title: HCC.high4

tag: tissue


title: HCC.high8

status: Public on Sep 10 2015

type: SRA

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Artificial sequences and ribosomal RNAs were identified and removed using TagDust and RNAdust.
Reads were aligned to the genome using BWA v0.5.9.
Transcription start sites (CAGE peaks) were identified using Paraclu.
Genome_build: hg19/GRCh37 for human and mm9/NCBI37 for mouse
Supplementary_files_format_and_content: Tab-delimited text files in the bed-like format including FDR, fold change, expression values (tpm) for 105 human samples

molecule: total RNA

organism: Mus musculus

source_name: Mdr2-KO liver

extract_protocol:
Total RNA of tissues were extracted using mirVana kit (Ambion) and the quality of the RNA samples was assessed using Agilent RNA 6000 nano kit.
Total RNA was used to synthesize cDNA with random primers. Full-length cDNAs were biotinylated and captured by streptavidin-coated magnetic beads. The cDNAs were released from cap-trapped RNAs, ligated to 5' linkers including barcode sequences, and digested with EcoP15I. The detailed protocol is described in Ref [PMID:22362160]

value: Liver

tag: etiology/histology

tag: gender

value: male


title: HCC.high5


title: HCC.high1


title: HCC.low15

value: female


title: HCC.high2


title: Input_Rif1-Flag_taz1∆

city: Tokyo

first: Yutaka

last: Kanoh

address: 2-1-6 Kamikitazawa, Setagaya-ku

department: Genome Medicine

institute: Tokyo Metropolitan Institute of Medical Science

description:
taz1∆
Rif1ChIP_taz1delta.bedgraph

library_source: genomic

data_processing:
All fastq files were aligned to S.pombe reference genomic ASM294v2 from Pombase by Bowtie1.0.0 with defalt setting.
The generated SAM files by Bowtie were converted to BAM and sorted by Samtools.
Peaks were called with Model-based analysis of ChIP-seq (MACS2.0.10) using following parameters; macs2 callpeak -t ChIP.sam -c Input.sam -f SAM -g 1.4e107 -n result_file -B -q 0.01 --nomodel
The generated treat_pileup.bedgraph files were loaded on Integrated Genome Browser.
Genome_build: ASM294v2
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: The stains were grown until mid log phase in YES medium at 30ºC. Cells containing nda3-KM311 mutation were arrested at M-phase at 20ºC for 5 hr. Cells were released into sequential cell cycle at 30ºC.

extract_protocol:
The cell wall was disrupted by zirconia beads and multi-beads shocker (Yasui Kikai Co.). Lysates were prepared by sonication and clarified by centrifugation. Protein and DNA complexes were immuno-precipitated by antibody conjugated with Protein G Dynabeads.
BrdU-incorporated genomic DNA was purified by Qiagen Genomic-tip and genomic buffer set. Purified genomic DNA was sheared by sonication. The fragmented DNA was heat-denatured and BrdU-substituted DNA was immuno-precipitated by Anti-BrdU antibody conjugated with anti-IgG1a-dynabeads.
ChIP, BrdUIP, and Input DNA was sheared to around 150bp by S220 Focused-ultrasonicators (COVARIS, INC.). The fragmented DNA were end-repaired, ligated to sequencing adapters and amplified according to the protocol of NEBNext® ChIP-Seq Library Prep Master Mix Set and NEBNext Multiplex Oligos for Illumina (New England Biolabs) to prepare library. The size and concentration of libraries were checked by Bioanalyzer 2000 and real-time PCR using KAPA Library Quantification Kits, respectively.

treatment_protocol:
Cells during G1 phase were fixed with 1% Formaldehyde at 20min after release.
Cells were arrested at early S-phase in 25mM HU at 60min after release from M-phase arrest and then the early replicated regions were labeled with 200µg/ml BrdU.

