title: SimpleChIP_LVshARID1A_Input_R1.fastq.gz

status: Public on Nov 10 2020

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: Input library from lentiviral shARID1A infected 12Z cells

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Library molecular complexity was then estimated from duplicate rates by ATACseqQC and preseqR, and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call narrow peaks (FDR < 0.05) on each ChIP replicate against the input control with flags `--nomodel --extsize 146` to bypass model building.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Differential abundance analysis was computed with csaw. Briefly, a consensus peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peaks called in each condition. The replicate intersection criteria used here are less stringent than the naïve overlap; any partial intersect between ChIP replicates was accepted as a query region tested for differential abundance. ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average logCPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a non-linear loess-based normalization to the peak count matrix, as is implemented in csaw, to assume a symmetrical MA distribution. A design matrix was then constructed from one “condition” variable, without an intercept. The count matrix and loess offsets were then supplied to edgeR for estimating dispersions and fitting the quasi-likelihood generalized linear model for hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kilobases, and the most significant probability was used to represent the merged region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate narrowPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping narrowPeaks. Non-thresholded differential abundance results from csaw are also reported as a tab-separated values (TSV) file.

source_name: 12Z cell line

growth_protocol: 12Z cells were cultured in DMEM/F12 media supplemented with 10% FBS, 1% L-glutamine, and 1% Penicllin-Streptomycin.

extract_protocol:
72 hours following lentiviral transduction, cells were treated with 1% formaldehyde in cell culture media for 15 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions, with the addition of 5 mM sodium butyrate included in Buffer A and ChIP Buffer. Antibodies used were 10 ug H3K27ac (Active Motif, 39133) or 5 ug H3K18ac (ab1191, Abcam) antibody. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).

treatment_protocol: Cells were transduced with lentiviral particles which expressed shRNA targeting ARID1A (shARID1A) or non-targeting control (shNONtg) at 100 units per cell multiplicity of infection. Growth media was replaced 24 hours after trandsuction.

tag: genotype/variation


title: samp_406441: Bio101_OTA_100uM

status: Public on Oct 22 2020

type: SRA

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).
Reads aligned to  reference genome (GENCODE human release 30 GRCh38) using STAR (v2.6.1d)
Aligned data were read into R and summarized as counts per gene using the Bioconductor GenomicAlignments package
Differential analysis was performed by the Bioconductor edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of gene counts, with Ensembl IDs in the first column, and the sample names in the header

molecule: total RNA

organism: Homo sapiens

source_name: 3D human kidney proximal tubule MPS

growth_protocol: The Nortis triple channel MPS devices (TSC™) were filled with 6 mg/mL of rat tail collagen I, and left overnight at room temperature to allow the collagen I matrix to solidify.  The mandrels of the MPS platforms were removed, leaving behind hollow channels through the collagen I matrix.  Cell chambers were coated with a 5 µg/mL mouse collagen IV to facilitate human PTECs adhesion.  T-flask cultures of PTECs were trypsinized to obtain single cell suspensions.  The cells were counted and resuspended with PTECs culture media at a concentration of 20 ×106 cells/mL and 2-2.5 µL were injected into the collagen IV-coated channels of the MPS.  Cells were allowed to attach for 3 hours before starting perfusion at a rate of 1.0 µL/min.  PTECs were cultured under flow for at least 6 days to form the tubule cell structures.  Prior to the beginning of experiments, a visual inspection under light microscope was performed to confirm complete (100%) coverage of PTEC tubule. Only kidney MPS that exhibited continuous media flow characteristics were selected for use in functional experiments.

extract_protocol:
Cells cultured within the kidney MPS were isolated after  OTA treatment, and total RNA was isolated using the Qiagen RNeasy Micro Kit
Total RNA was normalized to 2ng/ul in a total volume of 9ul and then transcribed to cDNA in a dedicated PCR clean workstation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Moutain View, CA).  Sequencing libraries were constructed from cDNA using the SMARTer ThruPLEX DNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Kidney MPS were exposed to 0, 0.1, 0.3, 1, 3, 10, 30 and 100 μM of OTA. Samples from donor Bio125 were exposed for 72 hrs and samples from donor Bio101 were exposed for 168 hrs.

tag: cell type

value: Human kidney proximal tubule epithelial cells (PTEC)

tag: treatment

tag: donor

tag: exposure time


title: RU2Zc_IGO_06937_19_S1_L002

status: Public on Nov 24 2020

city: New York

first: John

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

library_source: genomic

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO v2)
Supplementary_files_format_and_content: raw counts table

molecule: genomic DNA

source_name: HAP1 cells

extract_protocol:
Ammonium acetate salt precipitation
TruSeq
CRISPR

tag: cell line

value: HAP1 cells

value: ZIKV

tag: replicate

value: C

tag: lane


title: SimpleChIP_LVshNONtg_Input

state: MI

description: Input library from lentiviral non-targeting shRNA control (LVshNONtg) infected 12Z cells

value: Control


title: samp_406442: Bio101_OTA_100uM


title: samp_406440: Bio101_OTA_100uM


title: samp_406439: Bio101_OTA_10uM


title: RU2Zb_IGO_06937_18_S3_L002

value: B


title: samp_406438: Bio101_OTA_10uM


title: samp_406437: Bio101_OTA_10uM


title: samp_406435: Bio101_OTA_1uM


title: samp_406436: Bio101_OTA_10uM


title: samp_406433: Bio101_OTA_1uM


title: samp_406434: Bio101_OTA_1uM


title: samp_406432: Bio101_OTA_0.1uM


title: samp_406428: Bio101_OTA_0uM


title: samp_406422: Bio125_OTA_10uM


title: samp_406431: Bio101_OTA_0.1uM


title: samp_406429: Bio101_OTA_0uM


title: samp_406423: Bio125_OTA_10uM


title: samp_406424: Bio125_OTA_30uM


title: RU2Za_IGO_06937_17_S10_L001

value: A


title: samp_406427: Bio125_OTA_100uM


title: RU2Mc_IGO_06937_13_S9_L002

value: mock


title: samp_406425: Bio125_OTA_30uM


title: samp_406421: Bio125_OTA_10uM


title: samp_406426: Bio125_OTA_30uM


title: samp_406430: Bio101_OTA_0uM


title: samp_406420: Bio125_OTA_3uM


title: samp_406418: Bio125_OTA_3uM


title: samp_406415: Bio125_OTA_1uM


title: samp_406414: Bio125_OTA_0.3uM


title: samp_406416: Bio125_OTA_1uM


title: samp_406413: Bio125_OTA_0.3uM


title: samp_406412: Bio125_OTA_0.3uM


title: samp_406411: Bio125_OTA_0uM


title: samp_406410: Bio125_OTA_0uM


title: samp_406409: Bio125_OTA_0uM


title: Liver, GP5L

status: Public on Aug 26 2020

description: Sample 22

data_processing:
Reads were aligned to the mouse GRCm38.p6 transcriptome (Gencode release M19) and estimated transcript-level abundance using the Salmon aligner (version 0.11.3), in quasi-mapping mode with the variational Bayesian EM algorithm.
Counts per transcript were imported into R using the Bioconductor tximport package (version 1.10.1), and then summarized to the gene level based on transcript to gene mappings from the Gencode release M19. Differential gene expression analysis between groups were performed using edgeR package (v3.24.3).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: sample_counts.txt contains gene counts

organism: Mus musculus

source_name: Liver

growth_protocol: Both conventional (CV) and germ-free (GF) mice were maintained on 12-h light/dark cycles, and the same autoclaved Breeder Chow #5021 (LabDiet, St. Louis, MO), autoclaved non-acidified water, and autoclaved Enrich-N’Pure bedding (The Andersons Inc., Maumee, OH) were provided ad libitum.  CV female mice of 8 weeks of age were mated with CV male mice overnight, and male mice were promptly separated from female mice in the morning. The day with the overnight housing was defined as gestation day (gd) 0. Due to difficulties in achieving pregnancies in GF mice, GF female mice of 11-15 weeks of age were mated with male mice for 72 h prior to separation from GF male mice. Day 2 after introduction of male mice to the cage was assumed to be gd 0. All pregnant mouse tissues were collected on gd 15 which was previously shown to be the optimal time point to observe peak levels of gene expression changes.

extract_protocol:
Liver tissues were removed, washed in cold saline, and immediately snap-frozen in liquid nitrogen. All samples were then stored at -80°C until analysis.  Total RNA was extracted from liver tissues using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols with NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

tag: strain

value: Germfree C57BL/6

tag: group

value: Pregnant

tag: age

tag: tissue

value: Liver


title: Input

status: Public on Oct 20 2020

description: Input library from wild-type 12Z cells

data_processing:
Raw reads for IPs and input were trimmed with cutadapt and Trim Galore!
Trimmed reads were aligned to GRCh38.p12 reference genome via Bowtie2 with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools.
Picard MarkDuplicates was used to remove PCR duplicates, followed by sorting and indexing.
MACS2 was used to call significant broad peaks (FDR < 0.05) on each ChIP replicate against the input control with otherwise default settings.
A naïve overlapping peak set, as defined by ENCODE, was constructed by calling peaks on pooled replicates followed by bedtools intersect to select for peaks of at least 50% overlap with each biological replicate.
The resulting peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tabular peak set files including blacklist-filtered ChIP replicate broadPeaks (FDR < 0.05 MACS2 output) and naïve replicate-overlapping broadPeaks.

extract_protocol:
Cells were treated with 1% formaldehyde in fresh DMEM/F12 media for 10 min at room temp. Formaldehyde was quenched by the addition of 0.125 M Glycine, and cells were washed with PBS. 1x10^7 crosslinked cells were used per IP. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) per the manufacturers’ instructions, followed by 30 seconds of sonication. IPs were performed using the SimpleChIP Enzymatic Chromatin IP Kit per the manufacturers’ instructions with 1:100 anti-BRG1 antibody (ab110641, abcam). Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input and IP material when available, and all material when less than 10 ng available, using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific).

