seq 2


title: R1RT2R4: Inplanta_root_race1_rep4

source_name: in planta root, race1


title: 15-T26-TTR-CI; Crohn's disease

tag: disease state

value: Crohn's disease

tag: pcr

tag: sescd global

tag: sescd local

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: age sample


title: HCA00101.A04

tag: cell id

tag: cell type

tag: cell line


title: R1RT2R3: Inplanta_root_race1_rep3

tag: isolate


title: R1RT2R2: Inplanta_root_race1_rep2


title: 16-S0-TTR-IH; Crohn's disease

tag: Sex

tag: treatment

tag: cdai

tag: exact location

value: ILEUM

tag: time

value: HEALTHY

tag: surgery

tag: age diagnostic


title: HCA00101.A02

tag: time point

tag: cell count


title: Control spleen CD4+ T cells RNA-seq 3

tag: cell surface marker

tag: genotype/variation

value: Empty Vector

tag: strain


title: 15-T26-TTR-CH; Crohn's disease

tag: disease state

value: FEMALE

tag: pcr

tag: sescd global

tag: sescd local

value: ASCENDING COLON

tag: patient id

tag: affected area

tag: involved

tag: active area

tag: transplant

tag: age sample


title: Control spleen CD4+ T cells RNA-seq 2


title: 14-TM48-TTR-III; Crohn's disease

tag: Sex

value: MALE

tag: treatment

tag: cdai

tag: exact location

tag: time

value: Post

tag: surgery


title: HCA00101.A01

tag: cell id

tag: cell type

value: colorectal carcinoma

tag: cell line

tag: time point

tag: cell count


title: R1RT2R1: Inplanta_root_race1_rep1

tag: isolate


title: 6462FR4: Invitro_race 1_rep4

source_name: in vitro, race1


title: TS45_THP-1_R1

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

data_processing:
Paired-end sequencing reads were aligned to the human genome (GRCh38) and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: TS45_counts.txt

growth_protocol: THP-1 and derived cell lines were cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

extract_protocol:
Total RNA was extracted from sensitive or resistant K562 cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK) and its quality confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: Resistant


title: HCA00101.O01


title: Control spleen CD4+ T cells RNA-seq 1

tag: cell surface marker

tag: genotype/variation

tag: strain


title: TS45_THP-1_S1

value: Sensitive


title: 14-T52-TTR-III; Crohn's disease

tag: disease state

value: NO

tag: pcr

tag: sescd global

tag: sescd local

tag: patient id

tag: affected area

tag: involved

value: INVOLVED

tag: active area

tag: transplant

tag: age diagnostic

tag: age sample


title: TS45_THP-1_S2

tag: cell line


title: 6462FR2: Invitro_race 1_rep2

tag: isolate


title: 6462FR1: Invitro_race 1_rep1


title: CASTAT5 spleen CD4+ T cells RNA-seq 1


title: 6462FR3: Invitro_race 1_rep3


title: 14-T52-TTR-CII; Crohn's disease

tag: Sex

tag: treatment

tag: cdai

tag: exact location

tag: time

value: COLON

value: INACTIVE

tag: surgery


title: TS45_THP-1_R2

tag: phenotype


title: HCA00101.A03

tag: cell id

tag: cell type

tag: time point

tag: cell count


title: 14-T106-TTR-III; Crohn's disease

tag: disease state

tag: pcr

tag: sescd global

tag: sescd local

tag: patient id

tag: affected area

tag: involved

tag: active area


title: 14-T106-TTR-CII; Crohn's disease

tag: Sex

tag: treatment

tag: cdai

tag: transplant

tag: age diagnostic

tag: age sample


title: TS98_11_556_T2_INPUT

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM v0.7.15 (5). Read duplicates were removed using Picard v2.1.0. Reads were further filtered using Bedtools v2.25.0 to keep only paired reads that mapped to standard chromosomes and to remove reads with a mapping quality of less than 10. Reads mapped to blacklisted regions defined by ENCODE were then removed using Bedtools (http://mitra.stanford.edu/kundaje).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: Primary AML

growth_protocol: Cyropreserved primary cells were thawed and immediately crosslinked for ChIP.

extract_protocol:
ChIP was performed using anti-H3K27Ac (ab4729, Abcam, Cambridge, UK). 10^8 cells (THP-1) or 107 cells (primary AML samples) were used for each precipitation using the method described by Lee et al. (2006). Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode, Liege, Belgium). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipitation performed overnight on a rotator at 4°C and 20rpm. After five washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1hr. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a NextSeq desktop sequencing system (Illumina) with 75bp, paired-end high output generating 65-80M (THP-1_S and THP-1_R) and 34-45M reads per sample (primary AML samples).

