title: H1_WT_PP2.RNA-Seq.replicate.1

description: RNA

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

source_name: H1 Control

extract_protocol:
RNA was isolated from cell samples using the RNeasy® Micro Kit (Qiagen) according to the manufacturer instructions.
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

value: Late pancreatic progenitor cells


title: H1_WT_PP2.RNA-Seq.replicate.2

status: Public on Jan 19 2021

type: SRA

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

country: USA

institute: UC San Diego

description: RNA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019).

tag: cell type

value: differentiated hESCs

tag: developmental stage


title: Breast biopsy UVABC4 10-cell sample 4

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description:
BCC6.Sample04
2020_02_06_breastcancer_allcompiled.csv

data_processing:
Adapters were trimmed using fastq-mcf with the following options:  -q 10 -t 0.01 -k 0 (quality threshold 10, 0.01% occurrence frequency, no nucleotide skew causing cycle removal).
Datasets were aligned to the human (GRCh38.p12)  transcriptome using RSEM. Reference ERCC sequences were also provided for the alignment.
RSEM options  --bowtie2 --single-cell-prior --paired-end (Bowtie2 transcriptome aligner, single-cell prior to account for dropouts)
Comma separated file includes read counts from RSEM
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: 2020_02_06_breastcancer_allcompiled.csv (read counts)

molecule: polyA RNA

source_name: Breast tumor

extract_protocol:
All samples were cryoembedded and sectioned on to glass slides (8µm sections). Cell samples were isolated with laser capture microdissection and poly(A) RNA extracted, reverse transcribed and poly(A) PCR amplified prior to library preparation
Amplified cDNA samples were diluted to 0.2 µg/ml for tagmentation with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s earlier recommendation to purify libraries with 180% (vol/vol) SPRI beads

tag: tumor

tag: sample type

value: 10-cell sample

tag: stage/grade

value: Stage 1 Grade 2


title: Breast biopsy UVABC4 10-cell sample 3

description:
BCC6.Sample03
2020_02_06_breastcancer_allcompiled.csv


title: U2OS PDPK1-FKBP(F36V) RNA-seq DMSO rep2 [DMSO-2]

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
DMSO-2
processed data file: U2OS-PDK1-count.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each Sample

source_name: U2OS PDPK1-FKBP(F36V) RNA-seq DMSO

growth_protocol: All cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment. RNA was submitted to GENEWIZ or the Vanderbilt Technologies for Advanced Genomics Core Laboratory for rRNA reduction, library preparation, and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: engineered genotype

value: endogenous C-terminal tag on PDPK1, FKBP(F36V)-2xHA

tag: treatment

value: 0.01% DMSO for 24 hours


title: Embryonic_pancreas.RNA-Seq

description: RNA

source_name: Primary Fetal Pancreas (combined from 2 embryos, 54 and 58 days gestation)

extract_protocol:
RNA was extracted using Trizol. Following DNaseI digestion, polyA RNA was purified for library preparation.
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

value: Primary fetal human pancreas

value: 54 and 58 days gestation


title: H1_WT_PP2.RNA-Seq.replicate.3

description: RNA


title: H1_WT_PP2.RNA-Seq.replicate.4

description: RNA


title: Breast biopsy UVABC4 10-cell sample 5

description:
BCC6.Sample05
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 6

description:
BCC6.Sample06
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 15

description:
BCC6.Sample15
2020_02_06_breastcancer_allcompiled.csv


title: dLAMA1Enh_Clone_2_PP2.RNA-Seq.replicate.2

description: RNA

source_name: H1 LAMA1 Enhancer Deletion


title: Breast biopsy UVABC4 10-cell sample 13

description:
BCC6.Sample13
2020_02_06_breastcancer_allcompiled.csv


title: hip joint synovial tissues, T2

city: Shenyang

first: Lei

last: Guo

state: Liaoning

address: Nanjing North Street

country: China

institute: First Affiliated Hospital, China Medical University

description: circRNA

data_processing:
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplice junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: Expression_circRNA.xlsx

source_name: hip joint synovial tissues

growth_protocol: The experimental tissues were obtained from the patients, who received revision operations for aseptic loosening after total hip arthroplasty. The control specimens were obtained from the patients, who received primary total hip arthroplasty after femoral neck fracture.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: tissue

value: synovial tissues of hip joint

tag: condition


title: Breast biopsy UVABC4 10-cell sample 2

description:
BCC6.Sample02
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 22

description:
BCC6.Sample22
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell sample 1

description:
BCC6.Sample01
2020_02_06_breastcancer_allcompiled.csv


title: dLAMA1Enh_Clone_2_PP2.RNA-Seq.replicate.1

description: RNA


title: dLAMA1Enh_Clone_1_PP2.RNA-Seq.replicate.2

description: RNA


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 19

description:
BCC6.Control19
2020_02_06_breastcancer_allcompiled.csv

value: Pool-and-split control


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 18

description:
BCC6.Control18
2020_02_06_breastcancer_allcompiled.csv


title: dLAMA1Enh_Clone_1_PP2.RNA-Seq.replicate.1

description: RNA


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 17

description:
BCC6.Control17
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 16

description:
BCC6.Control16
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 20

description:
BCC6.Control20
2020_02_06_breastcancer_allcompiled.csv


title: dCRB2Enh_Clone_2_PP2.RNA-Seq.replicate.1

description: RNA

source_name: H1 CRB2 Enhancer Deletion


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 15

description:
BCC6.Control15
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.H3K4me1.replicate.1

description: Histone modification

library_source: genomic

molecule: genomic DNA

source_name: Cyt49 Control

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

value: Early pancreatic progenitor cells


title: dCRB2Enh_Clone_1_PP2.RNA-Seq.replicate.1

description: RNA


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 13

description:
BCC6.Control13
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 14

description:
BCC6.Control14
2020_02_06_breastcancer_allcompiled.csv


title: dCRB2Enh_Clone_1_PP2.RNA-Seq.replicate.2

description: RNA


title: Cyt49_DE.ChIP-Seq.H3K4me1.replicate.1

description: Histone modification

value: Definitive endoderm cells


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 10

description:
BCC6.Control10
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 12

description:
BCC6.Control12
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.CTCF.replicate.2

description: Transcription factor


title: Cyt49_ES.ChIP-Seq.H3K4me1.replicate.1

description: Histone modification

value: Embyonic stem cells


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 11

description:
BCC6.Control11
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.SOX9.replicate.1

description: Transcription factor


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 9

description:
BCC6.Control09
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.CTCF.replicate.1

description: Transcription factor


title: Cyt49_PP2.ChIP-Seq.SOX9.replicate.2

description: Transcription factor


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 8

description:
BCC6.Control08
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 7

description:
BCC6.Control07
2020_02_06_breastcancer_allcompiled.csv


title: dCRB2Enh_Clone_2_PP2.RNA-Seq.replicate.2

description: RNA


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 6

description:
BCC6.Control06
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 4

description:
BCC6.Control04
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.CTCF.replicate.1

description: Transcription factor


title: Cyt49_GT.ChIP-Seq.CTCF.replicate.1

description: Transcription factor

value: Gut tube cells


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 2

description:
BCC6.Control02
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 3

description:
BCC6.Control03
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ChIP-Seq.CTCF.replicate.2

description: Transcription factor


title: Cyt49_ES.ChIP-Seq.CTCF.replicate.2

description: Transcription factor


title: Cyt49_ES.ChIP-Seq.CTCF.replicate.1

description: Transcription factor


title: Cyt49_DE.ChIP-Seq.CTCF.replicate.2

description: Transcription factor


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 1

description:
BCC6.Control01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC4 10-cell pool-and-split control replicate 5

description:
BCC6.Control05
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 32

description:
BCC10.Sample32
2020_02_06_breastcancer_allcompiled.csv

value: Stage 1 Grade 3


title: Breast biopsy UVABC3 10-cell sample 30

description:
BCC10.Sample30
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_DE.ChIP-Seq.CTCF.replicate.1

description: Transcription factor


title: Breast biopsy UVABC3 10-cell sample 31

description:
BCC10.Sample31
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 27

description:
BCC10.Sample27
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 26

description:
BCC10.Sample26
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.HNF6.replicate.1

description: Transcription factor

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019). iAEC2 cells were maintained and differentiatied as previously described (Hurley et al 2020)

value: Late pancreatic progenitor

tag: chip antibody

value: Rabbit anti-HNF6

tag: antibody manufacturer

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: Cyt49_PP2.ChIP-Seq.PDX1.replicate.2

description: Transcription factor

value: differentiated hESCs

value: Rabbit anti-PDX1

value: Beta Cell Biology Consortium


title: Cyt49_PP2.ChIP-Seq.HNF6.replicate.2

description: Transcription factor


title: Cyt49_PP2.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

value: Rabbit anti-H3K27ac

value: Active Motif


title: Cyt49_PP2.ChIP-Seq.GATA6.replicate.2

description: Transcription factor

value: Rabbit anti-GATA6


title: Cyt49_PP1.ChIP-Seq.CTCF.replicate.2

description: Transcription factor


title: Breast biopsy UVABC3 10-cell sample 24

description:
BCC10.Sample24
2020_02_06_breastcancer_allcompiled.csv

value: 10-cell sample


title: Cyt49_PP2.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker

value: Rabbit anti-H3K4me1

value: Abcam


title: Breast biopsy UVABC3 10-cell sample 22

description:
BCC10.Sample22
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 23

description:
BCC10.Sample23
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 21

description:
BCC10.Sample21
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 19

description:
BCC10.Sample19
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.GATA6.replicate.1

description: Transcription factor


title: Breast biopsy UVABC3 10-cell sample 18

description:
BCC10.Sample18
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 20

description:
BCC10.Sample20
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.GATA4.replicate.1

description: Transcription factor

value: Goat anti-GATA4


title: Cyt49_PP2.ChIP-Seq.Input.replicate.1

description: Input


title: Breast biopsy UVABC3 10-cell sample 17

description:
BCC10.Sample17
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP2.ChIP-Seq.FOXA2.replicate.2

description: Transcription factor

value: Goat anti-FOXA2


title: Cyt49_PP2.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor

value: Goat anti-FOXA1


title: Cyt49_PP2.ChIP-Seq.GATA4.replicate.2

description: Transcription factor


title: Cyt49_PP2.ChIP-Seq.FOXA2.replicate.1

description: Transcription factor


title: Breast biopsy UVABC3 10-cell sample 16

description:
BCC10.Sample16
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.Input.replicate.1

description: Input

value: Early pancreatic progenitor


title: Cyt49_PP2.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: Breast biopsy UVABC3 10-cell sample 25

description:
BCC10.Sample25
2020_02_06_breastcancer_allcompiled.csv

value: Stage 1 Grade 3


title: Breast biopsy UVABC3 10-cell sample 15

description:
BCC10.Sample15
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 14

description:
BCC10.Sample14
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_PP1.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: Breast biopsy UVABC3 10-cell sample 13

description:
BCC10.Sample13
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 11

description:
BCC10.Sample11
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 9

description:
BCC10.Sample09
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

value: Gut tube


title: Breast biopsy UVABC3 10-cell sample 8

description:
BCC10.Sample08
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ChIP-Seq.H3K4me1.replicate.2

description: Histone marker


title: Cyt49_ES.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

value: Embryonic stem cell


title: Cyt49_ES.ChIP-Seq.Input.replicate.1

description: Input


title: Breast biopsy UVABC3 10-cell sample 7

description:
BCC10.Sample07
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_DE.ChIP-Seq.Input.replicate.1

description: Input

value: Definitive endoderm


title: Breast biopsy UVABC3 10-cell sample 6

description:
BCC10.Sample06
2020_02_06_breastcancer_allcompiled.csv


title: sgZFP36L2_sg2_rep2

city: New York

first: Hua

last: Zhou

state: NY

address: 550 First Avenue, Smilow 1307

department: PATHOLOGY

institute: NYU SCHOOL OF MEDICINE

data_processing:
Raw counts were transformed and normalized using the voom method (ref. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR doi: 10.12688/f1000research.9005.2).
Reads were aligned with STAR (2.5.3) using the GRCh38.p7 (May 2017) human assembly (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files) and gene level expression were quantified using HTSeq (ref. HTSeq—a Python framework to work with high-throughput sequencing data doi:10.1093/bioinformatics/btu638).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM  and DE values for the samples as well as the bigwig files.

