title: Wild-type 2 (2)

description: mRNA and LncRNA

extract_protocol:
Nine-day-old wild-type  seedlings grown on MS plates were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was removed by Ribo-zeroTM Rrna Removal Kit (Epicentre),
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library and sequencing was done on Illumina Hiseq 2500 platform.

tag: cultivar

value: Nine-day-old


title: SMRT_6mA_3w

status: Public on Apr 16 2018

type: SRA

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

library_source: genomic

data_processing:
Library strategy: SMRT-seq
Each of the raw data in bax.h5 format was first aligned to Arabidopsis TAIR10 genome using pbalign in base modification identification mode. The polymerase kinetics information was further loaded after alignment by loadChemistry.py and loadPulses scripts. Then post-aligned datasets were sorted by using cmph5tools. Finally, the 6mA was identified using ipdSummary.py script. We then filtered out 6mAs with less than 25 coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: The gff file is the PacBio standard analysis protocol result for DNA modification containing the 6mA sites information, genome locus, strand, coverage, IPD ratio and context sequence

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: Arabidopsis thaliana plants were grown on MS plates in growth chambers under long day conditions (16 hr light/8 hr dark) at 23°C ± 2°C.

extract_protocol:
3-week-old wild-type seedlings grown on MS plates were harvested and genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
The DNA libraries have been prepared following the PacBio instructions and sequenced on 16 SMRT cells using Pacific Biosciences RSII sequencing technology (Pacific Biosciences). The SMRT bell was produced using the DNA Template Prep Kit 1.0 (Pacific Biosciences). SMRTbell templates were bound to polymerases by using the DNA/Polymerase Binding Kit P6 v2 (Pacific Biosciences). 10 μg of Arabidopsis genomic DNA were mechanically sheared to an average size distribution of 10 kb.  Polymerase-template complexes were bound to magbeads by using Magbead Binding Kit (Pacific Biosciences), and sequencing was carried out on the PacBio RSII by using the DNA Sequencing Kit 4.0 (Pacific Biosciences). Movie lengths were 240 min for each of 16 SMRT cells. Subread filtering was performed by using Pacific Biosciences’ SMRT analysis software (v2.3.1).

tag: ecotype

tag: age


title: Wild-type 6

library_source: transcriptomic

data_processing:
Alignment: TopHat v2.0.9 using default settings; expression levels: Cufflinks v2.1.1 using default settings
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

extract_protocol:
3-week-old wild-type  seedlings grown on MS plates were harvested and total RNA were extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was removed by Ribo-zeroTM Rrna Removal Kit (Epicentre),
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library and sequencing was done on Illumina Hiseq 2500 platform.

tag: genotype/variation


title: Wild-type 1 (2)

description: mRNA and LncRNA


title: Wild-type 5


title: Wild-type 3 (2)

description: mRNA and LncRNA


title: SMRT_6mA

data_processing:
Each of the raw data in bax.h5 format was first aligned to Arabidopsis TAIR10 genome using pbalign in base modification identification mode. The polymerase kinetics information was further loaded after alignment by loadChemistry.py and loadPulses scripts. Then post-aligned datasets were sorted by using cmph5tools. Finally, the 6mA was identified using ipdSummary.py script. We then filtered out 6mAs with less than 25 coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: The gff file is the PacBio standard analysis protocol result for DNA modification containing the 6mA sites information, genome locus, strand, coverage, IPD ratio and context sequence

