title: PCA.50: prostate_cancer_primary_50

tag: igg production


title: Cohort2_P_Patient7

status: Public on Nov 18 2020

type: SRA

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

library_source: transcriptomic

data_processing:
Reads were mapped to the GRCh38.p10 Ensembl human genome using STAR v.2.5.2a with default parameters.
Cohort 1 and 2 were analyzed indenpendetly of one another. Genes with less than 10 raw counts in all conditions were excluded from the analysis to sort out lowly expressed genes.
Reads per kilobase million (RPKM) values were calculated and can be found in the processed data files.
Genome_build: GRCh38
Supplementary_files_format_and_content: Table with gene expression levels in excel format

molecule: polyA RNA

organism: Homo sapiens

source_name: Gut

extract_protocol:
Laser capture microdissection - please refer to paper for further details.
Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

tag: gut segment type

value: Perioperative

tag: patient


title: m3_DTL3_a

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

country: USA

institute: NHLBI

data_processing:
For renal tubule RNA-seq, the sequencing reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a.  For single-cell RNA-seq, the raw sequencing reads were mapped to Ensembl Release 96 using cellranger 3.0.2.
Transcript abundances in TPM were calculated by rsem 1.3.0. Single-cell RNA-seq data was processed by cellranger followed by SoupX and Seurat

organism: Mus musculus

growth_protocol: Pathogen-free male C57BL/6 had free access to ad libitum drinking water and normal rodent chow before experiment.

extract_protocol: Total RNA was extracted using the Direct-zol(tm) RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then purified by AmPure XP magnetic beads (Beckman Coulter Genomics). The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: Kidney

tag: tissue preparation

value: Microdissected renal tubule

tag: Sex

value: male

tag: age

value: 6-8 weeks


title: Cohort2_C_Patient4

value: Common channel


title: diffuse glioma_EORTC 26101_100

type: genomic

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description:
tumor_DNA_FFPE
EORTC 26101_100

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

molecule: genomic DNA

source_name: diffuse glioma IDH wt

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: gender

value: female


title: PCA.49: prostate_cancer_primary_49

type: RNA

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: Decipher Biosciences, Inc.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

