title: single_cell_RNAseq [s_dot_ogp102]

description:
s_dot_ogp102
Gene_expression_matrix.csv


title: single_cell_RNAseq [s_dot_ogp1]

status: Public on Feb 28 2019

type: SRA

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
s_dot_ogp1
Gene_expression_matrix.csv

library_source: transcriptomic

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL) using STAR_2.4.0g1.
Expression level of each gene was quantified in unites by transcript per million (TPM) using RSEM rsem-1.2.18 with default parameters.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene_expression_matrices (TPM value) of each gene in each cells in CSV format and Gene_expression_matrix_population (TPM) of each gene in population in xlsx format

molecule: total RNA

organism: Mus musculus

growth_protocol: C57BL/6 male mice of 2, 7, 23 and 25 months of age were used. Male C57BL/6 mice were purchased from Janvier or bred in house at the DKFZ Center for Preclinical Research facility.  Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. SVZs from 2 mice of 2 or 4 mice of 22 months of age were pulled per replicate. Single cell suspension was obtained using the Neural Tissue Dissociation kit with Trypsin (or Papain when staining for CD31+ and CDd11b+ cells) and Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200), GLAST(ACSA-1)-PE (Miltenyi, 1:20), Prom-APC, PSA-NCAM PE-Cy7 Miltenyi, 1:75), CD31-PE (BD, 1:100) and CD11b-APC (BD, 1:100). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. For single cell RNA-seq, we sorted for CD45-O4-CD133+GLAST+, cells. Single NSCs were handpicked and libraries according to Smartseq2 were prepared. For Bulk sequencing we sorted 1000 events of different populations based on the following marker combinations: Endothelial CD45-CD31+, Microglia CD45+Cd11b+, NSCs CD45-CD133+GLAST+, Neuroblasts CD45-GLAST-PSA-NCAM+.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability, we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000 or 3000.

tag: age

value: 23 MO

tag: strain

tag: tissue

value: SVZ

tag: gender

value: Male


title: 16E7_A

city: Philadelphia

first: Elizabeth

middle: A

last: White

state: PA

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

country: USA

institute: University of Pennsylvania

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Sequenced reads were filtered to remove adapters and low-quality reads
Clean reads were mapped to hg19 using STAR (v2.5). STAR used  the method of Maximal Mappable Prefix (MMP).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Genome_build: hg19
Supplementary_files_format_and_content: gene expression quantification table, calculated all genes' FPKM

molecule: polyA RNA

organism: Homo sapiens

source_name: G5-Ep primary human forekin keratinocyte

growth_protocol: Primary human keratinocytes stably harboring retroviral expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 0.5 ug/ml puromycin

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit in White Laboratory and polyA RNA was isolates using oligo dT beads at Novogene Corporation
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation

tag: retrovirus

value: Tranduced with HPV16 E7 retrovirus (MSCV-IP N-HA 16E7)

tag: cell line

value: Primary human foreskin keratinocytes selected with puromycin post retroviral transduction


title: population_RNAseq [N2PSA]

description:
N2PSA
Gene_expression_matrix_population.xlsx

growth_protocol: C57BL/6 male mice of 2, 7 and 19 months of age were used. Male C57BL/6 mice were purchased from Janvier or bred in house at the DKFZ Center for Preclinical Research facility.  Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. SVZs from 2 mice of 2 or 4 mice of 2 months of age were pulled per replicate. Single cell suspension was obtained using the Neural Tissue Dissociation kit with Trypsin (or Papain when staining for CD31+ and CDd11b+ cells) and Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200), GLAST(ACSA-1)-PE (Miltenyi, 1:20), Prom-APC, PSA-NCAM PE-Cy7 Miltenyi, 1:75), CD31-PE (BD, 1:100) and CD11b-APC (BD, 1:100). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. For single cell RNA-seq, we sorted for CD45-O4-CD133+GLAST+, cells. Single NSCs were handpicked and libraries according to Smartseq2 were prepared. For Bulk sequencing we sorted 1000 events of different populations based on the following marker combinations: Endothelial CD45-CD31+, Microglia CD45+Cd11b+, NSCs CD45-CD133+GLAST+, Neuroblasts CD45-GLAST-PSA-NCAM+.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability, we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000 or 3000.

value: 2 MO


title: cont_A

value: Tranduced with control retrovirus (MSCV-IP N-HA empty)


title: cont_B


title: single_cell_RNAseq [s_dot_ogp107]

description:
s_dot_ogp107
Gene_expression_matrix.csv


title: cont_C


title: population_RNAseq [N2_CD31]

description:
N2_CD31
Gene_expression_matrix_population.xlsx


title: population_RNAseq [N1PSA]

description:
N1PSA
Gene_expression_matrix_population.xlsx


title: population_RNAseq [N1_CD11b]

description:
N1_CD11b
Gene_expression_matrix_population.xlsx


title: 16E7_B


title: population_RNAseq [N2_CD11b]

description:
N2_CD11b
Gene_expression_matrix_population.xlsx


title: population_RNAseq [N1_CD31]

description:
N1_CD31
Gene_expression_matrix_population.xlsx


title: total RNA from RKO_H3-Hemi DNA mut

type: RNA

city: Baltimore

first: Wenbing

last: Xie

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Department of Oncology

institute: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD, PHD and SRA domains mutant H3-Hemi DNA mut

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (G4845A) were used, which contain 43,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

extract_protocol: Total RNA was isolated from cell pallets using TriZol reagent (Invitrogen) followed by RNeasy Mini Kit with DNase on-column digestion (Qiagen). RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.

value: RKO

value: Colon

source_name: RKO Mock cells


title: total RNA from RKO_H3 mut

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD and PHD domains mutant H3 mut


title: population_RNAseq [N2GP]

description:
N2GP
Gene_expression_matrix_population.xlsx


title: total RNA from RKO_DAEA

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 PHD domain mutant DAEA


title: total RNA from HCT_H3-Hemi DNA mut

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD, PHD and SRA domains mutant H3-Hemi DNA mut

source_name: HCT116 Mock cells


title: total RNA from HCT_H3 mut

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD and PHD domains mutant H3 mut


title: 27738 LA1 10days

city: Saint Louis

first: Roheena

last: Panni

address: 660S Euclid Ave, Campus box 8109

institute: Washington University in Saint Louis

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, agilent 10x blocking reagent and kreatech Kreablock onto Agilent 8x60K microarrays at 65oC for 20 min

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing:
Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.
Intensity values were Feature Extraction processed signal values (called rProcessedSignal) in log2 scale. Control probes were filtered off and duplicate probes were averaged before quantile-normalization. Only probes included in the matrix sheet are those with a detected call by the rIsWellAboveBG parameter in at least 1 of the study samples.

source_name: Tumor

label_protocol: cDNAs were amplified using the Sigma-WTA2 kit, and chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics) and Cy5-labeled cDNAs were hybridized to Agilent Mouse Gene Expression Microarrays 8x60K (G4852B-07809)

extract_protocol: Total RNA was isolated using ENZO total RNA kit.

value: Female

value: tumor (orthotopic pancreatic cancer model)

tag: treatment

value: ADH 503

tag: time


title: total RNA from RKO_YATA

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant YATA


title: total RNA from RKO_G448D

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant G448D


title: total RNA from RKO_WT

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous wild type UHRF1


title: 27740 LA1 10days


title: population_RNAseq [N1GP]

description:
N1GP
Gene_expression_matrix_population.xlsx


title: total RNA from RKO_EV

description: Endogenous UHRF1 depleted RKO cells

source_name: Endogenous UHRF1 depleted RKO cells


title: 27737 Vehicle

value: Vehicle

value: control


title: total RNA from RKO_Y188A

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD domain mutant Y188A


title: population_RNAseq [Old_psa_1]