tag: cell type

value: Primary AML

tag: chip antibody


title: 15-T52-TTR-CH; Crohn's disease

tag: exact location

tag: time

value: Pre

tag: surgery


title: 13-TM48-TTR-IIA; Crohn's disease

tag: disease state

value: Crohn's disease

tag: pcr

tag: sescd global

value: ACTIVE


title: 14-TM48-TTR-CII; Crohn's disease

tag: sescd local

tag: patient id

tag: affected area


title: 14-T26-TTR-CI; Crohn's disease

tag: Sex

tag: involved

tag: active area


title: TS98_10_727_T1

value: anti-H3K27Ac (ab4729, Abcam, Cambridge, UK)


title: TS98_9_497_T2


title: 13-TM36-TTR-III; Crohn's disease

tag: treatment

tag: cdai

value: ILEUM

tag: transplant


title: 14-T26-TTR-II; Crohn's disease

tag: age diagnostic

tag: age sample


title: 13-TM48-TTR-CII; Crohn's disease

value: FEMALE

tag: exact location

value: RECTUM


title: 13-TM48-TTR-CH; Crohn's disease

value: ASCENDING COLON

tag: time

value: HEALTHY


title: 13-TM36-TTR-CII; Crohn's disease

value: Post

tag: surgery


title: TS98_6_380_T1

tag: cell type

tag: chip antibody


title: TS98_5_171_T3


title: TS98_8_54_T2


title: 13-TM36-TTR-CH; Crohn's disease

tag: disease state

tag: pcr

tag: sescd global


title: TS98_4_546_T6


title: TS98_3_14_T10


title: 13-T52-TTR-II; Crohn's disease

tag: sescd local

tag: patient id

tag: affected area


title: TS98_1_556_T2


title: 13-T106-TTR-III; Crohn's disease

tag: Sex

tag: involved

tag: active area


title: 13-T106-TTR-CII; Crohn's disease

tag: treatment

tag: cdai

tag: transplant


title: 13-T52-TTR-CI; Crohn's disease

tag: exact location

tag: age diagnostic

tag: age sample


title: TS98_7_338_T2

tag: cell type


title: TS54_THP-1_R2

tag: cell line

tag: phenotype

value: Resistant

tag: chip antibody


title: 13-T106-TTR-CH; Crohn's disease

tag: disease state

tag: pcr

tag: sescd global

tag: time

tag: surgery


title: TS54_THP-1_S2


title: Hemocytes, INT3d, rep2

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

description:
Replicate 2 of library INT3d
CK_INT3d.xlsx
CK-INT3d all gene model.xlsx

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the reference genome of G. mellonella with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening of differentially expressed genes was performed in the paired library of the indicated time-point/CK. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Galleria mellonella (NCBI BioProjects: PRJNA498111)
Supplementary_files_format_and_content: Excel files, including Gene ID, FPKM values for each replicate, log2(fold change), p-value, FDR-value and gene discription  for the paired sample.

organism: Galleria mellonella

source_name: Hemocytes

growth_protocol: Conidia suspension (5 ul, 10e5conidia ml-1) of B. bassiana were injected into G. mellonella. The infected larvae were incubated at 25°C.

extract_protocol:
Hemocytes were ground into powder in liquid nitrogen. Total RNA was isolated from cellullar lysate r using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina assay.

treatment_protocol: Hemocytes were sampled at the indicated time-point, including 1, 2, and 3 days post infection. In addition, the hemocytes of the un-infected larvae were also sampled.

value: Hemocytes

tag: infection

value: Beauveria bassiana

value: 3 days post infection


title: LPS treated whole brain + dura (2) [LPS_12h_K74]

city: Brussels

first: Daliya

last: Kancheva

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
Raw data bcl files were first demultiplexed using Cellranger mkfastq
Demultiplexed data was then processed using the Cellranger count pipeline
The output count matrices of Cell Ranger count were then aggregated using Cellranger aggr
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited tekst files including raw counts for each sample individually (output Cellranger count) and the aggregated samples (output Cellranger aggr)