tag: genotype/variation

tag: epitope-tag

tag: antibody

tag: strain


title: HCC.low14


title: HCC.low11


title: HCC.high3


title: FlagChIP_Rif1-Flag_rap1∆

description:
rap1∆
Rif1ChIP_rap1delta.bedgraph

value: ANTI-FLAG M2 Monoclonal Antibody(Sigma), Subclass; IgG1, Clone; M2, Cat No.; F1804


title: HCC.low12


title: HCC.low16


title: NIH3T3_RRBS_C3

city: Ipswich

first: Guoqiang

last: Zhang

state: Massachusetts

address: 240 County Road

country: USA

institute: New England Biolabs Inc

description: processed data file: RRBS_CpG_methylation_call.txt

data_processing:
For RRBS, adaptor and low quality sequences (Phred score < 20) were trimmed from RRBS reads using the trim_galore package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter of --RRBS --paired. Reads were mapped to the mouse reference genome mm10 using Bismark with Bowtie2. CpG methylation was extracted from uniquely mapped reads using Bismark methylation extractor with the parameter of -p --no_overlap. Differential methylation analysis was carried out using the methylKit package, where logistic regression test was implemented on single CpG sites or genomic region sliding windows (window size 5 kb, step size 5 kb). The p-value of differential methylation test was corrected to q-values using the sliding linear model method. CpG sites or genomic regions with q-values < 0.01 were considered significantly differentially methylated.
For RNA-seq, sequencing reads were mapped to mm10 using TopHat2 (-r 60 --library-type fr-firststrand) with a known transcriptome file supplied (UCSC May 23, 2014). The number of reads mapped to each known gene were counted using htseq-count tools (-t exon -s reverse -i gene_id) and analyzed with DESeq2, where a negative binomial generalized linear model test is implemented on raw counts. The p-value of differential expression was corrected using Benjamini-Hochberg adjustment method and adjusted p-value was obtained. Genes with adj p-value < 0.01 were considered significantly differentially expressed. Sample distance was calculated using Euclidean distance on the rlog-transformed counts. Heatmap were generated using the Z-scored-transformed rlog values of significantly changed genes. Gene ontology analysis was carried out using the AmiGO 2 tools. Multiple comparisons were corrected using Bonferroni correction.
Genome_build: mm10
Supplementary_files_format_and_content: RRBS_CpG_methylation_call.txt: tab-delimited text file including the coordinates of CpG sites (1-based), strand, pvalue, qvalue and meth.diff
Supplementary_files_format_and_content: RNA-seq_log2fdc.txt: gene symbol, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj of each gene

source_name: NIH3T3_RRBS_control clone

growth_protocol: NIH3T3 stable clones were cultured in DMEM media supplemented with 10% of Fetal Bovine Serum.

extract_protocol:
Genomic DNA were extracted using Easy-DNA™ gDNA Purification Kit (Life Technologies). Total RNA were extracted using TRIZol reagent.
For RRBS, 1 μg of genomic DNA from stable clones overexpressing 14-3-3ε or control vector was digested by MspI, end-repaired and dA-tailed according to manufacturer’s conditions (New England Biolabs). Methylated NEB Illumina loop adaptor was ligated to digested DNA (E7370S, New England Biolabs). Ligation product was size-selected for 150 to 400 bp fragments on 2% agarose gels and bisulfite converted using the EZ DNA Methylation Kit (Zymo Research). Libraries were enriched by PCR using EpiMark Hot Start Taq DNA Polymerase (New England Biolabs). For RNA-seq, libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) per the manufacturer’s instructions. Average insert size of libraries was 200 bp.

treatment_protocol: 14-3-3ε was cloned into p3xFLAG-CMV-10 vector (Sigma-Aldrich). NIH3T3 stable cell line overexpressing 14-3-3ε was generated by selecting the cells transfected with 14-3-3ε constructs in 800 μg/mL of G418. After a week in culture single colonies were picked up and verified by western blotting using anti-FLAG antibody.