extract_protocol:
Nine-day-old wild-type seedlings grown on MS plates were harvested and genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
The DNA libraries have been prepared following the PacBio instructions and sequenced on 13 SMRT cells using Pacific Biosciences RSII sequencing technology (Pacific Biosciences). The SMRT bell was produced using the DNA Template Prep Kit 1.0 (Pacific Biosciences). SMRTbell templates were bound to polymerases by using the DNA/Polymerase Binding Kit P6 v2 (Pacific Biosciences). 10 μg of Arabidopsis genomic DNA were mechanically sheared to an average size distribution of 10 kb.  Polymerase-template complexes were bound to magbeads by using Magbead Binding Kit (Pacific Biosciences), and sequencing was carried out on the PacBio RSII by using the DNA Sequencing Kit 4.0 (Pacific Biosciences). Movie lengths were 240 min for each of 13 SMRT cells. Subread filtering was performed by using Pacific Biosciences’ SMRT analysis software (v2.3.1).
SMRT sequencing


title: Patient: 12 Technique: Vivo Region: Whole Tissue: Primary Melanoma

status: Public on Oct 25 2018

type: RNA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

country: USA

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

organism: Homo sapiens

source_name: Primary Melanoma

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: patient

tag: technique

value: Vivo

tag: region

value: Whole

tag: tissue

value: Primary Melanoma


title: Patient: 9 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 15 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 13 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 6 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 10 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: ECMO_30

status: Public on Dec 31 2019

city: Taipei

first: Sung-Liang

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: SAMPLE 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw signal data were normalized using quantile normalized by GenoStudio v2011.1 software

source_name: PBMC

label_protocol: cRNA were prepared with TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: course

value: Acute myocardial infarction

tag: gender

value: F

tag: outcome

value: Success


title: Patient: 8 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 14 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 11 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 4 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 16 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 3 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 5 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 1 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: Patient: 7 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: 12m_LK-_Bx11

status: Public on Apr 14 2017

city: Rochester

first: Walter

last: Park

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description:
12m_LK-_Bx11
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx

hyb_protocol: Standard Illumina hybridization protocol (hybridized to a Human HT-12v4.0 Expression (illumina Inc., San Diego, CA, USA)).  Briefly, 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.) for 16 hours. The BeadChip underwent a washing and streptavidin-Cy3 (GE Healthcare Bio-Sciences) conjugate staining protocol.

data_processing: Quantile normalization performed using R.

label: Biotin

source_name: 18-gauge kidney allograft biopsy

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep Amplification kit (Ambion-Life technologies).  200 ng of total RNA was reverse transcribed, biotin labeled.  Biotinylated cRNA was prepared according to the standard Illumina protocol

extract_protocol: RNA isolation performed using TRIzol, followed by Qiagen clean-up.

treatment_protocol: Specimens are frozen in RNALater and stored at -80 oC until use.

value: Liver-Kidney Transplant

tag: crossmatch

value: Negative

tag: protocol

value: 12m protocol bx

value: 18-gauge kidney allograft biopsy


title: 12m_LK-_Bx12

description:
12m_LK-_Bx12
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx15

description:
12m_XM-_Bx15
Kidney Transplant; Negative Crossmatch; 12m protocol bx

value: Kidney Transplant


title: 12m_XM-_Bx12

description:
12m_XM-_Bx12
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx11

description:
12m_XM-_Bx11
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK+_Bx9

description:
12m_LK+_Bx9
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx

value: Positive


title: 12m_XM-_Bx14

description:
12m_XM-_Bx14
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx13

description:
12m_XM-_Bx13
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx15

description:
12m_XM+_Bx15
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK-_Bx10

description:
12m_LK-_Bx10
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx14

description:
12m_XM+_Bx14
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK+_Bx8

description:
12m_LK+_Bx8
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx10

description:
12m_XM+_Bx10
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM-_Bx16

description:
12m_XM-_Bx16
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK+_Bx7

description:
12m_LK+_Bx7
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK-_Bx7

description:
12m_LK-_Bx7
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx12

description:
12m_XM+_Bx12
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM-_Bx9

description:
12m_XM-_Bx9
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx11

description:
12m_XM+_Bx11
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx9

description:
12m_XM+_Bx9
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK-_Bx9

description:
12m_LK-_Bx9
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK-_Bx8

description:
12m_LK-_Bx8
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx8

description:
12m_XM-_Bx8
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx7

description:
12m_XM-_Bx7
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx13