source_name: LPS treated whole brain + dura

growth_protocol: not applicable

extract_protocol:
Processing and tissue-collection of whole brain and dura mater was performed as previously described (Van Hove et al., 2019, doi: https://doi.org/10.1038/s41593-019-0393-4). Cellular suspensions were loaded on a Chromium Chip B (10x Genomics, No.1000074) on a GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in emulsion (GEM). GEMs  were prepared using the GemCode Single Cell 3' Gel Bead according to the manufacturer's instructions. Briefly, GEM reverse transcription incubation was performed in a 96-deep-well reaction module at 53C for 45 min, 85C for 5 min and ending at 4C. Next, GEMs were broken and complementary DNA (cDNA) was cleaned up with DynaBeads MyOne Silane Beads (10x Genomics, No. 2000048) and SPRIselect Reagent Kit (Beckman Coulter, No. B23318). Full-length, barcoded cDNA was PCR amplified with a 96-deep-well reaction module at 98C for 3 min, eleven cycles at 98C for 15 seconds, 63C for 20 seconds and 72C for 1 min, followed by one cycle at 72C for 1 min and ending at 4C.
scRNAseq libraries were prepared using the Library Kit (v3, 10xGenomics, No. 1000075) and the Chromium i7 Multiplex Kit (10x Genomics, No. 120262) according to the manufacturer's instructions. Following cleaning up with the SPRIselect Reagent Kit and enzymatic fragmentation, library construction to generate Illumina-ready sequencing libraries was performed by the addition of R1 (read 1 primer), P5, P7, i7 sample index and R2 (read 2 primer sequence) via end-repair, A-tailing, adapter ligation, post-ligation SPRIselect cleanup/size selection and sample index PCR.

treatment_protocol: Female, 9-week old C57BL/6 mice were injected i.p. with PBS (Control) (n = 4, included in sample Ctrl_PBS_12h_K72)  or 2.5 mg/kg LPS (n = 3 for LPS_12h_K73, n = 3 for LPS_12h_K74).

tag: strain

value: lipopolysaccharide (LPS)

tag: tissue

value: whole brain and dura mater

tag: number of cells


title: TS54_THP-1_R_input

value: Sensitive


title: Hemocytes, INT3d, rep1

description:
Replicate 1 of library INT3d
CK_INT3d.xlsx
CK-INT3d all gene model.xlsx


title: TS98_2_225_T15

value: Primary AML


title: TS54_THP-1_R1


title: TS54_THP-1_S1


title: genomic DNA from malignant melanoma clinical sample 1615M

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description:
SAMPLE 46
Malignant melanoma clinical sample.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from primary cell culture or clinical samples using QIAamp DNA FFPE Tissue Kit according to standard instructions.

tag: gender

value: Male

tag: age

value: malignant melanoma

value: lymph node

tag: stage (ajcc 7th)


title: TS54_ THP-1_S_input


title: genomic DNA from malignant melanoma clinical sample 1608P

description:
SAMPLE 43
Malignant melanoma clinical sample.

value: Female

value: skin

tag: tumor thickness


title: LPS treated whole brain + dura (1) [LPS_12h_K73]

tag: treatment


title: Control whole brain + dura [Ctrl_PBS_12h_K72]

source_name: Control whole brain + dura


title: Hemocytes, INT2d, rep2

description:
Replicate 2 of library INT2d
CK_INT2d.xlsx
CK-INT2d all gene model.xlsx

tag: cell type

value: 2 days post infection


title: 21 days post-partum SCARKO mutant - unsynchronized (115236)

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.12.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2b.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.12.
Gene expressoin matrix was generated using Drop-seq tools v1.12.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: testis

growth_protocol: Ar fl/fl females (Chakraborty et al., 2014) were crossed with Amh-cre tg/+ (Lécureuil et al., 2002); yielding ~50% of the resulting males lacking AR in Sertoli cells (hereafter referred to as SCARKO). The Amh-Cre- male littermates were used as wild type (WT) controls.

extract_protocol:
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation.
A total of 600 pg of amplified cDNA per sample was used for a Nextera XT library preparation (Illumina).

treatment_protocol: WIN 18,446 was administered to pups orally from 2-8 dpp at a dose of approximately 100 mg/kg/day. At 9 dpp, pups were given an IP injection of RA (100ug/animal). Testes were collected between 8 to 16 days following the RA injection. For 21dpp samples, testes were collected in untreated WT or SCARKO pups at 21dpp.

value: testis

tag: Sex


title: 21 days post-partum WT mutant - unsynchronized (115235)


title: genomic DNA from malignant melanoma clinical sample 1604P

description:
SAMPLE 40
Malignant melanoma clinical sample.


title: Hemocytes, INT2d, rep1

description:
Replicate 1 of library INT2d
CK_INT2d.xlsx
CK-INT2d all gene model.xlsx


title: genomic DNA from malignant melanoma clinical sample 1605P

description:
SAMPLE 41
Malignant melanoma clinical sample.


title: SKOV-3 cisplatin-resistant cells rep 2

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: ovarian cancer cells, ascites

growth_protocol: SKOV3 and OVCAR5 ovarian cancer cells were routinely cultured and maintained in their required medium.