tag: cell line

tag: cell type

value: Mouse embryonic fibroblast cell line

tag: clone id

value: Control clone 3

value: control


title: HCC.low13


title: Input_Rif1-Flag_rap1∆

description:
rap1∆
Rif1ChIP_rap1delta.bedgraph


title: HCC.low10


title: ZUMA-0029

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

description: NSUMA technique to assess the methylation status of Alu repeats

data_processing:
Pre-processing. Reads sequences were obtained from the Illumina instruments  qseq format and were pre-processed in different steps in order to remove misleading reads and improve the mapping accuracy. Bases at the 3’ end of the reads with low quality (PHRED score <= 2) were end clipped. The adapters sequence used in the PCR amplification were also removed using iterative searches of 5’ to 3’ fragments. Ambiguous bases (Ns) at both ends of the read were also removed. Finally, reads shorter than 10 bp or with more than 30% of ambiguous bases were filtered out from the analysis.
Mapping. Once trimmed and cleaned, reads were mapped to the human reference genome (build GRCh37/hg19) with Bowtie 0.12.7 using the following parameters: -S –p 8 –v 2 –phred64-quals –best –l 28 –k 2. The value of option v is the number of mismatches allowed.
Post-processing. Once mapped, ambiguous reads (those that are mapped in several genome locations) were disambiguated when the number of mismatches allowed the assignment of a unique position in the human genome with a higher probability, otherwise they were rejected. Reads mapped in unknown chromosome were annotated as chrUn (scaffolds and contigs which could not be placed on chromosomes) and excluded from further analyses. The unambiguous reads (including uniquely mapped reads) were selected for further analysis. The information was stored using the standard SAM/BAM format.
Counting of reads in regions of interest (NSUMA universe) was performed using coverageBed of the bedtools suite 2.16.2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized number of reads by NSUMA amplicon for each sample.
Supplementary_files_format_and_content: ZUMA-xxxx_coverage.txt The file contains describes the amplicon location and its coverage according to the NSUMA technique in the sample. Consists in a BED6+ file depicting the (chromosome, start, end, amplicon_type, amplicon_numeric_identifier and strand) of the amplicon; plus four coverage columns, namely (number of reads in the amplion, number of bases of the amplicon covered with at lesat one read, the length of the amplicon, the fraction of bases of the amplicon that had non-zero coverage).

organism: Homo sapiens

source_name: Blood

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a Genome Analyzer II instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits. Each flow cell ran on the Genome Analyzer IIx contained a PhiX control lane (loaded at a concentration of 4pM) that was used to monitor run quality.

value: Blood


title: HCC.low8


title: HCC.low9


title: HCC.high6


title: HCC.low7


title: Input_Rif1-Flag_WT

description:
Wild_Type
Rif1ChIP_WT.bedgraph


title: HCC.low6


title: HCC.low5


title: HCC.low4


title: HCC.low2


title: HCC.low3


title: Adenoma4


title: CB4_input

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) for human GC B cells using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-5 for MLL2 and 10^-15 for H3K4me1 and H3K4me3.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively. The fourth column is the maximum peak height normalized per million mapped reads in each library.

source_name: germinal center B cells from tonsil tissues

growth_protocol: Tonsillar germinal center B cells were isolated by  by magnetic cell separation (CD38high, CD77+), as described in Klein et al, Proc Natl Acad Sci U S A, 2003.

extract_protocol:
ChIP was performed on two independent pools of GC cells, each comprising 3-5 donors. Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 4ug of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 10nM, pooled and sequenced in an Illumina HiSeq 2500 instrument as single-end 101 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Purified cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.

value: tonsil

value: germinal center B cell

tag: gc cell pool

tag: chip antibody


title: CB5_input


title: Adenoma1


title: Inflammation2

value: Inflammation


title: Adenoma2


title: CB4_MLL2

value: anti-MLL2 (Sigma, catalog# HPA035977, lot# A69497)


title: BrdUIP_Rif1BS_II:4255kb_mut3

description:
Rif1BS_II:4255kb_mut3
BrdUIP_HU_rif1BS_II_4255kb_mut3.bedgraph

value: adh1-Thymidine kinase

value: Anti-bromodeoxyuridine (MBL), Subclass; mouse IgG1, Clone; 2B1, Cat No.; MI-11-3,


title: CB5_MLL2


title: CB5_H3K4me1

value: anti-H3K4me1 (Abcam, catalog# ab8895, lot# GR61294-1)