description:
Old_psa_1
Gene_expression_matrix_population.xlsx

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. SVZs from 2 mice of 2 or 4 mice of 19 months of age were pulled per replicate. Single cell suspension was obtained using the Neural Tissue Dissociation kit with Trypsin (or Papain when staining for CD31+ and CDd11b+ cells) and Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used: O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200), GLAST(ACSA-1)-PE (Miltenyi, 1:20), Prom-APC, PSA-NCAM PE-Cy7 Miltenyi, 1:75), CD31-PE (BD, 1:100) and CD11b-APC (BD, 1:100). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACSAriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27 at a density of approx. 1cell/ul.  Immediately after sorting cells were manually picked with a thin gel-loading micropipette under continuous visual inspection in a Zeiss microscope. To ensure that only one cell was picked, we transferred sequentially 1ul of the cell suspension to the picking plate where a single cell was immediately picked in 0.3ul with another pipette before the addition of a new cell to the plate. Cells were directly transferred to ice-cold lysis buffer (0.2%Triton X-100 containing RNAse inhibitors, Clontech) and frozen at -80ºC until library preparation. For single cell RNA-seq, we sorted for CD45-O4-CD133+GLAST+, cells. Single NSCs were handpicked and libraries according to Smartseq2 were prepared. For Bulk sequencing we sorted 1000 events of different populations based on the following marker combinations: Endothelial CD45-CD31+, Microglia CD45+Cd11b+, NSCs CD45-CD133+GLAST+, Neuroblasts CD45-GLAST-PSA-NCAM+.
RNA-seq libraries were prepared using Smart-seq2 technology as previously described. Briefly, lysed cells were thawed and subject to reverse transcription using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). In a randomly selected set of samples we included ERCC Spike-Ins (Ambion) at a 1:1000000 dilution. Full-length cDNAs were amplified by 20 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). Amplified cDNAs for every single cell were quantified and run on a High Sensitivity Bioanalyzer chip (Agilent). Samples containing no material or in which the cDNA appeared degraded were excluded (approx. 5-10%) from further processing. cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol with minor modifications. Specifically, we extended the tagmentation step to 8 minutes and performed a double cleanup with 0.8X AMPure XP SPRI beads (Agencourt) after PCR amplification for 9 cycles. To control for technical variability, we performed two replicate DNA libraries with cDNA from the same cell. For population studies, approx. 1ng of total RNA from 1000 cells was subject to SMARTer Ultra Low RNA kit (Clontech) according to the manufacturer’s instructions. cDNA products were quantified, run in a Bioanalyzer and subject to Illumina library preparation according to NEBNext Ultra DNA Library Preparation Kit (NEB). Libraries were quantified, pooled at equal concentrations and the multiplex was cleaned up again with 1X AMPure beads and measured in a Bioanalyzer prior to 101bp paired-end sequencing in an Illumina HiSeq 2000 or 3000.

value: 19 MO


title: total RNA from RKO_R491A

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant R491A


title: total RNA from RKO_H741A

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 RING domain mutant H741A


title: population_RNAseq [Old_cd11b_2]

description:
Old_cd11b_2
Gene_expression_matrix_population.xlsx


title: population_RNAseq [Old_psa_2]

description:
Old_psa_2
Gene_expression_matrix_population.xlsx


title: 27744 Vehicle


title: 27739 Vehicle


title: total RNA from HCT_R491A

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant R491A


title: population_RNAseq [Old_cd11b_1]

description:
Old_cd11b_1
Gene_expression_matrix_population.xlsx


title: 27741 LA1 48hrs


title: population_RNAseq [Old_cd31_2]

description:
Old_cd31_2
Gene_expression_matrix_population.xlsx


title: total RNA from HCT_G448D

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant G448D


title: population_RNAseq [Old_cd31_1]

description:
Old_cd31_1
Gene_expression_matrix_population.xlsx


title: total RNA from HCT_H741A

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 RING domain mutant H741A


title: 27745 Vehicle


title: 27741 Vehicle


title: total RNA from HCT_YATA

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant YATA


title: BulkATAC-MiSeq-21-S20

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues.
For all subsequent analysis we discarded peaks falling within these regions. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script.
All samples/libraries passed QC (none were filtered in downstream analyses)
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy for variants specific to individual colonies

molecule: genomic DNA

source_name: donor 3_CD34+ hematopoietic cells

growth_protocol: MethoCult H4034 Optimum culture

extract_protocol:
NP 40 lysis
ATAC-seq

tag: donor id

value: donor 3

tag: cell type

value: primary hematopoietic cells


title: population_RNAseq [Old_gp_2]

description:
Old_gp_2
Gene_expression_matrix_population.xlsx


title: population_RNAseq [Old_gp_1]

description:
Old_gp_1
Gene_expression_matrix_population.xlsx


title: BulkATAC-MiSeq-20-S19


title: total RNA from HCT_Y188A

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD domain mutant Y188A


title: BulkATAC-MiSeq-19-S18


title: BulkATAC-MiSeq-18-S17


title: 27742 LA1 48hrs


title: BulkATAC-MiSeq-17-S16


title: 27743 Vehicle


title: 27752 LA1 48hrs


title: 27748 LA1 10days


title: 27750 LA1 10days


title: total RNA from HCT_DAEA

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 PHD domain mutant DAEA


title: total RNA from HCT_WT

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous wild type UHRF1


title: total RNA from HCT_EV

description: Endogenous UHRF1 depleted HCT116 cells

source_name: Endogenous UHRF1 depleted HCT116 cells


title: 27747 LA1 10days


title: BulkATAC-MiSeq-15-S14


title: BulkATAC-MiSeq-16-S15


title: BulkATAC-MiSeq-11-S10


title: BulkATAC-MiSeq-07-S6


title: 27746 LA1 48hrs


title: BulkATAC-MiSeq-09-S8


title: BulkATAC-MiSeq-14-S13


title: BulkATAC-MiSeq-10-S9


title: BulkATAC-MiSeq-08-S7


title: BulkATAC-MiSeq-06-S5


title: BulkATAC-MiSeq-13-S12


title: 27751 LA1 48hrs


title: BulkATAC-MiSeq-12-S11


title: BulkATAC-MiSeq-03-S3


title: BulkATAC-MiSeq-02-S2


title: BulkATAC-MiSeq-04-S4


title: cS2-1-6_24

city: Kyoto

first: Jose

last: Ichisima

state: Kyoto

address: 53, Shogoin-Kawahara cho, Sakyo

department: Clinical Application Research

country: Japan

institute: Center for iPS cell research and application (CiRA), Kyoto University

description: Bulk RNA-Seq data

data_processing:
All sequence reads were extracted in FASTQ format as described in "library construction protocol" section
base-calling: CASAVA ver 1.8.2
raw read quality filtering: FASTX-Toolkit 0.0.13
alignment: Tophat ver 2.1.0
normalization: Cufflinks ver 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Corrected iPSCs-derived d24 neural progenitor cells

growth_protocol:
iPSC clones were cultured on Laminin511-E8 fragment iMatrix-511-coated tissue culture plates with StemFit AK02N medium at 37 °C.
neural differentiation protocol: iPSCs were dissociated into single cells and quickly re-aggregated in DFK 5% medium (DMEM/F-12 Ham medium (SIGMA) containing KnockOut™ Serum Replacement (Thermo Fisher Scientific), NEAA (Gibco™), 2-mercaptoethanol (Nacalai), GlutaMAX (Gibco™), SB-431542, Dorsomorphin (Tocris), and Y-27632 (Tocris)) (9,000 cells/well) using a Nunclon Sphera Microplates 96U-Well Plate (Thermo Fisher Scientific).
definitive endodermal cell differentiation protocol: iPSCs were dissociated, resuspended with RPMI1640 (Sigma) medium containing 1× B27 supplement (Invitrogen), 100 ng/mL rhActivin A (R&D SYSTEMS), 1 μM CHIR99021 (Calbiochem), and 10 μM Y-27632 (Tocris) and seeded on culture dishes coated with Matrigel (Corning) at a density of 1 × 105 cells/cm2. On the next day, Y27632 was removed from the medium, and 0.5 mM NaB (Wako) was added in the culture medium.

extract_protocol:
Total RNA was extracted using the RNeasy kit, and the quality was tested with a Bioanalyzer.
RNA-seq libraries were prepared by using a SureSelect Strand Specific RNA Library Preparation Kit (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 1500 (Illumina) in 100-base pair-end mode.