source_name: MOLM13 human AML cell line

growth_protocol: MOLM13 AML cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% PenStrep

extract_protocol:
MOLM13 cells were transduced with two independent sgRNAs targeting ZFP36L2 and compared to non-targeting sgRNA (sgRosa). After 6 days post-transduction, cells were washed with 1x PBS and total RNA was extracted using Rneasy Plus Mini Kit (Qiagen) and QIAshredder, which were performed according to manufacturer's protocol. For poly(A) mRNA isolation, magnetic isolation (NEB) was performed using ~1ug of total mRNA.
RNA-seq libraries were generated using NEXTflex Rapid Directional (Bioo Scientific) protocol and NEXTflex RNA-seq barcodesand sequenced using Hi-Seq4000 (50 cycles single end)

value: MOLM13 human AML cell line

tag: sgrna


title: sgZFP36L2_sg1_rep2


title: Breast biopsy UVABC3 10-cell sample 5

description:
BCC10.Sample05
2020_02_06_breastcancer_allcompiled.csv


title: sgZFP36L2_sg2_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 27

description:
BCC10.Control27
2020_02_06_breastcancer_allcompiled.csv

value: Pool-and-split control


title: Cyt49_DE.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker

value: differentiated hESCs


title: Breast biopsy UVABC3 10-cell sample 1

description:
BCC10.Sample01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell sample 3

description:
BCC10.Sample03
2020_02_06_breastcancer_allcompiled.csv


title: Cyt49_GT.ChIP-Seq.Input.replicate.1

description: Input


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 26

description:
BCC10.Control26
2020_02_06_breastcancer_allcompiled.csv


title: sgRosa_rep3

value: Non-targeting sgRNA


title: Breast biopsy UVABC3 10-cell sample 2

description:
BCC10.Sample02
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 25

description:
BCC10.Control25
2020_02_06_breastcancer_allcompiled.csv


title: THP1_IP_rep2

data_processing:
Library strategy: eCLIP
The eCLIP data was processed similarly as described previously [pubmed ID 28766298] and is outlined shortly in the following. First, adapter sequences were trimmed from both reads of all read-pairs using cutadapt version 1.14 . Then, all remaining reads longer than 16 bases were aligned against the human reference genome sequence hg19/GRCh37 using STAR version 2.5.0c [REF ]. Only uniquely mapped reads were kept. Read-pair duplicates by position were removed using picard tools version 2.6.0. To identify binding sites, we first ran a custom script to identify clusters of overlapping reads that had a read-depth of at least 10 reads. Then, we calculated significant enrichments for all such identified clusters by comparing IP-samples versus input-samples using edgeR. More specifically, we ran bamutils count version 0.5.7 to counted stranded reads within all identified clusters for all samples. Using this output, we calculated differential coverage between IP-vs-input for each cluster with edgeR after normalizing for total sequencing depth per replicate (resulting in counts per million/CPM per cluster). Final binding sites were called by applying logFC > 2 and FDR < 0.05 thresholds between IP-vs-input.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include ZFP36L2 binding sites for the samples.

source_name: THP1 human AML cell line

growth_protocol: MOLM13 and THP1 AML cells were grown in RPMI-1640 medium supplemented with 10% FBS and 1% PenStrep

extract_protocol:
20 million MOLM-13 and THP-1 cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation, and snap frozen. Cells were then lysed and treated with RNase I to fragment RNA as previously described. Anti-ZFP36L2/TIS11D antibody (ab70775) was then pre-coupled to Sheep anti-Rabbit Dynabeads (Thermo Fisher), added to lysate, and incubated overnight at 4 deg C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, while the remainder was magnetically separated and processed using the standard eCLIP protocol. eCLIP was performed by excising the area from ~30 kDa to ~105 kDa.
RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed in duplicates by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end seCLIP protocol

value: THP1 human AML cell line

tag: eclip antibody

value: Anti-ZFP36L2/TIS11D antibody (ab70775)


title: sgRosa_rep2


title: sgRosa_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 24

description:
BCC10.Control24
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 23

description:
BCC10.Control23
2020_02_06_breastcancer_allcompiled.csv


title: THP1_IP_rep1


title: THP1_Input_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 21

description:
BCC10.Control21
2020_02_06_breastcancer_allcompiled.csv


title: THP1_IgG_rep2

value: IgG


title: THP1_IgG_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 22

description:
BCC10.Control22
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 20

description:
BCC10.Control20
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 19

description:
BCC10.Control19
2020_02_06_breastcancer_allcompiled.csv


title: MOLM13_IP_rep2


title: MOLM13_IP_rep1


title: Breast biopsy UVABC3 10-cell sample 4

description:
BCC10.Sample04
2020_02_06_breastcancer_allcompiled.csv

value: 10-cell sample


title: sgZFP36L2_sg1_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 117

description:
BCC10.Control17
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 118

description:
BCC10.Control18
2020_02_06_breastcancer_allcompiled.csv


title: MOLM13_IgG_rep2


title: MOLM13_IgG_rep1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 10

description:
BCC10.Control10
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 16

description:
BCC10.Control16
2020_02_06_breastcancer_allcompiled.csv


title: siZNF213 3

city: Shenzhen

first: Juntao

last: Xu

state: Guangdong

address: Yuehai Subdistrict, Nanshan District

institute: Philrivers

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siZNF213 or sicontrol

tag: passages

value: 15-18 passage


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 12

description:
BCC10.Control12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 9

description:
BCC10.Control09
2020_02_06_breastcancer_allcompiled.csv


title: MOLM13_Input_rep1


title: sicontrol 3

value: control


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 8

description:
BCC10.Control08
2020_02_06_breastcancer_allcompiled.csv


title: siZNF213 1


title: siZNF213 2


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 5

description:
BCC10.Control05
2020_02_06_breastcancer_allcompiled.csv


title: sicontrol 2


title: sicontrol 1


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 7

description:
BCC10.Control07
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 4

description:
BCC10.Control04
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 27

description:
BCC5.Sample27
2020_02_06_breastcancer_allcompiled.csv

value: Stage 2 Grade 2


title: Breast biopsy UVABC2 10-cell sample 28

description:
BCC5.Sample28
2020_02_06_breastcancer_allcompiled.csv


title: siRNF181_2

treatment_protocol: cells were treated with 50nM siRNF181 or sicontrol


title: siRNF181_1


title: Breast biopsy UVABC2 10-cell sample 26

description:
BCC5.Sample26
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 25

description:
BCC5.Sample25
2020_02_06_breastcancer_allcompiled.csv


title: MOLM13_Input_rep2


title: sicontrol_2


title: Breast biopsy UVABC3 10-cell pool-and-split control replicate 14

description:
BCC10.Control14
2020_02_06_breastcancer_allcompiled.csv


title: sicontrol_1


title: Breast biopsy UVABC2 10-cell sample 24

description:
BCC5.Sample24
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 22

description:
BCC5.Sample22
2020_02_06_breastcancer_allcompiled.csv


title: BMDMs, KO-2, Input

city: Xi’an

first: Huilong

last: Yin

state: Shaanxi

address: No.169, Changle West Road

institute: Fourth Military Medical University

description:
1461, input
Methylated_RNA_sites.mRNA
1461.mRNA.m6A.bed

data_processing:
Library strategy: m6A-seq
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited coordinates of m6A peaks

organism: Mus musculus

source_name: BMDMs

growth_protocol: Briefly, bone marrow was extracted from femur and tibia of C57BL/6 mice, and red blood cells were lysed. Resultant bone marrow cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 mg/mL streptomycin in the presence of 40 ng/mL M-CSF for 7 days prior to treatment.

extract_protocol:
Total RNA was isolated from BMDMs using Trizol .
Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

tag: strain

value: Bone Marrow

value: BMDMs

tag: age

value: 8 weeks

tag: genotype

tag: ip antibody


title: Breast biopsy UVABC2 10-cell sample 21

description:
BCC5.Sample21
2020_02_06_breastcancer_allcompiled.csv

tag: tumor

tag: sample type


title: BMDMs, KO-2, IP

description:
1461, IP
Methylated_RNA_sites.mRNA
1461.mRNA.m6A.bed

tag: cell type


title: Breast biopsy UVABC2 10-cell sample 23

description:
BCC5.Sample23
2020_02_06_breastcancer_allcompiled.csv

tag: stage/grade


title: BMDMs, KO-1, Input

description:
1391, input
Methylated_RNA_sites.mRNA
1391.mRNA.m6A.bed


title: Breast biopsy UVABC2 10-cell sample 20

description:
BCC5.Sample20
2020_02_06_breastcancer_allcompiled.csv


title: siRNF181_3

tag: cell line

tag: treatment


title: Breast biopsy UVABC2 10-cell sample 17

description:
BCC5.Sample17
2020_02_06_breastcancer_allcompiled.csv


title: BMDMs, WT-2, IP

description:
1463, IP
Methylated_RNA_sites.mRNA
1463.mRNA.m6A.bed

tag: tissue

value: wild type


title: Breast biopsy UVABC2 10-cell sample 19

description:
BCC5.Sample19
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 18

description:
BCC5.Sample18
2020_02_06_breastcancer_allcompiled.csv


title: BMDMs, WT-2, Input

description:
1463, input
Methylated_RNA_sites.mRNA
1463.mRNA.m6A.bed


title: BMDMs, KO-1, IP

description:
1391, IP
Methylated_RNA_sites.mRNA
1391.mRNA.m6A.bed


title: BMDMs, WT-1, Input

description:
1393, input
Methylated_RNA_sites.mRNA
1393.mRNA.m6A.bed


title: Breast biopsy UVABC2 10-cell sample 16

description:
BCC5.Sample16
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 15

description:
BCC5.Sample15
2020_02_06_breastcancer_allcompiled.csv


title: sicontrol_3


title: Breast biopsy UVABC2 10-cell sample 13

description:
BCC5.Sample13
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 14

description:
BCC5.Sample14
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 12

description:
BCC5.Sample12
2020_02_06_breastcancer_allcompiled.csv


title: ATACseq-GRKO-GFP-GRdim_NT_rep1

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control
ChIP- and ATAC-seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
RNA-seq alignment was performed by STAR (2.7) with STAR --sjdbOverhang 50  --readFilesIn INPUT_R1.pair.fastq.gz INPUT_R2_R2.pair.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outTmpDir --outFileNamePrefix bam/rnaseq_STAR/OUTPUT . Dex regulated genes were defined with DESeq2 through HOMER program version 4.9.
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over control, 4x fold enrichment over local background, and >75 tags per site. In addition, untreated GR ChIP sample was used to further filter out noise from GR samples using default parameters on getDifferentialPeaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, ATAC

growth_protocol: Mouse adenocarcinoma and MEF cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit.
Libraries were prepared for sequencing using standard Illumina protocols.
For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.

treatment_protocol: Mouse adenocarcinoma and MEF cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq and ATAC-seq, and for 2 h in RNA-seq, prior extraction.