extract_protocol:
RNA was harvested using Trizol reagent. gDNA was removed using QIAGEN Rneasy mini kit. And then mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

treatment_protocol:
SKOV3 and OVCAR5 cisplatin (CDDP) resistant cells were generated by treating cells with 3 or 4 repeated doses of cisplatin for 24 hours. Surviving cells were allowed to recover for 3 to 4 weeks before receiving the next treatment. 2-3 millions of wild type and cisplatin resistant cells were used for RNA extraction.
30,000-50,000 OVCAR5_ALDH(+)CD133(+) DP and OVCAR5_ALDH(-)CD133(-) DN cells were FACS sorted based on their aldehyde dehydrogenase (ALDH) enzymatic activity and expression level of CD133 and were used for RNA extraction.
30,000-50,000 OVCAR5_FZD7(+) and OVCAR5_FZD7(-) cells were FACS sorted by using FZD7 antibody and were used for RNA extraction.
Extract protocol: RNA was extracted with a RNeasy Micro Kit and treated with DNase to remove gDNA contamination. mRNA was isolated from 500ng of total RNA extracted from OVCAR5_FZD7(+) and OVCAR5_FZD7(-) OC cells; 200ng of total RNA extracted from OVCAR5_ALDH(+)CD133(+)_DP and OVCAR5_ ALDH(-)CD133(-)_DN cells; and 1g of total RNA extracted from OVCAR5/SKOV3 cisplatin resistant and cells and OVCAR5/SKOV3 wild type cells.

value: SKOV-3 cisplatin-resistant cells

tag: tumor stage

value: high grade serous

tag: passage


title: genomic DNA from malignant melanoma clinical sample 1610P

description:
SAMPLE 44
Malignant melanoma clinical sample.

tag: disease state


title: Hemocytes, INT1d, rep2

description:
Replicate 2 of library INT1d
CK_INT1d.xlsx
CK-INT1d all gene model.xlsx

value: 1 day post infection


title: genomic DNA from malignant melanoma clinical sample 1607P

description:
SAMPLE 42
Malignant melanoma clinical sample.


title: 16 days past RA injection SCARKO mutant (115238)


title: Hemocytes, CK, rep2

description:
Replicate 2 of library CK
CK_INT1d.xlsx; CK_INT2d.xlsx; CK_INT3d.xlsx
CK-INT1d all gene model.xlsx
CK-INT2d all gene model.xlsx
CK-INT3d all gene model.xlsx

value: Hemocytes

value: control

value: no infection


title: SKOV-3 cisplatin-resistant cells rep 1


title: SKOV-3 wildtype cells rep 3

value: SKOV-3 wildtype cells


title: Hemocytes, CK, rep1

description:
Replicate 1 of library CK
CK_INT1d.xlsx; CK_INT2d.xlsx; CK_INT3d.xlsx
CK-INT1d all gene model.xlsx
CK-INT2d all gene model.xlsx
CK-INT3d all gene model.xlsx


title: SKOV-3 wildtype cells rep 2


title: genomic DNA from malignant melanoma clinical sample 1513M

description:
SAMPLE 32
Malignant melanoma clinical sample.


title: SKOV-3 wildtype cells rep 1


title: 13 days past RA injection SCARKO mutant (117698)


title: 8 days past RA injection WT (117507)


title: genomic DNA from malignant melanoma clinical sample 1602P

description:
SAMPLE 38
Malignant melanoma clinical sample.


title: WTB_16: Mycelium - WT - Rep6

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Custom GE microarray (8X60K, Design 085497  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 085497_D_F_20180419). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}.
We firstly selected control probes and probes targeting Penicillium expansum PEXP transcripts (GeneNames begining by 'PEXP_') giving a dataset with 12341 entries. We next selected the spots with a minimal weight of 1 for 9 out of 11 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 10054 spots out of 12341 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth method using the qsmooth function from the qsmooth R library. The resulting matrix has 33665 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Penicillium expansum

source_name: Mycelium

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Five and six MEA Petri dishes were inoculated with PeΔBrlA  (KO_BrlA) and Wild Type (WT) strains, respectively. Before the inoculation, Petri dishes were overlaid with a sterile cellophane layer. Then, the cultures were incubated at 25°C for 5 days in the dark.

