title: TST+/IGRA+ subject#7

type: protein

city: Bronx

first: Jacqueline

last: Achkar

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: IgG

hyb_protocol: Arrays were blocked with 3% BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected by goat anti-human biotin-labeled IgG (Jackson Immunoresearch), followed by a Streptavidin probe tagged with SureLight®P3 Cy5 (Cayman Chemicals). Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The slides were scanned using the GenePix 4000 Microarray scanner system. Scanned images were analyzed with by the image-processing software Spotfinder (http://www.tm4.org/spotfinder.html).

data_processing: The median pixel intensity of each feature was background subtracted. A minimum value of pixel intensity (400) was determined by the median pixel intensity of the spots with low quality, which was determined by the software quality control score for each spot depending on signal-to-noise ratio and spot shape. The scanned images were visually inspected. The spots with obvious local artifacts were excluded from analysis. The array features were printed in duplicates. The final data were averaged from the duplicates.

label: SureLight P3 Cy5

molecule: protein

source_name: Serum

label_protocol: SureLight®P3 Cy5

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:50

tag: infection states

value: Asymptomatic controlled Mtb infection


title: TST+/IGRA+ subject#6

status: Public on Dec 10 2019

country: USA

description: IgG

organism: Homo sapiens


title: C1HTsmall_s8_1911015030_Col06_S227

type: SRA

city: Barcelona

first: Atefeh

last: Lafzi

address: Baldiri Reixac 4

department: CNAG

country: Spain

institute: Center for Genomic Regulation

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv

library_source: transcriptomic

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11), R2 = cDNA

molecule: polyA RNA

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

growth_protocol: NIH3T3-GFP, MDCK-TurboFP650 and HEK293-RFP were cultured at 37ºC in an atmosphere of 5% (v/v) carbon dioxide in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% (w/v) fetal bovine serum, 100 U penicillin, and 100 µg/L streptomycin (Invitrogen).

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.

treatment_protocol: Untreated cells and donors.

tag: protocol

tag: centre

value: Stanford

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: TST+/IGRA+ subject#4

description: IgG


title: TST+/IGRA+ subject#5

description: IgG


title: Pfalciparum_SA250_hour6

city: Durham

first: Steven

last: Haase

state: North Carolina

department: Biology

institute: Duke University

data_processing:
Reads were aligned using STAR_2.4.1d with parameters --runMode alignReads --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFilterIntronMotifs RemoveNoncanonical
Aligned, sorted SAM files were created with cuffquant v2.2.1 with parameter --library-type=fr-firststrand
Samples from each strain were normalized by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using cuffnorm v2.2.1 with parameter --library-type=fr-firststrand
Genome_build: The Sanger Institute's P. falciparum 3D7 v3.0 genome
Supplementary_files_format_and_content: Tab-delimited text files for each strain with FPKM values for all genes per timepoints, which are given in hours

molecule: total RNA

organism: Plasmodium falciparum

source_name: in vitro culture

growth_protocol: Parasites were synchronized by alanine treatment and temperature cycling as decribed in Haynes and Moch 2002 (PMID:12125145). For the course of the experiment, strains were grown at 37C in RPMI 1640 with 10% human serum and 4% hematocrit. Flasks were gassed with 5% CO2, 5% O2, 90% N2. Cultures were sampled every 3 hours, and sampling began between late schizont and early ring stages.

extract_protocol:
Samples were spun down, media aspirated, and pellet snap frozen and stored at -80C. Total RNA was extracted using a phenol-chloroform protocol as described in Leman et al 2014 (PMID: 24906319), except citrate-buffered phenol was substituted for acid phenol. The ratios of reagent to sample as found in the cited protocol were retained, with the exception of the initial thawing in TES buffer, which was changed to a 2:1 ratio of TES to sample.
Libraries were prepared using Stranded Total RNA Kapa kits with rRNA Ribo-Zero Globin depletion

tag: strain


title: C1HTsmall_s8_1911015030_Col05_S228


title: 44265_P2 TFH

city: Pittsburgh

first: Smita lab

last: Lab

state: PA

address: 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh

description:
44265 CD4 TFH cell
44265P2

data_processing: Prior to analysis, genes with fewer than 30 counts per million reads were filtered, leaving 6,455 genes. Differential expression analyses were conducted using the limma-voom Bioconductor pipeline.

organism: Macaca mulatta

source_name: Lymph node

extract_protocol:
CD4 T cell subsets were sorted from frozen lymph nodes. Collected cells were flash frozen in RLT buffer and extracted using the Qiagen RNA isolation kit according to manufacturers instructions.
RNA converted to ds DNA. dsDNA fragmented the ends are repaired and ‘A’ tailed, adapters are ligated on, size selection is carried out, then PCR performed to generate the final library ready for sequencing according to Illumina protocols
3′-Tag-Seq (QuantSeq) Gene Expression Profiling

value: primary sorted CD4 T cells

tag: cd4 subsets

value: CD4 TFH cell

tag: gender

value: female

tag: time point post vacc

value: Week 2 post protein+ALFQ boost


title: TST+/IGRA+ subject#3

description: IgG


title: Pfalciparum_SA250_hour9


title: 44265_P1 Naïve Cell

description:
44265 Naive CD4 T cell
44265P1

value: Naive CD4 T cell


title: Pfalciparum_SA250_hour3


title: 44164_P4 mem non-THF

description:
44164 CD4 mem non-TFH cell
44164P4

value: CD4 mem non-TFH cell


title: TST+/IGRA+ subject#1

description: IgG


title: Pfalciparum_SA250_hour0


title: C1HTsmall_s8_1911015030_Col10_S224


title: C1HTsmall_s8_1911015030_Col02_S237


title: 44164_P3 mem- TFH

description:
44164 CD4 mem-TFH cell
44164P3

value: CD4 mem-TFH cell


title: Pfalciparum_FVO-NIH_hour66

value: FVO-NIH


title: TST- subject as control

description: IgG

value: Uninfected control


title: C1HTsmall_s8_1911015030_Col01_S221


title: C1HTsmall_s8_1911015030_Col04_S238


title: 44265_P3 mem- TFH

description:
44265 CD4 mem-TFH cell
44265P3


title: Pfalciparum_FVO-NIH_hour69


title: 44164_P2 TFH

description:
44164 CD4 TFH cell
44164P2


title: TST+/IGRA+ subject#2

description: IgG


title: TB patient #13

description: IgG

value: Symptomatic uncontrolled Mtb infection/TB disease


title: 44164_P1 Naïve Cell

description:
44164 Naive CD4 T cell
44164P1


title: TB patient #12

description: IgG


title: Pfalciparum_FVO-NIH_hour63


title: C1HTsmall_s7_1911011090_Col20_S209


title: C1HTsmall_s7_1911011090_Col19_S210


title: ddSEQ_Sample10

description:
cryopreserved HCA reference
ddSEQ_human_exp_mat.tsv, ddSEQ_human_metada.tsv, ddSEQ_mouse_exp_mat.tsv, ddSEQ_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (8-14,25-31,42-48), UMI (1-7);  R2 = cDNA

value: ddSEQ

value: Biorad


title: TB patient #11

description: IgG


title: C1HTsmall_s7_1911011090_Col18_S216


title: TB patient #10

description: IgG


title: Pfalciparum_FVO-NIH_hour57


title: ddSEQ_Sample8


title: C1HTsmall_s8_1911015030_Col03_S222


title: C1HTsmall_s7_1911011090_Col17_S215


title: Pfalciparum_FVO-NIH_hour54


title: TB patient #9

description: IgG


title: C1HTsmall_s7_1911011090_Col16_S214


title: C1HTsmall_s7_1911011090_Col15_S213


title: ddSEQ_Sample7


title: Pfalciparum_FVO-NIH_hour51


title: Pfalciparum_D6_hour48


title: ddSEQ_Sample5


title: TB patient #8

description: IgG


title: TB patient #7

description: IgG


title: TB patient #6

description: IgG


title: ddSEQ_Sample9


title: Pfalciparum_FVO-NIH_hour48


title: C1HTsmall_s7_1911011090_Col14_S212


title: Pfalciparum_FVO-NIH_hour60


title: Pfalciparum_FVO-NIH_hour45


title: ddSEQ_Sample4


title: C1HTsmall_s7_1911011090_Col13_S211


title: TB patient #5

description: IgG


title: Pfalciparum_FVO-NIH_hour42


title: C1HTsmall_s7_1911011090_Col12_S203


title: ddSEQ_Sample3


title: Pfalciparum_FVO-NIH_hour39


title: C1HTsmall_s7_1911011090_Col11_S219


title: Pfalciparum_FVO-NIH_hour36


title: C1HTsmall_s7_1911011090_Col10_S204


title: ddSEQ_Sample2


title: ddSEQ_Sample1


title: ddSEQ_Sample6


title: TB patient #2

description: IgG


title: ddSEQ_KKSample6


title: Pfalciparum_FVO-NIH_hour33


title: ddSEQ_KKSample5


title: C1HTsmall_s7_1911011090_Col09_S220


title: C1HTsmall_s7_1911011090_Col08_S205


title: C1HTsmall_s7_1911011090_Col07_S206


title: Pfalciparum_FVO-NIH_hour27


title: ddSEQ_KKSample3


title: Pfalciparum_FVO-NIH_hour21


title: ddSEQ_KKSample2


title: SCRBseq_N708

description:
cryopreserved HCA reference
SCRBseq_human_exp_mat.tsv, SCRBseq_human_metada.tsv, SCRBseq_mouse_exp_mat.tsv, SCRBseq_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-16); R2 = cDNA

value: gmSCRB-seq

value: LMU -Munich


title: TST+/IGRA+ subject#10

description: IgG

value: Asymptomatic controlled Mtb infection


title: TST+/IGRA+ subject#9

description: IgG


title: Pfalciparum_FVO-NIH_hour24


title: TB patient #4

description: IgG


title: Pfalciparum_FVO-NIH_hour18


title: ddSEQ_KKSample4


title: TB patient #3

description: IgG


title: C1HTsmall_s7_1911011090_Col06_S207

value: Stanford


title: ddSEQ_KKSample1

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: SCRBseq_N707


title: C1HTsmall_s7_1911011090_Col04_S218


title: SingleNuclei_nextseq2

description:
cryopreserved HCA reference
SingleNuclei_human_exp_mat.tsv, SingleNuclei_human_metada.tsv, SingleNuclei_mouse_exp_mat.tsv, SingleNuclei_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-16), UMI (17-26); R2 = cDNA

value: Single-Nuclei

value: Broad


title: C1HTsmall_s7_1911011090_Col05_S208


title: SCRBseq_N706


title: Pfalciparum_FVO-NIH_hour15


title: SCRBseq_N705


title: Pfalciparum_FVO-NIH_hour30


title: TB patient #1

description: IgG


title: SingleNuclei_nextseq1


title: Pfalciparum_FVO-NIH_hour9


title: SCRBseq_N704


title: TST+/IGRA+ subject#8

description: IgG


title: C1HTsmall_s7_1911011090_Col01_S201


title: QUARTZseq_P5S8

description:
cryopreserved HCA reference
QUARTZseq_human_exp_mat.tsv, QUARTZseq_human_metada.tsv, QUARTZseq_mouse_exp_mat.tsv, QUARTZseq_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-15), UMI (16-23), R2 = cDNA

value: RIKEN


title: C1HTsmall_s6_1911011085_Col20_S189


title: Pfalciparum_FVO-NIH_hour3


title: QUARTZseq_P4S7


title: SCRBseq_N703


title: Pfalciparum_FVO-NIH_hour0


title: SCRBseq_N702


title: SCRBseq_N701


title: QUARTZseq_P2S5


title: QUARTZseq_P3S6


title: C1HTsmall_s7_1911011090_Col03_S202


title: Pfalciparum_FVO-NIH_hour12


title: C1HTsmall_s7_1911011090_Col02_S217


title: Pfalciparum_FVO-NIH_hour6


title: C1HTsmall_s6_1911011085_Col19_S190


title: MTG_AD_rep71

status: Public on Dec 09 2019

type: RNA

city: Göttingen

first: Roy

last: Lardenoije

address: Robert-Koch-Str. 40

country: Germany

institute: University Medical Center Göttingen

description:
SAMPLE 71
AD middle temporal gyrus sample

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Raw data was exported from Illumina’s GenomeStudio with the Expression Module.