molecule: total RNA

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

tag: psa

tag: grade group

tag: race

value: Black

tag: non-organ confined

value: No

tag: palsma cell content

tag: inflammation signature

tag: ifng signature

tag: nk activity


title: PCA.48: prostate_cancer_primary_48

value: Yes

tag: igg production


title: m1_PTS3_a


title: Cohort2_C_Patient2

tag: gut segment type


title: PCA.57: prostate_cancer_primary_57


title: m1_PTS3_b


title: Cohort2_A_Patient14

value: Alimentary limb

tag: patient


title: m2_PTS3_a

tag: strain


title: diffuse glioma_EORTC 26101_096

description:
tumor_DNA_FFPE
EORTC 26101_096


title: diffuse glioma_EORTC 26101_099

description:
tumor_DNA_FFPE
EORTC 26101_099


title: Cohort2_P_Patient11


title: PCA.62: prostate_cancer_primary_62


title: m2_PTS3_b

tag: tissue


title: Cohort2_C_Patient9


title: PCA.47: prostate_cancer_primary_47


title: PCA.46: prostate_cancer_primary_46


title: PCA.45: prostate_cancer_primary_45


title: diffuse glioma_EORTC 26101_095

description:
tumor_DNA_FFPE
EORTC 26101_095


title: diffuse glioma_EORTC 26101_107

description:
tumor_DNA_FFPE
EORTC 26101_107


title: Cohort2_A_Patient7


title: m3_PTS3_a

tag: tissue preparation


title: PCA.44: prostate_cancer_primary_44


title: PCA.43: prostate_cancer_primary_43


title: diffuse glioma_EORTC 26101_098

description:
tumor_DNA_FFPE
EORTC 26101_098


title: Cohort2_P_Patient6


title: m3_PTS3_b

tag: Sex


title: diffuse glioma_EORTC 26101_093

description:
tumor_DNA_FFPE
EORTC 26101_093


title: m1_DTL1_a

tag: age


title: Cohort2_C_Patient15


title: diffuse glioma_EORTC 26101_097

description:
tumor_DNA_FFPE
EORTC 26101_097

tag: gender


title: PCA.42: prostate_cancer_primary_42

tag: psa


title: PCA.41: prostate_cancer_primary_41

tag: grade group


title: Cohort2_B_Patient14

value: Biliopancreatic limb


title: m3_DTL1_b


title: m3_DTL1_a


title: Cohort2_A_Patient11


title: diffuse glioma_EORTC 26101_092

description:
tumor_DNA_FFPE
EORTC 26101_092


title: Cohort2_P_Patient10


title: Cohort2_C_Patient8


title: m5_DTL1_b


title: m1_IMCD_a

source_name: IMCD


title: PCA.39: prostate_cancer_primary_39

tag: race


title: m1_IMCD_b


title: PCA.37: prostate_cancer_primary_37

tag: non-organ confined


title: PCA.40: prostate_cancer_primary_40

tag: palsma cell content


title: diffuse glioma_EORTC 26101_090

description:
tumor_DNA_FFPE
EORTC 26101_090


title: diffuse glioma_EORTC 26101_088

description:
tumor_DNA_FFPE
EORTC 26101_088


title: diffuse glioma_EORTC 26101_089

description:
tumor_DNA_FFPE
EORTC 26101_089


title: Cohort2_C_Patient5


title: PCA.36: prostate_cancer_primary_36

tag: inflammation signature


title: m1_IMCD_c


title: PCA.38: prostate_cancer_primary_38

tag: ifng signature


title: Cohort2_B_Patient8


title: m2_IMCD_a


title: Cohort2_A_Patient6


title: m2_IMCD_b


title: diffuse glioma_EORTC 26101_087

description:
tumor_DNA_FFPE
EORTC 26101_087


title: Cohort2_P_Patient5


title: m2_IMCD_c


title: Cohort2_B_Patient3


title: Cohort2_C_Patient14


title: PCA.34: prostate_cancer_primary_34

tag: nk activity


title: diffuse glioma_EORTC 26101_086

description:
tumor_DNA_FFPE
EORTC 26101_086


title: m3_IMCD_b


title: PCA.33: prostate_cancer_primary_33

tag: igg production


title: PCA.32: prostate_cancer_primary_32


title: diffuse glioma_EORTC 26101_085

description:
tumor_DNA_FFPE
EORTC 26101_085


title: diffuse glioma_EORTC 26101_084

description:
tumor_DNA_FFPE
EORTC 26101_084


title: PCA.31: prostate_cancer_primary_31


title: PCA.35: prostate_cancer_primary_35


title: m3_IMCD_a


title: Cohort2_B_Patient11

tag: gut segment type


title: PCA.30: prostate_cancer_primary_30


title: m3_IMCD_c


title: Cohort2_A_Patient10

tag: patient


title: diffuse glioma_EORTC 26101_081

description:
tumor_DNA_FFPE
EORTC 26101_081


title: diffuse glioma_EORTC 26101_082

description:
tumor_DNA_FFPE
EORTC 26101_082


title: Cohort2_P_Patient9


title: diffuse glioma_EORTC 26101_083

description:
tumor_DNA_FFPE
EORTC 26101_083


title: PCA.29: prostate_cancer_primary_29


title: PCA.28: prostate_cancer_primary_28


title: m3_DTL2_a

tag: strain


title: m2_DTL2_b

tag: tissue


title: m3_DTL2_b

tag: tissue preparation


title: Cohort2_B_Patient4


title: PCA.27: prostate_cancer_primary_27


title: diffuse glioma_EORTC 26101_080

description:
tumor_DNA_FFPE
EORTC 26101_080


title: Cohort2_C_Patient7


title: Cohort2_B_Patient7


title: m3_DTL2_c

tag: Sex


title: m4_ATL_b

source_name: ATL

tag: age


title: diffuse glioma_EORTC 26101_077

description:
tumor_DNA_FFPE
EORTC 26101_077

tag: gender


title: diffuse glioma_EORTC 26101_078

description:
tumor_DNA_FFPE
EORTC 26101_078


title: diffuse glioma_EORTC 26101_079

description:
tumor_DNA_FFPE
EORTC 26101_079


title: PCA.25: prostate_cancer_primary_25

tag: psa


title: Cohort2_B_Patient2


title: diffuse glioma_EORTC 26101_091

description:
tumor_DNA_FFPE
EORTC 26101_091


title: diffuse glioma_EORTC 26101_076

description:
tumor_DNA_FFPE
EORTC 26101_076


title: diffuse glioma_EORTC 26101_094

description:
tumor_DNA_FFPE
EORTC 26101_094


title: diffuse glioma_EORTC 26101_075

description:
tumor_DNA_FFPE
EORTC 26101_075


title: m1_DTL2_a


title: PCA.23: prostate_cancer_primary_23

tag: grade group


title: m1_DTL2_b


title: Cohort2_P_Patient15


title: m6_ATL_a


title: PCA.24: prostate_cancer_primary_24

tag: race


title: Cohort2_C_Patient11


title: diffuse glioma_EORTC 26101_073

description:
tumor_DNA_FFPE
EORTC 26101_073


title: PCA.21: prostate_cancer_primary_21

tag: non-organ confined


title: diffuse glioma_EORTC 26101_072

description:
tumor_DNA_FFPE
EORTC 26101_072


title: m3_PTS1_a


title: Cohort2_A_Patient5


title: Cohort2_B_Patient10


title: Cohort2_A_Patient3


title: PCA.22: prostate_cancer_primary_22

tag: palsma cell content


title: diffuse glioma_EORTC 26101_070

description:
tumor_DNA_FFPE
EORTC 26101_070


title: diffuse glioma_EORTC 26101_069

description:
tumor_DNA_FFPE
EORTC 26101_069


title: m3_GL_a

source_name: Glomerulus


title: m2_DTL2_a


title: Cohort2_A_Patient9


title: Cohort2_P_Patient8


title: diffuse glioma_EORTC 26101_071

description:
tumor_DNA_FFPE
EORTC 26101_071


title: diffuse glioma_EORTC 26101_068

description:
tumor_DNA_FFPE
EORTC 26101_068


title: PCA.19: prostate_cancer_primary_19

tag: inflammation signature


title: PCA.20: prostate_cancer_primary_20

tag: ifng signature


title: PCA.18: prostate_cancer_primary_18

tag: nk activity


title: diffuse glioma_EORTC 26101_067

description:
tumor_DNA_FFPE
EORTC 26101_067


title: Cohort2_C_Patient6


title: m3_GL_b


title: m2_DTL3_a


title: m1_DTL3_a


title: PCA.16: prostate_cancer_primary_16

tag: igg production


title: Cohort2_A_Patient4

tag: gut segment type


title: PCA.17: prostate_cancer_primary_17


title: m2_ATL_b


title: Cohort2_B_Patient5

tag: patient


title: diffuse glioma_EORTC 26101_066

description:
tumor_DNA_FFPE
EORTC 26101_066


title: PCA.15: prostate_cancer_primary_15


title: PCA.14: prostate_cancer_primary_14


title: PCA.26: prostate_cancer_primary_26


title: Cohort2_P_Patient3


title: PCA.13: prostate_cancer_primary_13


title: m1_MTAL_a

source_name: MTAL

tag: strain


title: PCA.12: prostate_cancer_primary_12


title: diffuse glioma_EORTC 26101_063

description:
tumor_DNA_FFPE
EORTC 26101_063


title: Cohort2_A_Patient15


title: diffuse glioma_EORTC 26101_064

description:
tumor_DNA_FFPE
EORTC 26101_064


title: m1_MTAL_b

tag: tissue


title: m3_DTL3_b

tag: tissue preparation


title: diffuse glioma_EORTC 26101_065

description:
tumor_DNA_FFPE
EORTC 26101_065


title: Cohort2_P_Patient2


title: diffuse glioma_EORTC 26101_074

description:
tumor_DNA_FFPE
EORTC 26101_074


title: Cohort2_P_Patient14


title: Cohort1_P_Patient24


title: diffuse glioma_EORTC 26101_109

description:
tumor_DNA_FFPE
EORTC 26101_109


title: PCA.10: prostate_cancer_primary_10


title: PCA.11: prostate_cancer_primary_11


title: diffuse glioma_EORTC 26101_062

description:
tumor_DNA_FFPE
EORTC 26101_062


title: Cohort1_P_Patient23


title: m2_MTAL_b

tag: Sex


title: diffuse glioma_EORTC 26101_061

description:
tumor_DNA_FFPE
EORTC 26101_061


title: m2_MTAL_a

tag: age


title: m3_MTAL_a


title: Cohort1_P_Patient22


title: m3_MTAL_b


title: diffuse glioma_EORTC 26101_057

description:
tumor_DNA_FFPE
EORTC 26101_057

tag: gender


title: diffuse glioma_EORTC 26101_058

description:
tumor_DNA_FFPE
EORTC 26101_058


title: Cohort1_P_Patient20


title: m1_DCT_a

source_name: DCT


title: Cohort1_P_Patient17


title: diffuse glioma_EORTC 26101_060

description:
tumor_DNA_FFPE
EORTC 26101_060


title: PCA.9: prostate_cancer_primary_9

tag: psa


title: PCA.8: prostate_cancer_primary_8

tag: grade group


title: m2_DCT_a


title: diffuse glioma_EORTC 26101_056

description:
tumor_DNA_FFPE
EORTC 26101_056


title: PCA.4: prostate_cancer_primary_4

tag: race


title: PCA.7: prostate_cancer_primary_7

tag: non-organ confined


title: Cohort1_P_Patient14


title: PCA.6: prostate_cancer_primary_6

tag: palsma cell content


title: PCA.5: prostate_cancer_primary_5

tag: inflammation signature


title: Cohort1_P_Patient12


title: PCA.3: prostate_cancer_primary_3

tag: ifng signature


title: m1_DCT_b


title: Cohort1_P_Patient15


title: m3_DCT_a


title: PCA.2: prostate_cancer_primary_2

tag: nk activity


title: PCA.1: prostate_cancer_primary_1

tag: igg production


title: m3_DCT_b


title: Cohort1_A_Patient9

tag: gut segment type


title: m2_DCT_b


title: Cohort1_B_Patient9

tag: patient


title: m1_CNT_a

source_name: CNT

tag: strain


title: diffuse glioma_EORTC 26101_052

description:
tumor_DNA_FFPE
EORTC 26101_052


title: m3_ATL_b

tag: tissue


title: diffuse glioma_EORTC 26101_053

description:
tumor_DNA_FFPE
EORTC 26101_053


title: diffuse glioma_EORTC 26101_051

description:
tumor_DNA_FFPE
EORTC 26101_051


title: m1_CNT_b

tag: tissue preparation


title: m2_CNT_a

tag: Sex


title: C017 Post: Vastus lateralis Post surgery

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

hyb_protocol: Following fragmentation, ~30ug of cRNA was hybridized at 45C for 16 hours on GeneChip Human Genome U1333 Plus 2.0 Array. GeneChips were washed and stained in Affymetrix Fluidics Station 450 (Fluids Protocol FS450_0001)

scan_protocol: After washing and staining, GeneChips were scanned on the Affymetrix GeneChip Scanner 3000 (GSC3000)

data_processing: Data was analyzed in Expression Console software. Signal intensity was determined with Probe Logarithmic Intensity Error (PLIER) Estimation. Resulting CHP files were analyzed in Partek Genomics Suite and raw intensity values were Log Transformed for statisitcal analysis.

label: Biotin

source_name: Vastus lateralis Post Roux-en-Y gastric bypass (RYGB) surgery

label_protocol: Biotinylated cRNA was prepared from ~500 ng total RNA according to standard Affymetrix Protocol (Manual Target Preparation for Gene Chip 3' Expression Arrays)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Subjects underwent RYGB. Samples from the vastus lateralis were colleced prior  (PRE) to and one year f(POST) ollowing surgery

value: Vastus Lateralis

tag: group

value: Control

tag: age (yr)

tag: weight (kg)

tag: body mass index


title: diffuse glioma_EORTC 26101_059

description:
tumor_DNA_FFPE
EORTC 26101_059

tag: gender


title: diffuse glioma_EORTC 26101_047

description:
tumor_DNA_FFPE
EORTC 26101_047


title: m2_CNT_b

tag: age


title: Cohort1_C_Patient23


title: Cohort1_A_Patient23


title: m3_CNT_a


title: diffuse glioma_EORTC 26101_055

description:
tumor_DNA_FFPE
EORTC 26101_055


title: Cohort1_B_Patient22


title: diffuse glioma_EORTC 26101_046

description:
tumor_DNA_FFPE
EORTC 26101_046


title: C015 Post: Vastus lateralis Post surgery


title: diffuse glioma_EORTC 26101_048

description:
tumor_DNA_FFPE
EORTC 26101_048


title: diffuse glioma_EORTC 26101_049

description:
tumor_DNA_FFPE
EORTC 26101_049


title: Cohort1_A_Patient24


title: m3_CNT_b


title: diffuse glioma_EORTC 26101_050

description:
tumor_DNA_FFPE
EORTC 26101_050


title: C016 Pre: Vastus Lateralis Pre surgery

source_name: Vastus Lateralis Pre Roux-en-Y gastric bypass (RYGB) surgery


title: C015 Pre: Vastus Lateralis Pre surgery


title: Cohort1_B_Patient20


title: C014 Post: Vastus lateralis Post surgery


title: diffuse glioma_EORTC 26101_044

description:
tumor_DNA_FFPE
EORTC 26101_044


title: Cohort1_A_Patient22


title: C017 Pre: Vastus Lateralis Pre surgery


title: m1_OMCD_a

source_name: OMCD


title: m1_OMCD_b


title: diffuse glioma_EORTC 26101_054

description:
tumor_DNA_FFPE
EORTC 26101_054


title: Cohort1_C_Patient20


title: Cohort1_C_Patient24


title: C014 Pre: Vastus Lateralis Pre surgery


title: Cohort1_B_Patient17


title: m2_OMCD_b


title: C013 Post: Vastus lateralis Post surgery


title: m3_OMCD_a


title: C016 Post: Vastus lateralis Post surgery


title: diffuse glioma_EORTC 26101_042

description:
tumor_DNA_FFPE
EORTC 26101_042


title: C013 Pre: Vastus Lateralis Pre surgery


title: m3_OMCD_b


title: Cohort1_A_Patient17


title: Cohort1_C_Patient17


title: C012 Post: Vastus lateralis Post surgery

value: Case


title: diffuse glioma_EORTC 26101_045

description:
tumor_DNA_FFPE
EORTC 26101_045


title: m4_OMCD_a


title: Cohort1_C_Patient15


title: m4_OMCD_b


title: C012 Pre: Vastus Lateralis Pre surgery


title: Cohort1_A_Patient15


title: C010 Post: Vastus lateralis Post surgery


title: diffuse glioma_EORTC 26101_043

description:
tumor_DNA_FFPE
EORTC 26101_043


title: diffuse glioma_EORTC 26101_040

description:
tumor_DNA_FFPE
EORTC 26101_040


title: diffuse glioma_EORTC 26101_038

description:
tumor_DNA_FFPE
EORTC 26101_038


title: Cohort1_B_Patient14


title: diffuse glioma_EORTC 26101_041

description:
tumor_DNA_FFPE
EORTC 26101_041


title: Cohort1_A_Patient14


title: Cohort1_C_Patient13


title: diffuse glioma_EORTC 26101_039

description:
tumor_DNA_FFPE
EORTC 26101_039


title: Cohort1_A_Patient13


title: Cohort1_B_Patient12


title: diffuse glioma_EORTC 26101_037

description:
tumor_DNA_FFPE
EORTC 26101_037


title: diffuse glioma_EORTC 26101_036

description:
tumor_DNA_FFPE
EORTC 26101_036


title: C09 Pre: Vastus Lateralis Pre surgery


title: diffuse glioma_EORTC 26101_035

description:
tumor_DNA_FFPE
EORTC 26101_035


title: diffuse glioma_EORTC 26101_034

description:
tumor_DNA_FFPE
EORTC 26101_034


title: C08 Post: Vastus lateralis Post surgery


title: simple Ti surface rep3

city: Shanghai

first: junyu

last: shi

address: 639 zhi-zao-ju road

department: Department of Implant Dentistry

country: China

institute: Shanghai Ninth People’s Hospital

description: gene expression in  rBMSCs after  cultured on Ti surface

hyb_protocol: Each slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

organism: Rattus norvegicus

source_name: marrow of rat tibias

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by NucleoSpin RNA Clean-up XS kit (Cat#740903, MN, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: rBMSCs were isolated from the marrow of rat tibias, cells were cultured on Ta-modified surface for 7 days, gene expression in  rBMSCs was measured.

tag: cell type

value: rBMSCs

tag: culture

value: simple Ti surface


title: C07 Post: Vastus lateralis Post surgery


title: Cohort1_C_Patient12


title: simple Ti surface rep2


title: C010 Pre: Vastus Lateralis Pre surgery


title: Ta-modified Ti surface rep2

description: gene expression in  rBMSCs after  cultured on Ta-modified surface

value: Ta-modified Ti surface


title: Ta-modified Ti surface rep3


title: C08 Pre: Vastus Lateralis Pre surgery


title: C06 Post: Vastus lateralis Post surgery


title: C06 Pre: Vastus Lateralis Pre surgery


title: H9_unmodifed [RNA-seq]

city: singapore

first: Aw

last: Jong Ghut Ashley

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Basecall samples with Albacore version 2.3.3 no filtering
Aligned samples with Graphmap 0.5.2
Aligned raw signal to sequence with Nanopolish 10.2
Calculated reactivity with PORE-cupine
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files were generated, higher values represent a higher possibiilty for single stranded region

source_name: Unmodified

extract_protocol:
Total RNA was extracted with TRIzol, RNA with poly A tail was enriched, adaptors were ligated at the 5' end and 3' end of the product from fragmented reversed transcribed RNA
Purified with columns or extracted with TRIzol with or without RNA with poly A tail
Purified RNA was ligated with a adpator at the 3' end and followed by a motor protein or adaptors were ligated at the 5' end and 3' end of the product from fragmented reversed transcribed RNA

tag: modifications


title: Tc1.E_2

city: Iowa City

first: Nitin

last: Karandikar

state: Iowa

address: C673 General Hospital

department: Pathology

institute: University of Iowa

data_processing:
Single-end 50 bp sequencing was performed on the Illumina HiSeq 2000. Basecalls were converted into FASTQs using the Illumina bcl2fastq and alignment was performed using kallisto with the GRCh38 human genome build.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited tsv files including lengths, counts and transcripts per million (TPM) for mRNA transcripts.

source_name: Naïve CD8+ T-cells

extract_protocol: Samples were submitted to the University of Chicago Genomics facility for RNA extraction, quality assessment and sequencing.

treatment_protocol: Naïve CD8+ T-cells were sorted from PBMC and resuspended at 1 million cells/ml in Stemline hematopoietic stem cell expansion serum-free media (Sigma S0192), followed by stimulation in various differentiation conditions as listed above. Cultures were activated with 0.5 ug/ml each of fixed anti-CD3 and anti-CD28 and incubated for 7 days at 37 degree Celsius. On day 7, aliquot of cultured CD8+ Tc0 and Tc1A-E cells were pelletized, snap frozen in liquid nitrogen, and stored at -80 C for shipment to Chicago for RNA extraction and sequencing.