tag: genotype

value: WT (Corrected)

value: Neural progenitor cells

tag: protocol

value: Neural differentiation protocol


title: BulkATAC-MiSeq-01-S1


title: cS2-1-6_5

description: Bulk RNA-Seq data

source_name: Corrected iPSCs-derived definitive endodermal cells

value: Definitive endodermal cells

value: Definitive endodermal cell differentiation protocol


title: cS2-1-6_12

description: Bulk RNA-Seq data

source_name: Corrected iPSCs-derived d12 neural progenitor cells


title: S2-2_24

description: Bulk RNA-Seq data

source_name: Disease iPSCs-derived d24 neural progenitor cells

value: MT (Clone 2)


title: S2-2_5

description: Bulk RNA-Seq data

source_name: Disease iPSCs-derived definitive endodermal cells


title: cS2-1-6_0

description: Bulk RNA-Seq data

source_name: Corrected iPSCs

value: iPSCs

value: Growth protocol


title: single_cell_RNAseq [s_dot_ogp100]

description:
s_dot_ogp100
Gene_expression_matrix.csv

value: 23 MO

value: SVZ

value: Male


title: S2-1_12

description: Bulk RNA-Seq data

source_name: Disease iPSCs-derived d12 neural progenitor cells

value: MT (Clone 1)


title: S2-1_5

description: Bulk RNA-Seq data


title: S2-2_0

description: Bulk RNA-Seq data

source_name: Disease iPSCs


title: S2-1_0

description: Bulk RNA-Seq data


title: B2_24

description: Bulk RNA-Seq data

source_name: Healthy control iPSCs-derived d24 neural progenitor cells

value: WT


title: S2-1_24

description: Bulk RNA-Seq data


title: B2_12

description: Bulk RNA-Seq data

source_name: Healthy control iPSCs-derived d12 neural progenitor cells


title: B2_0

description: Bulk RNA-Seq data

source_name: Healthy control iPSCs


title: S2-2_12

description: Bulk RNA-Seq data


title: CK: spores

city: Zhenjiang

first: Qiya

last: Yang

address: Xuefu ROAD 301

country: China

institute: Jiangsu University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Penicillium expansum

source_name: spores

growth_protocol: Penicillium expansum  treated with Meyerozyma guilliermondii was inoculated in NYDB medium, an was incubated at 25C, 120 rpm. For 24 h.

extract_protocol:
Spores were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sample  of Y is treated with  Meyerozyma guilliermondii, sample CK was the control group.

value: spores

value: spores in NYDB medium


title: Y: spores induced by Meyerozyma guilliermondii

value: spores induced by Meyerozyma guilliermondii in NYDB medium


title: ChIP_CPSF73_siPCF11_R1

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
ChIP-seq reads were mapped with bowtie2 with hg19 genome index.
Macs2 was used to detect significant enrichments – broad peaks, q-value < 0.01.
For visualisation genome-wide coverage within 50 bp was calculated normalised for sequencing depth (rpm). Reads were calibarted additionally for D.melanogaster content. BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: Bed: Table with three columns: chr, start, end; contains peak coordinates
Supplementary_files_format_and_content: bigWig: created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
ChIP was performed as described in accompanying paper. Antibodies used are indicated for each sample.
Sample 1-12: genomic libraries were prepared using NEBNext ChIP-Seq master-mix kit. Sample 13-25: Diagenode MicroPlex library preparation kit v2 (C05010012) was used to prepare libraries for sequencing, following manufacturer’s instructions.

treatment_protocol: siRNAs from Dharmacon were transfected for 48 hrs according to RNAiMAX reagent protocol at the concentrations indicated.

value: HeLa cells

tag: molecule subtype

value: CPSF73 bound DNA

tag: genotype/treatment

value: PCF11 knock-down (5 nM)

tag: antibody

value: Rabbit polyclonal anti-CPSF73 Bethyl Cat# A301-091A

tag: calibration

value: Drosophila spike-in


title: ChIP_CPSF73_siPCF11_R2


title: ChIP_input_CPSF73_siPCF11_R2

value: input DNA


title: ChIP_input_CPSF73_siPCF11_R1


title: Mice: S02 - CRR-2-03

city: hunan

first: Rongrong

last: Cui

address: 139，renming road

institute: The second Xiangya hospital of central south university

description: Biological replicate 3 of 3.  VSMCs, treated with TNF-α, harvested after several passages.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the  signals using a LOWESS filter (Locally-weighted Regression).
Averages are derived from LOWESS normalized data from all probes per miRNA.

source_name: VSMCs

label_protocol: The assay started from 2 to 5 µg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada),following the manufacturer's recommended protocol.

value: C57BL/6 mice

value: 8 weeks

value: abdominal aorta

value: Vascular smooth muscle cells (VSMCs)

value: TNF-α


title: Mice: S02 - CRR-2-02


title: Mice: S02 - CRR-2-01

description: Biological replicate 1 of 3.  VSMCs, treated with TNF-α, harvested after several passages.


title: ChIP_CPSF73_siLUC_R2

value: siLUC control for knock-down (5 nM)


title: ChIP_CPSF73_siLUC_R1


title: Mice: S01 - CRR-1-03

description: Biological replicate 3 of 3. Control VSMCs, untreated, harvested after several passages.

value: none (untreated control)


title: Mice: S01 - CRR-1-02

description: Biological replicate 2 of 3. Control VSMCs, untreated, harvested after several passages.


title: ChIP_input_CPSF73_siLUC_R2


title: Mice: S01 - CRR-1-01

description: Biological replicate 1 of 3. Control VSMCs, untreated, harvested after several passages.


title: ChIP_PCF11-Int_R2

value: PCF11 bound DNA

value: untreated

value: Rabbit polyclonal anti-PCF11 (PCF11-Int) Bethyl Cat# A303-705A


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_H741A

type: genomic

description: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 domain mutant

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing: Data were extracted using Illumina’s GenomeStudio V2011.1 software. Methylation status of each CpG site was presented as beta value based on following definition: beta value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy5 and Cy3

source_name: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 RING domain mutant H741A

label_protocol: DNA bisulfite conversion was carried out using EZ DNA Methylation Kit (Zymo Research) by following manufacturer’s manual with modifications for Illumina Infinium Methylation Assay. Briefly, 0.5 – 1.0 ug of genomic DNA was first mixed with 5 ul of M-Dilution Buffer and incubate at 37C for 15 minutes and then mixed with 100 ul of CT Conversion Reagent prepared as instructed in the kit’s manual. Mixtures were incubated in a thermocycler with 16 thermal cycles at 95C for 30 seconds and 50C for one hour. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification. Concentration of eluted DNA was measured using Nanodrop-1000 spectrometer. Bisulfite-converted DNA was analyzed using Illumina’s Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer’s manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer's instructions. Genomic DNA quality was assessed by low concentration agarose gel (0.6%) electrophoresis and spectrometry of OD260/280 and OD 260/230 ratio.


title: genomic DNA from RKO_DAEA

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 domain mutant

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium MethylationEPIC BeadChip Kit (WG-317-1002) by following manufacturer’s manual. Beadchip contains more than 850,000 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 PHD domain mutant DAEA

value: RKO


title: genomic DNA from HCT_R491A

description: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 domain mutant

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant R491A


title: genomic DNA from RKO_YATA

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant YATA


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_G448D

source_name: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 SRA domain mutant G448D


title: genomic DNA from RKO_G448D

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant G448D


title: ChIP_PCF11-Int_R1

value: HeLa cells

value: siLUC (5 nM)


title: genomic DNA from HCT_H741A

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 RING domain mutant H741A


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_R491A

source_name: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 SRA domain mutant R491A


title: ChIP_PCF11-Ct_R2

value: Rabbit polyclonal anti-PCF11 (PCF11-Ct) Abcam Cat# ab134391


title: genomic DNA from RKO_Mock

description: RKO Mock cells

source_name: RKO Mock cells


title: genomic DNA from RKO_H3-Hemi DNA mut

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD, PHD and SRA domains mutant H3-Hemi DNA mut


title: genomic DNA from RKO_Y188A

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD domain mutant Y188A


title: genomic DNA from RKO_H741A

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 RING domain mutant H741A


title: HeyA8-MDR cells, rep1

city: Houston

first: Lingegowda

middle: Selanere

last: Mangala

state: TX

address: 1881 East Rd

department: Gynecological Oncology

institute: M.D. Anderson Cancer Center

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom S array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA) normalization procedures.

label: biotin

source_name: HeyA8-MDR cells

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the GeneChip WT PLUS Reagent Kit ( Affymetrix).

growth_protocol: HeyA8-MDR cells were maintained in RPMI 1640 medium supplemented with 15% FBS, 300 ng/ml paclitaxel, and 0.1% gentamicin sulfate.