label: biotin

source_name: middle temporal gyrus, AD

label_protocol: Standard Illumina protocol.

extract_protocol: RNA was extracted with the Qiagen RNeasy Mini Kit in accordance with the prescribed protocol provided with the kit.

value: Male

tag: age

tag: tissue

value: brain, middle temporal gyrus

tag: disease state

value: AD


title: MTG_AD_rep73

description:
SAMPLE 73
AD middle temporal gyrus sample

value: Female


title: MTG_AD_rep76

description:
SAMPLE 76
AD middle temporal gyrus sample


title: MTG_Control_rep77

description:
SAMPLE 77
Control middle temporal gyrus sample

source_name: middle temporal gyrus, Control

value: Control


title: MTG_Control_rep56

description:
SAMPLE 56
Control middle temporal gyrus sample


title: MTG_AD_rep58

description:
SAMPLE 58
AD middle temporal gyrus sample


title: MTG_Control_rep55

description:
SAMPLE 55
Control middle temporal gyrus sample


title: MTG_Control_rep68

description:
SAMPLE 68
Control middle temporal gyrus sample


title: MTG_AD_rep57

description:
SAMPLE 57
AD middle temporal gyrus sample


title: MTG_Control_rep74

description:
SAMPLE 74
Control middle temporal gyrus sample


title: MTG_Control_rep65

description:
SAMPLE 65
Control middle temporal gyrus sample


title: MTG_Control_rep70

description:
SAMPLE 70
Control middle temporal gyrus sample


title: MTG_AD_rep78

description:
SAMPLE 78
AD middle temporal gyrus sample


title: MTG_AD_rep75

description:
SAMPLE 75
AD middle temporal gyrus sample


title: MTG_Control_rep64

description:
SAMPLE 64
Control middle temporal gyrus sample


title: MTG_AD_rep72

description:
SAMPLE 72
AD middle temporal gyrus sample


title: MTG_AD_rep54

description:
SAMPLE 54
AD middle temporal gyrus sample


title: MTG_AD_rep67

description:
SAMPLE 67
AD middle temporal gyrus sample


title: MTG_AD_rep53

description:
SAMPLE 53
AD middle temporal gyrus sample


title: MTG_Control_rep61

description:
SAMPLE 61
Control middle temporal gyrus sample


title: MTG_Control_rep63

description:
SAMPLE 63
Control middle temporal gyrus sample


title: MTG_AD_rep49

description:
SAMPLE 49
AD middle temporal gyrus sample


title: MTG_Control_rep66

description:
SAMPLE 66
Control middle temporal gyrus sample


title: MTG_Control_rep69

description:
SAMPLE 69
Control middle temporal gyrus sample


title: MTG_AD_rep51

description:
SAMPLE 51
AD middle temporal gyrus sample


title: MTG_Control_rep50

description:
SAMPLE 50
Control middle temporal gyrus sample


title: MTG_Control_rep62

description:
SAMPLE 62
Control middle temporal gyrus sample


title: MTG_Control_rep59

description:
SAMPLE 59
Control middle temporal gyrus sample


title: MTG_Control_rep60

description:
SAMPLE 60
Control middle temporal gyrus sample


title: MTG_Control_rep52

description:
SAMPLE 52
Control middle temporal gyrus sample


title: MTG_AD_rep48

description:
SAMPLE 48
AD middle temporal gyrus sample


title: MTG_AD_rep45

description:
SAMPLE 45
AD middle temporal gyrus sample


title: MTG_AD_rep44

description:
SAMPLE 44
AD middle temporal gyrus sample


title: MTG_Control_rep36

description:
SAMPLE 36
Control middle temporal gyrus sample


title: MTG_AD_rep40

description:
SAMPLE 40
AD middle temporal gyrus sample


title: MTG_Control_rep35

description:
SAMPLE 35
Control middle temporal gyrus sample


title: MTG_AD_rep37

description:
SAMPLE 37
AD middle temporal gyrus sample


title: MTG_AD_rep34

description:
SAMPLE 34
AD middle temporal gyrus sample


title: MTG_Control_rep23

description:
SAMPLE 23
Control middle temporal gyrus sample


title: MTG_AD_rep47

description:
SAMPLE 47
AD middle temporal gyrus sample


title: MTG_Control_rep32

description:
SAMPLE 32
Control middle temporal gyrus sample


title: MTG_AD_rep42

description:
SAMPLE 42
AD middle temporal gyrus sample


title: MTG_AD_rep43

description:
SAMPLE 43
AD middle temporal gyrus sample


title: MTG_Control_rep33

description:
SAMPLE 33
Control middle temporal gyrus sample


title: MTG_AD_rep41

description:
SAMPLE 41
AD middle temporal gyrus sample


title: MTG_AD_rep29

description:
SAMPLE 29
AD middle temporal gyrus sample


title: MTG_Control_rep30

description:
SAMPLE 30
Control middle temporal gyrus sample


title: MTG_Control_rep27

description:
SAMPLE 27
Control middle temporal gyrus sample


title: MTG_AD_rep46

description:
SAMPLE 46
AD middle temporal gyrus sample


title: MTG_AD_rep39

description:
SAMPLE 39
AD middle temporal gyrus sample


title: MTG_AD_rep31

description:
SAMPLE 31
AD middle temporal gyrus sample


title: MTG_AD_rep28

description:
SAMPLE 28
AD middle temporal gyrus sample


title: MTG_AD_rep26

description:
SAMPLE 26
AD middle temporal gyrus sample


title: MTG_Control_rep24

description:
SAMPLE 24
Control middle temporal gyrus sample


title: MTG_Control_rep25

description:
SAMPLE 25
Control middle temporal gyrus sample


title: MTG_AD_rep20

description:
SAMPLE 20
AD middle temporal gyrus sample


title: MTG_AD_rep21

description:
SAMPLE 21
AD middle temporal gyrus sample


title: MTG_Control_rep18

description:
SAMPLE 18
Control middle temporal gyrus sample


title: MTG_AD_rep19

description:
SAMPLE 19
AD middle temporal gyrus sample


title: MTG_Control_rep38

description:
SAMPLE 38
Control middle temporal gyrus sample


title: MTG_AD_rep15

description:
SAMPLE 15
AD middle temporal gyrus sample


title: MTG_AD_rep17

description:
SAMPLE 17
AD middle temporal gyrus sample


title: MTG_Control_rep22

description:
SAMPLE 22
Control middle temporal gyrus sample


title: MTG_AD_rep13

description:
SAMPLE 13
AD middle temporal gyrus sample


title: MTG_AD_rep16

description:
SAMPLE 16
AD middle temporal gyrus sample


title: MTG_Control_rep12

description:
SAMPLE 12
Control middle temporal gyrus sample


title: MTG_AD_rep14

description:
SAMPLE 14
AD middle temporal gyrus sample


title: M0_3

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 4.5 μg of cDNAs were hybridized for 16 hours at 450C, 60 rpm on Human GeneChip® HG-U133 plus 2.0 arrays (Affymetrix).  The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) using the FS450_0004 script

scan_protocol: Chips were scanned with GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

data_processing: CEL files were processed processed with Affymetrix Expression Console software version 1.4.1 to calculate probeset signal intensities, using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Bone marrow

label_protocol: Biotinylated double strand cDNA targets were prepared from 0.3 to 35 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: RNA was extracted using either the RNeasy Micro or Mini Kits (Qiagen), depending on cell numbers

treatment_protocol: Mononuclear cells were isolated by Ficoll gradient centrifugation.

tag: leukemia type

value: AML

tag: leukemia subtype

value: M0 AML

tag: batch

value: L

value: Bone marrow


title: M0_31


title: M0_5


title: MTG_AD_rep9

description:
SAMPLE 9
AD middle temporal gyrus sample


title: M0_29


title: M0_9


title: MTG_AD_rep6

description:
SAMPLE 6
AD middle temporal gyrus sample


title: M0_30


title: N13

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description:
N13_S38_L004
processed data file: dhmc.PN.p001.csv

library_source: genomic

data_processing:
library strategy: hMeDIP-Seq
Processing of sequencing data was performed as previously described. Briefly, FASTQ sequence files from biological replicates were concatenated and aligned to the Homo sapiens reference genome (GRCh37/hg19) using Bowtie 0.12.6, keeping only unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp. Hydroxymethlation levels on each CpG site were evaluated by read counts. To determine differentially hydroxymethylated CpG sites/regions, we used edgeR (Version: edgeR_3.8.6) to normalize read counts, estimate dispersion and perform differential tests. P-values smaller than 0.01 are considered significant to call DhMRs.
Motif detection within DhMRs was performed with Homer. DhMRs were resized to 50bp windows fixed at the center. Homer (v 4.8.3) was used to scan DhMRs for motifs using “findMotifsGenome.pl” with standard background (random genomic sequences sampled according to GC content of peak sequences) and parameters (mask repeats/lower case sequence, using 200bp fragment size for motif finding).
Genome_build: hg19
Supplementary_files_format_and_content: differentially hydroxymethylated CpG sites/regions; csv file with seqnames,start,end,logFC,logCPM,LR,PValue

molecule: genomic DNA

source_name: distant normal gastric tissue (Normal/N)

extract_protocol:
Genomic DNA was isolated from brain samples with standard protocols. Tissues were homogenized on ice and then treated with proteinase K (0.667 µg/µl) in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl) at 55°C for overnight. The second day, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube, and the genomic DNA precipitated with 600 μl isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion).
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method. DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. All sequencing libraries were run on Illumina Hi-seq 2000 machines.