value: CD8+ T-cells

tag: condition

tag: donor

tag: diagnosis

value: Healthy


title: C07 Pre: Vastus Lateralis Pre surgery


title: simple Ti surface rep1


title: Tc0_2

value: No cytokine added control


title: Tc1.D_2

value: 10 ng/ml IL-12


title: diffuse glioma_EORTC 26101_031

description:
tumor_DNA_FFPE
EORTC 26101_031

value: male


title: C09 Post: Vastus lateralis Post surgery


title: Cohort1_A_Patient12

tag: gut segment type

tag: patient


title: diffuse glioma_EORTC 26101_029

description:
tumor_DNA_FFPE
EORTC 26101_029


title: diffuse glioma_EORTC 26101_030

description:
tumor_DNA_FFPE
EORTC 26101_030

value: female


title: diffuse glioma_EORTC 26101_032

description:
tumor_DNA_FFPE
EORTC 26101_032


title: Tc1.C_2

value: anti-IL-4, 10 ng/ml IL-12


title: Tc1.B_2

value: 10 ng/ml IL-12, 10 ng/ml IL-2


title: C05 Pre: Vastus Lateralis Pre surgery

tag: tissue


title: Ta-modified Ti surface rep1


title: diffuse glioma_EORTC 26101_033

description:
tumor_DNA_FFPE
EORTC 26101_033


title: 18_RH31 H5

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Lesion
Gene expression data from human periventricular brain region

hyb_protocol: 12µg of cRNA molecules were heat fragmented and applied to the Human U133 plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the AGCC software package to prepare the .CEL files

data_processing: The data were analyzed with Transcriptome Analysis Console v4.1.1 (Affymetrix) using Robust Multi-Array Average (RMA) as normalization method.

source_name: Lesion 7

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix IVT protocol

extract_protocol:
Periventricular regions were obtained from post-mortem human brains. This region was captured using PixCell II laser-capture microdissection system (Arcturus BioScience).
RNA was isolated using the Arcturus PicoPure RNA isolation kit according to manufacturer’s protocol.

tag: sample type

value: Laser captured cells from human white matter

value: Cells from white matter lesion


title: 17_RH49 H4

source_name: Lesion 6


title: 16_RH62 H7

source_name: Lesion 5


title: C05 Post: Vastus lateralis Post surgery


title: 15_RH13 H5

source_name: Lesion 4


title: diffuse glioma_EORTC 26101_026

description:
tumor_DNA_FFPE
EORTC 26101_026

source_name: diffuse glioma IDH wt


title: Tc1.E_1


title: diffuse glioma_EORTC 26101_025

description:
tumor_DNA_FFPE
EORTC 26101_025


title: Tc1.D_1


title: diffuse glioma_EORTC 26101_027

description:
tumor_DNA_FFPE
EORTC 26101_027


title: Tc1.C_1


title: Tc0_1


title: Tc1.B_1


title: diffuse glioma_EORTC 26101_024

description:
tumor_DNA_FFPE
EORTC 26101_024


title: Fibroblasts 72 hpi 2

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
samples.txt
hff.txt

data_processing:
The MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
In read1, the first 5 positions are ignored, the next 4 positions (6-9) are the batch barcode, and the next 37 positions (10-46) are the insert that was used for the alignment.
In read2, the first 7 positions (1-7) are the sample barcode, and the next 8 positions (8-15) are the UMI (unique molecular identifier).
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per sample.

source_name: Fibroblasts infected with HCMV TB40

growth_protocol: Primary human foreskin fibroblasts (HFF) (ATCC CRL-1634) were maintained in DMEM with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 100 units/ml penicillin and streptomycin (Beit-Haemek, Israel).

extract_protocol:
PBMC were isolated from fresh venous blood, obtained from HSCT patients, using Lymphoprep (Stemcell Technologies) density gradient
RNA libraries were generated from samples of ~10,000 cells according to the MARS-seq protocol (Jaitin et al., 2014; Keren-Shaul et al., 2019).
The library is 3' RNA-seq

treatment_protocol: Fibroblasts were infected with HCMV strain TB40/E

value: Fibroblast


title: diffuse glioma_EORTC 26101_022

description:
tumor_DNA_FFPE
EORTC 26101_022


title: diffuse glioma_EORTC 26101_023

description:
tumor_DNA_FFPE
EORTC 26101_023


title: 13_RH14 H5

source_name: Lesion 2


title: Fibroblasts 72 hpi 1

description:
samples.txt
hff.txt


title: diffuse glioma_EORTC 26101_021

description:
tumor_DNA_FFPE
EORTC 26101_021


title: Fibroblasts 8 hpi 2

description:
samples.txt
hff.txt


title: 11_RH16 H6

description:
Pre-Lesion
Gene expression data from human periventricular brain region

source_name: Pre-Lesion 3

value: Cells from pre-lesion


title: diffuse glioma_EORTC 26101_019

description:
tumor_DNA_FFPE
EORTC 26101_019


title: meningeal_cell_preparation

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

country: Switzerland

institute: University of Bern

data_processing:
Illumina RTA 1.18.66.3 was used for base calling
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v3.1.0 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v3.1.0 quant was used to map the demultiplexed reads to the reference genome (mm10, v3.0.0, 10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts per droplet and estimate the number of ce
Seurat v3.1.4 was used under R v3.6.3 to remove low quality cells, keeping cells with more than 500 and less than 50% mitochondrial genes for further analysis. The filtered cells were clustered by similarity in gene expression and visualized using Seurat.
Differentially expressed genes were determined using the MAST v1.12.0 algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with UMI counts per gene per cell after filtering in Seurat

source_name: meninges

extract_protocol:
Mice were perfused with PBS and the top layer of the brain was scraped off with a scalpel. The tissue was dissociated using collagenase / dispase for 30 min at 37°C, treated with myelin-removal beads (MACS Miltenyi, # 130-096-433) and enriched for KIT+ ce
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v3.1 and i7 Mutiplex kit (10X Genomics) according to the manufacturers instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommen

tag: strain

tag: genotype

value: wildtype

value: 9 weeks

tag: treatment

value: untreated


title: MA1L liver tumor cells transduced with vector control, replicate 3

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Raw FASTQ reads were quantified to the mm10 transcriptome using Kallisto. Differential expression analysis was performed using Sleuth
For neoantigen prediction, RNA-seq reads were aligned to the mm10 genome using STAR, then mutations were called using the RNA-seq mode of Strelka v2. The resultant mutations were annotated using VEP, then neoantigens were predicted using pVACtools with H-2Kb and H-2Db as the candidate MHCI alleles.
To analyze expression of transposable elements, the raw FASTQ reads were first re-aligned using STAR with modified settings (outFilterMultimapNmax 100, winAnchorMultimapNmax 100). Transposable elements were quantified by TEcount from TEToolkit. Differential expression was assessed using the raw counts of all genes and transposable elements with DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file of transcript counts, from Kallisto

source_name: mouse liver tumor cells

growth_protocol: DMEM + 10% FBS+ 1% pen/strep

extract_protocol:
RNA from control and Kmt2d-mutant cells was extracted using TRIzol Reagent (Invitrogen) by following standard RNA extraction protocols.
PolyA selected RNA-seq with Illumina TruSeq v2

value: Vector


title: 10_RH5 H6

source_name: Pre-Lesion 2


title: 14_RH51 H5

source_name: Lesion 3


title: CLL-C44_LN_sc

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Libraries were sequenced on NovaSeq (Illumina) and processed by Cell Ranger Single Cell Software Suite 3.0.1 (Zheng et al., 2017).
Genes expressed in < 3 cells and cells with < 200 genes detected or > 10% mitochondrial gene content were filtered.
Downstream analyses were performed on Seurat v3 (Stuart et al., 2019).
For each sample, gene expression was normalized to count per 10,000 and the top 2,000 variable genes were identified and scaled with effects of total number of detected genes and mitochondrial gene content regressed out using Seurat functions ‘FindVariableFeatures’ and ‘ScaleData’ respectively.
Genome_build: hg38
Supplementary_files_format_and_content: ZIP file contains cellRanger count matrix output folder (filtered_feature_bc_matrix (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz))

extract_protocol: Individually barcoded single-cell libraries were created from peripheral blood mononuclear cells and lymph node single cell suspensions with the Chromium Single Cell 3′ Reagent Kit V2.

value: lymph node

tag: Sex

value: M


title: MA1L liver tumor cells transduced with vector control, replicate 2


title: 9_RH52 H7

description:
Control
Gene expression data from human periventricular brain region

source_name: Control 7

value: Normal control material


title: diffuse glioma_EORTC 26101_020

description:
tumor_DNA_FFPE
EORTC 26101_020


title: 7_RH23 H3

source_name: Control 5


title: 8_RH40 H7

source_name: Control 6


title: Tc1.A_2

value: CD8+ T-cells

value: anti-IL-4, 10 ng/ml IL-12, 10 ng/ml IL-2

value: Healthy


title: CLL-C33_LN_sc


title: MA1L liver tumor cells transduced with vector control, replicate 1


title: diffuse glioma_EORTC 26101_017

description:
tumor_DNA_FFPE
EORTC 26101_017

value: male


title: diffuse glioma_EORTC 26101_015

description:
tumor_DNA_FFPE
EORTC 26101_015


title: 6_RH37 H5

source_name: Control 4


title: 5_RH20 H4

source_name: Pre-Lesion 1


title: diffuse glioma_EORTC 26101_014

description:
tumor_DNA_FFPE
EORTC 26101_014


title: Tc1.A_1

source_name: Naïve CD8+ T-cells


title: MA1L liver tumor cells transduced with sgKmt2d, replicate 3


title: CLL-C24_LN_sc


title: diffuse glioma_EORTC 26101_013

description:
tumor_DNA_FFPE
EORTC 26101_013


title: diffuse glioma_EORTC 26101_012

description:
tumor_DNA_FFPE
EORTC 26101_012

value: female


title: 12_RH8 H4

source_name: Pre-Lesion 4


title: MA1L liver tumor cells transduced with sgKmt2d, replicate 2


title: MA1L liver tumor cells transduced with sgKmt2d, replicate 1


title: diffuse glioma_EORTC 26101_009

description:
tumor_DNA_FFPE
EORTC 26101_009


title: CLL-C44_PB_sc

value: peripheral blood


title: 3_RH11 H6

source_name: Control 3

value: Laser captured cells from human white matter


title: 10X_LC4754

data_processing:
The raw sequencing reads were mapped to Ensembl Release 96 using cellranger 3.0.2.
Transcript abundances in TPM were calculated by rsem 1.3.0. Single-cell RNA-seq data was processed by cellranger followed by SoupX and Seurat.

extract_protocol: 10X Genomics Chromium v3 Single Cell 3’ protocol: 3-6,000 cells/lane.

value: Kidney

tag: tissue preparation

value: single-cell RNA-seq

value: 6-8 weeks


title: CLL-C11_LN_sc

value: F


title: diffuse glioma_EORTC 26101_028

description:
tumor_DNA_FFPE
EORTC 26101_028

tag: gender


title: CLL-C03_LN_sc

tag: age


title: 4_RH45 H4

source_name: Lesion 1

tag: cell type

value: Cells from white matter lesion


title: 10X_LC4731


title: diffuse glioma_EORTC 26101_011

description:
tumor_DNA_FFPE
EORTC 26101_011

source_name: diffuse glioma IDH wt


title: 2_RH22 H6

source_name: Control 2


title: CLL-C33_PB_sc


title: CLL-C24_PB_sc


title: 10X_LC4726


title: diffuse glioma_EORTC 26101_010

description:
tumor_DNA_FFPE
EORTC 26101_010


title: A549/DDP

city: Shiyan

first: Fuyun

last: Ji

state: Hubei

address: South Renmin Road

department: Department of Medical Biology, School of Basic Medical Science

institute: Hubei University of Medicine

description:
Gene expression data from non-small cell lung cancer cells after ZNF300 was overexpressed
A549_DDP_NS

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: The data were analyzed with Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Affy packages in R.

label: Biotiin

source_name: Non-small cell lung caner cells cultured in vitro

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Conventional cell culture.

treatment_protocol: Cells were resuspended with  0.25%trypsin and collected for RNA extraction.