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

treatment_protocol: HeyA8-MDR cells were treated with miR-204-5p-inhibitor.


title: genomic DNA from HCT_Y188A

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD domain mutant Y188A


title: HeyA8-MDR cells, rep2


title: ChIP_input_PCF11_R2


title: genomic DNA from RKO_WT

description: Endogenous UHRF1 depleted RKO cells complemented with exogenous wild type UHRF1


title: genomic DNA from RKO_EV

description: Endogenous UHRF1 depleted RKO cells

source_name: Endogenous UHRF1 depleted RKO cells


title: genomic DNA from HCT_WT

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous wild type UHRF1


title: genomic DNA from HCT_YATA

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant YATA


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_Mock

description: 3A(-/-)3B(-/-)MT1(+/-) HCT116 Mock cells


title: genomic DNA from HCT_H3 mut

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD and PHD domains mutant H3 mut


title: HeyA8-MDR miR204, rep2

source_name: HeyA8-MDR miR204


title: PrEC

city: Cleveland

first: Shiv

middle: Shankar

last: Verma

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description:
prostate Control
total RNA enriched with small RNA
Total RNA  was isolated from three biological replicates of cells. The quality control was analyzed using Bio-Analyzer 2100 and subsequently used for miRNA-microarray platform. The signals were labeled with F635,

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Arrays were scanned using the GenePix 4100A Personal Scanner with GenePix Pro 6.0 software (Axon Instruments Inc., Union City, CA).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Primary Prostate Epithelial Cells,Normal, Human (HPrEC)

label_protocol: Microarray assay was performed using a service provider (Genosensor, Arizona) started from 0.5 µg total RNA samples that were first subject to dephosphorylation reaction to remove 5’ phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3’ end of sample (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contains a tag segment for capturing fluorescent dye during a later Cy5 dye staining process.

growth_protocol: The base culture medium for cells is RPMI-1640 with 10% FBS. Cells was maintained in an incubator at 37°C with 5% CO2.

extract_protocol: Cells were plated at 3.1 × l0 s per 6-cm dish in Phenol Red-free DMEM with 10% FBS. Twenty-four hour later, the medium was removed; the cells were washed twice with phosphate-buffered saline PBS, and DMEM with 1% BSA (Sigma). At 3 and 6 day after factor addition, cells were trypsinized and counted with an electrical resistance counter (CoulterElectronics, Inc., Hialeah, FL). On Day 3, cultures were refed with the same medium and additives.

value: PrEC


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_Y188A

source_name: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 TTD domain mutant Y188A


title: genomic DNA from HCT_G448D

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 SRA domain mutant G448D


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_DAEA

source_name: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous UHRF1 PHD domain mutant DAEA


title: 72h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep2

city: Charleston

first: Kai-Shu

last: Ling

state: SC

address: 2700 Savannah Hwy

institute: USDA-ARS

data_processing:
Standard Illumina pipeline including CASSAVA
The raw data were preprocessed to remove low quality reads, clip adapter sequences, and remove rRNA, tRNA and snRNA sequences.
Small RNA reads were counted for each sample
Supplementary_files_format_and_content: tab-delimited text files include small RNA read counts for each sample

organism: Bemisia tabaci

source_name: 72h after whitefly feed on TYLCV virus-infected tomato

growth_protocol: Whitefly Bemisia tabaci MEAM1 colony was maintained at the USDA-ARS, U.S. Vegetable Laboratory on broccoli (Brassica oleraceaL. var. botrytis) in a greenhouse (26 °C ± 5 °C). Approximately 1,500 adult whiteflies were transferred to TYLCV-infected or uninfected tomato (Solanum lycopersicum cv. Moneymaker) cuttings and allowed to feed for 24, 48, or 72 h. Tomato cuttings were placed in a flask of water, sealed with parafilm, and placed inside of an insect-proof cage within a growth chamber set to 28 ± 1°C, 14:10 (L:D) h photoperiod, and ~60% humidity. At the end of each time point, 200-500 living whiteflies were collected and immediately stored at -80°C until processing.

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Thermo Fisher, USA) according to the manufacturer’s protocol, and purified with the Direct-zol RNA MiniPrep kit (Zymo, USA). Small RNAs were run and purified from PAGE gel.
small RNA sequencing libraries were prepared for sequencing using standard Illumina protocols

tag: fed on

value: whole body


title: genomic DNA from HCT_H3-Hemi DNA mut

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 TTD, PHD and SRA domains mutant H3-Hemi DNA mut


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_WT

description: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells complemented with exogenous wild type UHRF1


title: 72h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep3


title: PC3

description:
prostate cancer
total RNA enriched with small RNA
Total RNA  was isolated from three biological replicates of cells. The quality control was analyzed using Bio-Analyzer 2100 and subsequently used for miRNA-microarray platform. The signals were labeled with F635,

source_name: PC3 are androgen receptor negative, do not express PSA


title: genomic DNA from RKO_H3 mut

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 TTD and PHD domains mutant H3 mut


title: genomic DNA from 3A(-/-)3B(-/-)MT1(+/-)_EV

description: Endogenous UHRF1 depleted 3A(-/-)3B(-/-)MT1(+/-) HCT116 cells


title: genomic DNA from HCT_DAEA

source_name: Endogenous UHRF1 depleted HCT116 cells complemented with exogenous UHRF1 PHD domain mutant DAEA


title: DU145

source_name: DU145 are androgen receptor negative, PTEN mutated


title: 72h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep1


title: 72h after whitefly feed on healthy tomato biorep 3

value: healthy tomato


title: 72h after whitefly feed on healthy tomato biorep 2


title: 48h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep3

source_name: 48h after whitefly feed on TYLCV virus-infected tomato


title: genomic DNA from HCT_EV

description: Endogenous UHRF1 depleted HCT116 cells

source_name: Endogenous UHRF1 depleted HCT116 cells


title: 22rV1

source_name: 22rV1 AR prositive, post castrated cell lines, express PSA


title: 48h after whitefly feed on healthy tomato biorep 2


title: 48h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep1


title: 48h after whitefly feed on healthy tomato biorep 1


title: 48h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep2


title: 24h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep3

source_name: 24h after whitefly feed on TYLCV virus-infected tomato


title: MONKEY_SPERM_ATACseq_Rep2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9, human reference genome hg19 and monkey reference genome rheMac8 using Bowtie2.  ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools.  To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS)  and  mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm9, hg19, rheMac8

organism: Macaca mulatta

source_name: Sperm

extract_protocol:
After sperm cells were counted, the nuclei from 100,000 sperm were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Purified sperm nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, sperm were treated with Proteinase K at 55°C for 2 hr, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation.
Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.

tag: strain background

value: sperm


title: 24h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep2

tag: strain


title: 24h after whitefly feed on tomato yellow leaf curl virus-infected tomato biorep1

tag: tissue


title: 24h after whitefly feed on healthy tomato biorep 3


title: 24h after whitefly feed on healthy tomato biorep 2


title: 24h after whitefly feed on healthy tomato biorep 1


title: HeyA8-MDR miR204, rep1


title: genomic DNA from HCT_Mock

description: HCT116 Mock cells

source_name: HCT116 Mock cells


title: genomic DNA from RKO_R491A

source_name: Endogenous UHRF1 depleted RKO cells complemented with exogenous UHRF1 SRA domain mutant R491A


title: LNCaP

source_name: LNCaP are androgen receptor, positive; estrogen receptor positive, and express PSA

value: LNCaP


title: control2

status: Public on Feb 27 2019

city: Guangzhou，China

first: jide

last: Wang

state: Guangdong ，China

address: 1838 Guangzhou Avenue North

department: Department of Digestive Medicine

institute: Nanfang Hospital, Southern Medical University

description: replicate 2

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).  1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were scanned using the Agilent DNA Microarray Scanner (part number G2505C).Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: colon cancer cells

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: DMEM supplemented with 10% FBS，37℃，5% CO2

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Stably transfected with LV-control and LV-miR-500a respectively.

value: LoVo

value: LV-control


title: miR-500a1

description: replicate 1


title: miR-500a3

description: replicate 3


title: miR-500a2

description: replicate 2


title: Control 04

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description: gene expression

hyb_protocol: Hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A) according to manufacturers protocol

scan_protocol: Arrays were scanned at 5 µm using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) and signal intensity data extracted using Agilent Feature Extraction software (v.9.5.3.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: HK-2 mRNA

label_protocol: Cyanine 3 (Cy3) labelled cRNA was generated with the LowInput QuickAmp Labeling Kit (5190-2305) for hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A).

growth_protocol: Proximal tubular human kidney cells (HK2) were cultured in Keratinocyte-Serum Free Medium (KSFM) containing 10% fetal bovine serum (FBS), 5 ng/ml recombinant epidermal growth factor (rEGF), 0.05 mg/ml bovine pituitary extract (BPE), 100 U/ml penicillin and 100µg/ml streptomycin. All cells were grown at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: After 24 hours total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol

treatment_protocol: After growth to confluency, cells were serum deprived for 24 hours. Thereafter cells were either treated with 0.5µM canagliflozin or left untreated and stimulated with high glucose (30mM).