tag: tissue type

value: Distant normal gastric tissue


title: N16

description:
N16_S39_L004
processed data file: dhmc.PN.p001.csv


title: MTG_AD_rep11

description:
SAMPLE 11
AD middle temporal gyrus sample


title: M0_7


title: M0_27


title: MTG_Control_rep10

description:
SAMPLE 10
Control middle temporal gyrus sample


title: MTG_Control_rep8

description:
SAMPLE 8
Control middle temporal gyrus sample


title: MTG_AD_rep4

description:
SAMPLE 4
AD middle temporal gyrus sample


title: MTG_AD_rep5

description:
SAMPLE 5
AD middle temporal gyrus sample


title: MTG_AD_rep1

description:
SAMPLE 1
AD middle temporal gyrus sample


title: M0_26


title: M0_24


title: M0_4


title: MTG_AD_rep7

description:
SAMPLE 7
AD middle temporal gyrus sample


title: M0_25


title: M0_28


title: MTG_AD_rep3

description:
SAMPLE 3
AD middle temporal gyrus sample


title: MTG_AD_rep2

description:
SAMPLE 2
AD middle temporal gyrus sample


title: N10

description:
N10_S37_L004
processed data file: dhmc.PN.p001.csv


title: N7

description:
N7_S36_L004
processed data file: dhmc.PN.p001.csv


title: M0_8


title: M0_23


title: P17

description:
P17_S51_L005
processed data file: dhmc.TN.p001.csv

source_name: adjacent gastric tissue to the tumor (Peripheral/P)

value: Adjacent gastric tissue to the tumor


title: P14

description:
P14_S50_L005
processed data file: dhmc.TN.p001.csv


title: N4

description:
N4_S35_L004
processed data file: dhmc.PN.p001.csv


title: N1

description:
N1_S34_L004
processed data file: dhmc.PN.p001.csv


title: M0_6


title: P8

description:
P8_S48_L005
processed data file: dhmc.TN.p001.csv


title: M0_21


title: P5

description:
P5_S47_L005
processed data file: dhmc.TN.p001.csv


title: T18

description:
T18_S45_L004
processed data file: dhmc.TPN.p001.csv

source_name: gastric tumor (Tumor/T)

value: Gastric tumor


title: P2

description:
P2_S46_L005
processed data file: dhmc.TN.p001.csv


title: T12

description:
T12_S43_L004
processed data file: dhmc.TPN.p001.csv


title: T15

description:
T15_S44_L004
processed data file: dhmc.TPN.p001.csv


title: T9

description:
T9_S42_L004
processed data file: dhmc.TPN.p001.csv


title: T6

description:
T6_S41_L004
processed data file: dhmc.TPN.p001.csv


title: T3

description:
T3_S40_L004
processed data file: dhmc.TPN.p001.csv


title: P11

description:
P11_S49_L005
processed data file: dhmc.TN.p001.csv


title: M0_20


title: M0_19


title: M0_17


title: M0_10


title: M0_22


title: M0_11


title: M0_18


title: M0_2


title: M0_16


title: M_CBF_8

value: Core Binding Factor AML


title: M0_12


title: M0_1


title: M_CBF_9


title: M_CBF_7


title: M_CBF_6


title: M_CBF_5


title: WT, pylorus, Aqp5Neg, biological rep 4

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

description: Gene expression data from Aqp5Neg pyloric stem cells from WT sorted by antibody

hyb_protocol: Microarray was performed using the Affymetrix Mouse ST v2.0 GeneChips (Affymetrix), which consists of more than 28,000 probes for previously annotated genes. The individual microarrays were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Hybridized probe fluorescence was detected using the Affymetrix G3000 GeneArray Scanner. Image analysis was carried out on the Affymetrix GeneChip Command Console v2.0 using the MAS5 algorithm.

data_processing: CEL files were generated for each array and used for gene expression analysis. The CEL files were then processed in R (v3.2.3) with the Bioconductor (v3.2) libraries ‘oligo’ (v1.34.2), ‘pd.mogene.2.0.st’ (v3.14.1) and ‘limma’ (v3.26.8). We used Robust Multi-array Average (RMA)39 to perform background correction and normalization with the ‘rma’ function implemented in the ‘oligo’ package (‘target’ parameter was set to ‘core’ to obtain expression values at the gene level). The experimental design was stored as a single factor with individual levels for each combination of Lgr5-GFP level (high, low, negative) and treatment (tamoxifen and control). Linear models were fitted to the expression data with the function ‘lmFit’ (default parameters). The relevant contrasts were fitted with ‘contrasts.fit’ (default parameters); differential expression was tested with ‘eBayes’ (default parameters). Differential gene expression was analyzed using Partek Genomics Suite software (Partek).

label: Biotin

organism: Mus musculus

source_name: Mouse adult pylorus

label_protocol: RNA quality was first determined by assessing the integrity of the 28s and 18s ribosomal RNA bands on Agilent RNA 60000 Pico LabChips in an Agilent 2100 Bioanalyser (Agilent Technologies). A minimum of 2ng of RNA was used to generate SPIA-amplified cDNA using the Ovation Pico WTA system (Nugen Technologies). Five micrograms of SPIA-amplified purified cDNA was then fragmented and biotin-labelled with the Nugen Encore Biotin module (Nugen Technologies).

growth_protocol: Mice were bred and housed in Biological Resource Centre (Singapore). All animal experiments were approved by the Institutional Animal Care and Use Committee of Singapore. For all experiments adult animals (not selected for gender) with a minimum age of 7-8 weeks were used. Mouse models used were Lgr5-EGFP-IRES-CreERT (Barker 2007, Nature), Lgr5-EGFP-DTR (Tian 2011, Nature) and wildtype mice.

extract_protocol: Murine pylorus was incubated in chelation buffer (5.6 mM sodium phosphate, 8 mM potassium phosphate, 96.2 mM sodium chloride, 1.6 mM potassium chloride, 43.4 mM sucrose, 54.9 mM D-sorbitol, 1 mM dithiothreitol) with 5 mM EDTA at 4oC for 2 hours. Glands were isolated by repeated pipetting of finely chopped pylorus tissue in cold chelation buffer. Chelation buffer containing isolated glands was filtered through 100μm filter mesh, and centrifuged at 720g at 4oC for 3 min. The pellet was resuspended in TrypLE (Life Technologies) with DNaseI (0.8U/μL)(Sigma) and incubated at 37oC for 10 min with intermittent trituration for digestion into single cells. Digestion was quenched by dilution with cold HBSS buffer. The suspension was centrifuged at 720g at 4oC for 3 min. For anti-Aqp5 antibody stain, the pellet was resuspended in HBSS with 2% fetal bovine serum (FBS, Hyclone) with anti-Aqp5-AF647 (Abcam, ab215225) at 1:500 dilution and incubated on ice at 30min in the dark. The pellet was subsequently washed twice with cold HBSS and spun at 800g for 3min at 4oC. The pellet was resuspended in HBSS with 2% fetal bovine serum (FBS, Hyclone). Before sorting, 1 μg/ml propidium iodide (Life Technologies) was added to the cell suspensions, filtered through a 40 μm strainer, and sorted on BD Influx Cell Sorter (BD Biosciences). Cells were collected in RLT Plus buffer (Qiagen) for RNA extraction or HBSS with 2% FBS and 1% PenStrep (Gibco) for organoid culture.   Cells were lysed in RLT Plus buffer (Qiagen). RNA was subsequently isolated with RNeasy Universal Plus kit (Qiagen).

treatment_protocol: Mice were not treated in any way, healthy mice were used for the experiment.

tag: mouse model

value: Wildtype

value: Pylorus

tag: population


title: WT, pylorus, Aqp5Neg, biological rep 2


title: M_CBF_3


title: M_CBF_2


title: M_CBF_4


title: WT, pylorus, Aqp5Neg, biological rep 3


title: M_CBF_10


title: M_CBF_1


title: WT, pylorus, Aqp5Pos, biological rep 4

description: Gene expression data from Aqp5Pos pyloric stem cells from WT sorted by antibody


title: WT, pylorus, Aqp5Pos, biological rep 3


title: WT, pylorus, Aqp5Neg, biological rep 1


title: WT, pylorus, Aqp5Pos, biological rep 2


title: M_8


title: WT, pylorus, Aqp5Pos, biological rep 1


title: M_9


title: Lgr5-EGFP-DTR, pylorus, Lgr5Neg, biological rep 2

description: Gene expression data from Lgr5neg pyloric differentiated cells from Lgr5-EGFP-DTR mouse model


title: Lgr5-EGFP-DTR, pylorus, Lgr5Neg, biological rep 3


title: M_6


title: M_5


title: Lgr5-EGFP-DTR, pylorus, Lgr5Lo, biological rep 3

description: Gene expression data from Lgr5Lo pyloric progenitor cells from Lgr5-EGFP-DTR mouse model


title: Lgr5-EGFP-DTR, pylorus, Lgr5Lo, biological rep 2


title: M_39


title: M_7


title: Lgr5-EGFP-DTR, pylorus, Lgr5Neg, biological rep 1


title: M_38


title: M_37


title: M_4


title: Lgr5-EGFP-DTR, pylorus, Lgr5Lo, biological rep 1


title: M_36


title: Lgr5-EGFP-IRES-CreERT2, colon, whole, biological rep 1

description: Gene expression data from whole colon from Lgr5-EGFP-IRES-CreERT2 mouse model

source_name: Mouse adult colon

value: Colon

value: Whole


title: Lgr5-EGFP-DTR, pylorus, Lgr5Hi, biological rep 1

description: Gene expression data from Lgr5Hi pyloric stem cells from Lgr5-EGFP-DTR mouse model


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Lo, biological rep 2

description: Gene expression data from Lgr5Lo differentiated colon cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Lo, biological rep 1


title: M_3


title: Lgr5-EGFP-DTR, pylorus, Lgr5Hi, biological rep 3


title: Lgr5-EGFP-DTR, pylorus, Lgr5Hi, biological rep 2


title: Lgr5-EGFP-IRES-CreERT2, colon, whole, biological rep 2


title: M_31


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Lo, biological rep 3


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Hi, biological rep 2

description: Gene expression data from Lgr5Hi colon stem cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: M_29


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Hi, biological rep 3


title: Lgr5-EGFP-IRES-CreERT2, small intestine, crypt, biological rep 2

description: Gene expression data from whole small intestinal crypts from Lgr5-EGFP-IRES-CreERT2 mouse model

source_name: Mouse adult small intestine

value: Small intestine


title: M_28


title: M_33


title: M_34


title: M_35


title: M_24


title: M_32


title: M_23


title: Lgr5-EGFP-IRES-CreERT2, small intestine, Lgr5Lo, biological rep 2

description: Gene expression data from Lgr5Lo small intestinal differentiated cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: Lgr5-EGFP-IRES-CreERT2, small intestine, crypt, biological rep 1


title: M_26


title: Lgr5-EGFP-IRES-CreERT2, small intestine, whole, biological rep 1

description: Gene expression data from whole small intestine from Lgr5-EGFP-IRES-CreERT2 mouse model


title: M_27


title: Lgr5-EGFP-IRES-CreERT2, colon, Lgr5Hi, biological rep 1


title: M_22


title: M_25


title: Lgr5-EGFP-IRES-CreERT2, small intestine, Lgr5Lo, biological rep 1


title: M_2


title: M_20


title: Lgr5-EGFP-IRES-CreERT2, small intestine, Lgr5Hi, biological rep 2

description: Gene expression data from Lgr5Hi small intestinal stem cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: Lgr5-EGFP-IRES-CreERT2, pylorus, whole, biological rep 2

description: Gene expression data from whole pyloric glands from Lgr5-EGFP-IRES-CreERT2 mouse model


title: M_19


title: Lgr5-EGFP-IRES-CreERT2, small intestine, Lgr5Hi, biological rep 1


title: Freeze-dried EVs rep2

city: Montpellier

first: Morille

last: Marie

address: 15 avenue Charles Flahault

department: UFR Sciences pharmaceutiques et biologiques, Bat C,

country: France

institute: ICGM UMR5253

description:
sample name: 5
miRNA
Freeze-dried EVs rep2
processed data file: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
The raw reads were trimmed using Cutadapt (version 2.3) to remove the sequencing adapter (TGGAATTCTCGGGTGCCAAGG) at the 3′-end. Additionally, 4 bases were also trimmed from the 5′-end and 3′-end of the reads as indicated in the manual of NEXTflex Small RNA-Seq Kit v3 from Bioo Scientific.
MicroRNA analysis was performed with miARma v1.7.3 pipeline. In this pipeline, alignment was performed with Bowtie v1.1.2 (--best --strata -M 1 --chunkmbs 1000 options) to the mouse genome (GRCm38). The microRNA annotation was retrieved from miRBase (v22). Counting of reads aligned to a miRNA was performed with Featurecounts v1.5.0-p1 (-s 1 -t miRNA -g Name options).
Genome_build: GRCm38
Supplementary_files_format_and_content: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt: Tab-separated text file. First column is the miRNA identifier (miRBase), the following columns are the raw counts for each sample.