value: Lung

tag: cell line

tag: disease state

value: Adenocarcinoma

tag: phenotype

value: chemoresistant


title: GFP- replicate 3

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

data_processing:
Zebrafish RNA-Seq was processed using Nextflow nf-core/rnaseq v1.4.2. See following two steps.
TrimGalore was used for adaptor and quality triming
Star v.2.6.1d was used to map the reads to the genome (danRer10) and featureCounts was used to summarize read counts per gene . Ensembl v80 for gene annotations (Ensembl v80 for gene annotations)
Datasets were processed using DESeq2 using default settings, to determine numbers of differentially expressed genes
Genome_build: danRer10
Supplementary_files_format_and_content: Normalised count data from DESeq2 (tab delimited)

organism: Danio rerio

source_name: GFP- (non-EVL) expressing cells

growth_protocol: Embryos were maintained in E3 until 6hpf

extract_protocol:
About 1500 6hpf Tg(krt18:krt18-GFP) embryos were dechorionated in pronase 1mg/ml in danieu solution. Embryos were collected, vortexed 3x 30 sec to prepare a cell suspension, cells centrifuged at 200g 3 min, resuspended in DMEM, and filtered with a 40um filter. 1x10^4 GFP+ cells were sortedand RNA was prepared using the RNeasy Micro Kit
Illumina libraries were prepared using the SMARTseq2 protocol and sequenced on a HiSeq2500 v4 to produce 50-nt single end reads

tag: developmental stage

value: 6 hpf

value: embryonic cells

tag: cell subtype

value: sroted GFP-  non-enveloping layer (non-EVL) cells


title: 1_RH4 H5

source_name: Control 1

value: Normal control material


title: CLL-C11_PB_sc


title: A549

description:
Gene expression data from non-small cell lung cancer cells
A549_NS

value: parental cell line


title: diffuse glioma_EORTC 26101_008

description:
tumor_DNA_FFPE
EORTC 26101_008

value: male


title: Kinate 8h

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

data_processing:
Readmapping was performed using STAR aligner, version STAR_2.5.1b_modified,  with the following options: --outFilterType BySJout , --outFilterMultimapNmax 20, --alignSJoverhangMin 8,  --alignSJDBoverhangMin 1,  --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMtype BAM SortedByCoordinate
Counting was performed using htseq-count with the following options: -r pos -s reverse -t exon -i gene_id --additional-attr gene_name, and using gencode.vM24 annations, HTSeq framework 0.11.4
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab delimited files with ensembl gene id, gene symbol and raw count

source_name: hippocampus of kinate treated mouse hippocampus

growth_protocol: 3 month old male C57/bl6 mice were housed with a 12 hours dark-light-schedule and experiments were performed during the dark cycle always at identical time points

extract_protocol:
For RNA isolation hippocampi were dissected from fresh brains, flash frozen and stored at -80 °C. Total RNA was isolated using TRItidy-reagent (Applichem), followed by an additional purification step using RNEasy columns (Qiagen)
Sequencing libraries were prepared from total RNA with TruSeq stranded total RNA library preparation kit (Illumina)

treatment_protocol: Kainic acid (Ascent scientific) (20 mg/kg, dissolved in PBS), SL327 (Sigma) (50mg/kg, dissolved in dimethylsulfoxide (DMSO) and mixed 1:1 with PBS) were administered by intraperitoneal injection. Mice treated with kainic acid and SL327 were administered with SL327 1 hour before kainic acid injections. Animals were sacrificed at given time points after onset of seizure or at corresponding time points after SL327 or vehicle injections as described before (Hermey et al, 2013)

tag: time

value: kainic acid

tag: tissue compartment

value: hippocampus


title: GFP- replicate 2


title: CLL-C03_PB_sc

tag: tissue

value: peripheral blood

value: M


title: A549-ZNF300

description: Gene expression data from non-small cell lung cancer cells after ZNF300 was overexpressed

tag: transfection

value: overexpressing ZNF300


title: Kinate 4h_2


title: Resistant Rep2

city: São Paulo

first: Sophie

last: Tandonnet

address: Rua do Matão, 277

country: Brazil

institute: Universidade de São Paulo

description: colony origin maintenance protocol: We used a laboratory colony of C. hominivorax, which contained OP-resistant individuals segregating the Gly137Asp and Trp251Ser mutations in the esterase E3 gene, collected from CaiapÃ´nia, GoiÃ¡s, Brazil. The colony was maintained for 11 generations in laboratory conditions according to Carvalho et al. (â€œDeep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance.â€ BMC Genomics. 2010; 11:695.)

data_processing:
To eliminate the low-quality region of the sequences, we used the program Trimmomatic. This program trimmed the sequences in order to remove read regions with an average quality lower than 15. After trimming, sequences shorter than 20 were discarded. We excluded identical reads to reduce the processing time of the sequences during assembly.
We assembled the transcriptome using the program Trinity (version trinityrnaseq_r20140717, --normalize_reads --full_cleanup) in pair-end mode. The single-end reads of the first replicate were inputted as left reads.   The completeness of the assembly was assessed by using BUSCO to search for complete single copy, complete duplicated, and fragmented orthologs within a Diptera database (â€œdiptera_odb9â€). The annotation of the transcriptome was carried out using FunctionAnnotator (eukaryotic mode), which uses the NCBI-nr database to find the closest BLAST hits and Blast2GO to assign GO terms.
We mapped separately the trimmed reads of each condition (Control and Resistant) to the reconstructed transcript set using Bowtie2 (version 2.2.3, '--local --very-sensitive-local' for first single-end replicate and '--local --very-sensitive-local --maxins 1000 --no-mixed --no-discordant' for the second paired-end replicate).
We obtained a table of counts using eXpress (v1.51) and RSEM (v1.2.25) with default parameters. Both programs use an expectation maximization approach and do not require a reference genome for counting. As RSEM does not support gapped alignments, we ran Bowtie2 without the gap argument (â€œ--sensitive --met-stderr --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1â€ and, additionally, â€œ--no-mixed --no-discordantâ€ for the pair-end libraries only).
To test for differential expression between the control and resistant conditions, we used two R packages of the Bioconductor repository; EdgeR (v1.2.25) and DESeq2. In both, counts were normalized by the library size. We considered for further examination the transcripts for which the false discovery rate (FDR) was below 0.05 and the absolute fold change higher than 2 in all analyses performed (eXpress or RSEM counting with either DESeq2 or EdgeR testing).
We conducted a variant analysis using the pipeline KisSplice (version 2.4.0). Briefly, kisSplice locally assembles the regions which surround variants (kissplice -s 1). The localisation of the polymorphic regions is then determined by aligning them to the transcriptome using BLAT (version 34, -minIdentity=80). The R package KissDE was then used to identify which variants were enriched in one condition versus the other. Finally, we filtered the polymorphisms predicted to have a functional impact (non-synonymous SNPs within the coding region) by using KisSplice2reftranscriptome (version 1.2.2), which uses the longest open reading frames (ORFs) identified by Transdecoder (version 3.0.1). For further analyses, we considered the condition specific, non-synonymous SNPs displaying (i) a magnitude of differential allelic expression of at least 20%, (ii) a coverage of at least 20 per replicate and (iii) an adjusted P-value below 0.01.
Genome_build: We used a de-novo assembled transcriptome (See second data processing step)
Supplementary_files_format_and_content: The fasta file contain the trinity-assembled transcripts of Cochliomyia hominivorax. The files â€œgenes.rsem.txtâ€ and â€œgenes.eXpress.txtâ€ contain the abundance measurements  of all transcripts, obtained using RSEM and eXpress, respectively.

organism: Cochliomyia hominivorax

source_name: L3 Larvae

extract_protocol:
Total RNA and DNA of resistant and control samples were isolated for each individual using TRIzol (InvitrogenTM, Thermo Fisher Scientific, Waltham, Massachusetts, USA) from whole bodies of 142 larvae: 44 and 58 surviving individuals respectively from the first and second replicates of the insecticide treatment, and 40 and 60 control larvae from the control group, first and second replicates, respectively. For RNA samples, DNase I (InvitrogenTM, Thermo Fisher Scientific, Waltham, Massachusetts, USA) was used to remove genomic DNA contamination and mRNA-enriched samples were further purified by using Nucleospin RNA Clean-up columns (Macherey & Nagel, DÃ¼ren, Germany). Quantification was performed using the fluorometer Qubit Quantitation Platform (InvitrogenTM, Thermo Fisher Scientific, Waltham, Massachusetts, USA).
RNA from single individuals of each replicate was pooled for sequencing. The sequencing was outsourced to the University of Veterinary Medicine, Vienna, Austria and a second biological replicate to LaboratÃ³rio MultiusuÃ¡rios Centralizado, ESALQ-USP (Piracicaba, Brazil). The RNA fragments resulting from the random breaking of the transcripts were converted into a cDNA library using the mRNA-Seq Sample Prep Kit (Illumina, San Diego, USA). The samples were sequenced using the HiSeq 2000 (Illumina, San Diego, USA).

treatment_protocol: For the resistant condition, a sample from the laboratory population was treated with the OP insecticide dichlorvos (2,2-dichlorovinyl dimethyl phosphate; C4H7Cl2O4P) at a lethal concentration (20 mg/L) for 90% of the population (LC90). The insecticide was directly mixed into the diet of the larvae consisting of fresh ground beef supplemented with bovine blood and water (2:1). A total of 500 second-instar larvae were maintained on the insecticide-containing diet for 24 h. Surviving individuals (resistant sample) were collected for total RNA extraction and subsequent analysis. Individuals of the control group were simply sampled from this laboratory population and maintained on the same diet without the insecticide.

value: resistant to insecticides

value: Esterase E3 Ser252

value: L3 larvae


title: diffuse glioma_EORTC 26101_005

description:
tumor_DNA_FFPE
EORTC 26101_005


title: Kinate 4h_1


title: GFP+ replicate 2

source_name: GFP+ (EVL) expressing cells

tag: strain

value: sroted GFP+ enveloping layer (EVL) cells


title: diffuse glioma_EORTC 26101_006

description:
tumor_DNA_FFPE
EORTC 26101_006


title: Control Rep2

value: susceptible and resistant to insecticides

tag: genotype

value: Esterase E3 Ser251 and Trp251


title: diffuse glioma_EORTC 26101_007

description:
tumor_DNA_FFPE
EORTC 26101_007

value: female


title: GFP+ replicate 1

value: 6 hpf

value: embryonic cells


title: Control Rep1

value: Esterase E3 Ser251 and Trp250


title: Untreated Control

source_name: hippocampus of untreated mouse hippocampus

tag: treatment

value: control


title: HT29 cells, NTSH_1

city: Houston

first: Shaolin

last: Ma

state: Tx

address: 1881 East Road

institute: MD Anderson Cancer Center

description:
RNASeq-sRNA-Annotation-AS-01-RNAcentral-exon.gtf
RNASeq-sRNA-align-featureCount-AS-01-combined.csv

data_processing:
For base calling, we use bcl2fastq v2.19.
We used bwa (version 0.7.17, with the parameters -n 1 -o 0 -e 0 -k 1) to align the short reads (using clean data) to the human genome (built GRCh38)
We downloaded the annotation file from RNACentral database (ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/genome_coordinates/gff3/).
We kept the 483947 exons annotated by “expert-database”. We used the function, countFeatures, from subread package (version 1.6.3) to count features in the annotation files.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text and csv files include count values for each Sample

source_name: HT29-nontargeting control sequence cells

extract_protocol:
exoRNeasy Midi and Maxi Kit (Qiagen, Hilden, Germany; Cat. # 77144
After sample QC, library was constructed by Small RNA Sample Pre Kit. The final cDNA library was ready after a round of sequencing adaptor ligation, reverse transcription, PCR enrichment, purification and size selection (18-40 nt).