title: FlagChIP_Rif1-Flag_WT

description:
Wild_Type
Rif1ChIP_WT.bedgraph


title: BrdUIP_rif1∆

description:
rif1∆
BrdUIP_HU_rif1delta.bedgraph


title: CB4_H3K4me1


title: BrdUIP_Rif1BS_I:2663kb_mut3

description:
Rif1BS_I:2663kb_mut3
BrdUIP_HU_rif1BS_I_2663kb_mut3.bedgraph


title: Inflammation1


title: BrdUIP_WT

description:
Wild_Type
BrdUIP_HU_WT.bedgraph


title: ZUMA-0023

organism: Pan troglodytes


title: WT6

source_name: WT liver

value: WT


title: WT5


title: ZUMA-0022


title: HCC.low1


title: CB5_H3K4me3

value: anti-H3K4me3 (Abcam, catalog# ab8580, lot# GR144288-1)


title: WT4

value: Liver


title: Inflammation3

value: male


title: WT3


title: ZUMA-0021


title: WT2


title: ZUMA-0028

organism: Pongo pygmaeus


title: Input_G1_WT

description:
Wild_type
Mcm4ChIP_G1_hsk1_89.bedgraph

value: No-tag


title: FlagChIP_Mcm4-Flag_hsk1-89

description:
hsk1-89
Mcm4ChIP_G1_hsk1_89.bedgraph

value: ANTI-FLAG M2 Monoclonal Antibody(Sigma), Subclass; IgG1, Clone; M2, Cat No.; F1804


title: FlagChIP_mock_WT

description:
Wild_Type
FlagChIP_mock_WT.bedgraph


title: Input_mock_WT

description:
Wild_Type
FlagChIP_mock_WT.bedgraph


title: ZUMA-0025


title: WT/DEL 14

status: Public on Sep 09 2015

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment counts for each gene were generated using HTseq (Anders S et al 2015) with the union option and were then transformed to FPKM (fragments per kilobase of gene per million fragments mapped) using a custom Perl script.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample.

source_name: 5A3+/del mice

extract_protocol:
CD150hi-HSC, CD150lo-HSC and CD150neg-MPP were sorted into 500 µL of TRIzol reagent (Life Technologies). RNA was isolated according to manufacturer’s instructions and precipitated with the addition of glycogen (New England BioLabs). The RNA was then treated with DNAse 1 (Ambion) and purified with the RNeasy MinElute Cleanup Kit (Qiagen).
For RNA-Seq analysis, total RNA (10 ng) were converted into double-stranded cDNA using the Ovation® RNA Amplification System V2 (NuGen, CA) per manufacturer’s recommendations. The amplified cDNA products were then used to generate RNA-seq libraries using the TruSeq RNA Sample Preparation Kit v2 reagents (Illumina®, CA) per manufacturer’s instructions, with 10 PCR amplification cycles. Library quality and quantity were assessed by the Agilent DNA1000 Chip (Agilent, CA) and qPCR (Kappa Biosystems Inc, MA).

value: CD150neg HSC

tag: age

value: 12.42 weeks

tag: genotype

value: WT/DEL


title: Adenoma3


title: CB4_H3K4me3


title: WT/DEL 12

value: 13.85 weeks


title: WT/DEL 6

value: CD150lo HSC

value: 13.28 weeks


title: WT/DEL 7


title: Input_HU_WT_for_BrdUIP

description:
Wild_Type
BrdUIP_HU_WT.bedgraph
BrdUIP_HU_rif1delta.bedgraph
BrdUIP_HU_rif1BS_I_2663kb_mut3.bedgraph
BrdUIP_HU_rif1BS_II_4255kb_mut3.bedgraph


title: WT/DEL 13


title: WT/DEL 5

value: CD150hi HSC

value: 12.85 weeks


title: WT/DEL 8


title: WT/DEL 9


title: WT/DEL 1


title: WT/WT 15

source_name: wildtype mice

value: WT/WT


title: WT/DEL 2


title: WT/DEL 4


title: WT/DEL 11


title: WT1


title: WT/WT 11


title: WT/WT 12


title: WT/WT 8


title: WT/DEL 3


title: WT/WT 10


title: WT/WT 14


title: WT/WT 7


title: WT/WT 6


title: WT/DEL 10


title: WT/WT 3


title: WT/WT 5


title: WT/WT 2


title: WT/WT 13


title: WT/WT 1


title: Smooth.24.1 [mRNA]

city: Dublin

first: Brendan

middle: J.