tag: condition

value: Wild-type

tag: chip antibody

value: none (input)


title: Liver, GP4L

description: Sample 21


title: Liver, GN5L

description: Sample 16

value: Nonpregnant


title: Liver, GN1L

description: Sample 12


title: Liver, GN6L

description: Sample 17


title: Liver, GN4L

description: Sample 15


title: Liver, CP5L

description: Sample 11

value: Conventional C57BL/6


title: Liver, GN3L

description: Sample 14


title: Liver, GN2L

description: Sample 13


title: Liver, GP2L

description: Sample 19


title: Liver, CP4L

description: Sample 10


title: Liver, CP3L

description: Sample 9


title: Liver, CN6L

description: Sample 6


title: Liver, GP3L

description: Sample 20


title: samp_406419: Bio125_OTA_3uM


title: Liver, CP2L

description: Sample 8


title: Liver, CN4L

description: Sample 4


title: Liver, CN5L

description: Sample 5


title: Liver, GP1L

description: Sample 18


title: Liver, CP1L

description: Sample 7


title: Liver, CN2L

description: Sample 2


title: Liver, CN3L

description: Sample 3


title: FS030_LM

status: Public on May 29 2020

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

data_processing:
STAR aligment
HTSeq gene coverage
Genome_build: hg38 + ERCC
Supplementary_files_format_and_content: Single cell by gene matrix reporting raw counts. columns = single cell index: <sample title>_<welI ID>_<sequencing batch ID>; rows = gene coverage counts.
Supplementary_files_format_and_content: Metadata.csv: Donor and cell identity information (well number, plate, donor, age, sex, pigmentation, FACS gate, anatomical sight, developmental stage, etc.)
Supplementary_files_format_and_content: HighResLouvain.csv: High resolution Louvain cluster assignments for melanocytes in PMID: 34475532 figure 1.
Supplementary_files_format_and_content: LowResLouvain.csv: Low resolution Louvain cluster assignments for melanocytes in PMID: 34475532 figure 1.

molecule: polyA RNA

source_name: skin

extract_protocol:
Tissue dissociation was started the same day as sample acquisition.  For adult and neonatal skin, the epidermis was enzymatically dissociated from the dermis with a dispase, neutral protease, grade II (Roche–Sigma-Aldrich), incubation for 14 hours at 4˚C.  Epidermal sheets were manually separated from dermis, finely minced, and incubated with 0.5% trypsin (Gibco) for 3 minutes at 37˚C.  After manual trituration, trypsin was deactivated using ice cold soybean trypsin inhibitor (Gibco), then diluted 2:3 in ice cold Hanks’ balanced salt solution, no Mg2+, no Ca2+ (Gibco).  The dissociated cell suspension was centrifuged at 500g, 4˚C , for 4 minutes, resuspended in FACS buffer (0.1% bovine serum albumin (Sigma) and 25mM Hepes (Gibco) in Dulbecco's phosphate-buffered saline (DPBS) (Gibco)) and strained with a 70µM filter to achieve a single cell suspension.  For fetal tissue, the developing epidermis was manually removed from the dermis following a 20 - 30 minute incubation with 10mM EDTA (Invitrogen), DPBS at 37˚C. The resulting epidermal layer was incubated with 0.5% trypsin (Gibco) for 1 min at 37˚C and manually triturated. Trypsin was deactivated using ice cold soybean trypsin inhibitor (Gibco), then diluted 2:3 in ice cold Hanks’ balanced salt solution (Gibco).  The dissociated cell suspension was centrifuged at 500g, 4˚C , for 4 minutes, resuspended in FACS buffer, and strained with a 70µM filter to achieve a single cell suspension.
smartseq2

value: skin

value: melanocytes

tag: age (years)

tag: site

value: foreskin


title: Liver, CN1L

description: Sample 1


title: FS043_LM


title: A1033M

value: thigh


title: A1026L

value: right thigh


title: A1025L

value: left thigh


title: samp_406417: Bio125_OTA_1uM

value: Human kidney proximal tubule epithelial cells (PTEC)


title: A1038LM

value: arch,calf,heel,shin


title: A1046M

value: shin,heel,arch,calf


title: A1021M

value: ankle or upper foot


title: 16WKM04

value: palm


title: GSMO10

status: Public on May 15 2020

city: chapel hill

first: Seth

last: Weir

address: 115 mason farm rd

institute: UNC Chapel Hill

description:
single-cell sequencing
GSMO_Working.rds

data_processing:
Raw sequence data were processed in a Linux environment using Drop-seq Tools V1.13. (https://github.com/broadinstitute/Drop-seq/releases) to generate a digital expression (DGE) matrix
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code: https://github.com/malawsky/Gershon_single-cell
Genome_build: mm10 genome
Supplementary_files_format_and_content: digital expression matrix

source_name: Medulloblastoma model

extract_protocol:
Brains were cut in half sagittally and drop-fixed in 4% paraformaldehyde for IHC, and half cerebellum or tumor collected for Drop-Seq.Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18
Drop-Seq libraries were prepared according to the Drop-seq protocol V3.1 (ref. 32), with full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL.
to high-throughput sequencing facility that does their own QC before running samples.
RNA libraries were prepared for sequencing using standard Illumina protocols (Multiplexed samples using nextera indexes so that libraries could be pooled)

tag: genotype

value: Cerebellum

value: Postnatal age 15


title: GSMO11

description:
single-cell sequencing
GSMO_Working.rds


title: A1015LM

value: arm


title: 9.5WK02

value: leg,arm


title: 12WK05

value: sole,leg,palm,arm


title: GSMO9

description:
single-cell sequencing
GSMO_Working.rds


title: A1016LM

value: anterior forearm


title: A1011L

value: skin


title: A1017LM

value: melanocytes

value: medial calf


title: GSMO7

description:
single-cell sequencing
GSMO_Working.rds


title: GSMO6

description:
single-cell sequencing
GSMO_Working.rds


title: 18WKM06

value: sole,leg,palm


title: A1012M


title: 10WK03

value: arm,palm,leg


title: 12WKM01

value: sole,palm,leg


title: Expanded_iEPs_Replicate_1

status: Public on Feb 14 2020

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description: Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry). BAM files and Gene-barcode matrices were generated using 10X Genomics Cellranger version 2(?)

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Induced endoderm progenitors converted from mouse embryonic fibroblasts

extract_protocol: 10x Genomcis Chromium single cell preparation


title: DEJ16_liver

status: Public on Nov 13 2019

city: Beijing

first: Yao

last: He

state: Haidian District

address: Room 307A, Intergrated Science Building 2, Peking University,, No.5 Yiheyuan Road

country: China

institute: BIOPIC

description:
UMI_counts_Droplet.mtx
UMI_counts_Droplet_barcodes.tsv
UMI_counts_Droplet_genes.tsv

data_processing:
Droplet-based sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.3, 10x Genomics) against the GRCh38 human reference genome. To call real cells from empty droplets, we used the emptyDrops() function from R package dropletUtils, (Lun et al., 2019  ), which assesses whether the RNA content associated with a cell barcode is significantly distinct from the ambient background RNA present within each sample. Cells with p < 0.01 (Benjamini–Hochberg-corrected) were considered for further analysis. Quality of cells were then assessed based on three metrics step by step: (1) The number of total UMI counts per cell (library size); (2) The number of detected genes per cell; (3) The proportion of mitochondrial gene counts. Low-quality cells were filtered if the library size or the number of detected genes (in log10 scale) was below the medians of all cells minus 3 × the median absolute deviation. Cells were filtered out if the proportion of mitochondrial gene counts was higher than the median of all cells minus 3 × the median absolute deviation.
We then tried to identify doublets cells following methods as previous described,  (Pijuan-Sala et al., 2019). Briefly, a doublet score was computed for each cell by applying the ‘doubletCells’ function (scran R package) to each 10x sample separately. We next identified clusters of cells in each sample by computing the first 50 principal components across all genes, building a shared nearest-neighbor graph (10 nearest neighbors; ‘buildSNNGraph’ function; scran R package), and applying the Louvain clustering algorithm (‘cluster_louvain’ function; igraph R package; default parameters) to it. Only HVGs (calculated separately for each sample) were used for the clustering. This procedure was repeated in each identified cluster to break the data into smaller clusters, ensuring that small regions of high doublet density were not clustered with large numbers of singlets. For each cluster, the median doublet score was considered as a summary of the scores of its cells, as clusters with a high median score were likely to contain mostly doublets. Doublet calls were made in each sample by considering a null distribution for the scores using a median-centered MAD-variance normal distribution, separately for each sample. The MAD estimate was calculated only on values above the median to avoid the effects of zero-truncation, as doublet scores cannot be less than zero. All cells in clusters with a median score at the extreme upper end of this distribution (Benjamini–Hochberg-corrected p < 0.1) were labeled as doublets. After removing doublet cells, a total of 66,187 cells were retained for downstream analysis.
The size factor of each cell was computed using a pooling strategy implemented in the R function computeSumFactors. Normalized counts were then computed by dividing the counts for each cell by the size factor for that cell. A log2 transformation was applied to normalized counts.
SMART-seq2 sequencing data were aligned with STAR, using genome reference hg38 and annotation downloaded from NCI GDC (Genomic Data Commons) (https://api.gdc.cancer.gov/data/254f697d-310d-4d7d-a27b-27fbf767a834).Gene-specific read counts were calculated using featureCounts (Liao et al., 2014) with parameters ‘-M -O–fraction -Q 30’. Quality of cells were then assessed based on three metrics step by step: (1) The number of total counts per cell (library size); (2) The number of detected genes per cell; (3) The proportion of mitochondrial gene counts. Low-quality cells were filtered if the library size or the number of detected genes was below the median of all cells minus 3 × the median absolute deviation. We also removed all cells with the proportion of mitochondrial gene counts higher than 10%. The size factor for each cell was computed using a pooling strategy implemented in the R function computeSumFactors in scran package. Normalized counts/expression were then computed by dividing the counts for each cell by the size factor for that cells. A log2 transformation was applied to normalized counts. A total of 7,099 cells were retained for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: UMI_counts_Droplet.mtx.gz: MTX file include UMI counts for all 10X samples; UMI_counts_Droplet_genes.tsv: tab-delimited plain text file containing gene annotation; UMI_counts_Droplet_cellinfo.tsv: tab-delimited text file containing cell information for 10X samples; UMI_counts_Droplet_barcodes.tsv: plain text file containing 10X data barcodes; read_counts_Smartseq2.csv: comma-delimited file include read counts for all Smartseq2 samples; gene_info_Smartseq2.tsv: tab-delimited file containing cell information for Smartseq2 samples; cell_info_Smartseq2.tsv: tab-delimited text file containing Smartseq2 cell information

source_name: CD45+ cells

extract_protocol:
Chromium 3' V2
Based on FACS analysis, single CD45+ cells (anti-human CD45, HI30, eBiocience) of the samples of patients DSF22, DSF27, DSM22, DSM27, DSA12, DSN09, DSD15, DEJ08, DEJ10 and DEJ16 were sorted into 1.5 mL low binding tubes (Eppendorf) with 50 mL sorting buffer for droplet-based scRNA-seq, or into wells of 96-well plates (Axygen) for plated-based scRNA-seq, prepared with lysis buffer which contained 1 μL 10 mM dNTP mix (Fermentas), 1 μL 10 μM Oligo dT primer, 1.9 μL 1% Triton X-100 (Sigma) plus 0.1 μL 40 U/μl RNase Inhibitor (Takara). The sealed plates were stored frozen at −80°C. For droplet-based scRNA-seq, single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (10x Genomics, Pleasanton) as per the manufacturer’s protocol (Zheng et al., 2017a). The loaded cell numbers of DSN09, DSD15, DEJ08 and DEJ10 were 10,000 for each sample, and the cell numbers of DEJ16 was 5,000 (Table S2). The cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 3′ adaptor and sample index attachment. Libraries were sequenced on an Illumina Hiseq 4000. For plated-based scRNA-seq, reverse transcription and transcriptome amplifications were performed following SMART-seq2 protocol. The amplified cDNA products were purified with 1x Agencourt XP DNA beads (Beckman), Following the first round of beads purification, the cDNA of each single cell was quantified with qPCR of GAPDH, and fragment analysis (using fragment analyzer AATI). The DNA products with high quality were further cleaned with 0.5x Agencourt XP DNA beads (Beckman) to eliminate short fragments (less than 500 bp). The concentration of each sample was then quantified with Qubit HsDNA kits (Invitrogen). The libraries were constructed with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech).