value: HT29 colon cancer cell

tag: passage number

value: nontargeting control sequence cells

tag: fraction

value: total RNA of small Evs


title: diffuse glioma_EORTC 26101_018

description:
tumor_DNA_FFPE
EORTC 26101_018

data_processing: BeadStudio software v3.2

tag: gender


title: HT29 cells, NTSH_2


title: diffuse glioma_EORTC 26101_002

description:
tumor_DNA_FFPE
EORTC 26101_002


title: HT29 cells, Shp53_1

source_name: HT29-p53 shRNA cells

value: p53 shRNA cells


title: Resistant Rep1

value: Esterase E3 Ser251

tag: age


title: Kinate 1h

value: kainic acid

value: hippocampus


title: diffuse glioma_EORTC 26101_016

description:
tumor_DNA_FFPE
EORTC 26101_016

value: male


title: Gut bacteria of hooded crane in the late period-120

status: Public on Nov 17 2020

city: Hefei

first: Yang

last: Zhuqing

address: School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China

institute: Anhui University

data_processing:
Raw sequencing data were pre-processed by QIIME (V.1.9)
Low-quality sequences with a sequence length ≤250 bp, or an average quality score <30, were eliminated.
UCLUST was used to cluster high-quality sequences into operational taxonomic units (OTUs) with 97% similarity, Chimeras and singleton OTUs were deleted
The most abundant sequence in each OTU was selected as the representative sequence and identified with the ribosomal database project Classifier
Representation was aligned using PyNAST
Genome_build: ribosomal database project Classifier (16s)
Supplementary_files_format_and_content: Different TXT files include different alpha multiplicity values
Supplementary_files_format_and_content: Different TXT files include different species classification levels
Supplementary_files_format_and_content: TXT file includes the specific intestinal bacteria information of each sample

organism: gut metagenome

source_name: The gut of the hooded crane

extract_protocol:
Faecal DNA was extracted using the faecal DNA extraction kit (QIAamp Fast DNA Stool Mini Kit, MP Biomedicals, Santa Ana, CA, USA), quantified by micro-spectrophotometer (NanoDrop ND-1000, Thermo Fisher Scientific, Waltham, MA, USA) and stored at -20 °C.
Purified DNA (30 μl) was extracted from each sample as an amplification template and sent to the Illumina Mi-seq platform of Shanghai Meiji Biological Company. The V4-V5 hypervariable region of the bacterial 16S rRNA gene fragment was amplified with primers F515/R907. Forward Primer: 515F（5’-GTGCCAGCMGCCGCGG-3’）;  Reverse Primer: 907R（5’-GGACTACHVGGGTWTCTAAT-3’）

treatment_protocol: stored at -20 °C

tag: species

value: Hooded crane

tag: winter period

value: Late period

tag: host

value: Grus monacha

tag: molecule

value: 16S rRNA


title: Gut bacteria of hooded crane in the early period-61 [Paired-end]

department: School of Resources and Environmental Engineering, Anhui University

value: Early period


title: Gut bacteria of hooded crane in the late period-119


title: Gut bacteria of hooded crane in the late period-118


title: Gut bacteria of bean goose in the late period-60 [Paired-end]

source_name: The gut of the bean goose

value: Bean goose


title: A549-LV5

description: Gene expression data from non-small cell lung cancer cells

value: control vector

tag: cell line


title: Gut bacteria of hooded crane in the late period-117


title: Gut bacteria of hooded crane in the late period-116


title: Gut bacteria of hooded crane in the late period-114


title: GFP- replicate 1

tag: developmental stage

value: 6 hpf

tag: cell type

value: embryonic cells

tag: cell subtype

value: sroted GFP-  non-enveloping layer (non-EVL) cells


title: Fibroblasts 8 hpi 1

description:
samples.txt
hff.txt

source_name: Fibroblasts infected with HCMV TB40

value: Fibroblast


title: Gut bacteria of hooded crane in the late period-113


title: Gut bacteria of hooded crane in the late period-112


title: Gut bacteria of hooded crane in the late period-111


title: Gut bacteria of hooded crane in the late period-110


title: Gut bacteria of hooded crane in the late period-108


title: HT29 cells, Shp53_2

value: HT29 colon cancer cell

value: total RNA of small Evs


title: diffuse glioma_EORTC 26101_004

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
tumor_DNA_FFPE
EORTC 26101_004

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions


title: Gut bacteria of hooded crane in the late period-109


title: diffuse glioma_EORTC 26101_003

description:
tumor_DNA_FFPE
EORTC 26101_003

value: female


title: Gut bacteria of hooded crane in the late period-105


title: GFP+ replicate 3

value: sroted GFP+ enveloping layer (EVL) cells


title: Gut bacteria of hooded crane in the late period-102


title: Gut bacteria of hooded crane in the late period-107


title: Gut bacteria of hooded crane in the late period-101


title: diffuse glioma_EORTC 26101_001

description:
tumor_DNA_FFPE
EORTC 26101_001


title: Gut bacteria of hooded crane in the middle period-99

value: Middle period


title: Gut bacteria of hooded crane in the middle period-100


title: Gut bacteria of hooded crane in the middle period-97


title: Gut bacteria of hooded crane in the middle period-93


title: Gut bacteria of hooded crane in the middle period-95


title: Gut bacteria of hooded crane in the middle period-98


title: Gut bacteria of hooded crane in the middle period-96


title: Gut bacteria of hooded crane in the middle period-92


title: Gut bacteria of hooded crane in the middle period-91


title: Gut bacteria of hooded crane in the late period-115


title: Gut bacteria of hooded crane in the middle period-89


title: Gut bacteria of hooded crane in the middle period-88


title: Gut bacteria of hooded crane in the middle period-87


title: Gut bacteria of hooded crane in the middle period-85


title: Gut bacteria of hooded crane in the middle period-83


title: Gut bacteria of hooded crane in the middle period-84


title: Gut bacteria of hooded crane in the early period-78


title: Gut bacteria of hooded crane in the early period-77


title: Gut bacteria of hooded crane in the early period-76


title: Gut bacteria of hooded crane in the middle period-81


title: Gut bacteria of hooded crane in the early period-80


title: Gut bacteria of hooded crane in the early period-79


title: Gut bacteria of hooded crane in the middle period-82


title: Gut bacteria of hooded crane in the early period-73


title: Gut bacteria of hooded crane in the middle period-94


title: Gut bacteria of hooded crane in the middle period-90


title: Gut bacteria of hooded crane in the early period-67


title: Gut bacteria of hooded crane in the early period-69


title: Gut bacteria of hooded crane in the early period-68


title: Gut bacteria of hooded crane in the early period-66


title: Gut bacteria of hooded crane in the early period-72


title: Gut bacteria of hooded crane in the early period-65


title: Gut bacteria of hooded crane in the early period-74


title: Gut bacteria of hooded crane in the early period-63


title: Gut bacteria of hooded crane in the early period-64


title: Gut bacteria of hooded crane in the early period-62


title: Gut bacteria of hooded crane in the early period-61


title: Gut bacteria of hooded crane in the middle period-86


title: Gut bacteria of bean goose in the late period-60

value: Anser fabalis


title: Gut bacteria of hooded crane in the early period-75

value: Hooded crane


title: Gut bacteria of bean goose in the late period-55

value: Late period


title: Gut bacteria of bean goose in the late period-54


title: Gut bacteria of hooded crane in the early period-70

value: Grus monacha


title: Gut bacteria of hooded crane in the early period-71

value: 16S rRNA


title: Gut bacteria of bean goose in the late period-48


title: Gut bacteria of bean goose in the late period-52


title: Gut bacteria of bean goose in the late period-46


title: Gut bacteria of bean goose in the late period-45


title: Gut bacteria of bean goose in the late period-42


title: Gut bacteria of bean goose in the late period-50


title: Gut bacteria of bean goose in the late period-47


title: Gut bacteria of bean goose in the middle period-39


title: Gut bacteria of bean goose in the middle period-38


title: Gut bacteria of bean goose in the middle period-37


title: Gut bacteria of bean goose in the middle period-36


title: Gut bacteria of bean goose in the late period-49


title: Gut bacteria of bean goose in the late period-59


title: Gut bacteria of bean goose in the middle period-34


title: Gut bacteria of bean goose in the late period-43


title: Gut bacteria of bean goose in the middle period-32


title: Gut bacteria of bean goose in the middle period-33


title: Gut bacteria of bean goose in the late period-57


title: Gut bacteria of bean goose in the middle period-35


title: Gut bacteria of bean goose in the late period-56


title: Gut bacteria of bean goose in the late period-51


title: Gut bacteria of bean goose in the middle period-30


title: Gut bacteria of bean goose in the middle period-29


title: Gut bacteria of bean goose in the late period-44


title: Gut bacteria of bean goose in the late period-41


title: Gut bacteria of bean goose in the middle period-40


title: Gut bacteria of bean goose in the early period-19

value: Early period


title: Gut bacteria of bean goose in the middle period-22

value: Bean goose


title: Gut bacteria of bean goose in the early period-20


title: Gut bacteria of bean goose in the middle period-26


title: Gut bacteria of bean goose in the middle period-25


title: Gut bacteria of bean goose in the early period-17


title: Gut bacteria of bean goose in the middle period-31


title: Gut bacteria of bean goose in the early period-5


title: Gut bacteria of bean goose in the middle period-27


title: Gut bacteria of bean goose in the early period-15


title: Gut bacteria of bean goose in the early period-6


title: Gut bacteria of bean goose in the early period-8


title: Gut bacteria of bean goose in the early period-7


title: Gut bacteria of bean goose in the early period-12


title: Gut bacteria of bean goose in the early period-14


title: Gut bacteria of bean goose in the early period-16


title: Gut bacteria of bean goose in the early period-3


title: Gut bacteria of bean goose in the early period-1


title: Gut bacteria of bean goose in the middle period-23


title: Gut bacteria of bean goose in the middle period-24


title: Gut bacteria of bean goose in the middle period-28


title: Gut bacteria of bean goose in the early period-9


title: Gut bacteria of bean goose in the early period-4


title: Microglia hC4B/- 2

city: Boston

first: Melis

last: Yilmaz

state: MA

address: 300 Longwood Avenue

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

data_processing:
fastq files were aligned to version 95 of mouse reference genome GRCm38 using STAR aligner
BAM files resulting from the alignments were summarized to genes using biomaRt package (Bioconductor)
Expression data was normalized using a weighted trimmed mean of the log expression ratios using edgeR (Bioconductor)
Gene annotations that did not have 3 cpm in at least 3 samples were dropped
Differentially expressed genes were identified using edgeR package (Bioconductor)
Genome_build: Mouse refernce genome GRCm38, release 95
Supplementary_files_format_and_content: tab-delimited text files raw gene counts for each sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Frontal Cortex

extract_protocol:
Microglia were first sorted from frontal cortex homogenates using the FACSAria. For each mouse, 1,000 microglia were sorted based on CD11bhigh and CD45low expression into 20 μl guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA was isolated using RNAClean XP beads (Agencourt A63987).
Template switching, cDNA synthesis, cDNA amplification and libraries were prepared using the Nextera kit (Illumina), following the manufacturer's instructions.

tag: tissue

value: Frontal cortex

value: Postnatal day 40

value: microglia


title: Microglia hC4B/- 1


title: Microglia hC4A/A 2


title: Microglia C4-/- 5


title: Microglia hC4A/- 4


title: Microglia hC4A/- 1


title: Microglia C4-/- 4


title: Microglia hC4A/A 1


title: Microglia hC4A/- 5


title: Microglia C4-/- 3


title: Microglia hC4B/- 3


title: Microglia hC4A/- 2


title: Microglia hC4B/- 4


title: mouse 1 Poly I/C

city: Mainz

first: Johannes

last: Braun

address: Langenbeckstr. 1

department: Center for Thrombosis and Hemostasis (CTH)

institute: University Medical Center, Johannes Gutenberg-University Mainz

hyb_protocol: According to standart Affimetrix protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data normalization by Robust Multi-array Average (RMA) approach and analysis of differentially expressed probe sets by Tukey's Bi-weight average algorithm and Analysis of Variance (ANOVA) were done with Affymetrix Expression Console Software and Affymetrix Transcriptome Analysis Console respectively.

source_name: spleen monocytes

label_protocol: Biotinylated cRNA were prepared according to standart Affimetrix protocol

extract_protocol: RNA was extracted with TRIzol reagent and processed with GeneChip™ WT PLUS Reagent Kit and hybridized on a GeneChip™ Mouse Gene 2.0 ST Array (Affymetrix)

treatment_protocol: selected EPCR WT monocytes were stimulated for 3 hours with IgG, HL7G (400ng/ml each), R848 (2µg/ml), CpG B (2.5 µM) or Poly I:C (1µg/ml)

value: Poly I/C


title: HCT-8 Control-shRNA cells-1

city: Beijing

first: shuang

last: shang

address: 2# Nan Wei Street

department: Pharmacology

institute: Institute of Material Medica

description: Gene expression data from HCT-8 cells stably expressing TRIB3-Control-shRNA-1

hyb_protocol: 3.5ug of cRNA were hybridized on Affymetrix Human Gene 2.0 ST Array at 45 degree C for 16 hours. Cartridge arrays were washed and stained using GeneChip Fluidic Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner with 7G upgrade.