source_name: mesenchymal stem cell-derived extracellular vesicles

growth_protocol: Mesenchymal stem cells (mMSC Bl6-GFP, designated as mMSC) were kindly provided by the team of Danièle Noël (IRMB, INSERM U1183, Montpellier), isolated and characterised following protocols previously described (Raisin et al. 2017, Morille et al, 2016). mMSC were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin, and grown in an incubator in optimal conditions of 37°C and 5% CO2. mMSC were cultured to reach 70% confluence. Cells were then washed with DPBS and further cultured in reduced serum medium Opti-MEM for 48h. The medium was collected and centrifuged at 300 g for 10 min at 4°C to eliminate dead cells. The supernatant was centrifuged at 2,000 g for 20 min at 4°C to eliminate cell debris, filtered (through a 0.22 µm membrane) to eliminate large vesicles and stored at 4°C overnight. This medium was then ultra-centrifuged in a 45Ti rotor (Beckman Coulter, USA) with an Optima XPN-80 Ultracentrifuge (Beckman Coulter, USA) at 100,000 g (35,800 rpm) for 110 min at 4°C to pellet small EVs (k factor: 209.6). The supernatant was discarded and EVs were washed with DPBS and centrifuged a second time under the same conditions. The EV pellet was finally resuspended in 1-2 mL of freezing buffer: DPBS, trehalose 25 mM in DPBS or trehalose 25 mM in DPBS supplemented with protease inhibitors. EVs were stored at 4°C, -20°C or -80°C until use. EVs characterised by western blot, lipidomics, proteomics, modified by physical processes, incubated with cells were previously stored at -80°C in trehalose 25 mM in DPBS with or without protease inhibitors.

extract_protocol:
EV pellets (freeze-dried or not) were resuspended in Qiazol lysis buffer and RNA was extracted following RNeasy Micro kit with a DNase treatment step (Qiagen, Courtaboeuf, France). RNA was then quantified spectrophotometrically (Nanodrop ND-1000, Wilmington DE) and RNA quality was assessed by capillary electrophoresis on an Agilent 2100 Bioanalyzer (Agilent Technologies Inc, Santa Clara, CA).
Libraries were constructed using the NEXTFLEX Small RNA-seq kit v3 (Perkin Elmer, NOVA-5132-05) following the manufacturer’s instructions. The resulting barcoded library was size selected on a Pippin HT (SAGE SCience) using 3 % agarose cassette (#HTG3004) and aiming for a size range between 126 base pairs (bp) and 169 bp.

treatment_protocol: EV suspensions were diluted to 0.25-5 x 1010 particles/mL in DPBS supplemented with trehalose 25 mM and frozen at -80°C, freeze-dried overnight (Heto PowerDry LL 3000 Freeze Dryer, ThermoScientific, USA) and resuspended in milliQ water. The resulting suspensions were then left to hydrate at 4°C for 1h and analysed by NTA.

value: C57BL/6-GFP transgenic mice

tag: freeze-dried or not

value: Freeze-dried


title: M_16


title: M_17


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Lo, biological rep 4

description: Gene expression data from Lgr5Lo pyloric differentiated cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: Freeze-dried EVs rep3

description:
sample name: 6
miRNA
Freeze-dried EVs rep3
processed data file: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt

value: mesenchymal stem cell-derived extracellular vesicles


title: M_21


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Lo, biological rep 2


title: M_18


title: Freeze-dried EVs rep1

description:
sample name: 4
miRNA
Freeze-dried EVs rep1
processed data file: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Hi, biological rep 3

description: Gene expression data from Lgr5Hi pyloric stem cells from Lgr5-EGFP-IRES-CreERT2 mouse model


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Lo, biological rep 1


title: M_14


title: Lgr5-EGFP-IRES-CreERT2, pylorus, whole, biological rep 1


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Lo, biological rep 3


title: M_12


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Hi, biological rep 4


title: T_Pre_AB_7

value: T-ALL

value: T-ALL (pre alpha beta lineage)

value: M


title: Unmodified EVs rep2

description:
sample name: 2
miRNA
Unmodified EVs rep2
processed data file: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt

value: Not freeze-dried


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Hi, biological rep 2


title: M_13

value: AML

value: L

value: Bone marrow


title: M_10


title: M_11


title: M_1


title: Unmodified EVs rep1

description:
sample name: 1
miRNA
Unmodified EVs rep1
processed data file: Morille_LyophilizedmiRNA_vs_NotLyophilizedmiRNA_Raw_Counts.txt


title: M_15


title: PB31-miR137 7 days OFF # 3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina Real Time Analysis software (RTA) 1.18.61 software was used for base calling
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus.GRCm38.82 genome using STAR (v. 2.4.0g, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus.GRCm38.82 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Mus musculus.GRCm38.82 transcriptome using STAR (v. 2.4.0g, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.19, Li and Dewey 2011).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated RSEM normalized TPM with Ensembl gene ID

source_name: ßTC3 cells

growth_protocol: ßTC3 cells were plated in 6-well plates in triplicate.

extract_protocol:
Cells were isolated and RNA was harvested using Trizol reagent. TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the 7 days DOX group, cells were cultured in DMEM media containing DOX (2µg/ml) for 7 days. For the DOX OFF group, DOX was withdrawn after 7 days, and were cultured in regular DMEM media for another 7 days. No DOX groups were cultured for 7 days in regular DMEM media.

tag: cell line

tag: plasmid

tag: group

tag: treatment

value: 7 Days DOX OFF

tag: replicate


title: PB31-miR137 7 days OFF # 2


title: Lgr5-EGFP-IRES-CreERT2, pylorus, Lgr5Hi, biological rep 1


title: PB31-miR137 7 days ON # 2

value: 7 days DOX


title: PB31-miR137 7 days OFF # 1


title: PB31-miR137 7 days ON # 3


title: PB31-miR137 7 days ON # 1


title: PB31-miR137 no dox # 3

value: no DOX


title: PB31-miR137 no dox # 1


title: T_Pre_AB_5


title: T_Pre_AB_6


title: T_Pre_AB_3


title: PB31-miR23b cluster 7 days OFF # 3

value: PB-31 miR-23b cluster

value: miR-23b cluster


title: T_Pre_AB_4


title: PB31-miR23b cluster 7 days OFF # 2


title: PB31-miR23b cluster 7 days ON # 3


title: PB31-miR23b cluster 7 days ON # 2


title: PB31-miR23b cluster 7 days OFF # 1


title: T_Pre_AB_2


title: T_IMG_7

value: Immature T-ALL (TR gamma rearrangement)


title: PB31-miR23b cluster no dox # 3


title: PB31-miR23b cluster 7 days ON # 1


title: T_IMG_6


title: PB31-miR137 no dox # 2


title: T_IMG_3


title: T_IMG_5


title: PB31-miR23b cluster no dox # 2


title: T_IMG_4


title: T_Pre_AB_1


title: T_IMG_2


title: PB31 7 days ON # 1

value: Control cells


title: PB31 7 days ON # 2


title: PB31 7 days ON # 3


title: PB31 no dox # 3


title: PB31 no dox # 2


title: PB31-miR23b cluster no dox # 1


title: PB31 no dox # 1


title: T_IMD_6

value: Immature T-ALL (TR delta rearrangement)


title: T_IMD_5


title: T_IMD_4


title: T_IMD_7


title: T_IMD_8


title: T_IMG_1


title: T_IMD_3


title: T_IMD_1


title: T_IMB_8

value: Immature T-ALL (TR beta rearrangement)


title: T_IMD_2


title: T_IMB_9


title: T_IMB_6


title: T_IMG_8


title: T_IMB_4


title: T_IMB_2


title: T_IMB_3


title: T_IMB_5


title: T_IMB_1


title: T_IM0_8

value: Immature T-ALL (no TR rearrangement)


title: T_IMD_9

value: T-ALL


title: T_IM0_6


title: TNBC sample46

city: Tampa

first: Douglas

last: Marchion

state: Florida

address: 12902 Magnolia Drive

department: Clinical Science Lab

institute: Moffitt Cancer Center

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).

source_name: TNBC 46 breast cancer tissue

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: breast cancer

tag: type

value: TNBC


title: TNBC sample53

source_name: TNBC 53 breast cancer tissue


title: TNBC sample51

source_name: TNBC 51 breast cancer tissue


title: TNBC sample47

source_name: TNBC 47 breast cancer tissue


title: TNBC sample50

source_name: TNBC 50 breast cancer tissue


title: TNBC sample40

source_name: TNBC 40 breast cancer tissue


title: T_IM0_11


title: TNBC sample44

source_name: TNBC 44 breast cancer tissue


title: T_IM0_1


title: TNBC sample49

source_name: TNBC 49 breast cancer tissue


title: TNBC sample39

source_name: TNBC 39 breast cancer tissue


title: T_IM0_3

source_name: Bone marrow


title: T_IM0_4


title: TNBC sample42

source_name: TNBC 42 breast cancer tissue


title: T_IM0_7


title: TNBC sample38

source_name: TNBC 38 breast cancer tissue


title: T_GD_4

value: T-ALL (gamma delta expression)

value: M


title: TNBC sample43

source_name: TNBC 43 breast cancer tissue


title: T_IM0_2

value: L


title: T_GD_2

value: Bone marrow


title: TNBC sample41

source_name: TNBC 41 breast cancer tissue


title: TNBC sample37

source_name: TNBC 37 breast cancer tissue


title: T_GD_3


title: TNBC sample35

source_name: TNBC 35 breast cancer tissue


title: T_GD_1


title: TNBC sample36

source_name: TNBC 36 breast cancer tissue


title: TNBC sample48

source_name: TNBC 48 breast cancer tissue


title: T_IM0_5


title: T_AB_4

value: T-ALL (alpha beta lineage)


title: T_AB_3


title: T_AB_1


title: TNBC sample34

source_name: TNBC 34 breast cancer tissue


title: T_AB_2


title: TNBC sample29

source_name: TNBC 29 breast cancer tissue


title: TNBC sample31

source_name: TNBC 31 breast cancer tissue


title: TNBC sample32

source_name: TNBC 32 breast cancer tissue


title: TNBC sample28

source_name: TNBC 28 breast cancer tissue


title: TNBC sample27

source_name: TNBC 27 breast cancer tissue


title: TNBC sample25

source_name: TNBC 25 breast cancer tissue


title: TNBC sample26

source_name: TNBC 26 breast cancer tissue


title: TNBC sample22

source_name: TNBC 22 breast cancer tissue


title: CD34+ CD1a+_2

source_name: Neonatal thymus

treatment_protocol: Neonatal thymi cell suspension were made, populations were flow-sorted according to markers reported in the literature