value: proximal tubule cell line


title: control1

description: replicate 1


title: Control 03

description: gene expression


title: control3

description: replicate 3


title: Control 01

description: gene expression


title: Canagliflozine 03

description: gene expression


title: Control 02

description: gene expression


title: Canagliflozine 04

description: gene expression


title: Canagliflozine 02

description: gene expression


title: S6

city: Seville

first: Belén

last: Gómez-González

email: gomezb@us.es, belen.gomez@cabimer.es

address: Cabimer/Avda Américo Vespucio, 24

country: Spain

institute: University of Seville

description: Whole genome sequencing

data_processing:
Library strategy: Whole genome sequencing
Paired-end reads were aligned to the yeast sacCer2 genome assembly using Novoalign 2.07.14 (http://novocraft.com), with the parameters for the mean and standard deviation of the expected size distribution set to 175 and 125, respectively. Alignments for 101bp paired-end reads were post-processed for removal of reads that could have arisen from PCR duplication (picard-tools 1.81; http://sourceforge.net/projects/picard/). Approximately 96% of paired reads were found to align concordantly to the reference genome resulting in a median coverage of 200x across all samples.
Base-level nucleotide counts were obtained using deepSNV 1.2.3 (Gerstung, et al. 2012) with a minimum base quality threshold of 30. SNV calling was performed simultaneously across the relevant sample groups per experiment using scripts written in Python. A minimum allele count of 5 and minimum allele frequency of 0.25 were applied for the rad53∆ chk1∆ exo1∆ (S64Bα vs W64Aα strain) and exo1∆ rad53∆ (YMS6 vs YGDP939 strain) genome sequencing experiments. These thresholds were increased to a minimum allele count of 20 and minimum allele frequency of 0.40 for the rad53∆ batch sequencing experiment (MMS-resistant, suppressor containing strains (SUP) vs YJT75 strain). Multiallelic loci and variants identified in any of the control samples with an allele frequency of 0.1 or above were discarded.
Variant annotation was performed with snpEff 3.0j (Cingolani, et al. 2012) using the sacCer2.61 ensembl genomic database provided by the package. SNVs that passed the above criteria were further filtered to only include those that were labelled as nonsynonymous mutations, and had a minimum allele frequency of 0.7.
Genome_build: sacCer2
Supplementary_files_format_and_content: Tab-delimited file for SNVs identified to be specific to suppressor samples.  Columns represent: "chrom" (chromosome), "pos" (genomic position), "ref" (sacCer2 reference nucleotide), "alt" (alternate allele identified in suppressor strain(s)), "maximum_allele_frequency" (maximum allele frequency across all suppressors), "num_suppressors_pass_0.7_allele_frequency" (number of suppressors with allele frequency equal or above 0.7), "upstream_gene" (closest upstream gene to SNV), "downstream_gene" (closest downstream gene to SNV), "overlapping_gene" (overlapping gene for SNV), "gene_effect" (snpEff derived effect type of SNV). The remainder of the columns in the file represent the allele frequency per sample strain.

organism: Saccharomyces cerevisiae

source_name: S64Balpha (MAT alpha sml1Δ::URA3 rad53Δ::HIS3 chk1Δ::LEU2 exo1Δ::TRP1 suppressor) W303 derivative

growth_protocol: Cells were grown in YPD medium (1% yeast extract, 2% bacto peptone, 2% glucose) media at 30 °C, shaking at 300 RPM in incubators and recovered at exponential growth (OD600 ~0.6).

extract_protocol:
DNA for whole-genome sequencing was extracted by the CTAB protocol. Briefly, cells were treated with 1M sorbitol-10mM EDTA pH 8-0.1% β-mercaptoethanol-2 mg/mL Zimoliase 20T at 30ºC during one hour to get sferoplasts. Speroplasts were then broken with cold water and treated with 1.4M NaCl-100mM Tris-Cl pH 7.6-25mM EDTA pH 8-2% CTAB , and then with RNase and Proteinase K. After centrifugation, pellet and supernatant were treated separately. The supernatant was extracted with 24:1 Cloroform:Isoamyl Alcohol and DNA precipitated with two volumes of 50 mM Tris-Cl pH 7.6-0 mM EDTA pH 8-1% CTAB and further resuspended in 1.4M NaCl-1 mM EDTA pH 8-10 mM Tris-Cl pH 7.6. The pellet pellet was resuspended directly in 1.4M NaCl-1 mM EDTA pH 8-10 mM Tris-Cl pH 7.6 and incubated during one hour at 50ºC, extracted with 24:1 Cloroform:Isoamyl Alcohol and rejoined with the supernatant DNA. The whole sample was precipitated then with one volume room temperature isopropanol, centrifuged, washed with 70% ethanol and resuspended in 10mM Tris-Cl pH 8.
Total extracted DNA was sheared using the Covaris S2 to ~300bp. The sheared DNA samples were end repaired, poly-A tailed and Illumina Single End Adapters were ligated (Paired End protocol. Illumina San Diego, CA, USA). The standard protocol by Illumina was adjusted to fit our samples.  We used Agencourt AMPure XP beads (AMPure bead protocol. Beckman Coulter, Inc.)  at 0.8x ratio to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems, Cape Town, South Africa).  Post PCR we used AMPure XP beads at a 1:1 ratio to maintain size integrity, which also helped us to optimise the pH and other salt concentrations to allow us to use the Invitrogen SizeSelect E-gel system (SizeSelect gel protocol. Life Technologies Corporation).  Unlike for the Illumina Paired End sample preparation protocol we ran the PCR before the gel. This improved visualisation of the product and removal of the correct band.  To aid us to remove any gel residue that would cause issues in later quality control (QC) and cluster formation we purified with QAIquick gel extraction kit (Gel purification protocol. QIAGEN Ltd.). After a final QC using the DNA 1000 BioAnalyser 2100 chip (Agilent, Santa Clara, CA, USA), the libraries were ready for Flowcell cluster formation on a cluster station  followed by Illumina paired-end sequencing on either the Genome Analyzer IIx or HiSeq 2500 with a read length of 36bp, 72bp or 101bp. Due to the increased output of the HiSeq 2500 we were able to multiplex 17 samples per lane.

value: yeast strains in small batch culture


title: Canagliflozine 01

description: gene expression


title: W6

description: Whole genome sequencing

source_name: W64Aalpha (MAT alpha sml1Δ::URA3 rad53Δ::HIS3 chk1Δ::LEU2 exo1Δ::TRP1) W303 derivative


title: 939

description: Whole genome sequencing

source_name: YGDP939 (MAT sml1Δ::URA3 rad53Δ::LEU2 exo1Δ::HIS3) W303 derivative


title: Tsg101 TG sample 1

city: Cincinnati

first: Kobina

last: Essandoh

state: OH

address: 231 Albert Sabin Way

institute: University of Cincinnati

description: countsTable.xls

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Heart

extract_protocol:
Total RNA from heart samples  were isolated using Trizol reagent (Invitrogen), and purified by the miRNeasy Mini kit (Qiagen). The quality and concentration of RNA was measured by the NanoDrop 2000 system (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/N

tag: age

value: 8 weeks

value: Heart

tag: genotype/variation

value: Tsg101 TG


title: WT sample 1

description: countsTable.xls

value: wild type


title: WT sample 3

description: countsTable.xls


title: Tsg101 TG sample 2

description: countsTable.xls


title: WT sample 2

description: countsTable.xls


title: NC_mimic

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: total RNA

data_processing:
All the reads were aligned to the reference transcriptome with bowtie2, no mismatch allowed
Differential analysis was performed with edgeR package.
Differentially expressed genes were selected by the logFC > 1 and p value <0.05
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files include RPKM values for each Sample

source_name: NC mimic

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: Tsg101 TG sample 3

description: countsTable.xls


title: mir34a_mimic

description: total RNA

source_name: mir34a mimic


title: MIR_PD

description: Pulldown RNA

source_name: MIR PD


title: MONKEY_SPERM_ATACseq_Rep1


title: NC_PD

description: Pulldown RNA

source_name: NC PD


title: 72h after whitefly feed on healthy tomato biorep 1


title: S7_T_S70_tumor_miRNA

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Basecalls performed using CASAVA version 1.8
miRNA-seq reads were aligned to the hg19 genome assembly using Novoalign version V3.08.02 with the following configurations: -a TCTGGAATTCTCGGGTGCCAAGGAACTCC -l 15 -t30 -h90 -r All 1 -c 32 -F ILM1.8
miRNA-seq were annotated using BCGSC miRNA Profiling Pipeline version 0.2.7 with miRBase 21 release.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include miRNA read count for all samples

source_name: pancreatic cancer patient tumour tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (15596026, Invitrogen).
All libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modification following the manufacturer’s instructions with 12 cycles of PCR amplification after ligation of the 3’ and 5’ adapters (5’ TCTGGAATTCTCGGGTGCCAAGGAACTCC). Individual libraries were prepared using a unique index primer in order to allow for pooling of multiple samples prior to sequencing. The library was quantified using qPCR. Sequencing was performed on a Hiseq2500 (Illumina Inc., San Diego, CA) and image processing and base calling were conducted using Illumina’s pipeline.