last: Loftus

address: Conway Institute, University College Dublin

department: School of Medicine & Medical Science

country: Ireland

institute: University College Dublin

data_processing:
Basecalls were performed using Illumina CASAVA v1.8.2
Adapters were trimmed from the 3' ends of sequenced reads using Fastx-toolkit
Reads were aligned to the human reference genome using the Star universal RNA-seq aligner
Read counts for genes were obtained using htseq-count, and only uniquely-aligning reads were counted for each gene
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of the numbers of reads mapped to all human genes in the Ensembl database

source_name: THP-1-derived macrophage

growth_protocol: THP-1 cells were obtained from the American Type Culture Collection (ATCC, TIB-202). The cells were grown in suspension in 75 cm2 flasks in RPMI medium supplemented with 10% heat-inactivated fetal bovine serum (FBS, Life technologies), 1% penicillin/streptomycin (Life technologies) and 2 mM L-Glutamine (Sigma) at 37 °C in humidified CO2 incubator. Antibiotics were used in the growth medium of THP-1 cells to avoid contamination of the propagating cells. To differentiate THP-1 cells into macrophages, the cells were seeded in 21 cm2 tissue culture dishes (CellStar) at a density of 107 cells/dish and incubated with 25 ng/mL of phorbol 12-myristate 13-acetate (PMA, Sigma) for 24 hours.

extract_protocol:
At 1, 4 and 24 hours post-infection, infected macrophages were washed twice with PBS and homogenized by adding Trizol reagent (Sigma). All the aliquots were stored at -80°C until required for RNA extraction. RNA extraction was performed by adding 200uL of chloroform (Sigma) to each sample and mixing by vortexing for 60 sec. The solution was then centrifuged for 15 min at 12000xg at 4°C. The aqueous phase was removed, transferred to a separate tube containing 500uL of isopropanol (Sigma), gently mixed and centrifuged 10 min at 12000xg at 4°C. The supernatant was discarded, the RNA pellet was resuspended in 1mL of 75% Ethanol, mixed by vortexing and centrifuged 5 min at 7500xg at 4°C. After discarding all the supernatants, the RNA was transferred to a miRNeasy mini kit column (Qiagen, Ldt.) and further purification steps were conducted according to the manufacturer’s instructions. In addition, the RNA was subjected to an on-column DNase treatment step (Qiagen Ltd.) to remove any DNA residues that could affect the downstream reaction. RNA quantity and quality was assessed using a NanoDrop TM 1000 spectrophotometer (Thermo Fisher Scientific Inc.) and on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Ltd.). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 7,5.
Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol. Briefly, the poly-A containing mRNA molecules were purified from 4ug of total RNA (extracted from not-infected and infected samples not bead-beaten) using poly-T oligo attached magnetic beads. The mRNA was then fragmented (to approximately 300bp) and the first strand cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random hexamers. The second strand of the cDNA was done by removing the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate a ds cDNA. dsDNA was then subjected to the addition of “A” bases to 3’ ends and ligation of the barcoded TruSeq adapters. Amplification of the fragments that had adapters ligated on both ends was performed by PCR using the primer cocktail supplied in the kit. Final libraries were analysed on an Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip (Agilent technology) to confirm that fragment size was ~200-260bp. All libraries were then quantified using a Qubit fluorometer and Qubit double stranded DNA High Sensitivity kit (Invitrogen). Libraries were loaded at a concentration of 10pM onto the flowcell and were single-end sequenced on Illumina HiSeq 2000 or Illumina MiSeq.

treatment_protocol: Before the infection, the medium was replaced with fresh RPMI/10% FBS/2mM L-Glutamine medium without antibiotics and cells were infected with mycobacteria to achieve a multiplicity of infection (MOI) of 10:1 (bacteria : cells). Non infected control macrophages received culture media only. Both not-infected and infected macrophages were prepared in triplicate in 21 cm2 tissue culture dishes and incubated at 37°C. After 1hpi, the infected macrophages were washed with sterile PBS to remove the extracellular mycobacteria and reincubated for 4hpi or 24hpi in culture media supplemented with 60ug/mL of amikacin (Sigma) at 37°C 5% CO2 until the macrophages were harvested. This was necessary to inhibit the growth of the remaining extracellular bacteria. In preliminary experiments, we confirmed that, at this concentration, amikacin did not influence intracellular viability of both strains of MAB  (data not shown).