tag: developmental stage

value: neonate

value: thymus


title: CD34+ CD1a- CD7-_1


title: CD34+ CD1a- CD7+_2


title: CD34+ CD1a- CD7-_3


title: TNBC sample24

source_name: TNBC 24 breast cancer tissue


title: CD34+ CD1a+_1


title: CD34+ CD1a- CD7-_2


title: TNBC sample21

source_name: TNBC 21 breast cancer tissue


title: CD34+ CD1a- CD7+_1


title: TNBC sample16

source_name: TNBC 16 breast cancer tissue


title: TNBC sample18

source_name: TNBC 18 breast cancer tissue


title: CD4 ISP_1

value: CD45+ CD3- CD8- CD4+ CD1a+


title: TNBC sample20

source_name: TNBC 20 breast cancer tissue


title: TNBC sample15

source_name: TNBC 15 breast cancer tissue


title: CD4 ISP_2


title: U2OS cells, WEE1i AZD1775, late

first: Hatice

middle: Ulku

last: Osmanbeyoglu

address: 5117 Centre Ave

data_processing:
Library strategy: Repli-seq
Raw Repli-seq reads were trimmed and filtered for quality using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned using bowtie2 (Langmead B & Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357-359.) against GRCh38(hg38). 13(5):819-839.).
Genome-wide replication timing (RT) profiles were constructed, scaled and pooled for analysis as previously described (Marchal C, et al. (2018) Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc
Briefly, Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph Genome-wide replication timing (RT) profiles: Log2 ratios of early versus late read counts were calculated for 50kb non-overlapping windows, Loess smoothed at 300kb windows.

source_name: U2OS cells

growth_protocol: RPMI supplemented with 10% FBS and pen/strep.

extract_protocol:
cells were fixed with EtOH, stained with PI, sorted into "early" and "late" S-phase based on DNA content, genomic DNA was extracted, sonicated, BrdU-labeled fragments were immunoprecipitated with an antibody
NEBNext kit (NEB#7370S) was used according to manufacturer's instructions. BrdU IP was performed after the end processing step and before indexing.

treatment_protocol: U2OS cells were treated with DMSO or 500nM AZD1775 for 30 minutes before labelling of the ongoing replication with 10uM BrdU.

tag: cell type

value: osteosarcoma

value: treated with 500nM AZD1775

tag: time point

value: late


title: TNBC sample17

source_name: TNBC 17 breast cancer tissue

tag: tissue


title: CD34+ CD1a+_3


title: U2OS cells, WEE1i AZD1775, early

value: early


title: U2OS cells, control, late

value: treated with DMSO


title: U2OS cells, control, early


title: DP TR Low_2

value: CD45hi CD4+ CD8+ TCRab_lo CD3-


title: DP TR High_1

value: CD45hi CD4+ CD8+ TCRab_hi CD3+


title: DP TR Low_1


title: TNBC sample14

source_name: TNBC 14 breast cancer tissue

value: breast cancer


title: S12 AQP5-

city: Singapore

first: Si Hui

last: Tan

address: 8A Biomedical Grove #06-06 Immunos

country: Singapore

institute: Institute of Medical Biology

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set12_Minus

data_processing:
Illumina Real-Time Analysis (RTA) software
Read Mapping: STAR version 2.5.3a with the following options issued: --outFilterType BySJout, --outFilterMultimapNmax 10, --alignSJoverhangMin 15, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 12, --outFilterMatchNminOverLread 0.4, --alignIntronMin 20, --alignIntronMax 2000000, --outSAMattrIHstart 0, --outSAMmapqUnique 244, --outMultimapperOrder Random, --outReadsUnmapped None, --outFilterIntronMotifs None, --outSAMmode Full, --outSAMattributes All --quantMode GeneCounts, --clip3pAdapterSeq AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
Counts per sample were concatenated in R version 3.2.3
Read Normalisation: TMM normalisation as implemented in edgeR version 3.12.1 (with limma_3.26.9).
Differential expression testing was performed with the edgeR function “glmQLFit” using a design matrix that took sample batches and AQP5 status into account.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text file include normalized read counts for individual samples, log2 fold change and FDR across AQP5+ and AQP5- samples.

source_name: Gastric pylorus

growth_protocol: Healthy pylorus tissue was resected from patients undergoing surgery to remove gastric tumour. Resected tissue was collected in Advanced DMEM/F-12 media with 10mM HEPES, 2mM Glutamax (incubation buffer, all from Life Technologies), supplemented with 1X Anti-Anti (Life Technologies) and 1mM N-acetylcysteine (Sigma).

extract_protocol:
After at least three washes in HBSS, the pylorus was chopped finely and digested in incubation buffer supplemented with 1mg/mL Collagenase (Gibco) and 2mg/mL Bovine Serum Albumin (Sigma) for 30min at 37oC with intermittent mixing. Glands were isolated by repeated pipetting of finely chopped pylorus tissue in cold chelation buffer. Chelation buffer containing isolated glands was filtered through 100μm filter mesh, and centrifuged at 720g at 4oC for 3 min. The pellet was resuspended in TrypLE (Life Technologies) with DNaseI (0.8U/μL)(Sigma) and incubated at 37oC for 10 min with intermittent trituration for digestion into single cells. Digestion was quenched by dilution with cold HBSS buffer. The suspension was centrifuged at 720g at 4oC for 3 min. For anti-Aqp5 antibody stain, the pellet was resuspended in HBSS with 2% fetal bovine serum (FBS, Hyclone) with anti-Aqp5-AF647 (Abcam, ab215225) at 1:500 dilution and incubated on ice at 30min in the dark. The pellet was subsequently washed twice with cold HBSS and spun at 800g for 3min at 4oC. The pellet was resuspended in HBSS with 2% fetal bovine serum (FBS, Hyclone). Before sorting, 1 μg/ml propidium iodide (Life Technologies) was added to the cell suspensions, filtered through a 40μm strainer, and sorted on BD Influx Cell Sorter (BD Biosciences). Cells were collected in RLT Plus buffer (Qiagen) for subsequent RNA extraction with RNeasy Micro Kit according to manufacturer's instructions.
Library was constructed with 10ng of input RNA using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian according to manufacturer's instructions.

tag: health status

value: Normal

tag: aqp5 expression


title: S13 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set13_Minus


title: S14 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set14_Minus


title: TNBC sample13

source_name: TNBC 13 breast cancer tissue

value: TNBC


title: S11 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set11_Minus


title: DP TR High_2


title: DP TR High_3


title: TNBC sample10

source_name: TNBC 10 breast cancer tissue


title: J4 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: AQP5_Minus


title: TNBC sample9

source_name: TNBC 9 breast cancer tissue


title: TNBC sample12

source_name: TNBC 12 breast cancer tissue


title: Chick_Fgf8+_3

city: Boston

first: Ryoji

last: Amamoto

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Cellular RNA

data_processing:
Quality control of RNA-seq reads were performed using fastqc version 0.10.1
RNA-seq reads were clipped and mapped onto onto the either the mouse genome (Ensembl GRCm38.90), chick genome (Ensembl GRCg6a.96), or Drosophila genome (BDGP6.22) using STAR version 2.5.2b. Parameters used were as follows: --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --clip3pAdapterSeq  --quantMode TranscriptomeSAM GeneCounts
Read counts were generated by HT-seq version 0.9.1. Sample parameters used were as follows: -i gene_name -s no
Genome_build: Ensembl GRCm38.90, Ensembl GRCg6a.96, BDGP6.22
Supplementary_files_format_and_content: Text files with the read counts for every gene for each sample.

organism: Gallus gallus

source_name: Chick Retina

extract_protocol:
The tissue was dissociated fresh or the tissue was frozen. Cells or nuclei were extracted, fixed, and labeled with appropriate SABER FISH probes. Specific cellular or nuclear populations were FACS isolated and the RNA was extracted from the cells or nuclei using the RecoverAll Kit. For live cells, Grik1-GFP plasmid was electroporated at P2 into the developing mouse retina. The retina was harvested at P40, and the cells were dissociated. GFP+ cells were FACS isolated into Trizol. The RNA was extracted based upon Trizol manual.
cDNA was generated using the SMART-Seq v.4 kit. The indices were added using the Nextera XT Kit.

tag: strain

value: White Leghorn

value: retina

tag: age

tag: rna marker


title: TNBC sample8

source_name: TNBC 8 breast cancer tissue


title: TNBC sample6

source_name: TNBC 6 breast cancer tissue


title: TNBC sample5

source_name: TNBC 5 breast cancer tissue


title: TNBC sample7

source_name: TNBC 7 breast cancer tissue


title: J3 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S3 (AQP5-)


title: Chick_Fgf8+_2

description: Cellular RNA


title: Chick_Fgf8+_1

description: Cellular RNA


title: Chick_Fgf8-_3

description: Cellular RNA


title: Chick_Fgf8-_2

description: Cellular RNA


title: Chick_Fgf8-_1

description: Cellular RNA


title: J2 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S2 (AQP5-)


title: Drosophila_esg+_3

description: Cellular RNA

organism: Drosophila melanogaster

source_name: Drosohpila midgut

value: Oregon-R

value: midgut

value: 7-10 days

value: esg+


title: J1 AQP5-

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S1 (AQP5-)


title: S14 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set14_Plus


title: Drosophila_esg+_2

description: Cellular RNA


title: Drosophila_esg+_1

description: Cellular RNA


title: Drosophila_esg-_3

description: Cellular RNA

value: esg-


title: Drosophila_esg-_2

description: Cellular RNA


title: Drosophila_esg-_1

description: Cellular RNA


title: S12 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set12_Plus


title: S13 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set13_Plus


title: TNBC sample3

source_name: TNBC 3 breast cancer tissue


title: TNBC sample1

source_name: TNBC 1 breast cancer tissue


title: S11 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: Set11_Plus


title: TNBC sample4

source_name: TNBC 4 breast cancer tissue


title: non-TNBC sample52

source_name: non-TNBC 52 breast cancer tissue

value: non-TNBC


title: non-TNBC sample53

source_name: non-TNBC 53 breast cancer tissue


title: TNBC sample2

source_name: TNBC 2 breast cancer tissue


title: MTG_AD_rep161

type: genomic

description: SAMPLE 161

hyb_protocol: (Oxidative) Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged with the Illumina iScan using standard recommended Illumina scanner settings.

data_processing:
Raw idat files from the scanner were used to determine the signal intensities with the minfi R package.
the 'MTG_processed_GA_illumina_methylation.txt' contains Average Beta (also determined with minfi) data.
the 'MTG_signal_intensities_GA_illumina_methylation.txt' contains Unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: middle temporal gyrus_AD

extract_protocol: Phenol-chloroform-isoamyl alcohol extraction combined with ethanol precipitation was used to isolate gDNA.

treatment_protocol: Tissue was frozen before DNA extraction.