data_processing: Intensity signals were normalized by RMA algorithm using Expression Console v1.4.1, Affymetrix. Statistical significant was determined by t-test. GO and KEGG analysis were performed by WebGestalt (updated on 1/30/2013). Heatmap was generated by R.

source_name: colon cancer cell line

label_protocol: 5.5 ug ss-cDNA was fragmented and labeled according to the standard Affymetrix protocol.

growth_protocol: HCT-8 cells were cultured in DMEM media.

extract_protocol: Total RNA was extracted by Trizol according to the manufacturer's instructions.

treatment_protocol: To generate cell populations stably expressing TRIB3-shRNA or Control-shRNA, plasmids were transfected into cells. After 24 hr of transfection, stable transfectants were selected in medium containing hygromycin for 14 days. After 2-3 passages in the presence of hygromycin, the cultured cells were used for experiments without cloning.

tag: genotype/variation

value: stably expressing TRIB3-Control-shRNA-1


title: HCT-8 Control-shRNA cells-3

description: Gene expression data from HCT-8 cells stably expressing TRIB3-Control-shRNA-3


title: mouse 2 unstimulated

value: unstimulated


title: mouse 1 CpGB

value: CpGB


title: Microglia hC4A/- 3


title: HCT-8 TRIB3-shRNA cells-1

description: Gene expression data from HCT-8 cells stably expressing TRIB3-shRNA -1

value: stably expressing TRIB3-shRNA-1


title: mouse 1 R848


title: mouse 1 unstimulated


title: HCT-8 TRIB3-shRNA cells-3

description: Gene expression data from HCT-8 cells stably expressing TRIB3-shRNA -3


title: HCT-8 Control-shRNA cells-2

description: Gene expression data from HCT-8 cells stably expressing TRIB3-Control-shRNA-2


title: mouse 2 HL7G


title: HCT-8 TRIB3-shRNA cells-2

description: Gene expression data from HCT-8 cells stably expressing TRIB3-shRNA -2


title: Microglia C4-/- 1


title: Microglia C4-/- 2


title: mouse 1 HL7G


title: Microglia WT 4

value: Wild type


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_H8412T1sgmga]

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm10 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: mouse lung tumor

extract_protocol:
Cells were stored in Trizol and RNA was isolated according to manufacturer instructions
RNA-seq libraries were prepared from total RNA using

treatment_protocol: Tumors from both groups were mechanically dissociated and re-suspended in Trizol

value: whole tumor mostly tumor cells plus immune and stromal cells

tag: viral vector used

value: lentiCRISPRv2cre sgMga


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_H8752T3sgmga]


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_G8814T1sgmga]


title: Microglia WT 2

tag: genotype


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_H8566T1sgmga]


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8692T1emp]

value: lentiCRISPRv2cre empty


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8553T1emp]


title: Microglia WT 3


title: Microglia WT 1


title: Lung Ricin 48h scRNA-seq

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Illumina Casava software used for basecalling.
Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10
Remove trailing low quality or N bases
Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than  7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30,  removed non-overlapping portions
Drop reads below the 26 bases long
Discard those reads that can not form paired. The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this.
Genome_build: mm10
Supplementary_files_format_and_content: files contained the 10X processed data of four samples

source_name: Lung

extract_protocol:
Lungs were removed, lyses into a single cells. The protoplast suspension was loaded into Chromium microfluidic chips with 3' (V3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics).
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3' v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

treatment_protocol: Distal lung parenchyma samples exposed to aerosolized PBS and ricin toxin at 8, 24, and 48 hours

tag: strain

value: lung

value: 48 hours post-injury

tag: treatment

value: Ricin-treated conditon from 48 hours post-injury


title: Empty KP cell line 1 bio rep#2

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to mm10 using TopHat v2.1.0.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1 & assigned to genes using Feature Counts

source_name: mouse lung cancer cell line

extract_protocol:
Cells were stored in Trizol and RNA extracted using the Zymogenetics directZol miniprep kit
RNA-seq libraries were prepared from total RNA using

treatment_protocol: Cell lines from both groups were cultured in 10% FBS containing DMEM with antibiotics (penicillin/ streptomycin)

value: mouse non small cell lung cancer cell


title: Lung Ricin 24h scRNA-seq

value: 24 hours post-injury

value: Ricin-treated conditon from 24 hours post-injury


title: Empty KP cell line 1 bio rep#1


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8444T1emp]


title: Empty KP cell line 1 bio rep#3


title: sgMga KP cell line 3 bio rep#2


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_H8692T2emp]


title: Lung Ricin 8h scRNA-seq

value: 8 hours post-injury

value: Ricin-treated conditon from 8 hours post-injury


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_G8814T2sgmga]


title: sgMga KP cell line 3 bio rep#1


title: Lung PBS Sham scRNA-seq

value: control

value: Sham condition


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8411T1emp]


title: Empty KP cell line 2 bio rep#2


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8409T2emp]


title: sgMga KP cell line 3 bio rep#3


title: Empty KP cell line 2 bio rep#3


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre sgMga lentivirus) [Sample_H8752T2sgmga]


title: Empty KP cell line 2 bio rep#1


title: Kras G12D LSL mouse (intratracheal instillation of LV2cre Empty lentivirus) [Sample_H8444T2emp]


title: sgMga KP cell line 2 bio rep#1


title: sgMga KP cell line 2 bio rep#3


title: sgMga KP cell line 1 bio rep#2


title: sgMga KP cell line 2 bio rep#2


title: sgMga KP cell line 1 bio rep#1


title: sgMga KP cell line 1 bio rep#3


title: Lung - mRNA_O3_Day1_Rep3

city: Morgantown

first: Quincy

middle: Alexander

last: Hathaway

state: WV

address: 1 Medical Center Road

department: Exercise Physiology

institute: West Virginia University

data_processing:
A mouse decoy-aware index was created using both the Ensembl primary assembly (release 99) and the transcriptome (release 99) through Salmon 1.1.0.
The index was then used to map the 51 bp paired end reads for quantification, specifying options “--validateMappings” and “gcBias” through Salmon 1.1.0.
Quantification files were imported into R (v3.6.3) using tximeta.
Differential gene expression performed through DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: quantification files produced by Salmon 1.1.0
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: lung homogenate

extract_protocol:
RNA was isolated from whole lung homogenate after pulverizing the lung tissues at -80 ° C. Total RNA was isolated using RNeasy Mini Kit (Qiagen 74106) and reverse transcription was performed using manufacturer’s protocol.
Libraries were built with the TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) and run on the HiSeq 2500 (Illumina) in 51bp paired end reads. Fastq files were mapped and quantified using the mapping-based mode of Salmon 1.1.0.

treatment_protocol: 8 week old male C57BL/6 mice were randomly divided into four groups ( air, carbon black, ozone and carbon black + ozone) and exposed to 2 ppm ozone (O3) for 3 hours, 10 mg/m3 carbon black (CB) for 3 hours, 10 mg/m3 CB and 2ppm ozone co-exposure (CB+O3) for 3 hours daily up to 4 days.

value: ozone

value: male

value: 8-12 weeks

value: wild type


title: Lung - mRNA_O3_Day4_Rep1


title: Lung - mRNA_CB_Day1_Rep3

value: carbon black


title: Lung - mRNA_CB_Day4_Rep2


title: Lung - mRNA_O3_Day4_Rep3


title: Lung - mRNA_CB_Day1_Rep1


title: Lung - mRNA_CB-O3_Day1_Rep4

value: carbon black + ozone


title: Lung - mRNA_CB_Day4_Rep3


title: Lung - mRNA_CB-O3_Day4_Rep1


title: Lung - mRNA_CB_Day4_Rep1


title: Lung - mRNA_CB_Day1_Rep2


title: Lung - mRNA_CB-O3_Day1_Rep2


title: Lung - mRNA_CB-O3_Day1_Rep3


title: Lung - mRNA_O3_Day1_Rep1


title: Lung - mRNA_CB-O3_Day4_Rep3


title: Lung - mRNA_O3_Day1_Rep4


title: Lung - mRNA_O3_Day1_Rep2


title: Lung - mRNA_CB-O3_Day4_Rep2


title: Lung - mRNA_Sham_Day4_Rep3

value: sham


title: Lung - mRNA_Sham_Day4_Rep2

value: lung


title: Lung - mRNA_Sham_Day4_Rep1


title: Lung - mRNA_Sham_Day1_Rep4


title: Lung - mRNA_CB-O3_Day1_Rep1


title: Lung - mRNA_O3_Day4_Rep2


title: Lung - mRNA_Sham_Day1_Rep3


title: Lung - mRNA_Sham_Day1_Rep2


title: Lung - mRNA_CB_Day1_Rep4


title: plasma small RNA-Seq VOVP98

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Fastq files were quality-controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads shorter than 14 nt were discarded.
The QC-passed reads were clipped from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics. The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasma

extract_protocol:
Total RNA from plasma samples was extracted with the miRNeasy plasma/serum mini kit (Qiagen) using the QiaCube extractor (Qiagen) following the manufacturer's instructions. RNA samples were stored until analysis at -80°C.
Small RNA transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs Inc., USA). Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction, and PCR amplification were performed according to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., Ipswich, MA, USA). After PCR amplification, the cDNA constructs were purified with the QIAQuick PCR Purification Kit (Qiagen, Germany) following the modifications suggested by the NEBNext Multiplex Small RNA Library Prep Protocol and loaded on the Bioanalyzer 2100 (Agilent Technologies, Milan, Italy) using the DNA High Sensitivity Kit (Agilent, Germany) according to the manufacturer’s protocol.