extract_protocol: At the end of the incubation period, mycelia were removed from cellophane layer and RNAs were extracted as described by Tannous et al ( 2014). Tannous J, El Khoury R, Snini SP, Lippi Y, El Khoury A, Atoui A, Lteif R, Oswald IP, Puel O. Sequencing, physical organization and kinetic expression of the patulin biosynthetic gene cluster from Penicillium expansum. Int J Food Microbiol. 2014 Oct 17;189:51-60

tag: genotype

value: WT

value: Mycelium


title: 13 days past RA injection WT (117697)


title: genomic DNA from malignant melanoma clinical sample 1519M

description:
SAMPLE 35
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1603P

description:
SAMPLE 39
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1613P

description:
SAMPLE 45
Malignant melanoma clinical sample.


title: WTB_7: Mycelium - WT - Rep5


title: genomic DNA from malignant melanoma clinical sample 1601P

description:
SAMPLE 37
Malignant melanoma clinical sample.


title: Hemocytes, INT1d, rep1

description:
Replicate 1 of library INT1d
CK_INT1d.xlsx
CK-INT1d all gene model.xlsx

value: Beauveria bassiana

tag: time


title: 8 days past RA injection SCARKO mutant (117508)

value: Male


title: BrlA_15: Mycelium - KO_BrlA - Rep5


title: 16 days past RA injection WT (115237)


title: OVCAR-5 cisplatin-resistant cells rep 3

value: OVCAR-5 cisplatin-resistant cells


title: OVCAR-5 cisplatin-resistant cells rep 2


title: OVCAR-5 cisplatin-resistant cells rep 1


title: ATAC-seq_SDHC_KO_vehicle_2

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Mapped reads were used to generate genomic coverage bedGraph files using bedtools v2.27.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed bedGraph files show genomic coverage.

source_name: immortalized mouse embryonic fibroblast cell line, SDHC KO + vehicle

growth_protocol: Cells grown in DMEM (low glucose) containing 10% FBS at 37 degrees Celsius in 5% CO2.

extract_protocol:
OMNI ATAC-seq performed on 50,000 cells. Amplified libraries were purified, and the sizes of library DNA were determined by the Fragment Analyzer (Advanced Analytical Technologies, IA) using the High Sensitivity NGS Fragment Analysis Kit (cat# DNF-486). The enrichment of accessible regions was determined by the quantification of the fold difference between positive and negative genomic loci using real-time PCR.
OMNI ATAC-seq library construction

treatment_protocol: Gene rearrangement induced by adding doxycycline to media at 1 microgram/mL final concentration.

tag: cell line

value: immortalized mouse embryonic fibroblast cell line (iMEF)

value: SDHC KO (R26M2rtTA/+;TetOcre;Sdhc-/-)

value: vehicle


title: ATAC-seq_SDHC_KO_vehicle_1


title: genomic DNA from malignant melanoma clinical sample 1504P

description:
SAMPLE 29
Malignant melanoma clinical sample.

value: malignant melanoma

value: skin


title: genomic DNA from malignant melanoma clinical sample 1423P

description:
SAMPLE 28
Malignant melanoma clinical sample.

value: Female


title: genomic DNA from malignant melanoma clinical sample 1513P

description:
SAMPLE 33
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1508P

description:
SAMPLE 31
Malignant melanoma clinical sample.


title: OVCAR-5 wildtype cells rep 3

value: OVCAR-5 wildtype cells

value: high grade serous


title: genomic DNA from malignant melanoma clinical sample 1514M

description:
SAMPLE 34
Malignant melanoma clinical sample.

value: lymph node


title: WTB_14: Mycelium - WT - Rep4


title: BrlA_10: Mycelium - KO_BrlA - Rep4


title: genomic DNA from malignant melanoma clinical sample 1421P

description:
SAMPLE 27
Malignant melanoma clinical sample.


title: ATAC-seq_SDHC_KO_HATi_2

source_name: immortalized mouse embryonic fibroblast cell line, SDHC KO + HATi

value: HATi


title: OVCAR-5 wildtype cells rep 2


title: WTB_10: Mycelium - WT - Rep3


title: ATAC-seq_SDHC_KO_HATi_1


title: OVCAR-5 wildtype cells rep 1


title: genomic DNA from malignant melanoma clinical sample 1519P

description:
SAMPLE 36
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1412P

description:
SAMPLE 25
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1414P

description:
SAMPLE 26
Malignant melanoma clinical sample.


title: HiC_KO

city: Singapore

first: Qi-Ling

last: Zhou

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Sigapore

data_processing:
The paired-end HiC reads are mapped and converted to .hic files using Juicertools with default setting
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .hic files are generated by Juicertools