tag: disease state

value: HCC

tag: individual

value: patient DEJ16

value: liver

value: CD45+ cells


title: DEJ16_ascites

value: ascites

tag: cell type


title: DEJ16_lymphnode

value: lymphnode


title: A1022M


title: DEJ10_tumorEdge

value: patient DEJ10

value: tumor


title: DEJ10_tumorCore


title: A1014L

value: thigh


title: DEJ10_liver


title: DEJ10_ascites


title: DEJ08_tumorCore

value: patient DEJ08


title: DEJ08_tumorEdge


title: DEJ08_liver


title: DEJ08_blood

value: blood


title: DSD15_liver

value: patient DSD15


title: DSN09_tumor_droplet

value: patient DSN09


title: DSN09_lymphnode_droplet


title: DSD15_tumor


title: DSD15_lymphnode


title: DSN09_blood_droplet


title: DSD15_blood


title: DSN09_liver_droplet


title: DSN09_ascites_droplet


title: DSN09_tumor_smartseq2

extract_protocol:
SMART-seq2
Based on FACS analysis, single CD45+ cells (anti-human CD45, HI30, eBiocience) of the samples of patients DSF22, DSF27, DSM22, DSM27, DSA12, DSN09, DSD15, DEJ08, DEJ10 and DEJ16 were sorted into 1.5 mL low binding tubes (Eppendorf) with 50 mL sorting buffer for droplet-based scRNA-seq, or into wells of 96-well plates (Axygen) for plated-based scRNA-seq, prepared with lysis buffer which contained 1 μL 10 mM dNTP mix (Fermentas), 1 μL 10 μM Oligo dT primer, 1.9 μL 1% Triton X-100 (Sigma) plus 0.1 μL 40 U/μl RNase Inhibitor (Takara). The sealed plates were stored frozen at −80°C. For droplet-based scRNA-seq, single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (10x Genomics, Pleasanton) as per the manufacturer’s protocol (Zheng et al., 2017a). The loaded cell numbers of DSN09, DSD15, DEJ08 and DEJ10 were 10,000 for each sample, and the cell numbers of DEJ16 was 5,000 (Table S2). The cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 3′ adaptor and sample index attachment. Libraries were sequenced on an Illumina Hiseq 4000. For plated-based scRNA-seq, reverse transcription and transcriptome amplifications were performed following SMART-seq2 protocol. The amplified cDNA products were purified with 1x Agencourt XP DNA beads (Beckman), Following the first round of beads purification, the cDNA of each single cell was quantified with qPCR of GAPDH, and fragment analysis (using fragment analyzer AATI). The DNA products with high quality were further cleaned with 0.5x Agencourt XP DNA beads (Beckman) to eliminate short fragments (less than 500 bp). The concentration of each sample was then quantified with Qubit HsDNA kits (Invitrogen). The libraries were constructed with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech).


title: DSN09_liver_smartseq2


title: DSN09_lymphnode_smartseq2


title: DEJ16_tumorEdge


title: DSN09_blood_smartseq2


title: DSA12_tumor

value: patient DSA12


title: DSA12_blood


title: DSA12_liver


title: DSM27_tumor

value: patient DSM27


title: DSM27_liver


title: DSM27_blood


title: DSM22_tumor

value: patient DSM22


title: DSF22_liver

value: patient DSF22


title: DSM22_blood

value: HCC


title: DSF27_tumor

value: patient DSF27


title: DSF22_tumor


title: DSF27_blood


title: DSF22_blood


title: DSD15_ascites


title: MAX_181019_raft17_A01_G001_0248-19

status: Public on Nov 02 2019

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
microRaft_processed.csv
SG35_142

data_processing:
MaGeCk was used to process data for lentiCRISPR bulk samples to quantify sgRNA abundances.
Targeted microRaft data was processed with CRaftID software (https://github.com/YeoLab/CRaftID)
Genome_build: hg19
Supplementary_files_format_and_content: [all.count_normalized.csv]  Table of normalized sgRNA counts (one column per sample) for bulk samples
Supplementary_files_format_and_content: [microRaft_processed.csv]   Read counts and sgRNA insert identified for each microRaft library. Libraries where no sgRNA insert were detected (sequencing failure) are not included in this file.

source_name: human embryonic kidney

growth_protocol: DMEM + 10%FBS

extract_protocol:
Quick Extract (Lucigen QE09050): Protocol according to manufacturers instructions.
[lentiCRISPR bulk]  gDNA was extracted and sonicated to ~1000bp. sgRNA containing fragments were recovered with biotinylated RNA probes targeting the flanking region on the lenticrispr v2 backbone and pulled down with streptavidin beads. gDNA fragments were PCRed first with primers flanking the sgRNA and second with Illumina sequencing adapters.
[targeted microRaft]  gDNA was extracted with in QuickExtract buffer and input into a PCR reaction containing barcoded primers that flank the gRNA insert. This PCR was cleaned up over a DNA purification column, and uniquely-barcoded products were pooled into a second PCR reaction using illumina sequencing primers.