description:
12m_XM+_Bx13
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM-_Bx6

description:
12m_XM-_Bx6
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: Patient: 2 Technique: Vivo Region: Whole Tissue: Primary Melanoma


title: 12m_XM-_Bx10

description:
12m_XM-_Bx10
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx4

description:
12m_XM+_Bx4
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx5

description:
12m_XM+_Bx5
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx3

description:
12m_XM+_Bx3
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx8

description:
12m_XM+_Bx8
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK+_Bx5

description:
12m_LK+_Bx5
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK+_Bx6

description:
12m_LK+_Bx6
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx6

description:
12m_XM+_Bx6
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK-_Bx6

description:
12m_LK-_Bx6
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK+_Bx4

description:
12m_LK+_Bx4
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_LK-_Bx3

description:
12m_LK-_Bx3
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx4

description:
12m_XM-_Bx4
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx5

description:
12m_XM-_Bx5
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK-_Bx5

description:
12m_LK-_Bx5
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM+_Bx7

description:
12m_XM+_Bx7
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: B6_H3K36me3_ChIPSeq

status: Public on Jun 30 2016

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
ChIP-Seq reads were filtered to keep only uniquely mapped reads
Two biological replicates for each sample were merged into one dataset
ChIP-Seq peaks were called using ZINBA v2.0.2.03
Genome_build: mm9

organism: Mus musculus

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. After high-speed spin soluble chromatin was removed and used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: spermatocytes

value: 14 days post-partum

tag: strain

tag: chip antibody


title: 12m_XM-_Bx3

description:
12m_XM-_Bx3
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK+_Bx2

description:
12m_LK+_Bx2
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM+_Bx2

description:
12m_XM+_Bx2
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 12m_XM-_Bx2

description:
12m_XM-_Bx2
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK-_Bx2

description:
12m_LK-_Bx2
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK-_Bx1

description:
12m_LK-_Bx1
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_XM-_Bx1

description:
12m_XM-_Bx1
Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK-_Bx4

description:
12m_LK-_Bx4
Liver-Kidney Transplant; Negative Crossmatch; 12m protocol bx


title: 12m_LK+_Bx3

description:
12m_LK+_Bx3
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 90d_XM-_Bx13

status: Public on Jun 08 2016

description: 18-gauge kidney allograft biopsy

data_processing: Quantile normalization performed in R.

value: kidney

tag: crossmatch type (positive =xm+, negative =xm-)

value: XM-

tag: protocol duration


title: 12m_XM+_Bx1

description:
12m_XM+_Bx1
Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 90d_XM-_Bx8

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx12

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx11

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx4

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx7

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx13

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx14

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx6

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx18

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx17

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx9

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx3

description: 18-gauge kidney allograft biopsy


title: 12m_LK+_Bx1

description:
12m_LK+_Bx1
Liver-Kidney Transplant; Positive Crossmatch; 12m protocol bx


title: 90d_XM+_C5+_Off_Bx12

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx10

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx15

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx5

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx16

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx1

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx8

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx9

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx10

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_Off_Bx11

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx6

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx7

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx5

description: 18-gauge kidney allograft biopsy


title: 90d_XM-_Bx2

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx4

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx11

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx3

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx12

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx18

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx7

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx3

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx9

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx4

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx2

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx14

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx8

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx10

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx2

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx13

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx5

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx15

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx1

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx16

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_NoC5_Bx6

description: 18-gauge kidney allograft biopsy


title: 90d_XM+_C5+_On_Bx1

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx17

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx14

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx12

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx13

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx9

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx8

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx5

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx6

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx1

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx2

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx11

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx14

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx10

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx7

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx3

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx8

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx6

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx4

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx2

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx9

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx1

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx11

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx5

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx15

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx13

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_C5+_On_Bx4

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx12

description: 18-gauge kidney allograft biopsy


title: 10d_XM+_NoC5_Bx10

description: 18-gauge kidney allograft biopsy


title: SCLtg LMO1tg #1

status: Public on Nov 05 2015

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

country: Canada

institute: Université de Montréal/IRIC

hyb_protocol: Hybridization to the probe array Mouse Genome 430A 2.0  (Affymetrix) was performed by the Ottawa Genome Center.