tag: bacterial infection

value: M. abscessus Smooth (MAB-S)-infected

tag: time point (hours post-infection)


title: Smooth.24.2 [mRNA]


title: ZUMA-0024

value: Blood


title: Smooth.4.3 [mRNA]


title: Smooth.1.3 [mRNA]


title: Smooth.4.2 [mRNA]


title: WT/WT 9


title: Smooth.1.2 [mRNA]


title: Smooth.1.1 [mRNA]


title: Rough.24.2 [mRNA]

value: M. abscessus Rough (MAB-R)-infected


title: Rough.24.3 [mRNA]


title: Rough.24.1 [mRNA]


title: Rough.1.3 [mRNA]


title: Rough.1.2 [mRNA]


title: Mac.24.1 [mRNA]

value: Uninfected control


title: Rough.4.1 [mRNA]


title: Mac.24.3 [mRNA]


title: Rough.4.2 [mRNA]


title: Rough.1.1 [mRNA]


title: Mac.24.2 [mRNA]


title: WT/WT 4


title: W81A3

city: Chapel Hill

first: Erin

middle: K

last: Shanle

state: NC

address: 3010 Genetic Medicine, 120 Mason Farm Road

department: Biochemistry and Biophysics

institute: University of North Carolina at Chapel Hill

data_processing:
Tophat 2.0.14,Default parameters, align to SacCer3 gtf
samtools, 0.1.19, -F 4, filter unmapped reads
htseq-count, 0.6.1p1, generate count table
DESeq2, 1.8.1, test for differential expression
Genome_build: sacCer3
Supplementary_files_format_and_content: text file of HTSeq counts

organism: Saccharomyces cerevisiae

extract_protocol:
Phenol chloroform extraction, Dnase treatment
Total RNA TruSeq-STRANDED (Ribo-Zero Gold) (Illumina)

tag: strain background

tag: genotype/variation background

value: taf14 deletant

tag: transformed with

tag: transformant genotype


title: W81A2


title: W81A1


title: Mac.4.3 [mRNA]


title: Mac.4.2 [mRNA]


title: Smooth.4.1 [mRNA]


title: Mac.4.1 [mRNA]


title: Mac.1.3 [mRNA]


title: FL3

value: full-length pRS313-TAF14-HA3-SSN6


title: Rough.4.3 [mRNA]


title: Mac.1.2 [mRNA]


title: Mac.1.1 [mRNA]


title: FL1


title: S_7

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

description: iliac crest needle biopsies

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: Young Woman

extract_protocol:
we obtained small needle bone biopsies from the posterior iliac crest of all subjects using an 8G needle under local anesthesia
total RNA was isolated using the RNeasy Micro Kit (Qiagen, Valencia, CA) and treated with the Turbo DNA-freeTM Kit (Life Technologies, Grand Island, NY) to remove potential contaminating DNA that may lead to false-positive amplification

tag: gender

value: Female

tag: tissue

value: bone

value: young


title: S_58

description: iliac crest needle biopsies


title: FL2


title: DV3

value: pRS313-HA3-SSN6 (empty vector)