treatment_protocol: 500 uM sodium arsenite, 1 hr

value: Colony from RBP-lentiCRISPR infected HEK293T

tag: time point

value: Day 10

tag: treatment

value: 500 um Sodium Arsenite, 1 hr

tag: isolation

value: targeted microRaft


title: MAX_181019_raft18_A01_G001_0204-15

description:
microRaft_processed.csv
SG23_131

tag: cell line


title: MAX_181019_raft17_A01_G001_0184-84

description:
microRaft_processed.csv
SG17_131


title: MAX_181019_raft17_A01_G001_0041-83

description:
microRaft_processed.csv
SG16_144


title: MAX_181019_raft17_A01_G001_0290-46

description:
microRaft_processed.csv
SG35_144


title: MAX_181019_raft15_A01_G001_0318-97

description:
microRaft_processed.csv
SG15_133


title: MAX_181019_raft18_A01_G001_0050-36

description:
microRaft_processed.csv
SG36_145


title: MAX_181019_raft15_A01_G001_0141-48

description:
microRaft_processed.csv
SG34_144


title: MAX_181019_raft15_A01_G001_0124-89

description:
microRaft_processed.csv
SG22_143


title: MAX_181019_raft15_A01_G001_0226-51

description:
microRaft_processed.csv
SG15_131


title: MAX_181019_raft14_A01_G001_0226-64

description:
microRaft_processed.csv
SG41_132


title: MAX_181019_raft12_A01_G001_0249-12

description:
microRaft_processed.csv
SG40_132


title: MAX_181019_raft12_A01_G001_0202-27

description:
microRaft_processed.csv
SG27_131


title: MAX_181019_raft15_A01_G001_0106-27

description:
microRaft_processed.csv
SG22_142


title: DSN09_ascites_smartseq2

value: ascites

value: CD45+ cells


title: MAX_181019_raft12_A01_G001_0046-52

description:
microRaft_processed.csv
SG27_130


title: MAX_181019_raft12_A01_G001_0026-89

description:
microRaft_processed.csv
SG35_145


title: MAX_181019_raft11_A01_G001_0072-92

description:
microRaft_processed.csv
SG14_142


title: MAX_181019_raft9_A01_G001_0202-42

description:
microRaft_processed.csv
SG38_132


title: MAX_181019_raft9_A01_G001_0301-16

description:
microRaft_processed.csv
SG36_143


title: MAX_181019_raft9_A01_G001_0205-86

description:
microRaft_processed.csv
SG11_133


title: MAX_181019_raft15_A01_G001_0187-19

description:
microRaft_processed.csv
SG22_145


title: MAX_181019_raft8_A01_G001_0305-29

description:
microRaft_processed.csv
SG32_142


title: MAX_181019_raft11_A01_G001_0069-5

description:
microRaft_processed.csv
SG34_133


title: MAX_181019_raft8_A01_G001_0196-14

description:
microRaft_processed.csv
SG31_133


title: MAX_181019_raft19_A01_G001_0144-87

description:
microRaft_processed.csv
SG39_143


title: MAX_181019_raft8_A01_G001_0058-32

description:
microRaft_processed.csv
SG37_144


title: MAX_181019_raft7_A01_G001_0097-5

description:
microRaft_processed.csv
SG29_130


title: MAX_181019_raft6_A01_G001_0316-84

description:
microRaft_processed.csv
SG31_130


title: MAX_181019_raft8_A01_G001_0128-57

description:
microRaft_processed.csv
SG28_145


title: MAX_181019_raft7_A01_G001_0098-46

description:
microRaft_processed.csv
SG34_131


title: MAX_181019_raft6_A01_G001_0166-42

description:
microRaft_processed.csv
SG34_143


title: MAX_181019_raft6_A01_G001_0143-38

description:
microRaft_processed.csv
SG33_133


title: MAX_181019_raft6_A01_G001_0152-50

description:
microRaft_processed.csv
SG34_142


title: MAX_181019_raft6_A01_G001_0109-12

description:
microRaft_processed.csv
SG9_130


title: MAX_181019_raft1_A01_G001_0089-14

description:
microRaft_processed.csv
SG33_143


title: MAX_181019_raft2_A01_G001_0080-7

description:
microRaft_processed.csv
SG6_142


title: MAX_181019_raft5_A01_G001_0035-73

description:
microRaft_processed.csv
SG25_130


title: MAX_181019_raft1_A01_G001_0039-58

description:
microRaft_processed.csv
SG20_142


title: GSMO8

description:
single-cell sequencing
GSMO_Working.rds

value: Cerebellum

value: Postnatal age 15


title: MAX_181019_raft9_A01_G001_0055-29

description:
microRaft_processed.csv
SG34_145


title: MAX_181019_raft17_A01_G001_0054-83

description:
microRaft_processed.csv
SG16_145


title: MAX_181019_raft17_A01_G001_0282-75

description:
microRaft_processed.csv
SG38_143


title: MAX_181019_raft6_A01_G001_0200-51

description:
microRaft_processed.csv
SG10_144


title: MAX_181019_raft4_A01_G001_0280-29

description:
microRaft_processed.csv
SG4_144


title: MAX_181019_raft17_A01_G001_0180-59

description:
microRaft_processed.csv
SG17_130


title: MAX_181019_raft11_A01_G001_0075-52

description:
microRaft_processed.csv
SG37_143


title: MAX_181019_raft9_A01_G001_0059-26

description:
microRaft_processed.csv
SG11_130


title: MAX_181019_raft7_A01_G001_0191-69

description:
microRaft_processed.csv
SG30_142


title: MAX_181019_raft15_A01_G001_0314-17

description:
microRaft_processed.csv
SG15_132


title: MAX_181019_raft2_A01_G001_0227-57

description:
microRaft_processed.csv
SG7_133


title: MAX_181019_raft2_A01_G001_0194-59

description:
microRaft_processed.csv
SG7_132


title: MAX_181019_raft5_A01_G001_0210-72

description:
microRaft_processed.csv
SG26_143


title: MAX_181019_raft10_A01_G001_0084-38

description:
microRaft_processed.csv
SG12_145


title: MAX_181019_raft7_A01_G001_0212-99

description:
microRaft_processed.csv
SG30_143


title: MAX_181019_raft7_A01_G001_0319-36

description:
microRaft_processed.csv
SG30_144


title: MAX_181019_raft9_A01_G001_0297-68

description:
microRaft_processed.csv
SG36_142


title: MAX_181019_raft13_A01_G001_0135-29

description:
microRaft_processed.csv
SG37_145


title: MAX_181019_raft17_A01_G001_0236-36

description:
microRaft_processed.csv
SG35_133


title: MAX_181019_raft19_A01_G001_0012-16

description:
microRaft_processed.csv
SG23_133


title: MAX_181019_raft17_A01_G001_0227-78

description:
microRaft_processed.csv
SG17_132


title: MAX_181019_raft13_A01_G001_0093-13

description:
microRaft_processed.csv
SG32_144


title: MAX_181019_raft5_A01_G001_0194-58

description:
microRaft_processed.csv
SG26_142


title: MAX_181019_raft1_A01_G001_0183-17

description:
microRaft_processed.csv
SG33_132


title: MAX_181019_raft6_A01_G001_0125-47

description:
microRaft_processed.csv
SG9_131


title: MAX_181019_raft2_A01_G001_0150-54

description:
microRaft_processed.csv
SG33_145


title: MAX_181019_raft4_A01_G001_0163-37

description:
microRaft_processed.csv
SG4_142


title: MAX_181019_raft5_A01_G001_0157-9

description:
microRaft_processed.csv
SG25_132


title: MAX_181019_raft4_A01_G001_0114-94

description:
microRaft_processed.csv
SG3_131


title: MAX_181019_raft9_A01_G001_0133-70

description:
microRaft_processed.csv
SG11_131


title: MAX_181019_raft4_A01_G001_0260-30

description:
microRaft_processed.csv
SG4_143


title: MAX_181019_raft6_A01_G001_0227-16

description:
microRaft_processed.csv
SG30_145


title: MAX_181019_raft7_A01_G001_0188-13

description:
microRaft_processed.csv
SG29_133


title: MAX_181019_raft12_A01_G001_0292-60

description:
microRaft_processed.csv
SG27_133


title: MAX_181019_raft5_A01_G001_0081-87

description:
microRaft_processed.csv
SG25_131


title: MAX_181019_raft15_A01_G001_0096-86

description:
microRaft_processed.csv
SG21_133


title: MAX_181019_raft2_A01_G001_0333-21

description:
microRaft_processed.csv
SG8_145


title: MAX_181019_raft16_A01_G001_0057-28

description:
microRaft_processed.csv
SG16_142


title: MAX_181019_raft8_A01_G001_0025-45

description:
microRaft_processed.csv
SG35_143


title: MAX_181019_raft7_A01_G001_0169-63

description:
microRaft_processed.csv
SG36_132


title: MAX_181019_raft4_A01_G001_0132-56

description:
microRaft_processed.csv
SG3_133


title: DEJ16_tumorCore

value: patient DEJ16

value: tumor


title: MAX_181019_raft10_A01_G001_0178-9

description:
microRaft_processed.csv
SG13_130


title: MAX_181019_raft5_A01_G001_0167-39

description:
microRaft_processed.csv
SG25_133


title: MAX_181019_raft19_A01_G001_0067-38

description:
microRaft_processed.csv
SG24_142


title: MAX_181019_raft10_A01_G001_0047-27

description:
microRaft_processed.csv
SG12_144


title: MAX_181019_raft16_A01_G001_0133-57

description:
microRaft_processed.csv
SG16_143


title: A1020LM

value: skin

value: melanocytes

value: arm


title: MAX_181019_raft6_A01_G001_0321-20

description:
microRaft_processed.csv
SG31_131


title: MAX_181019_raft3_A01_G001_0245-77

description:
microRaft_processed.csv
SG5_133


title: MAX_181019_raft4_A01_G001_0032-16

description:
microRaft_processed.csv
SG3_130


title: MAX_181019_raft14_A01_G001_0083-1

description:
microRaft_processed.csv
SG21_130


title: MAX_181019_raft15_A01_G001_0217-69

description:
microRaft_processed.csv
SG15_130


title: MAX_181019_raft14_A01_G001_0177-8

description:
microRaft_processed.csv
SG21_131


title: MAX_181019_raft6_A01_G001_0216-55

description:
microRaft_processed.csv
SG10_145


title: MAX_181019_raft2_A01_G001_0155-58

description:
microRaft_processed.csv
SG7_131


title: MAX_181019_raft2_A01_G001_0145-84

description:
microRaft_processed.csv
SG36_144


title: MAX_181019_raft18_A01_G001_0138-76

description:
microRaft_processed.csv
SG23_130


title: MAX_181019_raft10_A01_G001_0215-15

description:
microRaft_processed.csv
SG35_131


title: Day7_rafts11-20_technical_rep2

description:
all.count_normalized.csv
EWG22_S33_L004_R1_001

extract_protocol:
DNeasy Blood & Tissue (Qiagen 69504): Protocol according to manufacturers instructions.
[lentiCRISPR bulk]  gDNA was extracted and sonicated to ~1000bp. sgRNA containing fragments were recovered with biotinylated RNA probes targeting the flanking region on the lenticrispr v2 backbone and pulled down with streptavidin beads. gDNA fragments were PCRed first with primers flanking the sgRNA and second with Illumina sequencing adapters.
[targeted microRaft]  gDNA was extracted with in QuickExtract buffer and input into a PCR reaction containing barcoded primers that flank the gRNA insert. This PCR was cleaned up over a DNA purification column, and uniquely-barcoded products were pooled into a second PCR reaction using illumina sequencing primers.

value: RBP-lentiCRISPR infected HEK293T

value: lentiCRISPR bulk


title: MAX_181019_raft2_A01_G001_0249-18

description:
microRaft_processed.csv
SG8_143


title: MAX_181019_raft5_A01_G001_0263-40

description:
microRaft_processed.csv
SG26_144


title: Day7_rafts11-20_technical_rep1

description:
all.count_normalized.csv
EWG21_S32_L004_R1_001


title: Day7_rafts1-10_technical_rep1

description:
all.count_normalized.csv
EWG19_S16_L003_R1_001


title: Day0_technical_rep2

description:
all.count_normalized.csv
EWG18_S15_L003_R1_001


title: MAX_181019_raft18_A01_G001_0210-85

description:
microRaft_processed.csv
SG42_132


title: Day0_technical_rep1

description:
all.count_normalized.csv
EWG17_S14_L003_R1_001


title: Day7_rafts1-10_technical_rep2

description:
all.count_normalized.csv
EWG20_S17_L003_R1_001


title: MAX_181019_raft1_A01_G001_0260-5

description:
microRaft_processed.csv
SG33_131


title: BT549-Vector-Rep2

status: Public on Jun 04 2019

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs.
RNA-seq reads were mapped against hg19 using STAR aligner.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include baseMean, lfcSE, stat etc

source_name: BT-549 cells

growth_protocol: Cells were cultured in DMEM/F-12 medium (Life Technologies, Grand Island, NY) supplemented with 10% FBS (Thermo Scientific Gibco, Waltham, MA) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy kit (Qiagen, Germantown, MD). On-column DNase treatment was given following the procedure provided by the manufacturer.
The library was prepared using Illumina TruSeq stranded total RNA kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

value: control


title: MCF7-NTshRNA-Rep1

source_name: MCF7 cells

value: MCF7 (HTB-22)


title: BT549-Vector-Rep1


title: MCF7-PTENshRNA-Rep2

value: PTEN knock-down


title: BT549-PTEN-Rep1

value: PTEN over-expressed


title: MCF7-PTENshRNA-Rep1


title: BT549-PTEN-Rep2


title: MCF7-PTENshRNA-PolII-Rep2

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs.
Reads were aligned against hg19 by using Bowtie2.
BAM files were normalized by depth after removal of PCR duplicates and blacklisted regions.
For generating heatmap and metagene plots, ngs.plot program was used.
Genome_build: hg19
Supplementary_files_format_and_content: Library normalized bigWig files (Rep1 and Rep2 merged) were provided.

extract_protocol:
Chromatin was immunoprecipitated using RNA Pol II antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. Input DNA isolated using the phenol-chloroform method.
10ng precipitated DNA was used to prepare library using Illumina TruSeq ChIP library preparation kit.

value: Rpb1 (D8L4Y) (Cell Signaling cat# 14958)


title: MAX_181019_raft1_A01_G001_0004-8

description:
microRaft_processed.csv
SG20_145

value: Colony from RBP-lentiCRISPR infected HEK293T

value: Day 10

value: 500 um Sodium Arsenite, 1 hr

value: targeted microRaft


title: MCF7-PTENshRNA-PolII-Rep1


title: MCF7-NTshRNA-PolII-Rep1


title: MCF7-NTshRNA-Input-Rep2


title: MCF7-NTshRNA-PolII-Rep2


title: MCF7-PTENshRNA-Input-Rep2


title: MCF7-PTENshRNA-Input-Rep1


title: MCF7-NTshRNA-Input-Rep1


title: MAX_181019_raft2_A01_G001_0084-48

description:
microRaft_processed.csv
SG40_143


title: BT549-PTEN-TET-Input

value: TET


title: BT549-PTEN-TET-PolII


title: BT549-PTEN-PolII-Rep2


title: BT549-PTEN-PolII-Rep1


title: BT549-PTEN-Input-Rep1


title: Neurosphere cultures transfected with miRNA-335 antisense (miR-335KO) - rep1

status: Public on Jul 31 2019

type: RNA

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

description: Array images were processed using CodeLink system software and global median normalization was used to generate normalized expression values

hyb_protocol: CodeLink protocol

scan_protocol: CodeLink protocol

label: 2 ug total RNA was used to generate biotin-labeled cRNA  amplification protocol using the CodeLink iExpress Kit (Applied Microarray, Tempe, AZ).