tag: gender

value: Male

tag: disease state

value: AD

value: brain; middle temporal gyrus

tag: conversion

value: oxBS


title: non-TNBC sample51

source_name: non-TNBC 51 breast cancer tissue


title: MTG_Control_rep159

description: SAMPLE 159

source_name: middle temporal gyrus_Control

value: Control


title: MTG_Control_rep160

description: SAMPLE 160

value: Female


title: MTG_AD_rep157

description: SAMPLE 157


title: MTG_AD_rep158

description: SAMPLE 158


title: MTG_Control_rep156

description: SAMPLE 156


title: non-TNBC sample49

source_name: non-TNBC 49 breast cancer tissue

value: breast cancer


title: MTG_AD_rep162

description: SAMPLE 162


title: non-TNBC sample50

source_name: non-TNBC 50 breast cancer tissue


title: J4 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: AQP5_Plus

source_name: Gastric pylorus

value: Normal


title: J3 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S6 (AQP5+)


title: non-TNBC sample48

source_name: non-TNBC 48 breast cancer tissue


title: non-TNBC sample47

source_name: non-TNBC 47 breast cancer tissue


title: MTG_AD_rep155

description: SAMPLE 155


title: J2 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S5 (AQP5+)


title: MTG_Control_rep154

description: SAMPLE 154


title: MTG_AD_rep153

description: SAMPLE 153


title: J1 AQP5+

description:
DifferentialExpression_AQP5_RNAseq_forGEO.txt
processed data header: S4 (AQP5+)


title: MTG_AD_rep151

description: SAMPLE 151


title: MTG_AD_rep150

description: SAMPLE 150


title: MTG_AD_rep152

description: SAMPLE 152


title: non-TNBC sample46

source_name: non-TNBC 46 breast cancer tissue


title: RB3

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

description: Illumina HiSeq 4000 (scRNA-seq), Illumina HiSeq 2500 (scTCR-seq)

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count" using a custom reference package of 30,727 genes from RefSeq gene models
TCR data processed with "cellranger vdj" and the custom reference package
Genome_build: GRCh38
Supplementary_files_format_and_content: Cellranger version 2.2.0

source_name: CD45+ immune cells

extract_protocol:
Surgical resections procured and separated into tumor and NAT compartments by reviewing pathologist.  Samples rinsed with PBS, digested with Collagenase D and DNAse from 15 minutes at 37° C, and subjected to a gentleMACS dissociator, followed by an additional 10-minute incubation at 37° C.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit
PolyA priming for single-cell RNA-seq.  TCR enrichment using the Chromium Single Cell V(D)J Enrichment Kit, Human T cell

treatment_protocol: Pre-treatment samples

tag: patient

tag: region

value: Blood

tag: phenotype

value: Renal cell carcinoma, clear cell


title: MTG_Control_rep148

description: SAMPLE 148


title: MTG_Control_rep145

description: SAMPLE 145


title: MTG_Control_rep144

description: SAMPLE 144


title: RN3

value: Normal adjacent tissue


title: RT3

value: Tumor


title: RB2


title: MTG_AD_rep146

description: SAMPLE 146


title: MTG_Control_rep142

description: SAMPLE 142


title: MTG_Control_rep141

description: SAMPLE 141


title: MTG_Control_rep143

description: SAMPLE 143


title: non-TNBC sample44

source_name: non-TNBC 44 breast cancer tissue


title: RN2


title: non-TNBC sample45

source_name: non-TNBC 45 breast cancer tissue


title: RT2


title: MTG_Control_rep140

description: SAMPLE 140


title: MTG_AD_rep139

description: SAMPLE 139


title: MTG_Control_rep147

description: SAMPLE 147


title: MTG_AD_rep149

description: SAMPLE 149


title: RB1


title: non-TNBC sample42

source_name: non-TNBC 42 breast cancer tissue


title: MTG_Control_rep138

description: SAMPLE 138


title: non-TNBC sample43

source_name: non-TNBC 43 breast cancer tissue


title: non-TNBC sample39

source_name: non-TNBC 39 breast cancer tissue


title: non-TNBC sample41

source_name: non-TNBC 41 breast cancer tissue


title: non-TNBC sample40

source_name: non-TNBC 40 breast cancer tissue


title: non-TNBC sample38

source_name: non-TNBC 38 breast cancer tissue


title: MTG_AD_rep136

description: SAMPLE 136

source_name: middle temporal gyrus_AD


title: non-TNBC sample37

source_name: non-TNBC 37 breast cancer tissue


title: MTG_Control_rep137

description: SAMPLE 137

source_name: middle temporal gyrus_Control


title: MTG_AD_rep135

description: SAMPLE 135


title: RN1


title: MTG_AD_rep132

description: SAMPLE 132


title: MTG_AD_rep131

description: SAMPLE 131


title: CT2

value: Colorectal adenocarcinoma


title: MTG_AD_rep130

description: SAMPLE 130


title: RT1


title: MTG_AD_rep134

description: SAMPLE 134


title: CN2


title: MTG_AD_rep129

description: SAMPLE 129


title: MTG_Control_rep128

description: SAMPLE 128


title: MTG_Control_rep127

description: SAMPLE 127


title: MTG_Control_rep133

description: SAMPLE 133


title: CN1


title: CT1


title: MTG_AD_rep126

description: SAMPLE 126


title: non-TNBC sample34

source_name: non-TNBC 34 breast cancer tissue


title: non-TNBC sample35

source_name: non-TNBC 35 breast cancer tissue


title: MTG_AD_rep124

description: SAMPLE 124


title: non-TNBC sample32

source_name: non-TNBC 32 breast cancer tissue


title: MTG_AD_rep125

description: SAMPLE 125


title: EN3

source_name: CD3+ immune cells

value: Endometrial adenocarcinoma


title: MTG_Control_rep123

description: SAMPLE 123

value: BS


title: non-TNBC sample36

source_name: non-TNBC 36 breast cancer tissue


title: MTG_Control_rep122

description: SAMPLE 122


title: ET3


title: MTG_Control_rep119

description: SAMPLE 119


title: EN2


title: MTG_AD_rep120

description: SAMPLE 120


title: MTG_AD_rep121

description: SAMPLE 121


title: MTG_AD_rep118

description: SAMPLE 118


title: MTG_AD_rep117

description: SAMPLE 117


title: EN1


title: ET2


title: MTG_Control_rep116

description: SAMPLE 116


title: MTG_Control_rep114

description: SAMPLE 114


title: MTG_AD_rep115

description: SAMPLE 115


title: ET1


title: MTG_Control_rep113

description: SAMPLE 113


title: MTG_Control_rep112

description: SAMPLE 112


title: LB6

source_name: CD45+ immune cells

value: Large cell neuroendocrine carcinoma


title: MTG_Control_rep111

description: SAMPLE 111


title: non-TNBC sample33

source_name: non-TNBC 33 breast cancer tissue

value: non-TNBC


title: LN6


title: non-TNBC sample29

source_name: non-TNBC 29 breast cancer tissue


title: MTG_Control_rep108

description: SAMPLE 108


title: MTG_AD_rep110

description: SAMPLE 110

value: Male


title: MTG_AD_rep109

description: SAMPLE 109

value: AD


title: LT6


title: MTG_AD_rep107

description: SAMPLE 107

value: brain; middle temporal gyrus


title: TNBC sample11

source_name: TNBC 11 breast cancer tissue

value: TNBC


title: non-TNBC sample31

source_name: non-TNBC 31 breast cancer tissue


title: non-TNBC sample24

source_name: non-TNBC 24 breast cancer tissue


title: non-TNBC sample30

source_name: non-TNBC 30 breast cancer tissue


title: non-TNBC sample27

source_name: non-TNBC 27 breast cancer tissue


title: MTG_Control_rep105

description: SAMPLE 105

value: Control

value: oxBS


title: non-TNBC sample28

source_name: non-TNBC 28 breast cancer tissue

value: breast cancer


title: non-TNBC sample25

source_name: non-TNBC 25 breast cancer tissue


title: LN5

value: Lung adenocarcinoma


title: LT5


title: MTG_AD_rep104

description: SAMPLE 104

source_name: middle temporal gyrus_AD

value: Female


title: non-TNBC sample26

source_name: non-TNBC 26 breast cancer tissue


title: non-TNBC sample22

source_name: non-TNBC 22 breast cancer tissue


title: non-TNBC sample21

source_name: non-TNBC 21 breast cancer tissue


title: MTG_Control_rep102

description: SAMPLE 102

source_name: middle temporal gyrus_Control


title: LN4

source_name: CD3+ immune cells


title: MTG_AD_rep101

description: SAMPLE 101


title: LT4


title: MTG_AD_rep100

description: SAMPLE 100


title: MTG_AD_rep106

description: SAMPLE 106


title: MTG_Control_rep99

description: SAMPLE 99


title: LN3

value: Lung squamous cell carcinoma, keratinizing


title: MTG_AD_rep98

description: SAMPLE 98


title: non-TNBC sample20

source_name: non-TNBC 20 breast cancer tissue


title: MTG_Control_rep96

description: SAMPLE 96


title: non-TNBC sample23

source_name: non-TNBC 23 breast cancer tissue


title: MTG_AD_rep94

description: SAMPLE 94


title: MTG_AD_rep95

description: SAMPLE 95


title: MTG_Control_rep93

description: SAMPLE 93


title: MTG_AD_rep92

description: SAMPLE 92


title: non-TNBC sample19

source_name: non-TNBC 19 breast cancer tissue


title: LT2

value: Lung squamous cell carcinoma, nonkeratinizing


title: non-TNBC sample18

source_name: non-TNBC 18 breast cancer tissue


title: non-TNBC sample16

source_name: non-TNBC 16 breast cancer tissue


title: LN2

value: Normal adjacent tissue


title: non-TNBC sample17

source_name: non-TNBC 17 breast cancer tissue


title: MTG_AD_rep91

description: SAMPLE 91


title: LN1


title: MTG_AD_rep97

description: SAMPLE 97


title: MTG_Control_rep89

description: SAMPLE 89


title: MTG_AD_rep90

description: SAMPLE 90


title: LT1

value: Tumor


title: MTG_AD_rep87

description: SAMPLE 87


title: MTG_Control_rep85

description: SAMPLE 85


title: MTG_Control_rep88

description: SAMPLE 88


title: MTG_AD_rep86

description: SAMPLE 86


title: LT3


title: non-TNBC sample14

source_name: non-TNBC 14 breast cancer tissue


title: non-TNBC sample15

source_name: non-TNBC 15 breast cancer tissue


title: MTG_Control_rep83

description: SAMPLE 83


title: MTG_AD_rep84

description: SAMPLE 84


title: MTG_AD_rep82

description: SAMPLE 82


title: MTG_AD_rep80

description: SAMPLE 80


title: MTG_AD_rep79

description: SAMPLE 79


title: MTG_Control_rep103

description: SAMPLE 103


title: MTG_Control_rep78

description: SAMPLE 78


title: MTG_AD_rep75

description: SAMPLE 75


title: MTG_AD_rep74

description: SAMPLE 74


title: MTG_AD_rep76

description: SAMPLE 76


title: MTG_Control_rep77

description: SAMPLE 77


title: non-TNBC sample13

source_name: non-TNBC 13 breast cancer tissue


title: MTG_Control_rep72

description: SAMPLE 72


title: pt257: Tumour_normal_rep37.2

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

hyb_protocol: Labelled cRNA was then hybridized to the Agilent SurePrint G3 gene expression 8 × 60 K microarray (AMADID: 047718).

scan_protocol: Arrays were washed and scanned on an Agilent G2565CA microarray scanner at 100% R+G PMT, 3μm resolution and 20 bit TIFF with no XDR. Agilent Feature Extraction Software (version 11.0.1.1) was used for images adquisition and intensity data extraction.