tag: diet

value: Vegan


title: plasma small RNA-Seq VOVP97

value: Vegetarian


title: plasma small RNA-Seq VOVP87


title: plasma small RNA-Seq VOVP91


title: plasma small RNA-Seq VOVP78


title: plasma small RNA-Seq VOVP95

value: Omnivorous


title: plasma small RNA-Seq VOVP81


title: plasma small RNA-Seq VOVP77


title: plasma small RNA-Seq VOVP80


title: plasma small RNA-Seq VOVP85


title: plasma small RNA-Seq VOVP71


title: plasma small RNA-Seq VOVP73


title: plasma small RNA-Seq VOVP70


title: Lung - mRNA_Sham_Day1_Rep1

tag: gender


title: plasma small RNA-Seq VOVP90


title: plasma small RNA-Seq VOVP69


title: plasma small RNA-Seq VOVP74


title: plasma small RNA-Seq VOVP94


title: plasma small RNA-Seq VOVP82


title: plasma small RNA-Seq VOVP67


title: plasma small RNA-Seq VOVP92


title: plasma small RNA-Seq VOVP96


title: plasma small RNA-Seq VOVP68


title: plasma small RNA-Seq VOVP88


title: plasma small RNA-Seq VOVP84


title: plasma small RNA-Seq VOVP75


title: plasma small RNA-Seq VOVP63


title: plasma small RNA-Seq VOVP72


title: plasma small RNA-Seq VOVP64


title: plasma small RNA-Seq VOVP79


title: plasma small RNA-Seq VOVP61


title: plasma small RNA-Seq VOVP62


title: plasma small RNA-Seq VOVP60


title: plasma small RNA-Seq VOVP53


title: plasma small RNA-Seq VOVP55


title: plasma small RNA-Seq VOVP44


title: plasma small RNA-Seq VOVP42


title: plasma small RNA-Seq VOVP45


title: plasma small RNA-Seq VOVP43


title: plasma small RNA-Seq VOVP54


title: plasma small RNA-Seq VOVP51


title: plasma small RNA-Seq VOVP40


title: plasma small RNA-Seq VOVP50


title: plasma small RNA-Seq VOVP59


title: plasma small RNA-Seq VOVP58


title: plasma small RNA-Seq VOVP38


title: plasma small RNA-Seq VOVP39


title: plasma small RNA-Seq VOVP4


title: plasma small RNA-Seq VOVP36


title: plasma small RNA-Seq VOVP56


title: plasma small RNA-Seq VOVP48


title: plasma small RNA-Seq VOVP34


title: plasma small RNA-Seq VOVP46


title: plasma small RNA-Seq VOVP41


title: plasma small RNA-Seq VOVP37


title: plasma small RNA-Seq VOVP47


title: plasma small RNA-Seq VOVP35


title: plasma small RNA-Seq VOVP32


title: plasma small RNA-Seq VOVP33


title: plasma small RNA-Seq VOVP28


title: plasma small RNA-Seq VOVP52


title: plasma small RNA-Seq VOVP29


title: plasma small RNA-Seq VOVP26


title: plasma small RNA-Seq VOVP24


title: plasma small RNA-Seq VOVP21


title: plasma small RNA-Seq VOVP23


title: plasma small RNA-Seq VOVP137


title: plasma small RNA-Seq VOVP19


title: plasma small RNA-Seq VOVP142


title: plasma small RNA-Seq VOVP136


title: plasma small RNA-Seq VOVP141


title: plasma small RNA-Seq VOVP140


title: plasma small RNA-Seq VOVP18


title: plasma small RNA-Seq VOVP20


title: plasma small RNA-Seq VOVP15


title: plasma small RNA-Seq VOVP134


title: plasma small RNA-Seq VOVP132


title: plasma small RNA-Seq VOVP133


title: plasma small RNA-Seq VOVP130


title: plasma small RNA-Seq VOVP144


title: plasma small RNA-Seq VOVP13


title: plasma small RNA-Seq VOVP135


title: plasma small RNA-Seq VOVP14


title: plasma small RNA-Seq VOVP139


title: plasma small RNA-Seq VOVP129


title: plasma small RNA-Seq VOVP131


title: plasma small RNA-Seq VOVP16


title: plasma small RNA-Seq VOVP127


title: plasma small RNA-Seq VOVP125


title: plasma small RNA-Seq VOVP124


title: plasma small RNA-Seq VOVP126


title: plasma small RNA-Seq VOVP25


title: plasma small RNA-Seq VOVP122


title: plasma small RNA-Seq VOVP121


title: plasma small RNA-Seq VOVP12


title: plasma small RNA-Seq VOVP119


title: plasma small RNA-Seq VOVP113


title: plasma small RNA-Seq VOVP116


title: plasma small RNA-Seq VOVP105


title: plasma small RNA-Seq VOVP107


title: plasma small RNA-Seq VOVP112


title: plasma small RNA-Seq VOVP110


title: plasma small RNA-Seq VOVP11


title: plasma small RNA-Seq VOVP114


title: plasma small RNA-Seq VOVP101


title: plasma small RNA-Seq VOVP115


title: plasma small RNA-Seq VOVP104


title: plasma small RNA-Seq VOVP108


title: plasma small RNA-Seq VOVP106


title: plasma small RNA-Seq VOVP102


title: plasma small RNA-Seq VOVP10


title: plasma small RNA-Seq VOVP09


title: plasma small RNA-Seq VOVP08


title: plasma small RNA-Seq VOVP117


title: plasma small RNA-Seq VOVP07


title: plasma small RNA-Seq VOVP06


title: plasma small RNA-Seq VOVP03


title: plasma small RNA-Seq VOVP02


title: plasma small RNA-Seq VOVP109


title: mRNAseq_293Tcells_siHSF1_rep2

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

description:
polyadenylation-selected total RNA
processed data file: mRNAseq_293Tcells_siHSF1_reps1to4_FPMnorm.bedgraph.tdf

data_processing:
The reads were filtered with fastx-toolkit (hannonlab.cshl.edu) usng fastq_quality_filter with -q 20 and -p 80 parameters.
After filtering the R1 and R2 reads, their correct pairing was restored with fastq_pair (https://github.com/linsalrob/fastq-pair).
The paired R1 and R2 reads were aligned to hg19 using tophat2
The bam files were sorted with samtools (http://www.htslib.org/doc/samtools.html), and depth-normalized bedgraph files were generated using genomeCoverageBed of the bedtools package (https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html). The bedgraphs were compacted to IGV-preferred .tdf format (http://software.broadinstitute.org/software/igv/).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph.tdf files providing replicate-combined and sequencing depth-normalized samples to be visualized in the IGV  (http://software.broadinstitute.org/software/igv/).

growth_protocol: 293T Human Embryonic Kidney (HEK) cells (ATCC CRL-1573) were grown at 37 °C in DMEM supplemented with 10% FBS and 91 μg mL-1 Normocin.

extract_protocol:
After 48 hours of transfection, RNA was extracted and purified from the cells using RNEasy extraction kit (Qiagen) according to the manufacturer’s instructions using QIAshredder columns for homogenization. From the total RNA, the polyadenylated RNA was enriched by GeneWiz.
Library preparation and Illumina sequencing of the polyadenylation-seleced RNA (mRNA) was conducted by GeneWiz.

treatment_protocol: The cells were transfected with siRNA targeting a scrabled RNA sequence, HSF1 mRNA, or CTCF mRNA. The transfections were conducted using Lipofectamine LTX (Invitrogen) according to the manufacturer’s protocol (MAN0007822)

value: Human Embryonic Kidney (HEK) cells

value: siHSF1 transfected (HSF1 knockdown)


title: mRNAseq_293Tcells_siHSF1_rep3


title: mRNAseq_293Tcells_siHSF1_rep1


title: plasma small RNA-Seq VOVP111


title: mRNAseq_293Tcells_siCTCF_rep4

description:
polyadenylation-selected total RNA
processed data file: mRNAseq_293Tcells_siCTCF_reps1to4_FPMnorm.bedgraph.tdf

value: siCTCF transfected (CTCF kockdown)


title: plasma small RNA-Seq VOVP100


title: mRNAseq_293Tcells_siCTCF_rep3


title: mRNAseq_293Tcells_siHSF1_rep4


title: mRNAseq_293Tcells_Scr_rep1

description:
polyadenylation-selected total RNA
processed data file: mRNAseq_293Tcells_Scr_reps1to4_FPMnorm.bedgraph.tdf

value: scrambled transfected (control)


title: mRNAseq_293Tcells_Scr_rep3


title: mRNAseq_293Tcells_Scr_rep4


title: mRNAseq_293Tcells_siCTCF_rep2


title: 9FTreg95

city: Berkeley

first: Allon

last: Wagner

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

data_processing:
Reads were pseuoaligned with Kallisto v0.46.0 to the Ensembl v96 human transcripome
Transcript TPMs were aggregated and summed for gene-level analysis, and then log2-transformed; non-protein-coding transcripts were excluded
Genome_build: GRCh38.96
Supplementary_files_format_and_content: linear-scale count matrix in csv format

source_name: iTreg

extract_protocol:
PBMCs were isolated from peripheral blood and Treg cells were single sorted into 96-well plates by FACS using CD4+CD25hiCD127lo/neg antibodies. For adipose tissue, we first performed collagenase digestion. Next, the lymphocytes were isolated from the sample by Ficoll gradient and centrifugation (as done with PBMC isolation) in a ratio of 9 mL of sample to 4 mL of Ficoll. The lymphocyte layer was removed and washed. The Treg cells were then single sorted by FACS using CD4+CD25hiCD127lo/neg antibodies.
Illumina TruSeq Stranded mRNA kit was used for library prep, and sequenced with a 2 × 100 bp paired-end protocol on the HiSeq 2000 Sequencing System (Illumina).