source_name: Neurosphere cultures; transfected with 2'-O-methyl (2'OMe)-base modified Treatment (2' O Me-335)

label_protocol: Labeled cRNA was applied to CodeLink (Mouse) genome arrays for an 18 h hybridization followed by washing, staining, and scanning as per the CodeLink protocol.

growth_protocol: We isolated cortical neuroepithelium from embryonic day 12.5 mouse fetuses (C57BL/6) from the dorsal telecephalic vesicles and cultured as neurosphere culture.  Extreme care was taken to avoid structural precursors of hippocampus and striatum. Precursor cultures were established at an initial density of 106 cells in serum-free mitogenic media DMEM/F12 (catalog#11330-032; Invitrogen, Carlsbad, CA), 20 ng/ml bFGF (basic fibroblast growth factor; catalog #13256-029; Invitrogen), 20 ng/ml hEGF (human epidermal growth factor; catalog #53003-018; Invitrogen), 0.15 ng/ml LIF (leukemia inhibitory factor; catalog #L200; Alomone Labs, Jerusalem, Israel), ITS-X (insulin-transferrin-selenium-X) supplement (catalog #51500-056; Invitrogen), 0.85 Us/ml heparin (catalog #15077-019; Invitrogen), and 20 nM progesterone (catalog #P6149; Sigma, St. Louis, MO). Cells treated with antisense KO reagents for microRNA miR-335 and control for 24

extract_protocol: Total RNA was isolated from control and Treated samples Trizol method (#15596-026 Invitrogen)

treatment_protocol: GD 12.5 mice were sacrificed and precursor of cortical neural epithelium was isolated and grown as Neurospheres

tag: C57Bl/6 Mice sacrified at GD12.5


title: Neurosphere cultures transfected with miRNA-335 antisense (miR-335KO) - rep3

data_processing: Array images were processed using CodeLink system software and global median normalization was used to generate normalized expression values

label: 2 ug total RNA was used to generate biotin-labeled cRNA amplification protocol using the CodeLink iExpress Kit (Applied Microarray, Tempe, AZ).

growth_protocol: We isolated cortical neuroepithelium from embryonic day 12.5 mouse fetuses (C57BL/6) from the dorsal telecephalic vesicles and cultured as neurosphere culture. Extreme care was taken to avoid structural precursors of hippocampus and striatum. Precursor cultures were established at an initial density of 106 cells in serum-free mitogenic media DMEM/F12 (catalog#11330-032; Invitrogen, Carlsbad, CA), 20 ng/ml bFGF (basic fibroblast growth factor; catalog #13256-029; Invitrogen), 20 ng/ml hEGF (human epidermal growth factor; catalog #53003-018; Invitrogen), 0.15 ng/ml LIF (leukemia inhibitory factor; catalog #L200; Alomone Labs, Jerusalem, Israel), ITS-X (insulin-transferrin-selenium-X) supplement (catalog #51500-056; Invitrogen), 0.85 Us/ml heparin (catalog #15077-019; Invitrogen), and 20 nM progesterone (catalog #P6149; Sigma, St. Louis, MO). Cells treated with antisense KO reagents for microRNA miR-335 and control for 24


title: Neurosphere cultures transfected with nonsense control - rep1

source_name: Neurosphere cultures; transfected with 2'-O-methyl (2'OMe)-base modified control (2' O Me-EGFP)


title: Neurosphere cultures transfected with nonsense control - rep2


title: Neurosphere cultures transfected with nonsense control - rep3


title: Neurosphere cultures transfected with miRNA-335 antisense (miR-335KO) - rep2


title: BT549-Vector-Input-Rep2


title: MCF7-NTshRNA-Rep2


title: BT549-Vector-Input-Rep1


title: BT549-Vector-PolII-Rep2


title: CD64Cre/+  x Irf8fl/fl brain

status: Public on Mar 27 2019

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: CD64Cre/+  x Irf8fl/fl brain of CD64Cre/+ x Irf8fl/fl mice

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq
Demultiplexed data was then processed using the Cell Ranger count pipeline
8bp I7 sample barcode
26bp read1 (16bp Chromium barcode and 10bp UMI)
98bp read2 (transcript)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output CellRanger Count) for each sample

source_name: brain

extract_protocol: All Methods listed in Van Hove et al.  A single-cell atlas of non-parenchymal brain macrophages reveals unique transcriptional identities that are shaped by ontogeny and tissue environment.  Nature Neuroscience. 2019.

tag: genotype/variation

value: CD64Cre/+  x Irf8fl/fl

value: brain

tag: strain

value: CD64Cre/+ x Irf8fl/fl

tag: platform

value: 10x  Genomics

tag: number of cells


title: Standard protocol choroid plexus

description: Standard protocol choroid plexus of C57BL/6JRj mice

source_name: choroid plexus

tag: protocol

value: Standard protocol

tag: tissue

value: choroid plexus

value: 10x Genomics


title: Standard protocol dura

description: Standard protocol dura of C57BL/6JRj mice

source_name: dura mater

value: dura


title: Actinomycin D protocol choroid plexus

description: Actinomycin D protocol choroid plexus of C57BL/6JRj mice

value: Actinomycin D protocol


title: Actinomycin D protocol dura

description: Actinomycin D protocol dura of C57BL/6JRj mice


title: Adult satellite cells RNA-Seq rep3 [Hind_C]

status: Public on Feb 13 2019

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing TPM expression estimates calculated by RSEM

source_name: Adult satellite cells RNA-Seq

extract_protocol:
RNA was isolated from sorted ZsGreen+ cells using Picopure kit (Thermoscientific) according to manufacturer's instructions.
Libraries were prepared using Illumina standard protocols

tag: age

value: 3 months-old

value: Tibialis anterior

value: hindlimb-derived muscle stem cells


title: Adult satellite cells RNA-Seq rep2 [Hind_B]


title: Adult satellite cells RNA-Seq rep1 [Hind_A]


title: Trisomic, Lymphoblast, Female, 20 Year old, replicate 2

status: Public on Jul 29 2016

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F20YR_2C

data_processing:
Basecalls performed using bcl2fastq_v1.8.4 with the following options (--mismatches 1 fastq-cluster-count 0 )
FASTQC v0.11.2 was used to determine sequence quality
fastqc-mcf was used to trim low quality bases, adapters and N content from 3’ end (<q10). Removed reads that were shorter than 30bp after trimming
Reads were mapped using Tophat2 (v2.0.13) with the following options (--b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand)
Reads with MAPQ > 10 were kept using Samtools (v0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Raw count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample

source_name: Lymphoblastoid

growth_protocol: Cells were passaged in DMEM with 10% FBS

extract_protocol:
RNA was prepared using the RNeasy Kit from Qiagen
Libraries were prepared using the Truseq Stranded Kit from Illumina

tag: condition

value: Trisomic

tag: gender

value: Female

value: 20 Year old

tag: batch


title: Disomic, Lymphoblast, Female, 18 Year old, replicate 2

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F18YR_2C

value: Disomic

value: 18 Year old


title: Trisomic, Lymphoblast, Female, 13 Year old, replicate 2

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F13YR_2B

value: 13 Year old


title: Trisomic, Lymphoblast, Female, 13 Year old, replicate 1

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F13YR_1B


title: Trisomic, Lymphoblast, Female, 9 Year old, replicate 2

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F9YR_2A

value: 9 Year old


title: Trisomic, Lymphoblast, Female, 9 Year old, replicate 1

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F9YR_1A


title: BT549-PTEN-Input-Rep2

value: PTEN over-expressed

tag: chip antibody


title: Disomic, Lymphoblast, Female, 14 Year old, replicate 2

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F14YR_2B

value: 14 Year old


title: Trisomic, Fibroblast, Female, 19 Year old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F19YR_2

source_name: Fibroblast

value: 19 Year old


title: Trisomic, Fibroblast, Male, 21 Year old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M21YR_2

value: Male

value: 21 Year old


title: Disomic, Lymphoblast, Female, 7 Year old, replicate 2

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F7YR_2A

value: 7 Year old


title: Trisomic, Fibroblast, Female, 14 Year old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F14YR_1


title: Trisomic, Fibroblast, Female, 14 Year old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F14YR_2


title: BT549-Vector-PolII-Rep1

value: control

value: Rpb1 (D8L4Y) (Cell Signaling cat# 14958)


title: CD64+/+ x Irf8fl/fl brain

description: CD64+/+ x Irf8fl/fl brain of CD64+/+ x Irf8fl/fl mice

value: CD64+/+ x Irf8fl/fl

value: brain

value: 10x Genomics


title: Trisomic, Fibroblast, Male, 1 Year old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M1YR_2

value: Trisomic

value: 1 Year old


title: Trisomic, Fibroblast, Female, 3 Day old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F3DA_1

value: Female

value: 3 Day old


title: Trisomic, Fibroblast, Male, 1 Year old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M1YR_1


title: Trisomic, Fibroblast, Male, 2 Year old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M2YR_2

value: 2 Year old


title: Trisomic, Fibroblast, Male, 2 Year old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M2YR_1


title: Disomic, Fibroblast, Male, 20 Year old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M20YR_2

value: Disomic

value: 20 Year old


title: Trisomic, Lymphoblast, Female, 20 Year old, replicate 1

description:
polyA RNA from Trisomic Lymphoblastoid cells
T21_F20YR_1C


title: Trisomic, Fibroblast, Female, 3 Day old, replicate 2

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F3DA_2


title: Disomic, Fibroblast, Female, 11 Year old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F11YR_2

value: 11 Year old


title: Disomic, Fibroblast, Male, 19 Year old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M19YR_2

value: 19 Year old


title: Disomic, Fibroblast, Male, 1 Year old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M1YR_1

value: Male


title: Disomic, Fibroblast, Male, 19 Year old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M19YR_1


title: Disomic, Lymphoblast, Female, 18 Year old, replicate 1

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F18YR_1C

value: 18 Year old


title: Disomic, Fibroblast, Female, 2 Year old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F2YR_1


title: Disomic, Fibroblast, Female, 11 Year old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F11YR_1


title: Disomic, Fibroblast, Female, 2 Year old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F2YR_2


title: Disomic, Fibroblast, Male, 1 Year old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M1YR_2


title: Disomic, Fibroblast, Female, 2 Day old, replicate 2

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F2DA_2

value: 2 Day old


title: Disomic, Fibroblast, Female, 2 Day old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_F2DA_1


title: Trisomic, Fibroblast, Male, 21 Year old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_M21YR_1