value: mouse adenocarcinoma

tag: stably expressing

value: A465T GFP-GRdim

value: no treatment

tag: concentration

tag: time


title: ATACseq-GRKO-GFP-GRdim_DEX_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, ATAC

value: Dexamethasone

value: 1 h


title: ATACseq-GRKO-GFP-GRdim_DEX_rep1


title: Breast biopsy UVABC2 10-cell sample 11

description:
BCC5.Sample11
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 10

description:
BCC5.Sample10
2020_02_06_breastcancer_allcompiled.csv


title: ATACseq-GRKO-GFP-GRdim_NT_rep2


title: Breast biopsy UVABC2 10-cell sample 8

description:
BCC5.Sample08
2020_02_06_breastcancer_allcompiled.csv


title: BMDMs, WT-1, IP

description:
1393, IP
Methylated_RNA_sites.mRNA
1393.mRNA.m6A.bed


title: Breast biopsy UVABC2 10-cell sample 7

description:
BCC5.Sample07
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 5

description:
BCC5.Sample05
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 2

description:
BCC5.Sample02
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 4

description:
BCC5.Sample04
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 1

description:
BCC5.Sample01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 20

description:
BCC5.Control20
2020_02_06_breastcancer_allcompiled.csv

value: Pool-and-split control


title: Breast biopsy UVABC2 10-cell sample 3

description:
BCC5.Sample03
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 9

description:
BCC5.Sample09
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 19

description:
BCC5.Control19
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell sample 6

description:
BCC5.Sample06
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 16

description:
BCC5.Control16
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 17

description:
BCC5.Control17
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 18

description:
BCC5.Control18
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siPVT1_rep4_Cy5

type: RNA

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: SurePrint G3 Human GE v3 8x60K Microarray - G4851C

hyb_protocol: Agilent Gene Expression Hybridization Kit were used and samples were applied to microarrays enclosed in Agilent Microarray Hybridization Chamber. After hybridization, slides were washed sequentially.

scan_protocol: Slides were scanned on the SureScan Microarray Scanner (Agilent) with a resolution of 2 μm.

data_processing: Images were processed using the Feature Extraction software (Agilent) for quality control, determination of feature intensities and ratios, and for background correction. The ISPosAndSignif flag was used to filter low intensity signal probes. Then, all genes that were not detected as expressed (i.e., whose microarray spot signal was below the filter cutoff) in the four replicates of at least one of the two experimental conditions were excluded.

source_name: LNCaP , Vehicle , siPVT1 , rep4

label_protocol: 200 ng of total RNA were amplified and labeled using Agilent Low Input Quick Amp Labeling Kit following manufacturer's instructions

growth_protocol: LNCaP human prostate carcinoma cell line originally purchased from the American Type Culture Collection was cultured at 37 oC, 5 % CO2 in RPMI medium (Gibco) supplemented with 10 % fetal bovine serum (Vitrocell), 4.5 g/L glucose, 1.5 g/L sodium hydrogen carbonate, 2.4 g/L HEPES, 1 % sodium pyruvate and penicillin (100 U/ml)/streptomycin (100 U/ml). Cells were grown until reaching approximately 50 % confluence, the standard medium was replaced by RPMI supplemented with charcoal-stripped fetal bovine serum (CSS, Sigma-Aldrich), totaling 48 h of hormone deprivation.

extract_protocol: Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions and purified  using RNeasy Mini Kit (Qiagen). RNA integrity was analyzed with Bioanalyzer 2100 and the 2100 Expert program (Agilent Technologies); only samples with RNA Integrity Number (RIN) value > 8 were used in all experiments.

treatment_protocol: LNCaP cells were transfected 300 pmol of a negative control oligonucleotide with scrambled sequence or 300 pmol of a combination of the PVT1_2 and PVT1_5 antisense oligonucleotides (150 pmol each). Cells were incubated for 24 h, and then 1.0 nM R1881 was added or in a parallel control in the absence of androgen, the corresponding volume of ethanol vehicle was added.

value: LNCaP (ATCC CRL-1740)

value: Vehicle

tag: transfection


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 15

description:
BCC5.Control15
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siPVT1_rep4_Cy5

source_name: LNCaP , Androgen , siPVT1 , rep4

value: Androgen


title: Androgen_siPVT1_rep2_Cy3

source_name: LNCaP , Androgen , siPVT1 , rep2


title: Androgen_siControl_rep2_Cy5

source_name: LNCaP , Androgen , siControl , rep2

value: siControl


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 13

description:
BCC5.Control13
2020_02_06_breastcancer_allcompiled.csv

source_name: Breast tumor


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 14

description:
BCC5.Control14
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siControl_rep2_Cy3


title: Vehicle_siPVT1_rep3_Cy5

source_name: LNCaP , Vehicle , siPVT1 , rep3


title: Vehicle_siControl_rep4_Cy3

source_name: LNCaP , Vehicle , siControl , rep4


title: Androgen_siPVT1_rep3_Cy5

source_name: LNCaP , Androgen , siPVT1 , rep3


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 12

description:
BCC5.Control12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 11

description:
BCC5.Control11
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siPVT1_rep1_Cy5

source_name: LNCaP , Vehicle , siPVT1 , rep1


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 10

description:
BCC5.Control10
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siControl_rep3_Cy3

source_name: LNCaP , Vehicle , siControl , rep3


title: Vehicle_siPVT1_rep2_Cy5

source_name: LNCaP , Vehicle , siPVT1 , rep2


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 9

description:
BCC5.Control09
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siControl_rep4_Cy3

source_name: LNCaP , Androgen , siControl , rep4


title: Vehicle_siControl_rep1_Cy3

source_name: LNCaP , Vehicle , siControl , rep1


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 8

description:
BCC5.Control08
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 7

description:
BCC5.Control07
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siPVT1_rep1_Cy3

source_name: LNCaP , Androgen , siPVT1 , rep1


title: Vehicle_siPVT1_rep4_Cy3


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 6

description:
BCC5.Control06
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siControl_rep3_Cy5


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 4

description:
BCC5.Control04
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siControl_rep2_Cy5

source_name: LNCaP , Vehicle , siControl , rep2


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 3

description:
BCC5.Control03
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 5

description:
BCC5.Control05
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 2

description:
BCC5.Control02
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siControl_rep1_Cy3

source_name: LNCaP , Androgen , siControl , rep1


title: Androgen_siControl_rep3_Cy5

source_name: LNCaP , Androgen , siControl , rep3


title: Breast biopsy UVABC2 10-cell pool-and-split control replicate 1

description:
BCC5.Control01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 28

description:
BCC2.Sample28
2020_02_06_breastcancer_allcompiled.csv

value: 10-cell sample

value: Stage 1 Grade 2


title: Breast biopsy UVABC1 10-cell sample 27

description:
BCC2.Sample27
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siControl_rep4_Cy5

description: SurePrint G3 Human GE v3 8x60K Microarray - G4851C


title: Breast biopsy UVABC1 10-cell sample 26

description:
BCC2.Sample26
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siPVT1_rep1_Cy5


title: Vehicle_siPVT1_rep3_Cy3


title: Androgen_siControl_rep1_Cy5


title: Vehicle_siPVT1_rep2_Cy3


title: Vehicle_siControl_rep4_Cy5


title: Breast biopsy UVABC1 10-cell sample 23

description:
BCC2.Sample23
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 22

description:
BCC2.Sample22
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siControl_rep2_Cy3


title: Androgen_siControl_rep3_Cy3


title: Breast biopsy UVABC1 10-cell sample 21

description:
BCC2.Sample21
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siPVT1_rep1_Cy3


title: Breast biopsy UVABC1 10-cell sample 20

description:
BCC2.Sample20
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siPVT1_rep4_Cy3


title: Breast biopsy UVABC1 10-cell sample 19

description:
BCC2.Sample19
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 18

description:
BCC2.Sample18
2020_02_06_breastcancer_allcompiled.csv


title: Androgen_siPVT1_rep2_Cy5


title: Androgen_siPVT1_rep3_Cy3


title: Breast biopsy UVABC1 10-cell sample 16

description:
BCC2.Sample16
2020_02_06_breastcancer_allcompiled.csv


title: Vehicle_siControl_rep1_Cy5


title: Breast biopsy UVABC1 10-cell sample 24

description:
BCC2.Sample24
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 25

description:
BCC2.Sample25
2020_02_06_breastcancer_allcompiled.csv


title: 16120T

city: Guangzhou

first: Fang

last: Zheng

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

description: lncRNA expression data

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: tissue

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of cyanine-3-CTP.

growth_protocol: The breast cancer cell lines 76N and MBA-MD-231 were cultured under normoxia (20%) or hypoxia (0.6%) conditions.

extract_protocol: Hypoxic cell lines 76N and MBA-MD-231 and 4 pairs of ground breast cancer and adjacent normal tissues were stored in TRIZOL, then were extracted according to protocol.

treatment_protocol: Hypoxic cell lines 76N and MBA-MD-231 were harvested.

value: Breast cancer


title: Breast biopsy UVABC1 10-cell sample 17

description:
BCC2.Sample17
2020_02_06_breastcancer_allcompiled.csv


title: 16120P

description: lncRNA expression data

value: Adjacent normal breast tissue


title: 1609P

description: lncRNA expression data


title: 1609T

description: lncRNA expression data


title: Breast biopsy UVABC1 10-cell sample 15

description:
BCC2.Sample15
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 14

description:
BCC2.Sample14
2020_02_06_breastcancer_allcompiled.csv


title: 1504P

description: lncRNA expression data


title: Breast biopsy UVABC1 10-cell sample 13

description:
BCC2.Sample13
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 12

description:
BCC2.Sample12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 11

description:
BCC2.Sample11
2020_02_06_breastcancer_allcompiled.csv


title: MDA-MB-231H

description: lncRNA expression data

source_name: breast cancer cell line

value: Breast cancer cell line

tag: condition

value: Hypoxia


title: 1531P

description: lncRNA expression data


title: MDA-MB-231N

description: lncRNA expression data

value: Normoxia


title: Breast biopsy UVABC1 10-cell sample 10

description:
BCC2.Sample10
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 9

description:
BCC2.Sample09
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V3_TB1_tube

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

description:
LTBI 30_v1_tb1 vs LTBI 30_v3_tb1_7125_1_4.txt
30_LTBI_v3_tb1

hyb_protocol: 300 ng of Cy3 or Cy5-labelled cRNA (specific activity >6.0 pmol Cy3 or Cy5 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the two colour scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel set to 'red and green',  and PMT set to 100%).

data_processing: Feature Extraction Software 12.0 (Agilent) using default parameters (protocol GE2_1200_Jun14 and grid template: 072363_D_F_20180928) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were   log-2 transformed and normalised using the Agilp expression array processing package in ‘R’ Language and Environment for Statistical Computing 3.5.2

source_name: Cultured whole blood from IGRA+ donor

label_protocol: Two-color low input Quick Amp Labelling kit (Agilent)

extract_protocol: Cultures were transferred to fresh tubes, blood cells separated from the liquid phase by centrifugation and lysed in RNA Protect (Qiagen). RNA extracted using RNEasy mini kit (Qiagen) with on-column DNAse treatment. Globin-depletion performed using GLOBINclear Kit (ThermoFisher).