tag: tissue disease state

value: Tumor

tag: subject id

tag: patient diagnosis

value: Pancreatic ductal adenocarcinoma (PDAC)


title: S7_N_S69_normal_miRNA

source_name: adjacent normal tissue

value: Normal


title: RNAseq

city: Pittsburgh

first: Svetlana

last: Yatsenko

address: 300 Halket St

institute: University of Pittsburgh

data_processing:
RNA library was processed on the Illumina HiSeq 2500 system. The output of 174 million reads, the Whole Transcriptome RNA Sequence, was then aligned using TopHat (Trapnell et al., 2009) and RefSeq alignment software according to the GRCh37/hg19 human reference genome Assembly.
Gene expression was calculated based on the FPKM (FragmentsPer Kilobase of exon per Million reads mapped) score.
Genome_build: hg19
Supplementary_files_format_and_content: txt, FPKM values

source_name: Fetal ovary

growth_protocol: Fresh tissue

extract_protocol:
The RNA was extracted using the RNeasy Mini Kit (Qiagen) and converted to cDNA using the TruSeq RNA Sample Preparation Kit (Illumina) as specified in the manufacturer’s protocols.
1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit according to the manufacturer's protocol..

treatment_protocol: no treatment

value: normal fetus

tag: developmental stage

value: 21 weeks of gestation

tag: Sex

value: female


title: S5_T_S66_tumor_miRNA


title: S6_T_S68_tumor_miRNA


title: S6_N_S67_normal_miRNA


title: S4_N_S63_normal_miRNA


title: S3_N_S61_normal_miRNA


title: S3_T_S62_tumor_miRNA


title: S5_N_S65_normal_miRNA


title: S4_T_S64_tumor_miRNA


title: S1_T_S58_tumor_miRNA


title: ITWB15

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

hyb_protocol: Hybridization was performed according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol version 7.3.

scan_protocol: The slides were scanned using Agilent Technologies Scanner G2505C US83800207. Images were quantified using Agilent Feature Extraction Software version 11.15.1.1.

data_processing: Genomic aberrations were analyzed using Agilent CytoGenomics software version 4.0.3.12.

organism: Bubalus bubalis

source_name: water buffalo Sample (ITWB15)

label_protocol: Genomic DNAs were digested with Alu I and Rsa I endonucleases, and labeled with the use of Agilent SureTag complete DNA labeling kit.

extract_protocol: Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).

value: Blood

source_name: Reference (Olimpia)


title: S1_N_S57_normal_miRNA


title: ITWB6

source_name: water buffalo Sample (ITWB6)


title: ITWB11

source_name: water buffalo Sample (ITWB11)


title: ITWB13

source_name: water buffalo Sample (ITWB13)


title: ITWB4

source_name: water buffalo Sample (ITWB4)


title: PARN KO1_small RNA

city: Seoul

first: Chanseok

last: Shin

address: 1 Gwanak-ro

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences were trimmed by cutadpat from the raw sequencing data
Reads of at least 18-nt in length were mapped to the human genome (hg38) using BWA for the removal of non-coding RNA (rRNA, tRNA) sequences.
The cleaned reads were selected and mapped to the human genome (hg38) and miRBase release 21.0 using BOWTIE 2.
Genome_build: hg38, miRBase release 21.0
Supplementary_files_format_and_content: miRNA counts

source_name: HeLa S3 cells

growth_protocol: HeLa S3 cells were cultured in Dulbecco's modiﬁed Eagle's medium supplemented with 10% (v/v) fetal bovine serum and a penicillin/streptomycin mix in 5% CO2.

extract_protocol:
Total RNA was prepared using the TRI Reagent following the manufacturer's instructions and further enriched for small RNA by mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Five micrograms of small RNA was fractionated in 15% denaturing polyacrylamide gel, followed by gel-purification of small RNA ranging between 18–30 nt. Small RNA library was prepared following TruSeq Small RNA Library Preparation Kits (Illumina)

value: Cervix adenocarcinoma

value: HeLa S3

tag: genotype

value: PARN KO1


title: PARN KO2_small RNA

value: PARN KO2


title: S2_N_S59_normal_miRNA


title: ITWB5

source_name: water buffalo Sample (ITWB5)


title: AR-high-shGREB1-DHT-3

city: New York

first: Eugine

last: Lee

address: 550 1st avenue

institute: NYU school of medicine

data_processing:
Reads were aligned to the human genome (hg19) using STAR (v2.4.2a). The number of RNA-seq fragments mapped to each gene was determined for all genes in the GENCODE database (v19) using the HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: prostate cancer cells

growth_protocol: LNCaP cells were maintained in RPMI + 10% FBS.

extract_protocol:
Total RNA was isolated using the QiaShredder kit (Qiagen, Germantown, MD) for cell lysis and the RNeasy kit (Qiagen) for RNA purification.
Libraries were prepared using TruSeq Stranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions

treatment_protocol: LNCaP cells with high AR activity (AR-high) were infected with shRNA against Renilla or GREB1 and treated with either vehicle or DHT for 24 hrs.

tag: cell type

value: prostate cancer cells

value: LNCaP

tag: androgen receptor activity

value: high

tag: treatment

value: DHTicle


title: ITWB8

source_name: water buffalo Sample (ITWB8)


title: ITWB7

source_name: water buffalo Sample (ITWB7)


title: ITWB14

source_name: water buffalo Sample (ITWB14)


title: AR-high-shGREB1-veh-2

value: vehicle


title: AR-high-shGREB1-veh-3


title: AR-high-shGREB1-veh-1


title: AR-high-shGREB1-DHT-1


title: S2_T_S60_tumor_miRNA


title: 48h after whitefly feed on healthy tomato biorep 3

value: healthy tomato

value: whole body


title: WT_small RNA

value: WT


title: ITWB3

source_name: water buffalo Sample (ITWB3)


title: AR-high-shGREB1-DHT-2


title: AR-high-shRenilla-DHT-3

value: shRenilla


title: AR-high-shRenilla-DHT-2


title: AR-high-shRenilla-veh-3


title: AR-high-shRenilla-veh-2


title: ITWB2

source_name: water buffalo Sample (ITWB2)


title: ITWB12

source_name: water buffalo Sample (ITWB12)


title: AR-high-shRenilla-DHT-1


title: AR-high-2


title: AR-low-2

value: low


title: AR-high-1


title: ITWB1

source_name: water buffalo Sample (ITWB1)


title: AR_high_shGREB1_input

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
The ChIP-seq reads were aligned to the human genome (hg19, build 37) using the program BWA (VN: 0.7.12; default parameters) within the PEMapper.
Duplicated reads were marked by the software Picard (VN: 1.124; http://broadinstitute.github.io/picard/index.html) and removed.
The software MACS2 (-q 0.1) was used for peak identification with data from ChIP input DNAs as controls.
Genome_build: hg19
Supplementary_files_format_and_content: Tdf files were generated from the bam files by Igvtools with default parameters for visualization in IGV

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA complexes were isolated with antibody.
Libraries were made using the KAPA Biosystems Hyper Library Prep Kit (Kapa Biosystems, Woburn, MA, KK8504), using 10 ng of DNA as input and 10 PCR cycles for library amplification.

tag: chip antibody


title: AR_high_shGREB1_ChIP

value: AR (Santa Cruz, sc-816)


title: AR_high_shRenilla_input


title: AR-high-shRenilla-veh-1


title: AR-low-1


title: tumor sample3

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

institute: Yunnan university of Chinese Medicine

description:
C_3
DE_circRNA.txt

data_processing:
Reads were aligned to the h19 genome assembly using bwa
circRNAs were detected by CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: text file with chromosome coordinates and signal

source_name: patient

extract_protocol:
Total RNA was isolated from cell lines using TRIzol reagent (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypopharynx

tag: disease state

value: tumor


title: tumor sample2

description:
C_2
DE_circRNA.txt


title: normal sample3

description:
N_3
DE_circRNA.txt

value: normal


title: AR_high_shRenilla_ChIP


title: normal sample1

description:
N_1
DE_circRNA.txt


title: normal sample2

description:
N_2
DE_circRNA.txt


title: 8505C-I

first: James

middle: C

last: Chen

state: NEW YORK

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm10) using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: (Human: NCBI/build37.2; Mouse: UCSC/mm10)
Supplementary_files_format_and_content: tab-delimited TPM reads

source_name: cell line 8505C

growth_protocol: Variable, human lines maintained according to recommendations by ATCC. B16F10 using standard DMEM 10% FBS protocols

extract_protocol:
Trizol RNA extraction, manufacturer protocols
Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500/HiSeq4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.