data_processing: Raw data were corrected for background noise using the normexp method and normalized using the loess method in Limma.

source_name: Fresh frozen tissue

label_protocol: 100 ng of total RNA was labeled using Low Input Quick Amp Labeling (protocol v6.7) following manufacturer's instructions. Tumour samples were labelled with Cy3 and Cy5 was used with normal tissue.

extract_protocol: Total RNA was extracted using Direct-zol mini kit (ZymoResearch) following manufacturer's instructions. RNA concentration and purity was determined by OD at 260/280/230 nm readings using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). RNA integrity was determined using the RNA 6000 Nano Lab-on-a-Chip kit on a Bioanalyzer 2100 (Agilent Technologies).

value: Tumour

value: M

tag: histology

value: squamous cell carcinoma

tag: tumour stage

tag: node stage

tag: differentiation

value: Moderate

value: Normal


title: non-TNBC sample10

source_name: non-TNBC 10 breast cancer tissue

tag: type

value: non-TNBC


title: non-TNBC sample11

source_name: non-TNBC 11 breast cancer tissue

tag: tissue


title: non-TNBC sample12

source_name: non-TNBC 12 breast cancer tissue


title: MTG_AD_rep81

description: SAMPLE 81

source_name: middle temporal gyrus_AD

value: AD

value: brain; middle temporal gyrus


title: pt236: Tumour_normal_rep28.2

value: adenocarcinoma


title: MTG_Control_rep71

description: SAMPLE 71

value: Control

value: BS


title: non-TNBC sample9

source_name: non-TNBC 9 breast cancer tissue

value: breast cancer


title: MTG_Control_rep70

description: SAMPLE 70

source_name: middle temporal gyrus_Control

value: Female


title: non-TNBC sample5

source_name: non-TNBC 5 breast cancer tissue


title: non-TNBC sample6

source_name: non-TNBC 6 breast cancer tissue


title: pt187: Tumour_normal_rep12.2

value: Poor


title: MTG_Control_rep69

description: SAMPLE 69

value: Male


title: pt289: Tumour_normal_rep42

value: Well


title: non-TNBC sample4

source_name: non-TNBC 4 breast cancer tissue


title: MTG_Control_rep73

description: SAMPLE 73

value: oxBS


title: MTG_Control_rep67

description: SAMPLE 67


title: Mouse_Probe-Seq_Cell_Grik1+_3

description: Cellular RNA

source_name: Mouse Retina

value: retina

value: Adult (>P30)


title: non-TNBC sample7

source_name: non-TNBC 7 breast cancer tissue


title: pt291: Tumour_normal_rep43

value: Tumour

value: M

value: squamous cell carcinoma


title: Mouse_Probe-Seq_Cell_Grik1+_2

description: Cellular RNA


title: MTG_AD_rep64

description: SAMPLE 64


title: MTG_AD_rep65

description: SAMPLE 65


title: MTG_AD_rep63

description: SAMPLE 63


title: pt265: Tumour_normal_rep40

value: Moderate

value: Normal


title: MTG_AD_rep68

description: SAMPLE 68

value: AD

value: brain; middle temporal gyrus


title: MTG_AD_rep62

description: SAMPLE 62


title: MTG_AD_rep61

description: SAMPLE 61


title: non-TNBC sample3

source_name: non-TNBC 3 breast cancer tissue

value: non-TNBC


title: non-TNBC sample8

source_name: non-TNBC 8 breast cancer tissue


title: Mouse_Probe-Seq_Cell_Grik1+_1

description: Cellular RNA


title: pt283: Tumour_normal_rep41

value: F


title: pt308: Tumour_normal_rep44

value: adenocarcinoma


title: MTG_Control_rep66

description: SAMPLE 66

value: Control

value: BS


title: pt259: Tumour_normal_rep39

value: Poor


title: MTG_AD_rep59

description: SAMPLE 59

value: Female


title: MTG_Control_rep60

description: SAMPLE 60

value: Male


title: MTG_AD_rep58

description: SAMPLE 58


title: pt257: Tumour_normal_rep37.1


title: pt255: Tumour_normal_rep36


title: MTG_Control_rep57

description: SAMPLE 57


title: Mouse_Live_Cell_Grik1+_3

description: Cellular RNA

value: retina


title: non-TNBC sample2

source_name: non-TNBC 2 breast cancer tissue

value: breast cancer


title: pt258: Tumour_normal_rep38

value: Tumour


title: MTG_AD_rep56

description: SAMPLE 56


title: Mouse_Live_Cell_Grik1+_2

description: Cellular RNA

value: Adult (>P30)


title: MTG_AD_rep55

description: SAMPLE 55


title: non-TNBC sample1

source_name: non-TNBC 1 breast cancer tissue


title: Mouse_Live_Cell_Grik1+_1

description: Cellular RNA


title: MTG_AD_rep54

description: SAMPLE 54


title: pt253: Tumour_normal_rep35

value: M


title: pt250: Tumour_normal_rep34

value: squamous cell carcinoma

value: Moderate


title: Mouse_Whole_Cell_Vsx2-_2

description: Cellular RNA


title: pt245: Tumour_normal_rep33

value: Normal


title: MTG_Control_rep53

description: SAMPLE 53

value: brain; middle temporal gyrus


title: MTG_Control_rep51

description: SAMPLE 51

value: oxBS


title: Mouse_Whole_Cell_Vsx2-_1

description: Cellular RNA


title: MTG_Control_rep49

description: SAMPLE 49


title: MTG_Control_rep50

description: SAMPLE 50


title: Mouse_Whole_Cell_Grik1+_2

description: Cellular RNA


title: MTG_Control_rep48

description: SAMPLE 48


title: MTG_AD_rep45

description: SAMPLE 45

value: AD


title: MTG_AD_rep46

description: SAMPLE 46


title: pt240: Tumour_normal_rep31

value: F


title: Mouse_Whole_Cell_Grik1-_2

description: Cellular RNA


title: Mouse_Whole_Cell_Grik1+_1

description: Cellular RNA


title: MTG_AD_rep43

description: SAMPLE 43


title: Mouse_Nuclei_Grik1+_C

description: Nuclear RNA


title: MTG_AD_rep52

description: SAMPLE 52


title: MTG_Control_rep42

description: SAMPLE 42

value: Control


title: MTG_AD_rep40

description: SAMPLE 40

value: BS


title: MTG_AD_rep39

description: SAMPLE 39


title: Mouse_Nuclei_Grik1+_7

description: Nuclear RNA


title: MTG_AD_rep38

description: SAMPLE 38


title: pt239: Tumour_normal_rep30


title: Mouse_Nuclei_Grik1+_6

description: Nuclear RNA


title: pt236: Tumour_normal_rep28.1

value: adenocarcinoma


title: MTG_AD_rep47

description: SAMPLE 47

value: Female


title: pt243: Tumour_normal_rep32

value: Poor


title: pt234: Tumour_normal_rep26


title: pt238: Tumour_normal_rep29


title: Mouse_Nuclei_Grik1-_C

description: Nuclear RNA

value: retina


title: MTG_AD_rep41

description: SAMPLE 41


title: MTG_AD_rep33

description: SAMPLE 33

value: Male


title: MTG_Control_rep37

description: SAMPLE 37


title: MTG_Control_rep32

description: SAMPLE 32


title: Mouse_Nuclei_Grik1-_6

description: Nuclear RNA


title: MTG_AD_rep34

description: SAMPLE 34


title: pt220: Tumour_normal_rep23

value: Tumour

value: Well


title: Mouse_Whole_Cell_Grik1-_1

description: Cellular RNA

value: Adult (>P30)


title: MTG_Control_rep36

description: SAMPLE 36


title: B_breve_CLA_3A

city: Piacenza

first: Maria Luisa

last: Callegari

state: Piacenza

address: via Emilia Parmense

department: DISTAS

country: Italy

institute: Università Cattolica del Sacro Cuore

description:
replicate 3
CLA_3A

data_processing:
SOAPnuke
FASTQ
HISAT
Bowtie2
RSEM
Genome_build: Bifbre
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.txt

organism: Bifidobacterium breve DSM 20213 = JCM 1192

growth_protocol: MRS-cys, MRS-cys-linoleic acid

extract_protocol:
acidic-phenol/guanidine-isothiocyanate protocol
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription:  Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random  primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair  and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA  fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification  were performed to enrich the purified cDNA template using PCR primer;5)Denature and  cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and  DNA ligase;6) Sequencing on BGISEQ-500 platform.

tag: treatment

value: MRS-cys-linoleic acid


title: pt218: Tumour_normal_rep22

value: Moderate


title: MTG_Control_rep30

description: SAMPLE 30


title: pt235: Tumour_normal_rep27

value: M

value: squamous cell carcinoma

value: Normal


title: pt221: Tumour_normal_rep24


title: MTG_Control_rep31

description: SAMPLE 31

value: brain; middle temporal gyrus


title: MTG_Control_rep29

description: SAMPLE 29


title: pt226: Tumour_normal_rep25

value: F


title: MTG_AD_rep35

description: SAMPLE 35

value: AD


title: MTG_AD_rep27

description: SAMPLE 27

value: BS


title: MTG_AD_rep26

description: SAMPLE 26


title: MTG_Control_rep28

description: SAMPLE 28

value: Control


title: Mouse_Nuclei_Grik1-_7

description: Nuclear RNA


title: B_breve_CLA_2A

description:
replicate 2
CLA_2A


title: MTG_AD_rep25

description: SAMPLE 25


title: MTG_Control_rep24

description: SAMPLE 24


title: B_breve_CLA_1A

description:
replicate 1
CLA_1A


title: B_breve_C_3A

description:
replicate 3
B_breve_3A

value: MRS-cys


title: MTG_AD_rep23

description: SAMPLE 23

value: Female


title: MTG_AD_rep21

description: SAMPLE 21


title: B_breve_C_2A

description:
replicate 2
B_breve_2A


title: MTG_Control_rep18

description: SAMPLE 18


title: MTG_AD_rep17

description: SAMPLE 17


title: MTG_AD_rep19

description: SAMPLE 19


title: MTG_AD_rep20

description: SAMPLE 20


title: B_breve_C_1A

description:
replicate 1
B_breve_1A


title: MTG_Control_rep16

description: SAMPLE 16


title: MTG_Control_rep15

description: SAMPLE 15


title: pt197: Tumour_normal_rep16


title: pt204: Tumour_normal_rep20


title: pt198: Tumour_normal_rep17

value: adenocarcinoma

value: Poor


title: MTG_AD_rep14

description: SAMPLE 14

value: Male


title: pt193: Tumour_normal_rep15

value: Tumour


title: pt206: Tumour_normal_rep21

value: Well


title: pt202: Tumour_normal_rep19


title: pt199: Tumour_normal_rep18


title: MTG_AD_rep13

description: SAMPLE 13


title: MTG_Control_rep12

description: SAMPLE 12


title: RGDhMSC rep 6

first: Andres

middle: Jose

last: Garcia

address: 1106 IBB Building

institute: Georgia Institute of Technology

data_processing:
Normalization and data analysis were performed using the JMP Genomics Basic Expression Workflow
Target gene signals normalized to mean of all genes for particular sample using the mean normalization method in JMP Genomics Basic Expression Workflow

label: EvaGreen

source_name: Explanted tissue from a radial segmental defect treated with peptide-functionalized, hMSC-laden hydrogels for 1 week

label_protocol: PCR assays were performed using a custom array of Taqman primers (ThermoFisher) following the Manufacturer’s instructions. cDNA synthesis was performed on total RNA (100 ng) using the High-Capacity RNA-to-cDNA Kit (Thermo Fisher). Quantitative PCR was performed using Fluidigm 96×96 nanofluidic arrays.