treatment_protocol: Venous blood was collected into lithium heparin tubes, and then transferred (1ml each) to the nil, TB1 and TB2 tubes from QuantiFERON-TB Gold Plus In-tube Assay, and incubated for 22 hours at 37oC

value: Blood

tag: group

value: IGRA+

tag: timepoint

tag: stimulus


title: Breast biopsy UVABC1 10-cell sample 5

description:
BCC2.Sample05
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 6

description:
BCC2.Sample06
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 7

description:
BCC2.Sample07
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell sample 4

description:
BCC2.Sample04
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V3_TB2_tube

description:
LTBI 30_v3_neg vs LTBI 30_v3_tb2_6674_1_3.txt
30_LTBI_v3_tb2


title: Breast biopsy UVABC1 10-cell sample 3

description:
BCC2.Sample03
2020_02_06_breastcancer_allcompiled.csv


title: 1504T

description: lncRNA expression data


title: Breast biopsy UVABC1 10-cell sample 8

description:
BCC2.Sample08
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 20

description:
BCC2.Control20
2020_02_06_breastcancer_allcompiled.csv


title: 1531T

description: lncRNA expression data


title: Breast biopsy UVABC1 10-cell sample 2

description:
BCC2.Sample02
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V3_nil_tube

description:
LTBI 30_v3_neg vs LTBI 30_v3_tb2_6674_1_3.txt
30_LTBI_v3_neg


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 19

description:
BCC2.Control19
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V2_TB1_tube

description:
LTBI 30_v2_neg vs LTBI 30_v2_tb1_6674_2_1.txt
30_LTBI_v2_tb1

value: Week 2


title: IGRA+ve_#30_V2_TB2_tube

description:
LTBI 30_v2_tb2 vs LTBI 27_v1_tb2_6733_1_4.txt
30_LTBI_v2_tb2


title: IGRA+ve_#30_V2_nil_tube

description:
LTBI 30_v2_neg vs LTBI 30_v2_tb1_6674_2_1.txt
30_LTBI_v2_neg


title: Breast biopsy UVABC1 10-cell sample 1

description:
BCC2.Sample01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 17

description:
BCC2.Control17
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#28_V3_nil_tube

description:
LTBI 28_v3_tb1 vs LTBI 28_v3_neg_6674_1_2.txt
28_LTBI_v3_neg


title: IGRA+ve_#28_V3_TB2_tube

description:
LTBI 28_v3_tb2 vs LTBI 24_v2_neg_6674_1_4.txt
28_LTBI_v3_tb2


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 16

description:
BCC2.Control16
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V1_TB1_tube

description:
LTBI 30_v1_tb1 vs LTBI 30_v3_tb1_7125_1_4.txt
30_LTBI_v1_tb1

value: Week 0


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 15

description:
BCC2.Control15
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#30_V1_TB2_tube

description:
LTBI 30_v1_tb2 vs LTBI 30_v1_neg_6733_2_3.txt
30_LTBI_v1_tb2


title: IGRA+ve_#30_V1_nil_tube

description:
LTBI 30_v1_tb2 vs LTBI 30_v1_neg_6733_2_3.txt
30_LTBI_v1_neg


title: IGRA+ve_#28_V3_TB1_tube

description:
LTBI 28_v3_tb1 vs LTBI 28_v3_neg_6674_1_2.txt
28_LTBI_v3_tb1


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 14

description:
BCC2.Control14
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 12

description:
BCC2.Control12
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 18

description:
BCC2.Control18
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#28_V2_TB1_tube

description:
LTBI 28_v2_tb1 vs LTBI 27_v1_tb1_7126_1_4.txt
28_LTBI_v2_tb1


title: IGRA+ve_#28_V1_TB2_tube

description:
LTBI 28_v1_tb1 vs LTBI 28_v1_tb2_6733_2_2.txt
28_LTBI_v1_tb2


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 11

description:
BCC2.Control11
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 10

description:
BCC2.Control10
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#27_V3_TB1_tube

description:
LTBI 12_v3_neg vs LTBI 27_v3_tb1_7125_2_3.txt
27_LTBI_v3_tb1


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 9

description:
BCC2.Control09
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#28_V2_TB2_tube

description:
LTBI 28_v2_neg vs LTBI 28_v2_tb2_6733_1_3.txt
28_LTBI_v2_tb2


title: IGRA+ve_#27_V2_TB2_tube

description:
LTBI 27_v3_neg vs LTBI 27_v2_tb2_6732_2_4.txt
27_LTBI_v2_tb2


title: IGRA+ve_#28_V1_nil_tube

description:
LTBI 28_v1_neg vs LTBI 13_v1_tb2_7125_1_2.txt
28_LTBI_v1_neg


title: IGRA+ve_#28_V1_TB1_tube

description:
LTBI 28_v1_tb1 vs LTBI 28_v1_tb2_6733_2_2.txt
28_LTBI_v1_tb1


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 8

description:
BCC2.Control08
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#27_V3_TB2_tube

description:
LTBI 27_v1_neg vs LTBI 27_v3_tb2_6733_2_4.txt
27_LTBI_v3_tb2


title: IGRA+ve_#27_V1_TB1_tube

description:
LTBI 28_v2_tb1 vs LTBI 27_v1_tb1_7126_1_4.txt
27_LTBI_v1_tb1


title: IGRA+ve_#27_V2_nil_tube

description:
LTBI 27_v2_tb1 vs LTBI 27_v2_neg_6733_1_2.txt
27_LTBI_v2_neg


title: IGRA+ve_#27_V1_TB2_tube

description:
LTBI 30_v2_tb2 vs LTBI 27_v1_tb2_6733_1_4.txt
27_LTBI_v1_tb2


title: IGRA+ve_#28_V2_nil_tube

description:
LTBI 28_v2_neg vs LTBI 28_v2_tb2_6733_1_3.txt
28_LTBI_v2_neg


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 13

description:
BCC2.Control13
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#27_V3_nil_tube

description:
LTBI 27_v3_neg vs LTBI 27_v2_tb2_6732_2_4.txt
27_LTBI_v3_neg


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 7

description:
BCC2.Control07
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#27_V1_nil_tube

description:
LTBI 27_v1_neg vs LTBI 27_v3_tb2_6733_2_4.txt
27_LTBI_v1_neg


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 6

description:
BCC2.Control06
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#27_V2_TB1_tube

description:
LTBI 27_v2_tb1 vs LTBI 27_v2_neg_6733_1_2.txt
27_LTBI_v2_tb1


title: IGRA+ve_#23_V3_TB2_tube

description:
LTBI 23_v3_tb2 vs LTBI 23_v3_neg_6732_2_3.txt
23_LTBI_v3_tb2


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 5

description:
BCC2.Control05
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#23_V3_nil_tube

description:
LTBI 23_v3_tb2 vs LTBI 23_v3_neg_6732_2_3.txt
23_LTBI_v3_neg


title: IGRA+ve_#23_V3_TB1_tube

description:
LTBI 23_v2_tb2 vs LTBI 23_v3_tb1_4319_2_3.txt
23_LTBI_v3_tb1


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 4

description:
BCC2.Control04
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 3

description:
BCC2.Control03
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#23_V2_TB2_tube

description:
LTBI 23_v2_tb2 vs LTBI 23_v3_tb1_4319_2_3.txt
23_LTBI_v2_tb2


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 1

description:
BCC2.Control01
2020_02_06_breastcancer_allcompiled.csv


title: Breast biopsy UVABC1 10-cell pool-and-split control replicate 2

description:
BCC2.Control02
2020_02_06_breastcancer_allcompiled.csv


title: IGRA+ve_#23_V2_nil_tube

description:
LTBI 10_v3_tb1 vs LTBI 23_v2_neg_4319_2_4.txt
23_LTBI_v2_neg


title: IGRA+ve_#23_V2_TB1_tube

description:
LTBI 10_v1_neg vs LTBI 23_v2_tb1_4319_1_4.txt
23_LTBI_v2_tb1


title: Interneuron_P2_KO_2

city: Geneva 4

first: Alexandre

last: Dayer

state: GE

address: Rue Michel-Servet 1

department: Basic Neuroscience

country: Switzerland

institute: University of Geneva

description: Gene expression of CGE-derived interneurons settling in the neocortex

hyb_protocol: Mouse Genome 430 2.0 Array (Affymetrix) and Affymetrix GeneChip Fluidis Station 450

scan_protocol: GC3000 scanner (Affymetrix)

data_processing:
Partek Genomics Suites version 6.6 beta
normalization with robust multy-array average (RMA). mRNA expression levels of genes (ProbeSet) compared with 2-way ANOVA and contrasted with uncorrected p<0.001

label: biotin

source_name: cortex, interneurons, P2

label_protocol: oligo(dT)_24 primer with T7 RNA promoter to the 5' poly(T) - Ambion MEGAscript T7 labeling kit (Ambion)

growth_protocol: Fresh cut brain slices

extract_protocol: Rneasy Mini Kit from Quiagen - manufacturer's protocol

value: brain, CGE-derived interneurons

tag: genotype/variation

tag: age


title: Interneuron_P2_KO_1


title: IGRA+ve_#22_V3_TB2_tube

description:
LTBI 11_v3_tb1 vs LTBI 22_v3_tb2_6732_2_2.txt
22_LTBI_v3_tb2


title: Interneuron_P2_CT_1


title: IGRA+ve_#22_V3_TB1_tube

description:
LTBI 22_v3_neg vs LTBI 22_v3_tb1_6732_2_1.txt
22_LTBI_v3_tb1


title: IGRA+ve_#22_V3_nil_tube

description:
LTBI 22_v3_neg vs LTBI 22_v3_tb1_6732_2_1.txt
22_LTBI_v3_neg


title: IGRA+ve_#22_V2_TB2_tube

description:
LTBI 10_v1_tb2 vs LTBI 22_v2_tb2_4319_2_2.txt
22_LTBI_v2_tb2


title: IGRA+ve_#23_V1_nil_tube

description:
LTBI 22_v1_tb1 vs LTBI 23_v1_neg_6732_1_2.txt
23_LTBI_v1_neg


title: IGRA+ve_#23_V1_TB1_tube

description:
LTBI 23_v1_tb2 vs LTBI 23_v1_tb1_6732_1_1.txt
23_LTBI_v1_tb1


title: Interneuron_E18.5_KO_3

description: Gene expression of CGE-derived interneurons invading the cortical plate