value: 21 Year old


title: Disomic, Lymphoblast, Female, 7 Year old, replicate 1

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F7YR_1A

value: 7 Year old


title: Disomic, Lymphoblast, Female, 14 Year old, replicate 1

description:
polyA RNA from Disomic Lymphoblastoid cells
D21_F14YR_1B

value: 14 Year old


title: Disomic, T cells, Female, 38 Year old [D21_M38YRB]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_M38YRB

source_name: T cells

extract_protocol:
RNA was prepared using the AllPrep Kit from Qiagen
Libraries were prepared using the Truseq Stranded Kit from Illumina

value: C


title: Disomic, T cells, Female, 22 Year old [D21_F22YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_F22YR


title: Trisomic, Fibroblast, Female, 19 Year old, replicate 1

description:
polyA RNA from Trisomic Fibroblastoid cells
TS_F19YR_1


title: Trisomic, T cells, Female, 13 Year old [T21_M13YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M13YR


title: Trisomic, T cells, Female, 33 Year old [T21_M33YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M33YR


title: Disomic, T cells, Female, 31 Year old [D21_F31YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_F31YR


title: Trisomic, T cells, Female, 12 Year old [T21_M12YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M12YR


title: Trisomic, T cells, Female, 1 Year old [T21_M1YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M1YR


title: Disomic, T cells, Female, 29 Year old [D21_F29YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_F29YR


title: Trisomic, T cells, Male, 4 Year old [T21_F4YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_F4YR


title: Disomic, T cells, Male, 31 Year old [D21_M31YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_M31YR


title: Disomic, Fibroblast, Male, 20 Year old, replicate 1

description:
polyA RNA from Disomic Fibroblastoid cells
DS_M20YR_1


title: Disomic, T cells, Female, 17 Year old [D21_F17YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_F17YR


title: Trisomic, T cells, Female, 13 Year old [T21_M13YRB]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M13YRB


title: Disomic, Monocyte, Male, 31 Year old [D21_F31YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_F31YR

source_name: Monocyte

value: B


title: Trisomic, T cells, Female, 45 Year old [T21_F45YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_F45YR

value: Trisomic


title: Disomic, Monocyte, Male, 38 Year old [D21_M38YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_M38YR


title: Trisomic, T cells, Female, 13 Year old [T21_M13YRA]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M13YRA


title: Disomic, T cells, Female, 38 Year old [D21_M38YRA]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
D21_M38YRA


title: Trisomic, Monocyte, Female, 33 Year old [T21_M33YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M33YR


title: Trisomic, T cells, Male, 32 Year old [T21_F32YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_F32YR


title: Trisomic, Monocyte, Female, 4 Year old [T21_F4YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_F4YR


title: Disomic, Monocyte, Male, 22 Year old [D21_F22YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_F22YR


title: Trisomic, Monocyte, Male, 13 Year old [T21_M13YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M13YR


title: Trisomic, Monocyte, Male, 12 Year old [T21_M12YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M12YR


title: Trisomic, Monocyte, Male, 14 Year old [T21_M14YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M14YR


title: Trisomic, Monocyte, Male, 1 Year old [T21_M1YR_5312016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M1YR


title: Trisomic, Monocyte, Female, 13 Year old [T21_M13YRB_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M13YRB

value: A


title: Trisomic, Monocyte, Female, 13 Year old [T21_M13YRA_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_M13YRA


title: Trisomic, Monocyte, Female, 45 Year old [T21_F45YR_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_F45YR


title: Trisomic, Monocyte, Female, 32 Year old [T21_F32YR_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
T21_F32YR


title: Disomic, Monocyte, Male, 38 Year old [D21_M38YR_5112016]


title: Disomic, Monocyte, Male, 31 Year old [D21_M31YR_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_M31YR


title: Disomic, Monocyte, Female, 29 Year old [D21_F29YR_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_F29YR


title: Disomic, Monocyte, Female, 17 Year old [D21_F17YR_5112016]

description:
polyA RNA from Monocyte cells
HTSeq_in_mon_counts.txt.gz
D21_F17YR


title: Trisomic, T cells, Female, 14 Year old [T21_M14YR]

description:
polyA RNA from T cells
HTSeq_in_tcells_counts.txt.gz
T21_M14YR


title: DSE001 RNA-S1

status: Public on Dec 06 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
Minimal glycolysis
Sequencing was performed using Illumina HiSeq 2500 and carried out by Basecelar (Leiden, The Netherlands).  Dataset of 51 bp single reads of at least 1-Gb were generated. The genome sequence of CEN.PK113-7D (Nijkamp JF et al  (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact 11(36): doi:10.1186/1475-2859-11-36.) was used for all analyses.

data_processing:
At Baseclear FASTQ sequence reads were generated using Illumina Casava pipeline version 1.8.2
Quality assesment was based on data passing the Ilumina Chastity filtering. Subsequently, reads containing adapters and/or PhiX control signal were removed using an in-house (At Baseclear) filtering protocol.
RNA-seq reads were mapped with BWA (version 0.5.9-r16) to S. cerevisiae CEN.PK113-7D whole genome
samtools (version 0.1.7-r510) was used to convert the BWA sam output to sorted bam format
cuffdiff, from the cufflinks packages (version 1.0.3), was used to calculate the differential expression between the CEN.PK113-7D reference strain and the Minimal glycolysis strain IMX372
genome build: ASM26988v1

organism: Saccharomyces cerevisiae

source_name: Aerobic batch fermentor

growth_protocol: Growth experiments were conducted in synthetic medium containing salts, trace elements and vitamins, prepared and sterilized as described previously (Verduyn C, Postma E, Scheffers WA & Vandijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeasts - A continuous culture study on the regulation of respiration and alcoholic fermentation. Yeast 8(7):501-517). Glucose was added to a final concentration of 20.0 g L-1. Aerobic batch cultivations were performed in 2 L laboratory fermenters (Applikon, Schiedam, The Netherlands) with 1 L working volume. SM medium was used and set at pH 5 before autoclaving at 121° C for 20 min. Antifoam Emulsion C (Sigma) was added to a concentration of 0.2 g L-1 from a 20% (v/v) solution autoclaved separately (121° C, 20 min). Prior to inoculation, glucose was added to a final concentration of 20 g L-1 from a sterile (110° C, 90 min) 50% glucose solution and 1 mL of a vitamin solution (Verduyn et al., 1992). The pH was maintained at 5 by the automatic addition of 2 M KOH. Compressed air  for aerobic cultivations, was sparged to the bioreactor at the rate of 500 mL min-1  via an Ion Science Saga digital flow meter (Cambridge, UK). Temperature in the fermenters was kept at 30° C. Complete mixing of the medium was ensured by stirring at 800 rpm. Four independent batch cultivations were performed for each condition and each strain. Pre-cultures were started by inoculating SMG shake-flasks with 1 stock vial of the appropriate strain. After ca. 16 h incubation these cultures were used to inoculate new SMG shake-flasks. The starting OD was tightly controlled as to reach an OD = 1 after 8 hours of incubation. These exponentially growing cultures were washed twice with demineralized water (spinning 5000 rpm, 4 minutes) and resuspended in 100 mL demineralized water, cell suspension that was used to inoculate fermenters with starting OD of 0.1.

extract_protocol:
Biomass samples for RNA extractions were sampled from mid-exponential phase of grown in aerobic batch cultivations in bioreactors with chemically defined medium . Sampling for transcriptome analysis from chemostat cultures and total RNA extraction was performed as described previously ( Hazelwood LA, Walsh MC, Pronk JT, Daran JM. 2010. Involvement of vacuolar sequestration and active transport in tolerance of Saccharomyces cerevisiae to hop iso- -acids. Appl. Environ. Microbiol. 76:318 –328. http://dx.doi.org/10.1128/AEM.01457-09.)
cDNA libraries for the Illumina platform were generated and sequenced at BaseClear BV (Leiden, The Netherlands). cDNA was used as input for library preparation using the Illumina TruSeq DNA library preparation kit (Illumina). Briefly, the DNA was fragmented by nebulization and subjected to end-repair, A-tailing, ligation of adaptors including sample-specific barcodes and size-selection to obtain a library with median insert-size around 200-400 bp. After PCR enrichment, the resultant library was checked on a Bioanalyzer (Agilent) and quantified. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2500 with paired-end protocol

treatment_protocol: Optical density (OD) of diluted cell suspensions (measured OD ranging between 0.1 and 0.3) was measured at 660 nm using a spectrophotometer Libra S11 (Biocrom, Cambridge, UK). Biomass dry weight was determined by filtration as previously described (103). The concentration of extracellular metabolite in culture supernatants was by HPLC analysis using a Aminex HPX-87H ion exchange column operated at 60° C with 5 mM H2SO4 as mobile phase at flow rate of 0.6 mL min-1.

value: MATa ura3-52 his3-1 leu2-3,112 MAL2-8c SUC2 glk1::SpHis5, hxk1::KlLEU2, tdh1::KlURA3, tdh2, gpm2, gpm3, eno1, pyk2, pdc5, pdc6, adh2, adh5, adh4


title: DSE002 RNA-S1


title: MEFs

status: Public on Oct 01 2015

city: Jerusalem

first: Yossi

last: buganim

address: Ein Karem 91120

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Illumina bcl2fastq, v2.15.0.4, was used for transforming basecalls to fastq files.
Sequenced reads were quality trimmed at both ends with PHRED score threshold of 32, trimmed for adaptor sequence with Trim Galore, v0.3.7, and filtered for low-quality reads with the FASTX package, v0.0.13. Reads were then mapped to GRCm38 (mouse) using TopHat v2.0.11 with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 18 --read-realign-edit-dist 5 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the Cufflinks package v2.2.1 with the programs cuffquant and cuffnorm, using parameters -b, -u and a masking file with all IG, TR, rRNA, tRNA, miRNA, snRNA, snoRNA and pseudo entries of the mouse GTF file.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts and FPKM values at gene level for each sample. Fields are Ensembl_Gene_ID, Ensembl_Transcript_ID, Gene_Full_Name, Gene_Symbol, Gene_Biotype, EntrezGene_ID, RefSeq_mRNA, UCSC_ID, First_replicate_count, Second_replicate_count, First_replicate_fpkm, Second_replicate_fpkm. Multiple data is separated by semicolon. Missing data is represented by a question mark.

source_name: embryonic fibroblasts

growth_protocol: TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium

extract_protocol:
Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: embryonic fibroblasts


title: mESC

source_name: embryonic stem cells

value: embryonic stem cells


title: Neurosphere cultures transfected with miR153 mimetic_rep2

status: Public on Aug 01 2014

hyb_protocol: 10μg labeled cRNA samples were fragmented at 94C for 20minutes, mixed with hybridization buffer (Applied Microarray, Tempe, AZ) and hybridized with CodeLink whole genome arrays (Applied Microarray) for 18 hours. Post‐hybridization processing and secondary‐labeling with Cy™5‐conjugated to Streptavidin were performed according to the manufacturer’s instructions (Applied Microarray).