treatment_protocol: Transfected with viral particles of PLOC vectors and placed on 5-day blasticidin selection at manufacturer recommended protocols

tag: sample type

value: in vitro culture

value: pLOC IKZF1, stable transfection


title: SKCM-R

source_name: cell line SKCM-MEC2

value: pLOC RFP, stable transfection


title: SF210-IKZF1

source_name: cell line SF210


title: TCCSUP-I

source_name: cell line TCCSUP


title: 8505C-R


title: NCIH441-R

source_name: cell line NCIH441


title: SKCM-I


title: DO4-I

source_name: cell line DO4


title: TCCSUP-R


title: DO4-R


title: SF210-RFP


title: C34 16S rRNA Seq

city: Nanjing City

first: Xingyin

state: Jiangsu Province

address: Long Mian Street No.1

institute: Nanjing Medical University

data_processing:
Paired-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Paired-end reads were merged using FLASH (http://ccb.jhu.edu/software/FLASH/). Quality filtering on the raw tags were performed under specific filtering conditions to obtain the high-quality clean tags according to the QIIME (http://qiime.org/index.html) quality controlled process.
The tags were compared with the reference database (Gold database, http://drive5.com/uchime/uchime_download.html) using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed.
Sequences analysis were performed by Uparse software (http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs.
For each representative sequence, the GreenGene Database (http://greengenes.lbl.gov/cgi-bin/nph-index.cgi) was used based on RDP classifier (http://sourceforge.net/projects/rdp-classifier/) algorithmto annotate taxonomic information. OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences.
Supplementary_files_format_and_content: OTUs data files were generated using Uparse software.

source_name: Feces

extract_protocol:
Total genome DNA of fecal samples was extracted using the kit (Tiangen Company, Beijing, China). The DNA concentration was performed using Qubit@ 2.0 Fluorometer (Thermo Scientific). DNA quality was also monitored on 1% agarose gels. PCR was performed to produce V4 regions of the 16S rDNA gene using the conserved primers 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’). PCR products and operate electrophoresis on 2% agarose gel for detection. Samples with bright main strip between 400-450bp were chosen for purifing with GeneJET Gel Extraction Kit (Thermo Scientific). PCR fragments were sequenced by Novogene Company (Tianjin, China).
Libraries was sequenced on an Illumina HiSeq platform and 250 bp paired-end reads were generated.

treatment_protocol: Fecal samples were obtained at the homes of each participant, and were immediately frozen in their home freezer. Frozen samples were stored within insulating polystyrene foam containers, and stored at -80 ℃ until analysis. The time span from sampling to delivery to the Affiliated Jiangsu Cancer Hospital of Nanjing Medical University was intended to be as short as possible with a maximum of 24 hours.

value: fecal tissue

value: HBVC


title: LNCCP-R

source_name: cell line LNCCP


title: NCIH441-I


title: C33 16S rRNA Seq


title: ITWB10

source_name: water buffalo Sample (ITWB10)

value: Blood

source_name: Reference (Olimpia)


title: C32 16S rRNA Seq


title: tumor sample1

description:
C_1
DE_circRNA.txt


title: C31 16S rRNA Seq


title: C30 16S rRNA Seq


title: C25 16S rRNA Seq


title: SF210-DLX4

value: pLOC DLX4 stable transfection


title: C24 16S rRNA Seq


title: C29 16S rRNA Seq


title: C23 16S rRNA Seq


title: C28 16S rRNA Seq


title: LNCCP-I


title: C22 16S rRNA Seq


title: C21 16S rRNA Seq


title: C18 16S rRNA Seq


title: C16 16S rRNA Seq


title: C15 16S rRNA Seq


title: C14 16S rRNA Seq


title: C17 16S rRNA Seq


title: C13 16S rRNA Seq


title: C12 16S rRNA Seq


title: C35 16S rRNA Seq


title: C19 16S rRNA Seq


title: C11 16S rRNA Seq


title: C10 16S rRNA Seq


title: C26 16S rRNA Seq


title: C9 16S rRNA Seq


title: C5 16S rRNA Seq


title: C7 16S rRNA Seq


title: C8 16S rRNA Seq


title: C6 16S rRNA Seq


title: C4 16S rRNA Seq


title: C2 16S rRNA Seq


title: C1 16S rRNA Seq


title: B22 16S rRNA Seq

value: NHBVC


title: C3 16S rRNA Seq


title: C20 16S rRNA Seq


title: B19 16S rRNA Seq


title: B18 16S rRNA Seq


title: B17 16S rRNA Seq


title: B21 16S rRNA Seq


title: B16 16S rRNA Seq


title: B13 16S rRNA Seq


title: B12 16S rRNA Seq


title: B11 16S rRNA Seq


title: B15 16S rRNA Seq


title: B10 16S rRNA Seq


title: B9 16S rRNA Seq


title: B14 16S rRNA Seq


title: B8 16S rRNA Seq


title: B5 16S rRNA Seq


title: B7 16S rRNA Seq


title: B2 16S rRNA Seq


title: B1 16S rRNA Seq


title: B4 16S rRNA Seq


title: B3 16S rRNA Seq


title: A32_16S rRNA Seq

value: healthy control


title: A33_16S rRNA Seq


title: B20 16S rRNA Seq


title: A31_16S rRNA Seq


title: A30_16S rRNA Seq


title: A27_16S rRNA Seq


title: A26_16S rRNA Seq


title: A28_16S rRNA Seq


title: A23_16S rRNA Seq


title: A22_16S rRNA Seq


title: A29_16S rRNA Seq


title: A24_16S rRNA Seq


title: A19_16S rRNA Seq


title: A18_16S rRNA Seq


title: A17_16S rRNA Seq


title: A21_16S rRNA Seq


title: B6 16S rRNA Seq


title: A16_16S rRNA Seq


title: A20_16S rRNA Seq


title: A11_16S rRNA Seq


title: A10_16S rRNA Seq


title: A13_16S rRNA Seq


title: A9_16S rRNA Seq


title: A8_16S rRNA Seq


title: A4_16S rRNA Seq


title: A5_16S rRNA Seq


title: A15_16S rRNA Seq


title: A3_16S rRNA Seq


title: A25_16S rRNA Seq


title: A7_16S rRNA Seq


title: A2_16S rRNA Seq


title: A12_16S rRNA Seq


title: A6_16S rRNA Seq


title: A1_16S rRNA Seq


title: A14_16S rRNA Seq


title: Participant ID and visit (v) number [phchp368v2]

city: Indianapolis

first: Dr. Alexander

middle: B.

last: Niculescu

state: IN

address: 320 W. 15th Street

department: Psychiatry

institute: Indiana University Medical School

description: Independent Test cohort blood gene expression data

hyb_protocol: Microarrays: Biotin labeled aRNA are hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips according to manufacturer’s protocols http://www.affymetrix.com/support/technical/manual/expression_manual.affx. All GAPDH 3’/5’ ratios should be less than 2.0 and backgrounds under 50.

scan_protocol: Arrays are stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/Absent calls are determined using GCOS software with thresholds set at default values

data_processing: The AP derived and DE derived lists of genes were combined, and the gene expression data corresponding to them was used for the validation analysis. The cohorts (Validation Clinically Severe Stress, alongside the Low Stress and High Stress groups in the Discovery cohort) were assembled out of Affymetrix .cel data that was RMA normalized by gender and diagnosis. We transferred the log transformed expression data to an Excel sheet, and non-log transformed the data by taking 2 to the power of the transformed expression value. We then Z-scored the values by gender and diagnosis.  We then imported the Excel sheets with the Z-scored by gender and diagnosis expression data into Partek, and  statistical analyses were performed using a one-way ANOVA for the stepwise changed probesets, and also attempted a stringent Bonferroni corrections for all the probesets tested (Figure 1F). We also wrote an R script that automatically analyzes the data directly from the Excel sheet, and used that to confirm our calculations.