source_name: cortex, interneurons, E18.5


title: Interneuron_P2_CT_3


title: IGRA+ve_#22_V2_nil_tube

description:
LTBI 22_v2_neg vs LTBI 22_v1_neg_4319_1_3.txt
22_LTBI_v2_neg


title: Interneuron_E18.5_KO_2


title: Interneuron_E18.5_KO_1


title: IGRA+ve_#22_V2_TB1_tube

description:
LTBI 22_v2_tb1 vs LTBI 22_v1_tb2_4319_2_1.txt
22_LTBI_v2_tb1


title: IGRA+ve_#16_V3_TB2_tube

description:
LTBI 4_v2_tb1 vs LTBI 16_v3_tb2_7126_2_2.txt
16_LTBI_v3_tb2


title: Interneuron_E18.5_CT_2


title: Interneuron_P2_CT_2


title: IGRA+ve_#16_V3_nil_tube

description:
LTBI 16_v3_neg vs LTBI 16_v2_tb1_7126_2_1.txt
16_LTBI_v3_neg


title: IGRA+ve_#16_V3_TB1_tube

description:
LTBI 16_v1_tb2 vs LTBI 16_v3_tb1_7126_2_4.txt
16_LTBI_v3_tb1


title: Interneuron_E18.5_CT_3


title: Interneuron_P2_KO_3


title: Interneuron_E18.5_CT_1


title: IGRA+ve_#16_V2_TB2_tube

description:
LTBI 16_v2_tb2 vs LTBI 14_v3_tb2_7127_2_1.txt
16_LTBI_v2_tb2


title: IGRA+ve_#22_V1_nil_tube

description:
LTBI 22_v2_neg vs LTBI 22_v1_neg_4319_1_3.txt
22_LTBI_v1_neg


title: IGRA+ve_#22_V1_TB1_tube

description:
LTBI 22_v1_tb1 vs LTBI 23_v1_neg_6732_1_2.txt
22_LTBI_v1_tb1


title: IGRA+ve_#22_V1_TB2_tube

description:
LTBI 22_v2_tb1 vs LTBI 22_v1_tb2_4319_2_1.txt
22_LTBI_v1_tb2


title: IGRA+ve_#23_V1_TB2_tube

description:
LTBI 23_v1_tb2 vs LTBI 23_v1_tb1_6732_1_1.txt
23_LTBI_v1_tb2


title: IGRA+ve_#16_V1_TB1_tube

description:
LTBI 16_v1_tb1 vs LTBI 14_v1_tb1_7114_2_4.txt
16_LTBI_v1_tb1


title: Interneuron_E14.5_CT_2

description: Gene expression of CGE-derived interneurons migrating tangentially

source_name: cortex, interneurons, E14.5


title: Interneuron_E14.5_KO_2


title: Interneuron_E14.5_KO_3


title: Interneuron_E14.5_CT_1


title: IGRA+ve_#15_V2_TB1_tube

description:
LTBI 14_v2_tb2 vs LTBI 15_v2_tb1_7126_1_3.txt
15_LTBI_v2_tb1


title: IGRA+ve_#16_V1_TB2_tube

description:
LTBI 16_v1_tb2 vs LTBI 16_v3_tb1_7126_2_4.txt
16_LTBI_v1_tb2


title: IGRA+ve_#16_V2_nil_tube

description:
LTBI 25_v1_neg vs LTBI 16_v2_neg_7127_1_3.txt
16_LTBI_v2_neg


title: Interneuron_E14.5_CT_3


title: IGRA+ve_#15_V2_TB2_tube

description:
LTBI 15_v2_neg vs LTBI 15_v2_tb2_7126_1_2.txt
15_LTBI_v2_tb2


title: IGRA+ve_#15_V3_TB1_tube

description:
LTBI 15_v3_tb1 vs LTBI 15_v1_neg_7127_1_1.txt
15_LTBI_v3_tb1


title: IGRA+ve_#16_V2_TB1_tube

description:
LTBI 16_v3_neg vs LTBI 16_v2_tb1_7126_2_1.txt
16_LTBI_v2_tb1


title: Sertoli valve of W/Wv mouse, biological rep3

city: Yayoi, Bunkyo-ku

first: Yoshiakira

last: Kanai

state: Tokyo

country: Japan

institute: The University of Tokyo

description:
WtesSV3
Gene expression data from Sertoli valve of W/Wv mouse.

hyb_protocol: cRNA was hybridized to Mouse Genome 430 2.0 Array (Affimetrix), and chips were washed and stained using the Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: Data were normalized by the MAS5.0 method using R.

source_name: Sertoli valve of W/Wv mouse

label_protocol: cRNA was synthesized using GeneChip 3' IVT PLUS Reagent Kiit (Affymetrix).

growth_protocol: 7-week-old W/Wv mice were purchased from SLC Japan.

extract_protocol: RNA was purified using the QIAGEN Rneasy Micro Kit.

treatment_protocol: Trypan blue solution (0.4%, Sigma-Aldrich) was injected through efferent ducts into the testes to visualize the place of rete testis (RT), Sertoli valve (SV) and convoluted seminiferous tubules (ST) and testes were submerged in RNAlater Stabilization Solution (Thermo Fisher Scientific). Testes were cut into each region using forceps and needles under a dissecting microscope.

tag: strain

value: W/Wv

value: 7 weeks

value: testis

tag: tissue subtype

value: Sertoli valve (SV)


title: IGRA+ve_#15_V2_nil_tube

description:
LTBI 15_v2_neg vs LTBI 15_v2_tb2_7126_1_2.txt
15_LTBI_v2_neg


title: rete testis of W/Wv mouse, biological rep3

description:
WtesRT3
Gene expression data from rete testis of W/Wv mouse.

source_name: rete testis of W/Wv mouse

value: rete testis (RT)


title: Sertoli valve of W/Wv mouse, biological rep2

data_processing:
Data were normalized by the MAS5.0 method using R.
Algorithm: ExpressionStat 5.0


title: IGRA+ve_#15_V1_TB2_tube

description:
LTBI 15_v3_tb2 vs LTBI 15_v1_tb2_7126_2_3.txt
15_LTBI_v1_tb2


title: IGRA+ve_#15_V3_TB2_tube

description:
LTBI 15_v3_tb2 vs LTBI 15_v1_tb2_7126_2_3.txt
15_LTBI_v3_tb2


title: convoluted seminiferous tubules of W/Wv mouse, biological rep1

value: convoluted seminiferous tubules (ST)


title: IGRA+ve_#16_V1_nil_tube

description:
LTBI 14_v1_tb2 vs LTBI 16_v1_neg_7127_2_3.txt
16_LTBI_v1_neg


title: convoluted seminiferous tubules of W/Wv mouse, biological rep2


title: convoluted seminiferous tubules of W/Wv mouse, biological rep3

description:
WtesST3
Gene expression data from convoluted seminiferous tubules of W/Wv mouse.


title: IGRA+ve_#15_V1_TB1_tube

description:
LTBI 4_v1_neg vs LTBI 15_v1_tb1_7127_2_4.txt
15_LTBI_v1_tb1


title: 90686 Cohort 1

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

country: Canada

institute: University Health Network

data_processing:
Samples were aligned using STAR 2.5.2b9 against GRCh38 and transcript sequences downloaded from Ensembl build 90. Default parameters were used except for the following: “--chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5”.
Counts were the obtained using HTSeq v0.7.2
HTSeq counts were imported into R (3.4.1) and normalized using RLE
Supplementary_files_format_and_content: normalized counts

source_name: Acute myeloid leukemia

extract_protocol:
AML patient samples were obtained as viably frozen material from the Leukemia Tissue Bank at Princess Margaret Cancer Centre/ University Health Network and  thawed by dropwise addition of X-VIVO + 50% fetal calf serum supplemented with DNase (100μg/mL final concentration, Roche).
RNA was extracted from bulk peripheral blood mononuclear cells (PBMC) using the RNeasy Micro Kit (Qiagen Inc.).
A paired-end 50 base-pair flow-cell lane Illumina High seq 2000 yielded an average of 240 million sequence reads aligning to genome per sample at the Genome Sciences Centre, BC Cancer Agency for cohort 1. Cohort 2 was subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Centre for Applied Genomics, Sick Kids Hospital.

tag: sample material

value: peripheral blood

tag: cohort

value: Cohort 1

tag: rnaseq sample name


title: 100818 Cohort 1


title: U251-Ctrl rep1

city: Chongqing

first: Liling

last: Tang

address: No 174 Shapinba St

institute: Chongqing University

description: RawCounts.txt

data_processing:
Illumina Casava1.7 software was used for basecalling.
Reads were trimmed for quality score and adaptor sequences were also removed. The high-quality reads (between 30-45 million) that passed quality filters were aligned to the human reference genome (GRCh38) using STAR aligner, allowing up to two mismatches in conjunction with the gene model from Ensemble 92. Reads were quantitated by counting the number of reads across exons.
A  gene was designated as ""differentially expressed"", if it  pass the FDR adjusted p < 0.05 in DEseq ( Anders and Huber 2010, Genome Biol., 11, R106 ) as well as in null model of hypothesis (Kani et al (2017, Mol. Cancer Ther., 16, 1645)
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized read counts

source_name: glioma cells

growth_protocol: cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose (Hyclone) at 37°C in 5% CO2. All media were supplemented with 10% FBS (Excell Bio) and 100 ug/ml penicillin and streptomycin to make complete medium. Media were change every other day.

extract_protocol:
A RNeasy Mini Kit (Qiagen 74104) was used to extract total RNA. The RNA products isolated using this kit were loaded on a 1% agarose gel and separated by electrophoresis. Then, bands for 28S RNA, 18S RNA, and 5S RNA were inspected to ensure that RNA was extracted correctly. Next, the RNA quality and concentration were assayed using a Nanodrop 2000 spectrophotometer (ThermoFisher Scientific).
Strand-specific libraries were generated by using the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPA Biosystem Wilmington, MA). Sequencing libraries were quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and validated using High-Performance Capillary Electrophoresis (HPCE) and the Agilent Tapestation 4200 (Agilent Technologies, CA, USA).he sequencing libraries were multiplexed and clustered on one lane of a Flow Cell. After clustering, the Flow Cell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.  RNA-seq was performed by GENEWIZ (Plainfield, NJ, USA)

treatment_protocol: Complete media with 1 ug/ml Puro was used to culture this purified stable cell line.