scan_protocol: Scanning performed by the Ottawa Genome Center.

data_processing:
Normalization and summarization were performed using Bioconductor packages in the R environment, according to the following pipeline: (i) probesets were summarized and normalized using the RMA procedure implemented in the Affy package [115]; (ii) absent/present probesets were detected using the MAS5 implementation of the Affy package, and probesets deemed absent in both conditions (Cd3ε-/- and Cd3ε-/-SCLtgLMO1tg) were removed from downstream analysis; and (iii) detection of differentially expressed genes was carried out using the Rank Products package.
Differentialy expressed genes between Cd3ε-/- and Cd3ε-/-SCLtgLMO1tg thymocytes that show a significant change (adjusted p-val <0.05)  were subsequently selected based on published association with self-renewal.

source_name: CD3e-/- primary thymocytes from SCLtg-LMO1tg, ectopically expressing SCL (under Sil promoter) and LMO1 (under Lck promoter)

label_protocol: The extract was labelled using the GeneChip Eukaryotic Small Sample Target Labelling protocol (Affymetrix).

growth_protocol: Thymus from 3 week-old mice were dissected out and kept in PBS 2% fetal bovine serum until RNA extraction.

extract_protocol: RNA was extracted and purified using Qiagen RNeasy Mini Kit (P/N 741104) and resuspended in 5 ml of RNase free water at a concentration of 0.05 mg/ul.

treatment_protocol: Untreated 3 week-old mice were use to obtain thymocytes.

value: Thymus

tag: genotype

value: CD3e-/- Sil-SCL Lck-LMO1

value: 3 week old


title: SCLtg LMO1tg #2

tag: age


title: control #3

source_name: CD3e-/- primary thymocytes


title: control #2


title: 10d_XM+_NoC5_Bx3

description: 18-gauge kidney allograft biopsy


title: control #1


title: 5_normal

status: Public on Aug 01 2014

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: normal skin

label_protocol: Affymetrix double amplification protocol

value: normal skin

tag: amplification

value: Double

tag: material

value: bulk biopsy


title: H12-4


title: SCLtg LMO1tg #3


title: H13-4


title: +XM/NoTG_Biopsy2_Pt5

status: Public on May 30 2012

hyb_protocol: Standard Affymetrix processing

scan_protocol: Standard Affymetrix processing

data_processing: Data is analyzed using R. Normalization is Fastlo (Ballman et al, Bioinformatics 2004; 20:2778-2786. PMID: 15166021).