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
For ChIPseq, cells were fixed with 1% formaldehyde and insoluble chromatin fraction were isolated. Chromatin were sonicated to 200 to 500 base pair and protein-DNA complexes were pulled down by antibodies.For RNAseq, cells were lysed with Trizol, RNAs were isolated using phenol-chloroform extraction. For HiC cells were fixed with 2% formaldehyde and then insoluble chromatin fraction were isolated following Arima HiC kit protocol.
For ChIPseq samples, libraries were prepared using ThruPLEX DNA-seq kit (R400428) according to manufacturer's instruction. Constructed libraries were PAGE purified and only libraries with 250 to 500bp were used for sequencing. For RNAseq samples,  libraries were prepared using SMART Seq v4 Ultra Low Input RNA kit from Takara and Nextera XT DNA library prep kit from Illumina according to the manufacturer’s instructions. For HiC samples, libraries were prepared using Arima HiC kit and Swift biosciences® Accel NGS® 2S plus DNA library kit following the low input procedure instructions.

value: CTCF KO

value: bone marrow

value: Hematopoietic stem and progenitor cells

tag: developmental stage

value: adult


title: flow sorted OVCAR-5 ALDH(+)CD133(+) cells rep 2

value: OVCAR-5 ALDH(+)CD133(+) cells


title: flow sorted OVCAR-5 ALDH(+)CD133(+) cells rep 1


title: BrlA_16: Mycelium - KO_BrlA - Rep3

value: Mycelium


title: input_ChIPseq_KO

data_processing:
The paired-end RNA-seq reads are mapped by STAR to the mouse reference genome GRCm38 (mm10).
Alignments with mapping quality below 20 are filtered out. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files are converted by bedGraphToBigWig from bedGraph generated by bedtools. Normalization between the samples was based on the proportionality of the numbers of the mapped reads.

tag: strain


title: genomic DNA from malignant melanoma clinical sample 1505P

description:
SAMPLE 30
Malignant melanoma clinical sample.

value: Male

tag: tissue


title: WTB_1: Mycelium - WT - Rep2

value: WT


title: flow sorted OVCAR-5 ALDH(-)CD133(-) cells rep 2

value: OVCAR-5 ALDH(-)CD133(-) cells


title: genomic DNA from malignant melanoma clinical sample 1410M

description:
SAMPLE 24
Malignant melanoma clinical sample.


title: genomic DNA from malignant melanoma clinical sample 1409P

description:
SAMPLE 23
Malignant melanoma clinical sample.


title: input_ChIPseq_WT


title: WTB_8: Mycelium - WT - Rep1


title: genomic DNA from malignant melanoma clinical sample 1408P

description:
SAMPLE 22
Malignant melanoma clinical sample.


title: BrlA_2: Mycelium - KO_BrlA - Rep1


title: flow sorted OVCAR-5 FZD7 positive cells rep 2

value: OVCAR-5 FZD7 positive cells


title: genomic DNA from malignant melanoma clinical sample 1407P

description:
SAMPLE 21
Malignant melanoma clinical sample.

value: malignant melanoma


title: flow sorted OVCAR-5 ALDH(-)CD133(-) cells rep 1


title: SKOV-3 cisplatin-resistant cells rep 3

value: SKOV-3 cisplatin-resistant cells


title: eHi-C_SDHC_KO_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Mapped reads were used to generate genomic coverage bedGraph files using bedtools v2.27.0.
Genome_build: mm10
Supplementary_files_format_and_content: hic

source_name: immortalized mouse embryonic fibroblast cell line

extract_protocol:
Cells harvested by trypsinization, and eHi-C performed on 1E6 cells as input.
Rubicon Genomics ThruPLEX DNA-seq 48 S kit.

tag: condition

value: SDHC KO


title: BrlA_9: Mycelium - KO_BrlA - Rep2


title: flow sorted OVCAR-5 FZD7 positive cells rep 1


title: eHi-C_SDHC_KO_1


title: genomic DNA from malignant melanoma clinical sample 1407M

description:
SAMPLE 20
Malignant melanoma clinical sample.

tag: gender

value: Female


title: eHi-C_Control_1

value: Control


title: flow sorted OVCAR-5 FZD7 negative cells rep 1

value: OVCAR-5 FZD7 negative cells

value: high grade serous


title: eHi-C_Control_2


title: Cut_and_run_IgG_SDHC_KO_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2.2.3
Mapped reads were used to generate genomic coverage bedGraph files using bedtools v2.27.0.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Cells harvested by trypsinization, and CUT&RUN performed using standard procedure.
Rubicon Genomics ThruPLEX DNA-seq 48 S kit.

tag: antibody

value: IgG


title: flow sorted OVCAR-5 FZD7 negative cells rep 2


title: Cut_and_run_IgG_SDHC_KO_3


title: genomic DNA from malignant melanoma clinical sample 1405P

description:
SAMPLE 18
Malignant melanoma clinical sample.