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Array images were processed using CodeLink TM software (Applied Microarray, AZ), and global median normalization was used to generate normalized expression values. The raw and normalized signal intensity was determined by CodeLink Expression Analysis Software (version 5.0.0.31312).

label: biotin

source_name: Neurosphere cultures transfected with miR-153 expression vector for 24 hours

label_protocol: 1.0μg of purified mRNA samples from either control or miR-153 mimetic treated groups mixed with 50pg RNA spike-in control were used to generate biotin labeled cRNA samples by a linear amplification method using Ambion’s MessageAmp™ II‐Biotin Enhanced Single Round aRNA Amplification Kits (#Am1791; Life Technologies, CA) aacording to manufacturer's protocols.

growth_protocol: We isolated cortical neuroepithelium from embryonic day 12.5 mouse fetuses (C57BL/6) from the dorsal telecephalic vesicles and cultured as neurosphere culture. Extreme care was taken to avoid structural precursors of hippocampus and striatum. Precursor cultures were established in constituted meduim containing serum-free mitogenic media DMEM/F12 (catalog#11330-032; Life Technologies, CA), 20 ng/ml bFGF (basic fibroblast growth factor; catalog #13256-029; Life Technologies, CA), 20 ng/ml hEGF (human epidermal growth factor; catalog #53003-018; Life Technologies, CA), 0.15 ng/ml LIF (leukemia inhibitory factor; catalog #L200; Alomone Labs, Jerusalem, Israel), ITS-X (insulin-transferrin-selenium-X) supplement (catalog #51500-056; Life Technologies, CA), 0.85 Us/ml heparin (catalog #15077-019; Life Technologies, CA), and 20 nM progesterone (catalog #P6149; Sigma, St. Louis, MO).

extract_protocol: Total RNA was isolated from control and treated samples using using mirVana™ miRNA Isolation Kit (#AM1560; Life Technologies, CA) according to the manufacturer’s protocol.

treatment_protocol: 3~4 million neural progenitors were exposed to 7 ug of miR-153 mimetic (miRNASelect™ pEGP-mmu-mir-153 Expression Vector, Cell Biolabs, CA) or control (miRNASelect™ pEGP-miR Null Control Vector, Cell Biolabs, CA) for 24 hours through transfection using an eletroporator (NEON electroporator with transfection kit, settings 1200V, 20ms, 2 pulses, Life Technologies, CA).

value: Mouse fetuses sacrified at GD12.5

tag: transfection

value: miR-153 expression vector


title: Neurosphere cultures transfected with miR153 mimetic_rep3


title: Neurosphere cultures transfected with null control_rep6

source_name: Neurosphere cultures transfected with null control vector for 24 hours

value: null control


title: Neurosphere cultures transfected with miR153 mimetic_rep5


title: Neurosphere cultures transfected with null control_rep4


title: Neurosphere cultures transfected with null control_rep5


title: GMP_HSC-WT-2

status: Public on Mar 07 2016

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: sorted wild-type newborn liver GMP (lin- Sca-1- c-kit+ FcgRII/IIIhi CD34+)

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix MG430 v2 microarrays (Affymetrix) and stained according to the manufacturer's instructions.

scan_protocol: scanning of the samples was performed according to the manufacturer's instructions

data_processing: Microarry data was normalized using the RMA method with R‐Bioconductor, and the differentially expressed genes were identified using the Significance Analysis for Microarrays (SAM) algorithm (Tusher et al. 2001) in TM4‐MeV software v.4.6 (Saeed et al. 2003) with the threshold set to 0 as a median number of falsely significant genes.

label_protocol: 10 ng of total RNA were used for linear amplification of cDNA using the Ovation Pico RNA Amplification Systm (Nugen), according to the manufacturer's instructions. 5 µg of cRNA were biotin-labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen).

growth_protocol: PU.1 Q202L heterozygous mice were bred normally and newborns were harvested directly after birth or shortly before. Littermates were used for the study.

extract_protocol: Short-term hematopoietic stem cells (lin- Sca-1+ c-kit+ CD150- CD48+) and GMP (lin- Sca-1- c-kit+ FcgRII/IIIhi CD34+) were sorted by FACS into RLT buffer, and RNA was prepared by RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.

tag: genotype

value: WT

value: sorted newborn liver cells

value: newborn


title: Neurosphere cultures transfected with null control_rep1


title: Neurosphere cultures transfected with miR153 mimetic_rep6


title: GMP_HSC-PU.1_Q202L-2

description: sorted PU.1 Q202L knock-in newborn liver GMP (lin- Sca-1- c-kit+ FcgRII/IIIhi CD34+)

value: Q202L knock-in


title: Neurosphere cultures transfected with null control_rep3


title: Neurosphere cultures transfected with miR153 mimetic_rep4


title: ST_HSC-WT-2

description: sorted wild-type newborn liver ST-HSC (lin- Sca-1+ c-kit+ CD150- CD48+)


title: ST_HSC-PU.1_Q202L-3

description: sorted PU.1 Q202L knock-in newborn liver ST-HSC (lin- Sca-1+ c-kit+ CD150- CD48+)


title: ST_HSC-PU.1_Q202L-2


title: ST_HSC-PU.1_Q202L-1


title: ST_HSC-WT-3


title: ST_HSC-WT-1


title: GMP_HSC-PU.1_Q202L-3


title: Neurosphere cultures transfected with miR153 mimetic_rep1


title: Neurosphere cultures transfected with null control_rep2


title: GMP_HSC-WT-3


title: GMP_HSC-PU.1_Q202L-1


title: GMP_HSC-WT-1


title: Leaf-cys-c1-REP3

status: Public on May 29 2013

city: Sevilla

first: Cecilia

last: Gotor

address: Avda. Américo Vespucio, 49

country: Spain

institute: Instituto de Bioquímica Vegetal y Fotosíntesis

description: Gene expression data from leaf cells (cys-c1)

hyb_protocol: Following fragmentation, 15 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Arabidopsis ATH1 Genome Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDT

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

organism: Arabidopsis thaliana

source_name: leaf, cysc-c1 mutant 14-days-old plants

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana (accession Col-0) and the cys-c1 mutant (SALK_022479) seeds were grown on solid Murashige & Skoog medium supplemented with 1% sucrosse. Plants were grown under a photoperiod of 16 h of white light (120 mE m-2 s-1) at 20ºC /8 h dark at 18ºC.

extract_protocol: Roots or leaves of 14-days-old plants grown under identical conditions on MS medium and RNA extracted from each sample. Total RNA was isolated with Trizol reagent (Invitrogen) followed by cleaning with the RNeasy Plant Mini Kit (Qiagen).

value: leaves


title: Leaf-cys-c1-REP1


title: Leaf-WildType-REP3

description: Gene expression data from leaf cells (wild type)

source_name: leaf, wild type 14-days-old plants

value: Wild Type


title: Leaf-cys-c1-REP2


title: Leaf-WildType-REP2


title: Leaf-WildType-REP1


title: Root-WildType-REP3

status: Public on Oct 01 2010

description: Gene expression data from root cells (wild type)

source_name: root, wild type 14-days-old plants

value: roots


title: Root-cys-c1-REP3

description: Gene expression data from root cells (cys-c1)

source_name: root, cysc-c1 mutant 14-days-old plants


title: Root-WildType-REP2


title: Root-WildType-REP1


title: Root-cys-c1-REP2


title: Root-cys-c1-REP1


title: B140 RA TNF t=0 PAXgene vs CRS red 80 PMT

status: Public on Jan 28 2010

city: Amsterdam

first: Lisa

last: van Baarsen

address: Meibergdreef 9

department: Div. of Clinical Immunology and Rheumatology

institute: EULAR & FOCIS Center of Excellence

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53053.gif

hyb_protocol: not provided

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: B140 RA TNF t=0 PAX

label_protocol: Indirect labelling of amplified RNA via aminoallyl; As described in: Gene expression profiling in rheumatology. Methods Mol Med. 2007;136:305-27  The following is a slight modification by Mitch Garber, Anatoly Urisman and subsequently by Lisa van Baarsen of a protocol developed by Joe DeRisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA).  Original document can be obtained at www.microarrays.org.   cDNA synthesis:  Two separate reaction vials for labeling: one for the experimental sample to be labeled with Cy3 (green) and one for the reference sample to be labeled with Cy5 (red).    1. For total RNA, mix 25 ug of the RNA with 5 ug of anchored oligo-dT [(dT)20-     VN] (Operon, HPLC purified) in a  total volume of 18 ul in 1,5 ml tubes. For   cRNA, use 5 ug of the amplified cRNA with 10 ug of Poly D(N)6 (Operon) primer   in a total volume of 18 ul in 1.5 ml tubes.  2. Heat to 70C for 10 minutes at 300 rpm  3. Cool on ice water for 5 minutes. 4. Make a nucleotide master mix  Nucleotide Mix per reaction: 6 ul 5X RT buffer 0.6 ul 50X dNTP stock solution* 3 ul 0.1 M DTT 1.5 ul 200 U/ul Superscript II RT (Gibco) 0.5 ul RNasin (Gibco)    *50X dNTP stock solution using a 4:1 ratio aminoallyl-dUTP to dTTP  10 ul each 100 mM dATP, dGTP, dCTP (Pharmacia)  8 ul 100 mM aminoallyl-dUTP** (Sigma, #A0410)  2 ul 100 mM dTTP **Dissolve 10 mg aminoallyl-dUTP in 170 uL water.  Add approx. 6.8 uL 1N NaOH.     Final pH is roughly 7.0 using pH paper.  5. Pipet 11.6 ul nucleotide mix in a 0.5 ml thin wall tube for both the Cy3 and Cy5 samples 4. Spin down and add the 18 ul of sample or reference  5. Incubate reaction for 1h at 42C 6. Add 1 ul reverse transcriptase and continue incubation at 42C for an additional 1h   Hydrolysis of RNA: 7. Add 15 ul of 0.1 N NaOH.  Incubate at 70C for 10 minutes if cRNA is used or 30 minutes if total RNA is used as template  8. Add 15 ul 0.1 N HCl.    9. Carefully add 450 ul RNAse-free water to each reaction.   Cleanup: 10. Apply the 500 ul neutralized, diluted reaction mix on a labeled Microcon-30 filter (Amicon), spin at 10,000g for 7 minutes and discard flow through 11. Pipet 450 ul water on the filter, spin at 10,000g for 7 minutes and discard flow through 12. Repeat washing step 11 13. Concentrate the probe to 10 ul by centrifugation in steps of 30 seconds. Check after each step the fluid level in the filter. Never let the membrane dry completely!! 14. If there is less then half a circle of fluid on top of the filter, invert the microcon in a clean labeled tube and spin at 10,000g for 1 minute to recover the aminoallyl labeled cDNA probe; adjust to 10 ul with water 15. Samples can now be stored at -20C or -80C   Coupling of aminoallyl-labeled cDNA to Cy3 or Cy5 16. Add 0.5 ul 1M sodium bicarbonate, pH 9.0 (50 mM final) to the 10 ul aminoallyl-labeled cDNA and transfer the sample to the right aliquot of dye () 17. Incubate 1h at RT in the dark.  Mix every 15 minutes.   Quenching and Cleanup 18. Add 4.5 ul 4M hydroxylamine  19. Incubate 15 minutes in the dark    To remove unincorporated/quenched Cy dyes, proceed with Qia-Quick PCR purification kit (QIAGEN). Use method as described by the manufacturer.   Use Cy3/5 labeled samples immediately for hybridisation; Protocol Type = Labeling; Performer: Cornelis,,Verweij