label: Biotin

source_name: Whole Blood

label_protocol: Sample Labeling:  Sample labeling is performed using the Ambion MessageAmp II-BiotinEnhanced aRNA amplification kit. The procedure is briefly outlined below and involves the following steps:     1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.    2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA.    3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.    4. In Vitro Transcription to Synthesize aRNA with Biotin-NTP Mix generates multiple copies of biotin-modified aRNA from the double- stranded cDNA templates; this is the amplification step.    5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol:
We used three independent cohorts: discovery (major psychiatric disorders), validation (major psychiatric disorders with clinically severe pain disorders), and testing (an independent major psychiatric disorders cohort for predicting pain state, and for predicting future ED visits for pain) (Figure 1A).
Subjects were recruited from the patient population at the Indianapolis VA Medical Center. All subjects understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards, per Indiana University IRB approved protocol. Subjects completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies, and up to six testing visits, 3–6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of rating scales, including a visual analog scale (1-10) for assessing pain and the SF-36 quality of life scale, which has two pain related items (items 21 and 22), and the blood was drawn. We collected whole blood (10 ml) in two RNA-stabilizing PAXgene tubes, labeled with an anonymized ID number, and stored at -80 degrees C in a locked freezer until the time of future processing. Whole-blood RNA was extracted for microarray gene expression studies from the PAXgene tubes, as detailed below.
Whole blood (2.5 ml) RNA extraction: 2.5-5 ml of whole blood was collected into each PaxGene tube by routine venipuncture.  PaxGene tubes contain proprietary reagents for the stabilization of RNA. The cells from whole blood will be concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing Proteinase K for protein digestion.  A second centrifugation step will be done to remove residual cell debris.  After the addition of ethanol for an optimal binding condition the lysate is applied to a silica-gel membrane/column.  The RNA bound to the membrane as the column is centrifuged and contaminants are removed in three wash steps.  The RNA is then eluted using DEPC-treated water.

tag: gender

value: Female

tag: diagnosis

value: MDD

tag: test cohort pain state

value: Yes

tag: test cohort all future emergency department visits with pain


title: Participant ID and visit (v) number [phchp361v3]

value: PTSD

tag: test cohort first year emergency department visits with pain


title: Participant ID and visit (v) number [phchp362v1]

value: Male


title: Participant ID and visit (v) number [phchp364v1]


title: Participant ID and visit (v) number [phchp358v1]


title: Participant ID and visit (v) number [phchp363v2]


title: Participant ID and visit (v) number [phchp360v3]

value: BP


title: Participant ID and visit (v) number [phchp358v2]


title: Participant ID and visit (v) number [phchp359v2]


title: Participant ID and visit (v) number [phchp362v3]


title: Participant ID and visit (v) number [phchp368v1]


title: Participant ID and visit (v) number [phchp359v3]


title: Participant ID and visit (v) number [phchp357v4]


title: Participant ID and visit (v) number [phchp365v1]


title: Participant ID and visit (v) number [phchp361v1]


title: Participant ID and visit (v) number [phchp359v1]


title: Participant ID and visit (v) number [phchp363v1]


title: Participant ID and visit (v) number [phchp361v2]


title: Participant ID and visit (v) number [phchp366v1]

value: SZ


title: Participant ID and visit (v) number [phchp356v1]


title: Participant ID and visit (v) number [phchp357v5]


title: Participant ID and visit (v) number [phchp358v3]


title: Participant ID and visit (v) number [phchp353v1]


title: Participant ID and visit (v) number [phchp357v3]


title: Participant ID and visit (v) number [phchp362v2]


title: Participant ID and visit (v) number [phchp360v1]


title: Participant ID and visit (v) number [phchp352v3]


title: Participant ID and visit (v) number [phchp357v1]


title: Participant ID and visit (v) number [phchp357v2]


title: Participant ID and visit (v) number [phchp351v2]


title: Participant ID and visit (v) number [phchp351v1]


title: Participant ID and visit (v) number [phchp337v2]


title: Participant ID and visit (v) number [phchp343v2]


title: Participant ID and visit (v) number [phchp333v2]


title: Participant ID and visit (v) number [phchp342v3]


title: Participant ID and visit (v) number [phchp348v1]


title: Participant ID and visit (v) number [phchp333v4]


title: Participant ID and visit (v) number [phchp345v1]


title: Participant ID and visit (v) number [phchp328v3]


title: Participant ID and visit (v) number [phchp337v3]


title: Participant ID and visit (v) number [phchp343v3]


title: Participant ID and visit (v) number [phchp333v3]


title: Participant ID and visit (v) number [phchp329v3]

value: SZA


title: Participant ID and visit (v) number [phchp343v1]


title: Participant ID and visit (v) number [phchp352v1]


title: Participant ID and visit (v) number [phchp330v1]


title: Participant ID and visit (v) number [phchp329v2]


title: Participant ID and visit (v) number [phchp327v1]


title: Participant ID and visit (v) number [phchp328v2]


title: Participant ID and visit (v) number [phchp331v1]


title: Participant ID and visit (v) number [phchp337v1]


title: Participant ID and visit (v) number [phchp325v3]


title: Participant ID and visit (v) number [phchp325v4]


title: Participant ID and visit (v) number [phchp342v2]


title: C27 16S rRNA Seq

tag: tissue


title: Participant ID and visit (v) number [phchp319v4]


title: Participant ID and visit (v) number [phchp320v2]


title: Participant ID and visit (v) number [phchp324v1]


title: Participant ID and visit (v) number [phchp320v1]


title: Participant ID and visit (v) number [phchp320v3]


title: Participant ID and visit (v) number [phchp325v1]


title: Participant ID and visit (v) number [phchp319v1]


title: Participant ID and visit (v) number [phchp319v2]


title: Participant ID and visit (v) number [phchp319v3]


title: Participant ID and visit (v) number [phchp318v3]


title: Participant ID and visit (v) number [phchp319v6]


title: Participant ID and visit (v) number [phchp316v3]


title: Participant ID and visit (v) number [phchp318v2]


title: Participant ID and visit (v) number [phchp315v1]


title: Participant ID and visit (v) number [phchp316v5]


title: Participant ID and visit (v) number [phchp318v1]


title: Participant ID and visit (v) number [phchp328v1]


title: Participant ID and visit (v) number [phchp316v4]


title: Participant ID and visit (v) number [phchp316v6]


title: Participant ID and visit (v) number [phchp316v1]


title: Participant ID and visit (v) number [phchp316v2]


title: Participant ID and visit (v) number [phchp314v3]


title: Participant ID and visit (v) number [phchp313v3]


title: Participant ID and visit (v) number [phchp313v2]


title: Participant ID and visit (v) number [phchp314v1]


title: Participant ID and visit (v) number [phchp314v2]


title: Participant ID and visit (v) number [phchp312v1]


title: Participant ID and visit (v) number [phchp309v1]


title: Participant ID and visit (v) number [phchp304v2]


title: Participant ID and visit (v) number [phchp313v1]


title: Participant ID and visit (v) number [phchp308v2]


title: Participant ID and visit (v) number [phchp309v3]


title: Participant ID and visit (v) number [phchp312v3]


title: Participant ID and visit (v) number [phchp308v1]


title: Participant ID and visit (v) number [phchp300v2]


title: Participant ID and visit (v) number [phchp309v2]


title: Participant ID and visit (v) number [phchp307v1]


title: Participant ID and visit (v) number [phchp308v3]


title: Participant ID and visit (v) number [phchp300v4]


title: Participant ID and visit (v) number [phchp304v3]


title: Participant ID and visit (v) number [phchp312v2]


title: Participant ID and visit (v) number [phchp308v4]


title: Participant ID and visit (v) number [phchp304v1]


title: Participant ID and visit (v) number [phchp300v5]


title: Participant ID and visit (v) number [phchp300v3]


title: Participant ID and visit (v) number [phchp299v5]


title: Participant ID and visit (v) number [phchp300v6]


title: Participant ID and visit (v) number [phchp333v1]


title: Participant ID and visit (v) number [phchp342v1]


title: Participant ID and visit (v) number [phchp352v2]


title: Participant ID and visit (v) number [phchp299v4]


title: Participant ID and visit (v) number [phchp300v1]


title: Participant ID and visit (v) number [phchp297v3]


title: Participant ID and visit (v) number [phchp297v4]


title: Participant ID and visit (v) number [phchp296v3]


title: Participant ID and visit (v) number [phchp298v3]


title: Participant ID and visit (v) number [phchp297v2]


title: Participant ID and visit (v) number [phchp299v1]


title: Participant ID and visit (v) number [phchp297v1]


title: Participant ID and visit (v) number [phchp292v1]


title: Participant ID and visit (v) number [phchp298v4]


title: Participant ID and visit (v) number [phchp299v3]


title: Participant ID and visit (v) number [phchp295v1]


title: Participant ID and visit (v) number [phchp298v1]


title: Participant ID and visit (v) number [phchp299v2]


title: Participant ID and visit (v) number [phchp296v2]


title: Participant ID and visit (v) number [phchp293v1]


title: Participant ID and visit (v) number [phchp293v2]


title: Participant ID and visit (v) number [phchp292v2]


title: Participant ID and visit (v) number [phchp286v1]


title: Participant ID and visit (v) number [phchp290v2]


title: Participant ID and visit (v) number [phchp290v1]


title: Participant ID and visit (v) number [phchp290v3]


title: Participant ID and visit (v) number [phchp292v3]