tag: age

value: skin

tag: stage (ajcc 7th)


title: HC-3 [re-used]

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis,11 was used to identify distinct cell populations and visualize cell clusters in graphs as in. 8 Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content.
Genome_build: GrCh38 genome
Supplementary_files_format_and_content: Raw dataframe csv files

molecule: polyA RNA

source_name: Skin tissue

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Experimental procedures followed established techniques using the Chromium Single Cell 3’ Library V2  kit (10x Genomics). Cell suspensions were separated by the Chromium System (10X Genomics) into  mini-reaction "partitions" or GEMs formed by oil micro-droplets, each containing a gel bead and a cell. A  1000-fold excess of partitions compared to cells assured that most partitions/GEMs had only one cell per  GEM. Gel beads contained an oligonucleotide scaffold composed of an oligo-dT section for priming  reverse transcription, and barcodes for each cell (10X Genomics) and each transcript (unique molecular   identifier, UMI), as described. 7,000 cells were loaded into the instrument to obtain data on ~4,000 cells  with a rate of ~3.1% of partitions showing more than one cell/partition. The following steps were all  performed using reagents and protocols developed by 10X Genomics.
The emulsions were transferred from the Chromium chip to a PCR cycler for cDNA synthesis. The emulsion was then broken using a recovery agent, and following Dynabead and SPRI clean up, cDNAs were amplified by PCR (C1000, Bio-Rad). cDNAs were sheared enzymatically into lengths of ~200bp. DNA fragment ends were repaired, A-tailed, and adaptors ligated.
Single Cell 10x Genomics 3' Library V2 Chemistry

value: Healthy control


title: genomic DNA from malignant melanoma clinical sample 1406P

description:
SAMPLE 19
Malignant melanoma clinical sample.

tag: tumor thickness


title: Cut_and_run_IgG_Control_2


title: HC-2 [re-used]


title: Cut_and_run_IgG_Control_1


title: HC-1 [re-used]


title: Cut_and_run_Butyryllysine_SDHC_KO_3

value: Butyryllysine

tag: antibody manufacturer and catalog number

value: PTM Biolabs cat# PTM-301


title: HiC_WT

value: bone marrow

tag: cell type

value: Hematopoietic stem and progenitor cells

value: adult


title: HC-4 [re-used]


title: CTCL-12 [re-used]

source_name: Skin tumor

tag: tumor stage

value: CTCL tumor


title: genomic DNA from malignant melanoma clinical sample 1403P

description:
SAMPLE 17
Malignant melanoma clinical sample.


title: Cut_and_run_Butyryllysine_Control_2


title: Cut_and_run_Propionyllysine_SDHC_KO_3

value: Propionyllysine

value: PTM Biolabs cat# PTM-201


title: PF42 CTR

data_processing:
The sequenced reads were mapped onto the GrCh38 homo sapiens reference genome, version GrCh38.v81 using CLC Genomics Workbench 12.0 (Qiagen) and gene expression values TPM (Transcripts per million) were calculated using CLC Genomics Workbench 12.0.
Paired-end raw read FASTq files were quality checked using the CLC Genomics Workbench 12.0 per default parameters. Failed reads were removed at this time.
Heatmaps were generated in TreeView3 using values normalized for each donor as follows: library size normalization is automatically performed using the TMM (trimmed mean of M values) method. For each desired comparison, gene differential expression was calculated from regularized log-fold-changes and multiple-testing-corrected P-values. Genes were considered to be differentially expressed when P < 0.05 and log2FC was >0.585 in either direction (which corresponds to FC > 1.5 in either direction). Volcano plots, PCA plots, and Venn diagrams were generated from genes that were initially filtered to exclude those with low overall expression in all samples.
Default parameters can be found at: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1200/index.php?manual=Introduction_CLC_Genomics_Workbench.html
Genome_build: GrCh38
Supplementary_files_format_and_content: Excel files with gene expression data

source_name: CD4+ cells from normal blood

growth_protocol: All cultures were performed in complete RPMI-1640 medium (ThermoFisher) containing rhIL-2 (10ng/ml, PeproTech) and IL-7 (5ng/ml, PeproTech).16 Cells were activated by the Dynabeads CD3/CD28 T cell Expander (ThermoFisher, bead-to-cell ratio: 1:1).