tag: cell type

value: U251MG cell line

tag: genotype

value: wild type


title: U251-Ctrl rep2

description: RawCounts.txt


title: 110500 Cohort 1


title: Interneuron_E14.5_KO_1

tag: tissue


title: U251-overexpression MDM2 rep2

description: RawCounts.txt

value: MDM2 overexpression


title: U251-overexpression MDM2 rep1

description: RawCounts.txt


title: 110260 Cohort 1


title: 80488 Cohort 1


title: IGRA+ve_#15_V1_nil_tube

description:
LTBI 15_v3_tb1 vs LTBI 15_v1_neg_7127_1_1.txt
15_LTBI_v1_neg


title: IGRA+ve_#14_V3_TB1_tube

description:
LTBI 4_v2_neg vs LTBI 14_v3_tb1_7127_1_4.txt
14_LTBI_v3_tb1


title: IGRA+ve_#14_V3_TB2_tube

description:
LTBI 16_v2_tb2 vs LTBI 14_v3_tb2_7127_2_1.txt
14_LTBI_v3_tb2


title: rete testis of W/Wv mouse, biological rep1


title: IGRA+ve_#14_V1_TB2_tube

description:
LTBI 14_v1_tb2 vs LTBI 16_v1_neg_7127_2_3.txt
14_LTBI_v1_tb2


title: 90582 Cohort 1


title: 110438 Cohort 1


title: rete testis of W/Wv mouse, biological rep2


title: IGRA+ve_#14_V2_TB1_tube

description:
LTBI 14_v2_tb1 vs LTBI 14_v2_neg_7126_1_1.txt
14_LTBI_v2_tb1


title: IGRA+ve_#14_V3_nil_tube

description:
LTBI 14_v1_neg vs LTBI 14_v3_neg_7127_1_2.txt
14_LTBI_v3_neg


title: Sertoli valve of W/Wv mouse, biological rep1


title: 100327 Cohort 1


title: IGRA+ve_#14_V2_TB2_tube

description:
LTBI 14_v2_tb2 vs LTBI 15_v2_tb1_7126_1_3.txt
14_LTBI_v2_tb2


title: IGRA+ve_#14_V1_nil_tube

description:
LTBI 14_v1_neg vs LTBI 14_v3_neg_7127_1_2.txt
14_LTBI_v1_neg


title: IGRA+ve_#14_V2_nil_tube

description:
LTBI 14_v2_tb1 vs LTBI 14_v2_neg_7126_1_1.txt
14_LTBI_v2_neg


title: 90184 Cohort 1


title: 110120 Cohort 1


title: IGRA+ve_#12_V3_TB2_tube

description:
LTBI 12_v3_tb1 vs LTBI 12_v3_tb2_7125_2_1.txt
12_LTBI_v3_tb2


title: IGRA+ve_#12_V3_nil_tube

description:
LTBI 12_v3_neg vs LTBI 27_v3_tb1_7125_2_3.txt
12_LTBI_v3_neg


title: IGRA+ve_#12_V2_TB2_tube

description:
LTBI 12_v2_tb1 vs LTBI 12_v2_tb2_6674_2_2.txt
12_LTBI_v2_tb2


title: 110102 Cohort 1


title: 90590 Cohort 1


title: 100885 Cohort 1


title: IGRA+ve_#12_V3_TB1_tube

description:
LTBI 12_v3_tb1 vs LTBI 12_v3_tb2_7125_2_1.txt
12_LTBI_v3_tb1


title: 100183 Cohort 1


title: 874 Cohort 1


title: IGRA+ve_#14_V1_TB1_tube

description:
LTBI 16_v1_tb1 vs LTBI 14_v1_tb1_7114_2_4.txt
14_LTBI_v1_tb1


title: 100255 Cohort 1


title: 100507 Cohort 1


title: 9677 Cohort 1


title: 90190 Cohort 1


title: 100274 Cohort 1


title: 100454 Cohort 1


title: 90668 Cohort 1


title: 858 Cohort 1


title: 80185 Cohort 1


title: IGRA+ve_#12_V1_TB2_tube

description:
LTBI 12_v1_tb2 vs LTBI 12_v1_tb1_7125_1_3.txt
12_LTBI_v1_tb2


title: IGRA+ve_#12_V1_nil_tube

description:
LTBI 12_v2_neg vs LTBI 12_v1_neg_6674_2_4.txt
12_LTBI_v1_neg


title: IGRA+ve_#12_V2_TB1_tube

description:
LTBI 12_v2_tb1 vs LTBI 12_v2_tb2_6674_2_2.txt
12_LTBI_v2_tb1


title: IGRA+ve_#10_V3_TB1_tube

description:
LTBI 10_v3_tb1 vs LTBI 23_v2_neg_4319_2_4.txt
10_LTBI_v3_tb1


title: IGRA+ve_#12_V1_TB1_tube

description:
LTBI 12_v1_tb2 vs LTBI 12_v1_tb1_7125_1_3.txt
12_LTBI_v1_tb1


title: IGRA+ve_#10_V3_nil_tube

description:
LTBI 10_v2_tb1 vs LTBI 10_v3_neg_4319_1_1.txt
10_LTBI_v3_neg


title: IGRA+ve_#10_V2_nil_tube

description:
LTBI 10_v2_neg vs LTBI 10_v1_tb1_4318_2_1.txt
10_LTBI_v2_neg


title: 90428 Cohort 1


title: 90135 Cohort 1


title: IGRA+ve_#9_V3_TB2_tube

description:
LTBI 9_v3_tb2 vs LTBI 7_v3_tb1_4318_1_3.txt
9_LTBI_v3_tb2


title: IGRA+ve_#10_V1_TB2_tube

description:
LTBI 10_v1_tb2 vs LTBI 22_v2_tb2_4319_2_2.txt
10_LTBI_v1_tb2


title: 840 Cohort 1


title: IGRA+ve_#12_V2_nil_tube

description:
LTBI 12_v2_neg vs LTBI 12_v1_neg_6674_2_4.txt
12_LTBI_v2_neg


title: IGRA+ve_#10_V1_TB1_tube

description:
LTBI 10_v2_neg vs LTBI 10_v1_tb1_4318_2_1.txt
10_LTBI_v1_tb1


title: 80534 Cohort 1


title: IGRA+ve_#10_V2_TB2_tube

description:
LTBI 10_v2_tb2 vs LTBI 10_v3_tb2_4318_2_3.txt
10_LTBI_v2_tb2


title: IGRA+ve_#10_V3_TB2_tube

description:
LTBI 10_v2_tb2 vs LTBI 10_v3_tb2_4318_2_3.txt
10_LTBI_v3_tb2


title: 90392 Cohort 1


title: 80008 Cohort 1


title: IGRA+ve_#10_V2_TB1_tube

description:
LTBI 10_v2_tb1 vs LTBI 10_v3_neg_4319_1_1.txt
10_LTBI_v2_tb1


title: IGRA+ve_#10_V1_nil_tube

description:
LTBI 10_v1_neg vs LTBI 23_v2_tb1_4319_1_4.txt
10_LTBI_v1_neg


title: IGRA+ve_#9_V3_TB1_tube

description:
LTBI 9_v3_tb1 vs LTBI 9_v3_neg_4318_1_1.txt
9_LTBI_v3_tb1


title: 90185 Cohort 1


title: IGRA+ve_#9_V2_TB1_tube

description:
LTBI 9_v2_neg vs LTBI 9_v2_tb1_4317_2_3.txt
9_LTBI_v2_tb1


title: IGRA+ve_#9_V1_TB2_tube

description:
LTBI 9_v1_neg vs LTBI 9_v1_tb2_4317_1_2.txt
9_LTBI_v1_tb2


title: IGRA+ve_#9_V3_nil_tube

description:
LTBI 9_v3_tb1 vs LTBI 9_v3_neg_4318_1_1.txt
9_LTBI_v3_neg


title: IGRA+ve_#9_V2_nil_tube

description:
LTBI 9_v2_neg vs LTBI 9_v2_tb1_4317_2_3.txt
9_LTBI_v2_neg


title: IGRA+ve_#9_V2_TB2_tube

description:
LTBI 7_v2_tb1 vs LTBI 9_v2_tb2_4317_2_1.txt
9_LTBI_v2_tb2


title: 512 Cohort 1


title: 100474 Cohort 1


title: 90521 Cohort 1


title: 90077 Cohort 1


title: 100006 Cohort 1


title: 100016 Cohort 1


title: 90295 Cohort 1


title: 100348 Cohort 1


title: 110283 Cohort 1


title: 90481 Cohort 1


title: 110484 Cohort 1


title: 90240 Cohort 1

value: peritoneal fluid


title: 713 Cohort 1


title: 100565 Cohort 1


title: 598 Cohort 1


title: IGRA+ve_#9_V1_nil_tube

description:
LTBI 9_v1_neg vs LTBI 9_v1_tb2_4317_1_2.txt
9_LTBI_v1_neg

value: Blood


title: IGRA+ve_#8_V3_TB2_tube

description:
LTBI 8_v3_neg vs LTBI 8_v3_tb2_4318_1_2.txt
8_LTBI_v3_tb2

value: IGRA+


title: 100770 Cohort 1


title: 90543 Cohort 1


title: IGRA+ve_#8_V3_TB1_tube

description:
LTBI 8_v2_tb1 vs LTBI 8_v3_tb1_4317_2_4.txt
8_LTBI_v3_tb1


title: IGRA+ve_#8_V3_nil_tube

description:
LTBI 8_v3_neg vs LTBI 8_v3_tb2_4318_1_2.txt
8_LTBI_v3_neg


title: IGRA+ve_#8_V2_TB1_tube

description:
LTBI 8_v2_tb1 vs LTBI 8_v3_tb1_4317_2_4.txt
8_LTBI_v2_tb1

value: Week 2


title: 90476 Cohort 1


title: IGRA+ve_#8_V1_TB1_tube

description:
LTBI 8_v1_TB1 vs LTBI 8_v1_neg_4317_1_1.txt
8_LTBI_v1_tb1

value: Week 0


title: IGRA+ve_#8_V1_TB2_tube

description:
LTBI 8_v1_tb2 vs LTBI 3_v1_tb1_4317_1_3.txt
8_LTBI_v1_tb2


title: 90444 Cohort 1


title: 90147 Cohort 1


title: 110002 Cohort 1


title: IGRA+ve_#8_V2_TB2_tube

description:
LTBI 8_v2_tb2 vs LTBI 8_v2_neg_4317_2_2.txt
8_LTBI_v2_tb2


title: IGRA+ve_#8_V2_nil_tube

description:
LTBI 8_v2_tb2 vs LTBI 8_v2_neg_4317_2_2.txt
8_LTBI_v2_neg


title: 90239 Cohort 1


title: IGRA+ve_#7_V1_nil_tube

description:
LTBI 7_v3_neg vs LTBI 7_v1_neg_4059_2_4.txt
7_LTBI_v1_neg


title: IGRA+ve_#7_V3_nil_tube

description:
LTBI 7_v3_neg vs LTBI 7_v1_neg_4059_2_4.txt
7_LTBI_v3_neg


title: IGRA+ve_#7_V2_TB1_tube

description:
LTBI 7_v2_tb1 vs LTBI 9_v2_tb2_4317_2_1.txt
7_LTBI_v2_tb1


title: IGRA+ve_#8_V1_nil_tube

description:
LTBI 8_v1_TB1 vs LTBI 8_v1_neg_4317_1_1.txt
8_LTBI_v1_neg


title: IGRA+ve_#7_V3_TB2_tube

description:
LTBI 1_v3_tb1 vs LTBI 7_v3_tb2_4059_2_2.txt
7_LTBI_v3_tb2


title: IGRA+ve_#7_V1_TB1_tube

description:
LTBI 7_v1_tb1 vs LTBI 2_v2_tb1_4317_1_4.txt
7_LTBI_v1_tb1


title: RNAseq-GRKO-GFP-GRdim_TNF+DEX_rep2

data_processing:
RTA 2.4.11 was used for Basecalling and Bcl2fastq 2.17 was used for demultiplexing allowing 1 mismatch.
Trimmomatic 0.36 was used for adapter and quality control.
ChIP- and ATAC-seq alignment was performed by Bowtie2 (2.1.0) with Bowtie2 –p 8 –x bowtie2_ref/genome_prefix –U read1.fastq –S result.sam.
RNA-seq alignment was performed by STAR (2.7) with STAR --sjdbOverhang 50  --readFilesIn INPUT_R1.pair.fastq.gz INPUT_R2_R2.pair.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outTmpDir --outFileNamePrefix bam/rnaseq_STAR/OUTPUT . Dex regulated genes were defined with DESeq2 through HOMER program version 4.9.
Peaks were called using HOMER program version 4.9 with findPeaks with following parameters; FDR<0.001, 4x fold enrichment over control, 4x fold enrichment over local background, and >75 tags per site. In addition, untreated GR ChIP sample was used to further filter out noise from GR samples using default parameters on getDifferentialPeaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (HOMER makeUCSCfile command) from alignment file.

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, TNF+Dex-treated, RNA

growth_protocol: Mouse adenocarcinoma cells were grown in Dulbecco's Modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 25 U/ml penicillin and 25 µg/ml streptomycin, and 2mM L-Glutamine, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator. Mouse adenocarcinoma cells were also supplemented with 5 µg/ml of tetracycline to supress GFP-GR expression.

extract_protocol:
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit.
Libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.

treatment_protocol: Mouse adenocarcinoma cells were grow in steroid-depleted medium (10% charcoal stripped FBS in DMEM) for 24 h, and the cells were subsequently left untreated or treated 100 nM of dexamethasone for 1 h in ChIP-seq and ATAC-seq, and for 2 h in RNA-seq, prior extraction.