tag: donor id

value: Fat

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

value: F

tag: donor group


title: 9FTreg96

tag: tissue


title: mRNAseq_293Tcells_Scr_rep2

tag: cell line

tag: cell type

tag: genotype/variation


title: 9FTreg92


title: 9FTreg88


title: 9FTreg89


title: mRNAseq_293Tcells_siCTCF_rep1


title: 9FTreg94


title: 9FTreg85


title: 9FTreg93


title: 9FTreg86


title: 9FTreg83


title: 9FTreg91


title: 9FTreg87


title: 9FTreg82


title: 9FTreg81


title: 9FTreg84


title: 9FTreg80


title: 9FTreg78


title: 9FTreg79


title: 9FTreg77


title: 9FTreg76


title: 9FTreg75


title: 9FTreg73


title: 9FTreg74


title: 9FTreg90


title: 9FTreg72


title: 9FTreg69


title: 9FTreg70


title: 9FTreg71


title: 9FTreg67


title: 9FTreg68


title: 9FTreg66


title: 9FTreg65


title: 9FTreg59


title: 9FTreg58


title: 9FTreg64


title: 9FTreg61


title: 9FTreg63


title: 9FTreg62


title: 9FTreg52


title: 9FTreg56


title: 9FTreg55


title: 9FTreg53


title: 9FTreg51


title: 9FTreg50


title: 9FTreg54


title: 9FTreg49


title: 9FTreg48


title: 9FTreg47


title: 9FTreg45


title: 9FTreg42


title: 9FTreg43


title: 9FTreg41


title: 9FTreg60


title: 9FTreg39


title: 9FTreg57


title: 9FTreg38


title: 9FTreg37


title: 9FTreg36


title: 9FTreg35


title: 9FTreg34


title: 9FTreg31


title: 9FTreg32


title: 9FTreg30


title: 9FTreg29


title: 9FTreg28


title: 9FTreg25


title: 9FTreg27


title: 9FTreg26


title: 9FTreg46


title: 9FTreg20


title: 9FTreg21


title: 9FTreg44


title: 9FTreg40


title: 9FTreg12


title: 9FTreg16


title: 9FTreg18


title: 9FTreg14


title: 9FTreg33


title: 9FTreg09


title: 9FTreg10


title: 9FTreg08


title: 9FTreg07


title: 9FTreg24


title: 9FTreg22


title: 9FTreg05


title: 9BTreg96

value: Blood


title: 9FTreg02


title: 9FTreg04


title: 9FTreg23


title: 9FTreg01


title: 9FTreg03


title: 9FTreg19


title: 9BTreg94


title: 9BTreg95


title: 9BTreg93


title: 9FTreg17


title: 9FTreg15


title: 9FTreg13


title: 9FTreg11


title: 9BTreg90


title: 9BTreg91


title: 9FTreg06


title: 9BTreg84


title: 9BTreg83


title: 9BTreg85


title: 9BTreg88


title: 9BTreg86


title: 9BTreg81


title: 9BTreg87


title: 9BTreg79


title: 9BTreg77


title: 9BTreg76


title: 9BTreg92


title: 9BTreg75


title: 9BTreg89


title: 9BTreg80


title: 9BTreg72


title: 9BTreg73


title: 9BTreg74


title: 9BTreg68


title: 9BTreg70


title: 9BTreg69


title: 9BTreg71


title: 9BTreg67


title: 9BTreg65


title: 9BTreg66


title: 9BTreg64


title: 9BTreg63


title: 9BTreg62


title: 9BTreg82


title: 9BTreg61


title: 9BTreg78


title: 9BTreg60


title: 9BTreg58


title: 9BTreg54


title: 9BTreg56


title: 9BTreg55


title: 9BTreg59


title: 9BTreg53


title: 9BTreg57


title: 9BTreg51


title: 9BTreg50


title: 9BTreg49


title: 9BTreg52


title: 9BTreg47


title: 9BTreg44


title: 9BTreg48


title: 9BTreg43


title: 9BTreg42


title: 9BTreg39


title: 9BTreg40


title: 9BTreg38


title: 9BTreg37


title: 9BTreg36


title: 9BTreg35


title: 9BTreg34


title: 9BTreg33


title: 9BTreg32


title: 9BTreg31


title: 9BTreg24


title: 9BTreg21


title: 9BTreg46


title: 9BTreg23


title: 9BTreg45


title: 9BTreg41


title: 9BTreg29


title: 9BTreg27


title: 9BTreg18


title: 9BTreg19


title: 9BTreg20


title: 9BTreg17


title: 9BTreg12


title: 9BTreg13


title: 9BTreg14


title: 9BTreg15


title: 9BTreg16


title: 9BTreg11


title: 9BTreg10


title: 9BTreg09


title: 9BTreg06


title: 9BTreg08


title: 9BTreg28


title: 9BTreg05


title: 9BTreg07


title: 9BTreg30


title: 9BTreg04


title: 9BTreg25


title: 9BTreg26


title: 8FTreg9

value: HC


title: 9BTreg01


title: 9BTreg03


title: 9BTreg02


title: 8FTreg93


title: 8FTreg96


title: 8FTreg95


title: 8FTreg94


title: 8FTreg92


title: 8FTreg8


title: 8FTreg89


title: 8FTreg82


title: 8FTreg84


title: 8FTreg88


title: 8FTreg86


title: 8FTreg85


title: 8FTreg87


title: 8FTreg81


title: 8FTreg83


title: 8FTreg80


title: 8FTreg78


title: 8FTreg7


title: 8FTreg79


title: 8FTreg77


title: 8FTreg76


title: 8FTreg75


title: 8FTreg74


title: 8FTreg90


title: 8FTreg91


title: 8FTreg71


title: 8FTreg72


title: 8FTreg73


title: 8FTreg70


title: 8FTreg6


title: 8FTreg69


title: 8FTreg67


title: 8FTreg66


title: 8FTreg68


title: 8FTreg65


title: 8FTreg61


title: 8FTreg64


title: 8FTreg63


title: 8FTreg60


title: 8FTreg59


title: 8FTreg58


title: 8FTreg5


title: 8FTreg55


title: 8FTreg62


title: 8FTreg54


title: 8FTreg52


title: 8FTreg57


title: 8FTreg51


title: 8FTreg4


title: 8FTreg50


title: 8FTreg53


title: 8FTreg56


title: 8FTreg49


title: 8FTreg48


title: 8FTreg40


title: 8FTreg47


title: 8FTreg41


title: 8FTreg43


title: 8FTreg46


title: 8FTreg45


title: 8FTreg44


title: 8FTreg42


title: 8FTreg3


title: 8FTreg39


title: 8FTreg37


title: 8FTreg34


title: 8FTreg35


title: 8FTreg38


title: 8FTreg36


title: 8FTreg32


title: 8FTreg33


title: 8FTreg29


title: 8FTreg28


title: 8FTreg30


title: 8FTreg2


title: 8FTreg31


title: 8FTreg26


title: 8FTreg27


title: 8FTreg25


title: 8FTreg23


title: 8FTreg24


title: 8FTreg1


title: 8FTreg22


title: 8FTreg21


title: 8FTreg18


title: 8FTreg17


title: 8FTreg15


title: 8FTreg19


title: 8FTreg14


title: 8FTreg16


title: 8FTreg20


title: 8FTreg12


title: 8FTreg10


title: 8FTreg13


title: 8BTreg95


title: 8BTreg94


title: 8FTreg11


title: 9BTreg22


title: 8BTreg92


title: 8BTreg93


title: 8BTreg91


title: 8BTreg90


title: 8BTreg87


title: 8BTreg89


title: 8BTreg86


title: 8BTreg85


title: 8BTreg84


title: 8BTreg83


title: 8BTreg82


title: 8BTreg80


title: 8BTreg76


title: 8BTreg78


title: 8BTreg75


title: 8BTreg74


title: 8BTreg77


title: 8BTreg81


title: 8BTreg79


title: 8BTreg70


title: 8BTreg96


title: 8BTreg73


title: 8BTreg71


title: 8BTreg68


title: 8BTreg67


title: 8BTreg72


title: 8BTreg65


title: 8BTreg66


title: 8BTreg69


title: 8BTreg64


title: 8BTreg62


title: 8BTreg61


title: 8BTreg60


title: 8BTreg88


title: 8BTreg58


title: 8BTreg59


title: 8BTreg63


title: 8BTreg57


title: 8BTreg55


title: 8BTreg54


title: 8BTreg56


title: 8BTreg53


title: 8BTreg48


title: 8BTreg52


title: 8BTreg50


title: 8BTreg46


title: 8BTreg51


title: 8BTreg49


title: 8BTreg47


title: 8BTreg42


title: 8BTreg39


title: 8BTreg44


title: 8BTreg40


title: 8BTreg45


title: 8BTreg36


title: 8BTreg41


title: 8BTreg37


title: 8BTreg35


title: 8BTreg34


title: 8BTreg33


title: 8BTreg29


title: 8BTreg31


title: 8BTreg32


title: 8BTreg30


title: 8BTreg27


title: 8BTreg26


title: 8BTreg25


title: 8BTreg21


title: 8BTreg23


title: 8BTreg20


title: 8BTreg17


title: 8BTreg24


title: 8BTreg28


title: 8BTreg22


title: 8BTreg12


title: 8BTreg38


title: 8BTreg14


title: 8BTreg10


title: 8BTreg43


title: 8BTreg08


title: 8BTreg16


title: 8BTreg05


title: 8BTreg04


title: 8BTreg01


title: 8BTreg19


title: 8BTreg06


title: 8BTreg13


title: 8BTreg15


title: 8BTreg03


title: 8BTreg07


title: 7FTreg96


title: 8BTreg09


title: 7FTreg94


title: 8BTreg18


title: 7FTreg93


title: 8BTreg11


title: 7FTreg92


title: 7FTreg90


title: 7FTreg87


title: 8BTreg02


title: 7FTreg89


title: 7FTreg85


title: 7FTreg83


title: 7FTreg82


title: 7FTreg95


title: 7FTreg75


title: 7FTreg74


title: 7FTreg76


title: 7FTreg77


title: 7FTreg72


title: 7FTreg71


title: 7FTreg70


title: 7FTreg91


title: 7FTreg88


title: 7FTreg67


title: 7FTreg63


title: 7FTreg86


title: 7FTreg65


title: 7FTreg81


title: 7FTreg84


title: 7FTreg64


title: 7FTreg79


title: 7FTreg59


title: 7FTreg60


title: 7FTreg62


title: 7FTreg61


title: 7FTreg80


title: 7FTreg78


title: 7FTreg73


title: 7FTreg58


title: 7FTreg57


title: 7FTreg53


title: 7FTreg54


title: 7FTreg69


title: 7FTreg55


title: 7FTreg52


title: 7FTreg51


title: 7FTreg68


title: 7FTreg56


title: 7FTreg66


title: 7FTreg48


title: 7FTreg47


title: 7FTreg46


title: 7FTreg45


title: 7FTreg44


title: 7FTreg42


title: 7FTreg43


title: 7FTreg41


title: 7FTreg37


title: 7FTreg39


title: 7FTreg38


title: 7FTreg36


title: 7FTreg35


title: 7FTreg34


title: 7FTreg33


title: 7FTreg30


title: 7FTreg31


title: 7FTreg50


title: 7FTreg29


title: 7FTreg32


title: 7FTreg40


title: 7FTreg28


title: 7FTreg26


title: 7FTreg24


title: 7FTreg49


title: 7FTreg23


title: 7FTreg27


title: 7FTreg22


title: 7FTreg25


title: 7FTreg21


title: 7FTreg20


title: 7FTreg19


title: 7FTreg18


title: 7FTreg16


title: 7FTreg15


title: 7FTreg14


title: 7FTreg13


title: 7FTreg11


title: 7FTreg12


title: 7FTreg10


title: 7FTreg08


title: 7BTreg96


title: 7FTreg05


title: 7FTreg06


title: 7FTreg03


title: 7FTreg07


title: 7FTreg02


title: 7BTreg95


title: 7BTreg92


title: 7FTreg01


title: 7BTreg91


title: 7BTreg89


title: 7BTreg90


title: 7BTreg93


title: 7FTreg17


title: 7BTreg87


title: 7BTreg86


title: 7BTreg85


title: 7BTreg84


title: 7BTreg83


title: 7BTreg82


title: 7BTreg80


title: 7BTreg79


title: 7FTreg09


title: 7FTreg04


title: 7BTreg77


title: 7BTreg94


title: 7BTreg81


title: 7BTreg74


title: 7BTreg75


title: 7BTreg76


title: 7BTreg73


title: 7BTreg71


title: 7BTreg72


title: 7BTreg88


title: 7BTreg66


title: 7BTreg67


title: 7BTreg69


title: 7BTreg70


title: 7BTreg65


title: 7BTreg68


title: 7BTreg64


title: 7BTreg63


title: 7BTreg62


title: 7BTreg60


title: 7BTreg61


title: 7BTreg59


title: 7BTreg78


title: 7BTreg58


title: 7BTreg57


title: 7BTreg55


title: 7BTreg56


title: 7BTreg54


title: 7BTreg53


title: 7BTreg52


title: 7BTreg50


title: 7BTreg51


title: 7BTreg46


title: 7BTreg48


title: 7BTreg45


title: 7BTreg49


title: 7BTreg43


title: 7BTreg44


title: 7BTreg42


title: 7BTreg41


title: 7BTreg36


title: 7BTreg34


title: 7BTreg40


title: 7BTreg39


title: 7BTreg35


title: 7BTreg37


title: 7BTreg30


title: 7BTreg31


title: 7BTreg32


title: 7BTreg33


title: 7BTreg29


title: 7BTreg28


title: 7BTreg26


title: 7BTreg27


title: 7BTreg25


title: 7BTreg24


title: 7BTreg23


title: 7BTreg47


title: 7BTreg22


title: 7BTreg21


title: 7BTreg20


title: 7BTreg18


title: 7BTreg19


title: 7BTreg17


title: 7BTreg15


title: 7BTreg38


title: 7BTreg16


title: 7BTreg12


title: 7BTreg14


title: 7BTreg13


title: 7BTreg11


title: 7BTreg10


title: 7BTreg09


title: 7BTreg07


title: 7BTreg06


title: 7BTreg05


title: 7BTreg08


title: 7BTreg02


title: 7BTreg04


title: 7BTreg01


title: 7BTreg03


title: 6FTreg92


title: 6FTreg93


title: 6FTreg95


title: 6FTreg94


title: 6FTreg96


title: 6FTreg91


title: 6FTreg90


title: 6FTreg89


title: 6FTreg87


title: 6FTreg86


title: 6FTreg88


title: 6FTreg85


title: 6FTreg84


title: 6FTreg83


title: 6FTreg82


title: 6FTreg77


title: 6FTreg76


title: 6FTreg79


title: 6FTreg75


title: 6FTreg81


title: 6FTreg74


title: 6FTreg80


title: 6FTreg78


title: 6FTreg73


title: 6FTreg71


title: 6FTreg70


title: 6FTreg72


title: 6FTreg68


title: 6FTreg67


title: 6FTreg69


title: 6FTreg66


title: 6FTreg64


title: 6FTreg63


title: 6FTreg62


title: 6FTreg60


title: 6FTreg65


title: 6FTreg59


title: 6FTreg58


title: 6FTreg61


title: 6FTreg56


title: 6FTreg54


title: 6FTreg55


title: 6FTreg57


title: 6FTreg53


title: 6FTreg52


title: 6FTreg51


title: 6FTreg49


title: 6FTreg48


title: 6FTreg47


title: 6FTreg46


title: 6FTreg44


title: 6FTreg45


title: 6FTreg43


title: 6FTreg39


title: 6FTreg41


title: 6FTreg40


title: 6FTreg36


title: 6FTreg38


title: 6FTreg35


title: 6FTreg32


title: 6FTreg33


title: 6FTreg37


title: 6FTreg31


title: 6FTreg34


title: 6FTreg28


title: 6FTreg29


title: 6FTreg30


title: 6FTreg27


title: 6FTreg25


title: 6FTreg24


title: 6FTreg23


title: 6FTreg50


title: 6FTreg22


title: 6FTreg20


title: 6FTreg18


title: 6FTreg26


title: 6FTreg17


title: 6FTreg16


title: 6FTreg14


title: 6FTreg15


title: 6FTreg42