label_protocol: Standard Affymetrix processing

extract_protocol: Trizol + Qiagen

value: Kidney Allograft Biopsy

tag: timepoint

value: ≥2 year biopsy - Banff:cg=0


title: +XM/NoTG_Biopsy2_Pt8


title: +XM/NoTG_Biopsy2_Pt11


title: +XM/NoTG_Biopsy2_Pt10


title: +XM/NoTG_Biopsy2_Pt6


title: H11-4


title: Control_Biopsy2_Pt7_repeat

value: ≥1 year biopsy - Banff:cg>0


title: +XM/NoTG_Biopsy2_Pt7


title: H10-4


title: +XM/NoTG_Biopsy2_Pt3


title: +XM/NoTG_Biopsy2_Pt2


title: H14-4


title: +XM/NoTG_Biopsy2_Pt9


title: +XM/NoTG_Biopsy2_Pt4


title: Control_Biopsy2_Pt6_repeat


title: Control_Biopsy2_Pt7

value: ≥1 year biopsy - Banff:cg=0


title: Control_Biopsy2_Pt8


title: Control_Biopsy2_Pt10


title: Control_Biopsy2_Pt3_repeat


title: +XM/NoTG_Biopsy2_Pt1


title: Control_Biopsy2_Pt5


title: Control_Biopsy1_Pt5

value: ≤1 year biopsy - Banff:cg=0


title: Control_Biopsy2_Pt9


title: Control_Biopsy2_Pt2


title: Control_Biopsy2_Pt4


title: Control_Biopsy2_Pt5_repeat


title: Control_Biopsy2_Pt6


title: Control_Biopsy1_Pt8


title: Control_Biopsy2_Pt4_repeat


title: Control_Biopsy2_Pt3


title: Control_Biopsy2_Pt1


title: Control_Biopsy1_Pt7


title: Control_Biopsy1_Pt4


title: Control_Biopsy1_Pt3


title: Control_Biopsy1_Pt2


title: Control_Biopsy1_Pt6


title: Control_Biopsy1_Pt10


title: Control_Biopsy1_Pt9


title: Control_Biopsy1_Pt1


title: +XM/TG+_Biopsy2_Pt10


title: 10d_XM+_NoC5_Bx7

description: 18-gauge kidney allograft biopsy


title: +XM/TG+_Biopsy2_Pt8


title: +XM/TG+_Biopsy2_Pt7


title: +XM/TG+_Biopsy2_Pt9


title: +XM/TG+_Biopsy2_Pt3


title: +XM/TG+_Biopsy2_Pt5


title: +XM/TG+_Biopsy2_Pt4


title: +XM/TG+_Biopsy2_Pt2


title: +XM/TG+_Biopsy1_Pt9


title: +XM/TG+_Biopsy2_Pt1


title: +XM/TG+_Biopsy1_Pt4


title: +XM/TG+_Biopsy1_Pt6


title: +XM/TG+_Biopsy1_Pt8


title: +XM/TG+_Biopsy1_Pt10


title: +XM/TG+_Biopsy1_Pt3


title: +XM/TG+_Biopsy1_Pt2


title: +XM/TG+_Biopsy1_Pt7


title: +XM/TG+_Biopsy1_Pt5


title: T12_KidneyBx_IFTA+i10

status: Public on Nov 01 2010

data_processing: Standard GCOS processing using MAS 5.0 algorithm.