tag: cell line

value: mouse adenocarcinoma

tag: stably expressing

value: A465T GFP-GRdim

tag: treatment

value: Tumor necrosis factor + Dexamethasone

tag: concentration

value: 10 ng per ul + 100 nM


title: RNAseq-GRKO-GFP-GRdim_TNF+DEX_rep1

tag: time


title: IGRA+ve_#7_V2_nil_tube

description:
LTBI 7_v2_neg vs LTBI 7_v2_tb2_7135_2_3.txt
7_LTBI_v2_neg

tag: group

tag: timepoint


title: IGRA+ve_#7_V2_TB2_tube

description:
LTBI 7_v2_neg vs LTBI 7_v2_tb2_7135_2_3.txt
7_LTBI_v2_tb2

tag: stimulus


title: IGRA+ve_#7_V1_TB2_tube

description:
LTBI 7_v1_tb2 vs LTBI 1_v1_neg_4058_2_3.txt
7_LTBI_v1_tb2


title: RNAseq-GRKO-GFP-GRdim_TNF_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, TNF-treated, RNA

value: Tumor necrosis factor

value: 10 ng per ul

value: 3 h


title: IGRA+ve_#6_V3_TB2_tube

description:
LTBI 6_v3_tb2 vs LTBI 6_v3_neg_4059_2_3.txt
6_LTBI_v3_tb2


title: IGRA+ve_#6_V3_TB1_tube

description:
LTBI 6_v3_tb1 vs LTBI 9_v1_tb1_4318_1_4.txt
6_LTBI_v3_tb1


title: IGRA+ve_#6_V2_TB1_tube

description:
LTBI 6_v2_tb1 vs LTBI 6_v2_neg_4059_1_2.txt
6_LTBI_v2_tb1


title: IGRA+ve_#6_V2_TB2_tube

description:
LTBI 6_v1_neg vs LTBI 6_v2_tb2_4058_2_4.txt
6_LTBI_v2_tb2


title: IGRA+ve_#6_V2_nil_tube

description:
LTBI 6_v2_tb1 vs LTBI 6_v2_neg_4059_1_2.txt
6_LTBI_v2_neg


title: IGRA+ve_#7_V3_TB1_tube

description:
LTBI 9_v3_tb2 vs LTBI 7_v3_tb1_4318_1_3.txt
7_LTBI_v3_tb1


title: IGRA+ve_#6_V3_nil_tube

description:
LTBI 6_v3_tb2 vs LTBI 6_v3_neg_4059_2_3.txt
6_LTBI_v3_neg


title: IGRA+ve_#6_V1_TB2_tube

description:
LTBI 6_v1_tb1 vs LTBI 6_v1_tb2_4058_2_2.txt
6_LTBI_v1_tb2


title: RNAseq-GRKO-GFP-GRwt_TNF+DEX_rep3

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, TNF+Dex-treated, RNA

value: wild-type GFP-GR


title: IGRA+ve_#6_V1_TB1_tube

description:
LTBI 6_v1_tb1 vs LTBI 6_v1_tb2_4058_2_2.txt
6_LTBI_v1_tb1


title: RNAseq-GRKO-GFP-GRwt_TNF+DEX_rep2


title: RNAseq-GRKO-GFP-GRdim_TNF_rep3


title: IGRA+ve_#5_V3_TB2_tube

description:
LTBI 5_v2_neg vs LTBI 5_v3_TB2_4057_2_4.txt
5_LTBI_v3_tb2


title: RNAseq-GRKO-GFP-GRwt_TNF_rep2

source_name: 3617-KOGR cells, stably integrated wild-type GFP-GR, TNF-treated, RNA


title: RNAseq-GRKO-GFP-GRwt_TNF_rep3


title: RNAseq-GRKO-GFP-GRwt_TNF+DEX_rep1


title: RNAseq-GRKO-GFP-GRdim_TNF_rep1


title: ECKI_IP

city: changsha

first: Zijun

state: hunan

address: N0.139 RENMIN MIDDLE ROAD

department: Dermatology

institute: Second Xiangya Hospital of Central South university

data_processing:
Basic statistics were  performed by FastX on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software
ChIP-seq reads were aligned to the mm10 genome assembly using BWA v0.7.12.
For single-end sequencing, the fragment size was estimated with MACS2 predicted method with default parameters(Model-based analysis of ChIP-Seq (MACS), Genome Biol).
Peaks were called using  MACS2 version 2.1.0 (model-based analysis of ChIP-seq)  with the following setting: A q value threshold of enrichment  of 0.05 was used for all data sets.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file was generated by MACS version 2.1.0.20150420

source_name: CD4+T cells

growth_protocol: Spleen derived CD4+ T cells from E4BP4-conditional CD4T knock-in mice were isolated

extract_protocol:
Lysates were clarified from sonicated nuclei and the chromatin was immunoprecipitated with antibody.
DNA Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Spleen

value: CD4+T cells

tag: chip antibody

value: DYKDDDDK Tag (D6W5B) Rabbit mAb (CST lot14793)


title: RNAseq-GRKO-GFP-GRmon_DEX_rep2

source_name: 3617-KOGR cells, stably integrated A465T/I634A GFP-GRmon, Dex-treated, RNA

value: A465T/I634A GFP-GRmon

value: Dexamethasone

value: 2 h


title: RNAseq-GRKO-GFP-GRmon_DEX_rep1


title: RNAseq-GRKO-GFP-GRmon_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T/I634A GFP-GRmon, non-treated, RNA

value: no treatment


title: RNAseq-GRKO-GFP-GRmon_DEX_rep3


title: RNAseq-GRKO-GFP-GRdim_DEX_rep3

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, Dex-treated, RNA


title: RNAseq-GRKO-GFP-GRmon_NT_rep1


title: RNAseq-GRKO-GFP-GRwt_TNF_rep1


title: IGRA+ve_#5_V3_nil_tube

description:
LTBI 5_v3_neg vs LTBI 5_v3_tb1_4059_2_1.txt
5_LTBI_v3_neg

value: Blood

value: IGRA+


title: IGRA+ve_#5_V2_TB2_tube

description:
LTBI 5_v2_tb2 vs LTBI 5_v2_tb1_4059_1_1.txt
5_LTBI_v2_tb2

value: Week 2


title: RNAseq-GRKO-GFP-GRdim_DEX_rep1

value: mouse adenocarcinoma

value: A465T GFP-GRdim


title: RNAseq-GRKO-GFP-GRdim_DEX_rep2


title: IGRA+ve_#6_V1_nil_tube

description:
LTBI 6_v1_neg vs LTBI 6_v2_tb2_4058_2_4.txt
6_LTBI_v1_neg

value: Week 0


title: IGRA+ve_#5_V3_TB1_tube

description:
LTBI 5_v3_neg vs LTBI 5_v3_tb1_4059_2_1.txt
5_LTBI_v3_tb1


title: IGRA+ve_#3_V3_TB2_tube

description:
LTBI 3_v3_tb2 vs LTBI 3_v3_tb1_4058_1_1.txt
3_LTBI_v3_tb2


title: RNAseq-GRKO-GFP-GRdim_NT_rep2

source_name: 3617-KOGR cells, stably integrated A465T GFP-GRdim, non-treated, RNA


title: IGRA+ve_#5_V2_TB1_tube

description:
LTBI 5_v2_tb2 vs LTBI 5_v2_tb1_4059_1_1.txt
5_LTBI_v2_tb1

source_name: Cultured whole blood from IGRA+ donor


title: IGRA+ve_#5_V1_TB1_tube

description:
LTBI 5_v1_neg vs LTBI 5_v1_tb1_4058_2_1.txt
5_LTBI_v1_tb1


title: RNAseq-GRKO-GFP-GRdim_NT_rep3


title: IGRA+ve_#5_V1_TB2_tube

description:
LTBI 1_v3_tb2 vs LTBI 5_v1_tb2_4058_1_4.txt
5_LTBI_v1_tb2


title: IGRA+ve_#3_V3_nil_tube

description:
LTBI 3_v3_neg vs LTBI 2_v3_tb2_4058_1_3.txt
3_LTBI_v3_neg


title: IGRA+ve_#3_V3_TB1_tube

description:
LTBI 3_v3_tb2 vs LTBI 3_v3_tb1_4058_1_1.txt
3_LTBI_v3_tb1


title: IGRA+ve_#3_V2_TB2_tube

description:
LTBI 3_v2_tb2 vs LTBI 1_v3_neg_4059_1_4.txt
3_LTBI_v2_tb2


title: IGRA+ve_#3_V1_TB2_tube

description:
LTBI 3_v1_neg vs LTBI 3_v1_TB2_4057_1_3.txt
3_LTBI_v1_tb2


title: IGRA+ve_#5_V2_nil_tube

description:
LTBI 5_v2_neg vs LTBI 5_v3_TB2_4057_2_4.txt
5_LTBI_v2_neg


title: IGRA+ve_#5_V1_nil_tube

description:
LTBI 5_v1_neg vs LTBI 5_v1_tb1_4058_2_1.txt
5_LTBI_v1_neg


title: IGRA+ve_#3_V1_TB1_tube

description:
LTBI 8_v1_tb2 vs LTBI 3_v1_tb1_4317_1_3.txt
3_LTBI_v1_tb1


title: IGRA+ve_#9_V1_TB1_tube

description:
LTBI 6_v3_tb1 vs LTBI 9_v1_tb1_4318_1_4.txt
9_LTBI_v1_tb1


title: IGRA+ve_#3_V2_nil_tube

description:
LTBI 3_v2_neg vs LTBI 3_v2_TB1_4057_2_1.txt
3_LTBI_v2_neg


title: IGRA+ve_#3_V2_TB1_tube

description:
LTBI 3_v2_neg vs LTBI 3_v2_TB1_4057_2_1.txt
3_LTBI_v2_tb1


title: RNAseq-GRKO-GFP-GRdim_NT_rep1


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 2 of Pierce's Disease_2

city: Davis

first: Mélanie

last: Massonnet

state: California

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

data_processing:
Adapter contamination removal and quality trimming of raw reads was done using Trimmomatic v.0.36 with the options LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 MINLEN:20.
Bowtie2 v.2.3.4.1 was used to map the processed reads onto the predicted protein-coding sequences of V. vinifera ‘PN40024’ (version V1 from http://genomes.cribi.unipd.it/grape/) with parameters: -q -end-to-end -sensitive -no-unal.
Counts of uniquely mapped reads (mapping quality Q > 30) were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91.
Genome_build: Predicted transcriptome of V. vinifera ‘PN40024’ (version V1 from http://genomes.cribi.unipd.it/grape/)
Supplementary_files_format_and_content: grape_raw_counts.txt : tab delimited text file, raw read counts determined by mapping the trimmed sequencing reads

organism: Vitis vinifera

growth_protocol: The experiment was conducted on potted Vitis Vinifera cv. ‘Cabernet Sauvignon’ plants propagated from cuttings in vermiculite trays and transplanted into one gallon pots after root and shoot establishment. Plants were arranged in a completely randomized design and were grown under greenhouse conditions. Optimal water and nutrients were provided on a consistent basis. X. fastidiosa subsp. fastidiosa was grown on PD3 agar media at 28°C for five days. Cells were harvested from PD3 agar plates with 1X PBS.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Grapevines were mechanically inoculated twice with either 20 μl of harvested X. fastidiosa cells (OD600nm = 0.25) or 20 μl of 1X PBS at the sixth internode of the stem using a 20-gauge needle. Stems (internode directly above the point of inoculation) were collected at two time points according the Pierce’s Disease symptoms: Phase 1 = one or two leaves with some scorching, Phase 2 = several leaves with some scorching and a few matchstick petioles.