extract_protocol: Total RNA was extracted with RNeasy Plus Micro Kit

tag: peptide

value: RGD


title: MTG_Control_rep22

description: SAMPLE 22


title: RGDhMSC rep 7


title: pt192: Tumour_normal_rep14

source_name: Fresh frozen tissue

value: Moderate


title: pt190: Tumour_normal_rep13

value: M


title: MTG_Control_rep11

description: SAMPLE 11


title: pt187: Tumour_normal_rep12.1

value: squamous cell carcinoma


title: MTG_Control_rep10

description: SAMPLE 10


title: MTG_AD_rep9

description: SAMPLE 9


title: RGDhMSC rep 5


title: RGDhMSC rep 4


title: MTG_AD_rep8

description: SAMPLE 8


title: MTG_AD_rep7

description: SAMPLE 7


title: RGDhMSC rep 3


title: pt185: Tumour_normal_rep11

value: Normal


title: MTG_AD_rep6

description: SAMPLE 6

value: brain; middle temporal gyrus


title: MTG_Control_rep5

description: SAMPLE 5


title: pt182: Tumour_normal_rep10


title: pt175: Tumour_normal_rep9


title: RGDhMSC rep 2


title: RGDhMSC rep 1


title: MTG_Control_rep4

description: SAMPLE 4


title: RDGhMSC rep 8

value: RDG


title: RDGhMSC rep 7


title: pt173: Tumour_normal_rep8

value: F


title: MTG_AD_rep3

description: SAMPLE 3

value: AD

value: BS


title: MTG_AD_rep1

description: SAMPLE 1


title: MTG_AD_rep2

description: SAMPLE 2


title: pt171: Tumour_normal_rep7


title: pt158: Tumour_normal_rep4


title: RDGhMSC rep 6


title: pt167: Tumour_normal_rep6


title: RDGhMSC rep 3


title: RDGhMSC rep 4


title: RDGhMSC rep 2


title: CS-R-3

city: Shanghai

first: Xianghui

last: Chen

address: No. 325 Guohe Rd

department: Department of Pharmaceutical Botany, School of Pharmacy

country: China

institute: Second Military Medical University

description:
ALL_Unigene.FA
ALL_Rpkm.txt

data_processing:
Illumina CASAVA(v1.8.2) software used for basecalling.
Adapter sequences, low quality bases and undetected bases were removed using Trimmomatic (v0.30)
Short reads were assembled by trinity (http://trinityrnaseq.sourceforge.net/). Contigs were clustered by CD-HIT to produce longer contigs (unigenes)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: TXT file of RPKM for all Sample, FASTA file of unigene for all sample

organism: Crocus sativus

source_name: Stigma

extract_protocol:
Total RNA from the three stages of stigmas (RED, -2DAY, and 0DAY) were extracted by grinding the tissue in liquid nitrogen to fine powder and isolated in three biological replicates using 1ml TRIzol reagent. Illumina NEBNext Ultra RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: RED

value: stigma

value: red stigma in closed bud inside the perianth tubes (0.8cm in length)

tag: genotype

value: wild type


title: RDGhMSC rep 5


title: RDGhMSC rep 1


title: CS-R-2

description:
ALL_Unigene.FA
ALL_Rpkm.txt

tag: age


title: MTG_Control_rep44

description: SAMPLE 44

tag: gender

value: Male

value: Control

value: oxBS


title: F2V2, rep2

city: Glasgow

first: Chris

last: Linington

address: 120 University Avenue

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

description: gene expression data from myelinating cultures 18 DIV treated withF2V2

hyb_protocol: Hybridized, washed and stained using GeneTitan hybridization, wash and stain kit for WT Array Plates and GeneTitan Operating Software, and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: GeneTitan scanner

data_processing: Partek Genomics Suite (version 6.6), probeset level data were normalised using GCRMA normalisation and summarised to transcript cluster level using One-Step Tukey's Biweight method.

organism: Rattus norvegicus

source_name: myelinating cultures, 19 DIV

label_protocol: Labelled with biotin using Ambion WT Expression Kit following the Affymetrix GeneChip WT Terminal Labeling kit

growth_protocol: Neurospheres were generated from striata of P1 Sprague-Dawley rats by resuspending enzymatically dissociated cells in 20ml neurosphere media [DMEM/F12 (1:1, DMEM containing 4,500 mg/L glucose), supplemented with 0.105 % NaHCO3, 2 mM glutamine, 5,000 IU/ml penicillin, 5µg/ml streptomycin, 5.0mM HEPES, 0.0001% bovine serum albumin, (all from Invitrogen), 25 µg/ml insulin, 100 µg/ml apotransferrin, 60M putrescine, 20nM progesterone, and 30nM sodium selenite (all from Sigma)] and plating them into a 75 cm3 tissue culture flask. The culture was supplemented with 20ng/ml mouse submaxillary gland epidermal growth factor (R&D Systems) and maintained at 37ºC in a humidified atmosphere of 7% CO2/93% air. Every 2-3 days, 5 ml NSM and 4 µl EGF were added to the flask. Neurosphere-derived astrocytes (NsAs) were obtained by triturating neurospheres and plating them onto Poly-L lysine (PLL, 13g/ml, Sigma) -coated coverslips (13 mm diameter, VWR International, Leicestershire, UK) in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine (Sigma) until they formed confluent monolayer.      Myelinating spinal cord cultures were derived from E15.5 Sprague-Dawley (SD) embryos. Spinal cords were dissected out, cleared of meninges, minced with a scalpel blade and enzymatically dissociated with 2.5% trypsin (Invitrogen) and 1.33% collagenase (ICN Pharmaceuticals, UK). Enzymatic activity was stopped by adding 1 ml of a solution containing 0.52 mg/ml soybean trypsin inhibitor, 3.0 mg/ml bovine serum albumin, and 0.04 mg/ml DNase (Sigma). The tissue was then triturated, centrifuged and resuspended in plating medium (PM, 50% DMEM, 25% horse serum, 25% HBSS) and 150,000 cells per 100 µl plated on cover slips coated with a confluent monolayer of NsAs. Coverslips were placed in 35-mm Petri dishes (3 per dish) and left in the incubator to attach for 2 hours, after which 300 µl of PM and 500 µl of differentiation medium (DM) [DMEM (4,500 mg/ml glucose), 10 ng/ml biotin, 0.5% hormone mixture (1 mg/ml apotransferrin, 20 mM Putrescine, 4 μM progesterone, and 6 μM selenium; formulation based on Bottenstein and Sato, 197940), 50 nM hydrocortisone, and 0.1 μg/ml insulin (all reagents from Sigma) ] were added. Cultures were fed every 2 days by removing 500 µl of media and replacing it with fresh DM media, after 12 days insulin was removed from the DM used to feed the cultures.  The effect of FGF2 variants on these in vitro myelinating cultures was investigated by adding them to the culture media from day 18 (i.e. when myelination has just begun)for 24 hoursin vitro.

extract_protocol: RNA was extracted using the Qiagen Rneasy Micro kit according to manufacturer's instructions

treatment_protocol: The in vitro myelinating cultures were either untreated or treated with hFGF2, wtFGF2 or F2V2. Samples were collected at 24 hours from the untreated and treated myelinating cultures.

tag: strain

value: Sprague-Dawley


title: F2V2, rep3


title: F2V2, rep4


title: wtFGF2, rep4

description: gene expression data from myelinating cultures 18 DIV treated with wt FGF2


title: GFOGERhMSC rep 8

value: GFOGER


title: pt157: Tumour_normal_rep3

value: Tumour

value: M

value: adenocarcinoma

value: Moderate


title: CS-2d-3

description:
ALL_Unigene.FA
ALL_Rpkm.txt

value: -2 DAY

value: two days before anthesis, dark red stigma in closed bud inside the perianth tubes (3cm)


title: CS-R-1

description:
ALL_Unigene.FA
ALL_Rpkm.txt


title: F2V2, rep1


title: GFOGERhMSC rep 7


title: TNF+ATRA 1

city: Santiago de Compostela

first: Carmen

last: Conde

state: A Coruña

address: Choupana s/n

institute: Hospital Clinico Universitario

description: Gene expression in pool of culture FLS from RA patients after 12h of indicated treatment

hyb_protocol: 600 ng of Cy3-labelled cRNA was hybridized at 65°C for 19h at 10 rpms using SureHyb hybridization chambers (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA), using default parameters (profile AgilentG3_GX_1Color).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE1-107_Sep09_mod and Grid: 072363_D_F_20150612.
Remove Control probes (negatives and positives): 58201 biological probes.
Filter Probesets based on Detected or Not Detected Flags: Use flag spot information in data files. Entities retained in which 100% of samples in 1 out of any 4 conditions (Basal, ATRA, TNF, TNF+ATRA) have Detected or Not Detected Flag.
Probes that are not detected in any of the 8 samples are removed. Probes pass the filter if it is detected in the two samples of at least one of the four groups. 23824 filtered probes.

source_name: Pool FLS from three RA patients

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the Low Input Quick Amp Labeling kit, One-Color (Agilent), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Speedtools Total RNA extraction kit (Biotools, Madrid, Spain). Its integrity was assessed with Agilent 2100 Bioanalyzer in combination with Agilent RNA 6000 Nano Chips.

treatment_protocol: FLS from six different RA patients were culture for 12h with 0.05% DMSO (Basal), 5mM ATRA, 10ng/ml TNF or 5mM ATRA+10ng/ml TNF in the serum-deprived medium.

value: Culture FLS

value: TNF (10ng/ml)+ATRA (5mM)


title: TNF+ATRA 2


title: wtFGF2, rep1


title: CS-2d-2

description:
ALL_Unigene.FA
ALL_Rpkm.txt


title: wtFGF2, rep2


title: wtFGF2, rep3


title: TNF 2

value: TNF (10ng/ml)


title: pt159: Tumour_normal_rep5

value: Normal


title: pt129: Tumour_normal_rep1

value: squamous cell carcinoma

value: Poor


title: pt146: Tumour_normal_rep2


title: GFOGERhMSC rep 6


title: GFOGERhMSC rep 5


title: ATRA 2

value: ATRA (5mM)


title: TNF 1


title: humanFGF2, rep4

description: gene expression data from myelinating cultures 18 DIV treated with human FGF2


title: CS-2d-1

description:
ALL_Unigene.FA
ALL_Rpkm.txt

value: stigma

value: wild type


title: ATRA 1


title: humanFGF2, rep3

value: Sprague-Dawley


title: humanFGF2, rep2


title: CS-0d-3

description:
ALL_Unigene.FA
ALL_Rpkm.txt

value: 0 DAY

value: day of anthesis, dark red stigma outside the perianth tubes


title: GFOGERhMSC rep 4

value: GFOGER


title: CS-0d-2

description:
ALL_Unigene.FA
ALL_Rpkm.txt


title: GFOGERhMSC rep 3


title: GFOGERhMSC rep 2


title: humanFGF2, rep1