source_name: IFTA+i

tag: histology

value: 1yr protocol bx - Banff:cg=0; i/ci>0


title: T12_KidneyBx_IFTA+i11


title: +XM/TG+_Biopsy1_Pt1

tag: tissue


title: T12_KidneyBx_IFTA+i7


title: +XM/TG+_Biopsy2_Pt6


title: T12_KidneyBx_IFTA+i13


title: T12_KidneyBx_IFTA+i8


title: T12_KidneyBx_IFTA+i15


title: T12_KidneyBx_IFTA+i14


title: T12_KidneyBx_IFTA+i16


title: T12_KidneyBx_IFTA+i12


title: T12_KidneyBx_IFTA+i9


title: T12_KidneyBx_IFTA+i4


title: T12_KidneyBx_IFTA+i5


title: T12_KidneyBx_IFTA+i6


title: T12_KidneyBx_IFTA+i3


title: T12_KidneyBx_IFTA20

source_name: IF/TA

value: 1yr protocol bx - Banff:i/cg=0; ci>0


title: T12_KidneyBx_IFTA19


title: T12_KidneyBx_IFTA16


title: T12_KidneyBx_IFTA+i2


title: T12_KidneyBx_IFTA23


title: T12_KidneyBx_IFTA18


title: T12_KidneyBx_IFTA22


title: T12_KidneyBx_IFTA11


title: T12_KidneyBx_IFTA15


title: T12_KidneyBx_IFTA+i1


title: T12_KidneyBx_IFTA13


title: T12_KidneyBx_IFTA12


title: T12_KidneyBx_IFTA6


title: T12_KidneyBx_IFTA8


title: T12_KidneyBx_IFTA2


title: T12_KidneyBx_IFTA7


title: T12_KidneyBx_IFTA10


title: T12_KidneyBx_IFTA9


title: T12_KidneyBx_IFTA3


title: T12_KidneyBx_IFTA5


title: T12_KidneyBx_IFTA4


title: T12_KidneyBx_Norm21

source_name: Normal

value: 1yr protocol bx - Banff:i/cg/ci=0


title: T12_KidneyBx_Norm19


title: T12_KidneyBx_Norm23


title: T12_KidneyBx_IFTA1


title: T12_KidneyBx_Norm24


title: T12_KidneyBx_IFTA17


title: T12_KidneyBx_Norm25


title: T12_KidneyBx_Norm22


title: T12_KidneyBx_Norm18


title: T12_KidneyBx_Norm13


title: T12_KidneyBx_Norm8


title: T12_KidneyBx_Norm12


title: T12_KidneyBx_Norm20


title: T12_KidneyBx_Norm16


title: T12_KidneyBx_IFTA24


title: T12_KidneyBx_Norm11


title: T12_KidneyBx_Norm6


title: T12_KidneyBx_Norm15


title: T12_KidneyBx_Norm17


title: T12_KidneyBx_Norm9


title: T12_KidneyBx_Norm10


title: T12_KidneyBx_Norm14


title: T12_KidneyBx_Norm1


title: Subclinical interstitial fibrosis (GIF#8 T=12m)

status: Public on Mar 30 2007

description: Standard Affymetrix

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: GCOS expression values

source_name: Human kidney bx

label_protocol: Standard Affymetrix (small sample protocol)

tag: T=12m bx - Fibrotic path (GIF/TA)


title: T12_KidneyBx_Norm5


title: Subclinical interstitial fibrosis (GIF#9 T=0)

description: Standard Affymetrix

tag: Time zero bx - Normal path


title: T12_KidneyBx_Norm3


title: T12_KidneyBx_Norm2


title: T12_KidneyBx_Norm4


title: Normal (Norm#5 T=12m)

description: Standard Affymetrix

tag: T=12m bx - Normal path


title: T12_KidneyBx_Norm7


title: Subclinical interstitial fibrosis (GIF#8 T=0)

description: Standard Affymetrix


title: Normal (Norm#8 T=0)

description: Standard Affymetrix


title: Normal (Norm#5 T=0)

description: Standard Affymetrix


title: Normal (Norm#10 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#7 T=12m)

description: Standard Affymetrix


title: Normal (Norm#6 T=12m)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#9 T=12m)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#6 T=12m)

description: Standard Affymetrix


title: Normal (Norm#8 T=12m)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#6 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#7 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#3 T=0)

description: Standard Affymetrix


title: T12_KidneyBx_IFTA21


title: Normal (Norm#6 T=0)

description: Standard Affymetrix


title: Normal (Norm#4 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#4 T=12m)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#4 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#2 T=12m)

description: Standard Affymetrix


title: Normal (Norm#2 T=12m)

description: Standard Affymetrix


title: T12_KidneyBx_IFTA14


title: Subclinical interstitial fibrosis (GIF#3 T=12m)

description: Standard Affymetrix


title: Normal (Norm#2 T=0)

description: Standard Affymetrix


title: Normal (Norm#4 T=12m)

description: Standard Affymetrix


title: Normal (Norm#1 T=0)

description: Standard Affymetrix

tag: Time zero bx - Normal pathology


title: Subclinical interstitial fibrosis (GIF#1 T=0)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#2 T=0)

description: Standard Affymetrix


title: Normal (Norm#1 T=12m)

description: Standard Affymetrix


title: Normal (Norm#10 T=12m)

description: Standard Affymetrix


title: Subclinical interstitial fibrosis (GIF#1 T=12m)

description: Standard Affymetrix

tag: 12month protocol bx (post-renal transplantation)