value: stem tissue

tag: cultivar

value: Cabernet Sauvignon

value: Xylella fastidiosa-inoculated

tag: infection phase


title: Woody stem from 1X PBS-inoculated plant at Phase 2 of Pierce's Disease_2

value: 1X PBS-inoculated


title: Woody stem from 1X PBS-inoculated plant at Phase 2 of Pierce's Disease_3


title: IGRA+ve_#3_V1_nil_tube

description:
LTBI 3_v1_neg vs LTBI 3_v1_TB2_4057_1_3.txt
3_LTBI_v1_neg


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 2 of Pierce's Disease_1


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 1 of Pierce's Disease_3


title: Woody stem from 1X PBS-inoculated plant at Phase 2 of Pierce's Disease_1


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 2 of Pierce's Disease_3


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 1 of Pierce's Disease_1


title: Woody stem from 1X PBS-inoculated plant at Phase 1 of Pierce's Disease_3


title: Woody stem from Xylella fastidiosa-inoculated plant at Phase 1 of Pierce's Disease_2


title: Woody stem from 1X PBS-inoculated plant at Phase 1 of Pierce's Disease_1


title: scRNA-seq zebrafish 4dpf, neuromast hair cells

city: Bethesda

first: Doris

middle: K

last: Wu

state: MD

address: 35A Convent Dr., Rm 1D-824

institute: NIDCD

description:
Z4dpf
Zebrafish
Single cell RNA-seq

data_processing:
Basecalls performed using Illumina’s RTA 2.0.12.
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings.
Secondary analysis was performed using SCANPY (version 1.4.4).
Genome_build: not provided
Supplementary_files_format_and_content: barcodes.tsv.gz: cell barcodes
Supplementary_files_format_and_content: features.tsv.gz: gene names
Supplementary_files_format_and_content: matrix.mtx.gz: expression matrix
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5: expression matrix in HDF5 format

organism: Danio rerio

source_name: P4 zebrafish hair-cell

extract_protocol:
Zebrafish larvae Tg(myo6b: RiboTag) at 4 dpf were dissected to remove the head, which included the ear. Approximately 400 dissected bodies in batches of 50 were dissociated by adding 0.5 ml of 0.5% trypsin (Gibco, cat# 15400054) and triturated with 1 ml pipette tip for 30 seconds at 30°C. The dissociated cells were filtered with 40 μm strainer (Pluriselect, cat# 43-50040-50) and washed with PBS twice before adding DMEM containing 10% FBS and spun down by centrifugation at 700g rpm for 5 min at 4°C. Cells were resuspended and kept in DMEM before processing for FACS.
scRNA-seq was carried out with 10X Genomics single cell platform (10X Genomics, Pleasanton, CA. USA). Approximately 5000 live cells after FACS in a maximum volume of 34 microliters were loaded on a 10X Genomics Chromium Controller (10x Genomics). Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics) was used for libraries preparation according to manufacturer’s instructions. Quality of the libraries was evaluated on a Fragment Analyzer instrument (Agilent) and sequenced on a NextSeq 500 sequencer Illumina with the following paired read lengths: 26 bp Read 1, 8 bp I7 Index and 98 bp Read 2.

tag: genotype/variation

tag: developmental stage

value: 4 dpf

value: Neuromast hair cells


title: Woody stem from 1X PBS-inoculated plant at Phase 1 of Pierce's Disease_2


title: IGRA+ve_#2_V3_TB1_tube

description:
LTBI 2_v3_tb1 vs LTBI 2_v3_neg_4058_1_2.txt
2_LTBI_v3_tb1


title: IGRA+ve_#2_V2_TB1_tube

description:
LTBI 7_v1_tb1 vs LTBI 2_v2_tb1_4317_1_4.txt
2_LTBI_v2_tb1


title: IGRA+ve_#2_V3_nil_tube

description:
LTBI 2_v3_tb1 vs LTBI 2_v3_neg_4058_1_2.txt
2_LTBI_v3_neg


title: IGRA+ve_#2_V3_TB2_tube

description:
LTBI 3_v3_neg vs LTBI 2_v3_tb2_4058_1_3.txt
2_LTBI_v3_tb2


title: IGRA+ve_#2_V2_TB2_tube

description:
LTBI 2_v2_TB2 vs LTBI 1_v2_neg_4057_2_3.txt
2_LTBI_v2_tb2


title: IGRA+ve_#2_V2_nil_tube

description:
LTBI 2_v1_TB2 vs LTBI 2_v2_neg_4057_1_4.txt
2_LTBI_v2_neg


title: IGRA+ve_#2_V1_nil_tube

description:
LTBI 2_v1_TB1 vs LTBI 2_v1_neg_4057_1_2.txt
2_LTBI_v1_neg


title: IGRA+ve_#1_V1_TB2_tube

description:
LTBI 1_v1_TB2 vs LTBI 1_v1_TB1_4057_1_1.txt
1_LTBI_v1_tb2


title: IGRA+ve_#1_V3_nil_tube

description:
LTBI 3_v2_tb2 vs LTBI 1_v3_neg_4059_1_4.txt
1_LTBI_v3_neg


title: IGRA+ve_#1_V1_TB1_tube

description:
LTBI 1_v1_TB2 vs LTBI 1_v1_TB1_4057_1_1.txt
1_LTBI_v1_tb1


title: IGRA+ve_#1_V2_TB2_tube

description:
LTBI 1_v2_TB1 vs LTBI 1_v2_TB2_4057_2_2.txt
1_LTBI_v2_tb2


title: IGRA+ve_#2_V1_TB1_tube

description:
LTBI 2_v1_TB1 vs LTBI 2_v1_neg_4057_1_2.txt
2_LTBI_v1_tb1


title: Healthy_Control_#54_V2_TB2_tube

description:
HC 54_v1_neg vs HC 54_v2_tb2_7113_1_3.txt
54_HC_v2_tb2

source_name: Cultured whole blood from healthy donor

value: Healthy control


title: IGRA+ve_#2_V1_TB2_tube

description:
LTBI 2_v1_TB2 vs LTBI 2_v2_neg_4057_1_4.txt
2_LTBI_v1_tb2


title: Healthy_Control_#55_V2_TB2_tube

description:
HC 55_v2_tb2 vs HC 55_v2_tb1_7113_1_4.txt
55_HC_v2_tb2


title: Healthy_Control_#55_V2_TB1_tube

description:
HC 55_v2_tb2 vs HC 55_v2_tb1_7113_1_4.txt
55_HC_v2_tb1


title: IGRA+ve_#1_V3_TB1_tube

description:
LTBI 1_v3_tb1 vs LTBI 7_v3_tb2_4059_2_2.txt
1_LTBI_v3_tb1


title: IGRA+ve_#1_V2_TB1_tube

description:
LTBI 1_v2_TB1 vs LTBI 1_v2_TB2_4057_2_2.txt
1_LTBI_v2_tb1


title: Healthy_Control_#55_V1_TB2_tube

description:
HC 55_v2_neg vs HC 55_v1_tb2_7113_2_2.txt
55_HC_v1_tb2


title: Healthy_Control_#55_V2_nil_tube

description:
HC 55_v2_neg vs HC 55_v1_tb2_7113_2_2.txt
55_HC_v2_neg


title: IGRA+ve_#1_V3_TB2_tube

description:
LTBI 1_v3_tb2 vs LTBI 5_v1_tb2_4058_1_4.txt
1_LTBI_v3_tb2


title: Healthy_Control_#54_V1_TB1_tube

description:
HC 54_v1_tb2 vs HC 54_v1_tb1_7113_2_3.txt
54_HC_v1_tb1


title: Healthy_Control_#55_V1_TB1_tube

description:
HC 55_v1_tb1 vs HC 55_v1_neg_7113_2_4.txt
55_HC_v1_tb1


title: Healthy_Control_#54_V2_TB1_tube

description:
HC 54_v2_tb1 vs HC 54_v2_neg_7113_2_1.txt
54_HC_v2_tb1


title: IGRA+ve_#1_V1_nil_tube

description:
LTBI 7_v1_tb2 vs LTBI 1_v1_neg_4058_2_3.txt
1_LTBI_v1_neg


title: Healthy_Control_#55_V1_nil_tube

description:
HC 55_v1_tb1 vs HC 55_v1_neg_7113_2_4.txt
55_HC_v1_neg


title: Healthy_Control_#54_V2_nil_tube

description:
HC 54_v2_tb1 vs HC 54_v2_neg_7113_2_1.txt
54_HC_v2_neg


title: IGRA+ve_#1_V2_nil_tube

description:
LTBI 2_v2_TB2 vs LTBI 1_v2_neg_4057_2_3.txt
1_LTBI_v2_neg


title: Healthy_Control_#53_V1_TB1_tube

description:
HC 53_v1_tb1 vs HC 53_v2_neg_7113_1_1.txt
53_HC_v1_tb1


title: Healthy_Control_#53_V1_TB2_tube

description:
HC 53_v1_tb2 vs HC 53_v2_tb1_7106_2_3.txt
53_HC_v1_tb2


title: Healthy_Control_#53_V1_nil_tube

description:
HC 53_v1_neg vs HC 53_v2_tb2_7106_2_1.txt
53_HC_v1_neg


title: Healthy_Control_#53_V2_TB2_tube

description:
HC 53_v1_neg vs HC 53_v2_tb2_7106_2_1.txt
53_HC_v2_tb2


title: Healthy_Control_#54_V1_TB2_tube

description:
HC 54_v1_tb2 vs HC 54_v1_tb1_7113_2_3.txt
54_HC_v1_tb2


title: Healthy_Control_#51_V1_nil_tube

description:
HC 51_v2_tb2 vs HC 51_v1_neg_7105_2_2.txt
51_HC_v1_neg


title: Healthy_Control_#53_V2_TB1_tube

description:
HC 53_v1_tb2 vs HC 53_v2_tb1_7106_2_3.txt
53_HC_v2_tb1


title: Healthy_Control_#54_V1_nil_tube

description:
HC 54_v1_neg vs HC 54_v2_tb2_7113_1_3.txt
54_HC_v1_neg


title: Healthy_Control_#51_V1_TB2_tube

description:
HC 51_v1_tb1 vs HC 51_v1_tb2_7105_1_2.txt
51_HC_v1_tb2


title: Healthy_Control_#53_V2_nil_tube

description:
HC 53_v1_tb1 vs HC 53_v2_neg_7113_1_1.txt
53_HC_v2_neg


title: Healthy_Control_#51_V1_TB1_tube

description:
HC 51_v1_tb1 vs HC 51_v1_tb2_7105_1_2.txt
51_HC_v1_tb1


title: Healthy_Control_#51_V2_nil_tube

description:
HC 51_v2_neg vs HC 51_v2_tb1_7105_1_4.txt
51_HC_v2_neg


title: ExVivoBlood_IGRA+ve_Donor_30_Visit_2

description:
LTBI 30_v2 vs LTBI 30_v1_6475_2_2.txt
30_LTBI_v2_pax

extract_protocol: PAXgene Blood miRNA Kit (Qiagen) with on-column DNAse treatment. Globin-depletion using GLOBINclear Kit (ThermoFisher)

treatment_protocol: Venous Blood was collected into PAXgene RNA tubes (PreAnalytix), inverted repetedly to mix, incubated at room temperature for 2 hours and frozen.


title: Healthy_Control_#51_V2_TB2_tube

description:
HC 51_v2_tb2 vs HC 51_v1_neg_7105_2_2.txt
51_HC_v2_tb2


title: Healthy_Control_#51_V2_TB1_tube

description:
HC 51_v2_neg vs HC 51_v2_tb1_7105_1_4.txt
51_HC_v2_tb1


title: ExVivoBlood_IGRA+ve_Donor_28_Visit_1

description:
LTBI 27_v3 vs LTBI 28_v1_6475_1_2.txt
28_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_30_Visit_3

description:
LTBI 30_v3 vs LTBI 16_v1_7135_1_1.txt
30_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_27_Visit_2

description:
LTBI 27_v1 vs LTBI 27_v2_7133_2_4.txt
27_LTBI_v2_pax


title: ExVivoBlood_IGRA+ve_Donor_28_Visit_3

description:
LTBI 28_v2 vs LTBI 28_v3_6475_1_1.txt
28_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_30_Visit_1

description:
LTBI 30_v2 vs LTBI 30_v1_6475_2_2.txt
30_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_23_Visit_1

description:
LTBI 23_v1 vs LTBI 23_v2_7135_2_1.txt
23_LTBI_v1_pax


title: ExVivoBlood_IGRA+ve_Donor_23_Visit_3

description:
LTBI 23_v3 vs LTBI 24_v1_7133_2_3.txt
23_LTBI_v3_pax


title: ExVivoBlood_IGRA+ve_Donor_27_Visit_1

description:
LTBI 27_v1 vs LTBI 27_v2_7133_2_4.txt
27_LTBI_v1_pax