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Blood samples were purified for CD4+ cells using EasySep enrichment kit (StemCell Technologies). RNA was isolated from samples obtained from SS (n=4), MF (n=3), and HC (n=3) independent donors on 48 hours of culture with/without STAT-6 inhibitor. Total RNA was isolated using the RNeasy purification Kit (Qiagen), and cDNA was obtained employing the High Capacity Reverse Transcription cDNA synthesis kit (Applied Biosystems). RNA was quantified by a Qubit Fluorometer (Invitrogen) and RNA integrity was checked using an Agilent Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies).
Libraries were prepared using ultra DNA library prep kits. RNA sequencing analysis was performed on Illumina NextSeq500 using 500-bp paired-end reads by Health Science Sequencing core facility at University of Pittsburgh. Between 10 and 30 million read pairs were generated per sample.

treatment_protocol: STAT-6 was inhibited by the STAT-6-specific inhibitor AS151749930 (100nM, Axon Medchem)

tag: treatment


title: Cut_and_run_Butyryllysine_Control_1


title: Cut_and_run_Propionyllysine_SDHC_KO_1


title: PF41 + STAT6i

value: STAT6 inhibitor


title: Cut_and_run_Propionyllysine_Control_2


title: genomic DNA from malignant melanoma clinical sample 1210P

description:
SAMPLE 11
Malignant melanoma clinical sample.

value: Male

tag: disease state

value: malignant melanoma


title: CTCL-8 [re-used]

value: IIB T3N0B0M0


title: genomic DNA from malignant melanoma clinical sample 1306P

description:
SAMPLE 14
Malignant melanoma clinical sample.

value: Female


title: PF41 CTR


title: CTCL-6 [re-used]

value: F IIB T3NxB0M0


title: genomic DNA from malignant melanoma clinical sample 1307P

description:
SAMPLE 15
Malignant melanoma clinical sample.


title: Cut_and_run_Propionyllysine_Control_1

tag: genotype

value: Control


title: genomic DNA from malignant melanoma clinical sample 1207P

description:
SAMPLE 9
Malignant melanoma clinical sample.

value: skin


title: genomic DNA from malignant melanoma clinical sample 1301P

description:
SAMPLE 12
Malignant melanoma clinical sample.


title: PF39 + STAT6i


title: genomic DNA from malignant melanoma clinical sample 1401P

description:
SAMPLE 16
Malignant melanoma clinical sample.


title: Cut_and_run_Acetyllysine_SDHC_KO_3

value: SDHC KO

value: Acetyllysine

value: PTM Biolabs cat# PTM-105


title: PF39 CTR


title: Cut_and_run_Butyryllysine_SDHC_KO_1

value: Butyryllysine

value: PTM Biolabs cat# PTM-301


title: MF8 + STAT6i

source_name: Skin Tumor

tag: tumor type

value: mycosis fungoides


title: genomic DNA from malignant melanoma clinical sample 1209P

description:
SAMPLE 10
Malignant melanoma clinical sample.


title: MF8 CTR


title: Cut_and_run_H3K27ac_SDHC_KO_3

value: Active Motif cat# 39134


title: genomic DNA from malignant melanoma clinical sample 1113M

description:
SAMPLE 5
Malignant melanoma clinical sample.

value: lymph node


title: Cut_and_run_Acetyllysine_Control_1


title: C103_H0

city: Houston

first: Noah

last: Shroyer

state: Texas

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

data_processing:
Pseudosalignment was performed using Kallisto (https://pachterlab.github.io/kallisto/) and raw gene counts were output as tsv files
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files with raw gene counts for every gene and every sample

source_name: Intestine

growth_protocol: Enteroids were grown in conditions indicated in the manuscript

extract_protocol:
RNA was isolated and enteroids according to E.Z.N.A.® Total RNA Kit I protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Enteroids were treated with either 1,25D3 (100nM) or an eqaul volume of Ethanol (Control)

value: Control (0nM)

tag: status

value: Undifferentiated

tag: segment

tag: patient line


title: Cut_and_run_H3K27ac_SDHC_KO_1


title: MF3 + STAT6i

value: STAT6 inhibitor


title: C103_H100


title: Cut_and_run_Acetyllysine_SDHC_KO_1


title: Cut_and_run_H3K27ac_Control_2


title: genomic DNA from malignant melanoma clinical sample 1304P

description:
SAMPLE 13
Malignant melanoma clinical sample.

value: malignant melanoma

tag: tissue


title: MF3 CTR


title: C103_D0

value: Differentiated


title: Cut_and_run_H3K27ac_Control_1

tag: condition


title: genomic DNA from malignant melanoma clinical sample 1202P

description:
SAMPLE 6
Malignant melanoma clinical sample.

tag: gender

value: Female


title: MF6 CTR


title: genomic DNA from malignant melanoma clinical sample 1203P

description:
SAMPLE 7
Malignant melanoma clinical sample.


title: SZ15 + STAT6i

source_name: CD4+ cells from SZ patient blood

value: Sezary syndrome


title: C104_H100