extract_protocol: Linear amplification of total RNA using Ambion kit; As described in: Gene expression profiling in rheumatology. van der Pouw Kraan TC, van Baarsen LG, Rustenburg F, Baltus B, Fero M, Verweij CL. Methods Mol Med. 2007;136:305-27  Protocol MessageAmp aRNA kit (Ambion #1750; version 0309A; updated 27-04-2004)  All incubation steps are performed in a thermal cycler block using thin wall tubes. When the incubation temperature is ??37??C a heated lid is used. Do not use a heated lid when incubation temperature is <37??C. Use as input 1 microgram (ug) total RNA in a maximal volume of 11 ul.  First strand synthesis: 1. Thaw samples and reagents 2. Set the temperature of the thermal cycler on 70 degrees Celcius (C)  3. Prepare the following mix:     - RNA sample (max 11 ul)        - 1 ul oligo T7 primer         - add RNAse free water to a final volume of 12 ul  4. Incubate samples 10 minutes at 70C in thermal cycler 5. Put on ice-water for 5 minutes 6. Prepare Reverse transcriptase mix at RT, use per reaction:     2 ul 10x First strand buffer          1 ul Ribonuclease inhibitor          4 ul dNTP mix    1 ul Reverse Transcriptase    7. Add 8 ul mastermix to each sample 8. Incubate for 2h at 42??C   Second strand synthesis: 9. Prepare second strand (SS) mix, use per reaction:        63 ul RNAse free water          10 ul 10x second strand buffer          4 ul dNTP mix            2 ul DNA polymerase                1 ul RNAse H                         10. Add 80 ul SS mix to each sample  11. Incubate for 2h at 16??C 12. (If desired; samples can be immediately stored at ?C20C until the next day)  cDNA Purification (fume hood): 13. Pre-heat RNAse free water at 50??C 14. Take 1 tube en 1 cDNA filter per cDNA sample 15. Add 50 ul cDNA binding buffer to the filter and incubate for 5 minutes at RT 16. Pipet 250 ul DNA binding buffer to the cDNA samples 17. Pipet cDNA sample mix on the pre-wetted filter, centrifuge 1 min at 10.000g and discard flowthrough  18. Add 500 ul cDNA wash buffer to the filter and centrifuge 1 min at 10.000g, discard flow through 19. Centrifuge another 1 min at 10.000g  20. Put filter in a clean 2 ml elution tube 21. Pipet 10 ul pre-heated (50C) RNAse free water on the filter, incubate 2 min at RT and centrifuge 2 min at 10.000 rpm 22. Repeat step 21 23. Discard filter 24. Measure in each sample the volume; should be 16-18 ul adjust if necessary 25. Store cDNA at ?C20C until the next day or at ?C80C for a longer time period)  In vitro transcription to synthesize aRNA 1. Set the temperature of the thermal cycler on 37C  2. Thaw the reagents needed for the in vitro transcription on ice and put them at RT once they are thawed 3. Prepare at RT the mix containing per sample:     4 ul of each ATP, CTP, GTP nucleotide vial (75 mM)     4 ul UTP Solution (75 mM)    4 ul T7 10x reaction buffer                 4 ul T7 Enzyme mix               4. Pipet 24 ul mix to the samples 5. Incubate for 5h at 37??C 6. Put the samples on ice  7. Add 2 ul DNAse I incubate for 30 min at 37C  aRNA Purification (fume hood RT) 8. Pre-heat 100 ul RNAse free water per sample at 50??C  9. Take 1 clean tube and 1 filter per cRNA sample  10. Pipet 100 ul RNA binding buffer on the filter and incubate for 5 min  11. Pipet 58 ul RNA elution solution to each cRNA sample, vortex and add 350 ul cRNA binding buffer to each sample and vortex 12. Transfer samples to a new 1.5 ml tube and add 250 ul 100% ethanol  13. Apply the 650 ul mix on the pre-wetted filter, spin 1 min at 10.000g and discard flow through 14. Add 650 ul aRNA wash buffer to the filter, spin 1 min at 10.000g  15. Spin 1 min at 10.000g and move the dry filter to a fresh 2 ml tube  16. Add 50 ul pre-heated RNAse free water, incubate 2 min  17. Spin 2 min at 10.000g and repeat step 16 18. Spin 2 min at 10.000 rpm and discard filter  19. Measure the quantity and quality of cRNA on Agilent BioAnalyzer or NanoDrop ND-1000 spectrophotometer and store at ?C80??C; Protocol Type = Amplification; Performer: Cornelis,,Verweij

tag: patient

tag: time(absolute)

value: 0 months

tag: clinical (delta das28)

tag: clinical (eular)

tag: clinical (ddasv2-v10)

label_protocol: not provided

extract_protocol: not provided

tag: reference


title: B143 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53052.gif

source_name: B143 RA TNF t=0 PAX


title: B155 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58735.gif

source_name: B155 RA TNF t=1 Paxgene 40 PMT

value: 1 months

source_name: CRSbatch00140 PMT

value: CRSbatch00140 PMT


title: B159 RA TNF t=0 PAXgene vs CRS red

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55921.gif

source_name: B159 RA TNF t=0 PAX 80 PMT

source_name: CRSbatch001 80 PMT

value: CRSbatch001 80 PMT


title: B153 RA TNF t=0 PAXgene vs CRS 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55862.gif

source_name: B153 RA TNF t=0 PAXgene 80 PMT


title: B153 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57879.gif

source_name: B153 RA TNF t=1 Paxgene 40 PMT

source_name: CRSbatch001 40 PMT

value: CRSbatch001 40 PMT


title: B160 RA TNF t=0 PAXgene vs CRS

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56741.gif

source_name: B160 RA TNF t=0 PAXgene  80 PMT


title: B154 RA TNF t=0 PAXgene vs CRS

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55920.gif

source_name: B154 RA TNF t=0 PAXgene 80 PMT


title: B125 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53083.gif

source_name: B125 RA TNF t=0 PAX


title: B128 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53055.gif

source_name: B128 RA TNF t=0 PAX


title: B145 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58752.gif

source_name: B145 RA TNF t=1 Paxgene 40PMT

source_name: CRSbatch001 40PMT

value: CRSbatch001 40PMT


title: B155 RA TNF t=0 PAXgene vs CRS red

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55882.gif

source_name: B155 RA TNF t=0 PAXgene 80 PMT


title: B149 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53082.gif

source_name: B149 RA TNF t=0 PAX


title: B154 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58880.gif

source_name: B154 RA TNF t=1 Paxgene 40 PMT


title: B142 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57884.gif

source_name: B142 RA TNF t=1 Paxgene 40 PMT


title: B128 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57889.gif

source_name: B128 RA TNF t=1 Paxgene 40 PMT


title: B145 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53075.gif

source_name: B145 RA TNF t=0 PAX


title: B160 RA TNF t=1 PAXgene vs CRS 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57875.gif

source_name: B160 RA TNF t=1 Paxgene 80 PMT


title: B140 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57885.gif

source_name: B140 RA TNF t=1 Paxgene 40 PMT


title: B149 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58754.gif

source_name: B149 RA TNF t=1 Paxgene 40 PMT


title: B157 RA TNF t=0 PAXgene vs CRS

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55883.gif

source_name: B157 RA TNF t=0 PAXgene 80 PMT

source_name: CRSbatch001 80 PMT


title: B159 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58755.gif

source_name: B159 RA TNF t=1 Paxgene 40PMT

source_name: CRSbatch001 40 PMT


title: B143 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57881.gif

source_name: B143 RA TNF t=1 Paxgene 40 PMT


title: B130.2 RA TNF t=0 PAXgene vs CRS red 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53846.gif

source_name: B130.2 RA TNF t=0 PAX


title: B129 RA TNF t=1 PAXgene vs  CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58458.gif

source_name: B129 RA TNF t=1 Paxgene 40 PMT


title: B125 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/57876.gif

source_name: B125 RA TNF t=1 Paxgene 40 PMT


title: B157 RA TNF t=1 PAXgene vs CRS 80 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59240.gif

source_name: B157 RA TNF t=1 Paxgene 80 PMT


title: Mouse cDNA microarray analysis of CHB50 cells, 022PATHU corresponds to replicate 1

status: Public on Dec 01 2006

description: To identify neuronal differentiation-associated gene candidates using CHB50 neuroblasts by comparing CHB50 cells from the permissive condition (proliferation) to the non-permissive condition (differentiation)

data_processing: After background correction and removal of flagged values (including controls and housekeeping genes) the log ratio (VALUE) was calculated by Ch1 (P1Signal) divided by Ch2 (P2BalancedSignal)

organism: Rattus norvegicus

source_name: CHB50 at 33C (permissive temperature/+tsTA/-p53))

growth_protocol: CHB50 cultures are maintained in DMEM, 10%Fetal Calf Serum, 100U/ml penicillin-streptomycin and 50ug/ml of G418

extract_protocol: Trizol method (Invitrogen) followed by poly-A-mRNA isolation with Qiagen's Oligotex mRNA kit

treatment_protocol: CHB50 cells cultured at the permissive temperature (33C)

tag: Conditionally immortalized CHB50 cells are cultured at 33C for expression of the large T antigen and attenuation of p53 (the proliferation condition)

source_name: CHB50 at 39C (non-permissive temperature/-tsTA/+p53)

growth_protocol: CHB50 cultures are maintained in serum-free medium in DMEM, 49%F-12, 1%N2 supplement, and 100U/ml penicillin-streptomycin

treatment_protocol: CHB50 cells cultured at the non-permissive temperature (39C) for 72 hours

tag: Conditionally immortalized CHB50 cells are cultured at 39C for suppression of the large T antigen and induction of p53 (the differentiation condition)


title: B130 RA TNF t=1 PAXgene vs CRS 40 PMT

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58612.gif

source_name: B130 RA TNF t=1 Paxgene 40 PMT