title: S_49

description: iliac crest needle biopsies


title: S_46

description: iliac crest needle biopsies


title: DV2


title: DV1


title: S_4

description: iliac crest needle biopsies


title: BY3

value: WT


title: S_40

description: iliac crest needle biopsies


title: S_34

description: iliac crest needle biopsies


title: S_28

description: iliac crest needle biopsies


title: S_22

description: iliac crest needle biopsies


title: BY2


title: BY1


title: S_13

description: iliac crest needle biopsies


title: S_16

description: iliac crest needle biopsies


title: S_19

description: iliac crest needle biopsies


title: S_1

description: iliac crest needle biopsies


title: S_25

description: iliac crest needle biopsies


title: S_31

description: iliac crest needle biopsies


title: S_60

description: iliac crest needle biopsies

source_name: Old Woman + Estrogen

value: old


title: S_9

description: iliac crest needle biopsies


title: S_52

description: iliac crest needle biopsies


title: S_57

description: iliac crest needle biopsies


title: S_54

description: iliac crest needle biopsies


title: S_10

description: iliac crest needle biopsies


title: S_6

description: iliac crest needle biopsies


title: S_43

description: iliac crest needle biopsies


title: S_48

description: iliac crest needle biopsies


title: S_42

description: iliac crest needle biopsies


title: S_51

description: iliac crest needle biopsies


title: S_39

description: iliac crest needle biopsies


title: S_45

description: iliac crest needle biopsies


title: S_36

description: iliac crest needle biopsies


title: S_3

description: iliac crest needle biopsies


title: S_37

description: iliac crest needle biopsies


title: S_30

description: iliac crest needle biopsies


title: S_33

description: iliac crest needle biopsies


title: Day2_Rep3

city: West lafayette

first: Natalia

last: Dudareva

state: IN

address: 175 S.University Street

department: Biochemistry

institute: Purdue University

data_processing:
Base calling:  CASAVA 1.8.2 [Illumina]
Adapter filtering and quality control trimming: Trimmomatic 0.22 (options: LEADING:20 TRAILING:20 MINLEN:30)
Transcriptome assembly: Trinity r2012-10-05 with normalization of 30
Mapping using TopHat and count matrix using HTSeq

organism: Petunia x hybrida

source_name: flowers

extract_protocol:
Corolla tissue was removed, frozen in liquid nitrogen, and RNA was isolated using Qiagen RNeasy kit. RNA was treated with DNase to eliminate genomic DNA using the TURBODNA-free kit (Ambion). Libraries were constructed using an Illumina mRNA-Seq kit.
RNA libraries were prepared for sequencing using the TruSeq RNA Library Preparation Kit.

tag: cultivar

value: Mitchell diploid

value: corolla

tag: developmental stage

value: day 2 postanthesis


title: Day2_Rep2


title: S_24

description: iliac crest needle biopsies


title: Bud_Rep3

value: bud


title: Day2_Rep1


title: Bud_Rep2


title: S_12

description: iliac crest needle biopsies


title: Bud_Rep1


title: S_56

description: iliac crest needle biopsies

source_name: Old Woman


title: S_47

description: iliac crest needle biopsies


title: S_44

description: iliac crest needle biopsies


title: S_8

description: iliac crest needle biopsies


title: S_41

description: iliac crest needle biopsies


title: S_35

description: iliac crest needle biopsies


title: S_59

description: iliac crest needle biopsies


title: S_53

description: iliac crest needle biopsies


title: S_27

description: iliac crest needle biopsies


title: S_5

description: iliac crest needle biopsies


title: open batch C

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

description:
eyes open from P14-P20
combined.fpkm.tsv
deseq2_closed_vs_open.tsv

data_processing:
Samples were processed with bcbio-nextgen version 0.7.9a which implements the following steps:
Quality, adapter and polyA trimming with AlienTrimmer version 0.3.2 with a quality cutoff of Phred < 5
Aligned to rn5 with the STAR aligner version 2.3.14z against an index built using the gene annotation from Ensembl release 74
Reads aligning to each gene were counted with FeatureCounts version 1.4.4
FPKM was estimated with Cufflinks version 2.1.1 using the gene annotation from Ensembl release 74
Gene-level differential expression was run with DESeq2 version 1.4.1 using the model formula ~ batch + eye_condition to correct for batch effects
Gene-level FPKM from Cufflinks were combined into the file combined.fpkm
Genome_build: rn5
Supplementary_files_format_and_content: Tab delimited files, combined.fpkm.tsv with FPKM values for each sample and deseq2_closed_vs_open.tsv which has the DESeq2 results of differential expression for each gene

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Superficial superior colliculus

extract_protocol:
Qiazol extraction followed by cleanup with the RNeasy MinElute kit
Illumina protocol (#1004898 Rev. D)

treatment_protocol: Storage of tissue in RNALater at -20C prior to total RNA extraction and library preparation

tag: strain

value: Sprague Dawley

tag: group

value: eyes open

tag: batch

value: C


title: open batch A

value: A


title: S_32

description: iliac crest needle biopsies


title: S_21

description: iliac crest needle biopsies


title: S_18

description: iliac crest needle biopsies


title: S_29

description: iliac crest needle biopsies


title: open batch B

value: B


title: S_38

description: iliac crest needle biopsies


title: closed batch A

description:
eyelids glued closed from P14-P20
combined.fpkm.tsv
deseq2_closed_vs_open.tsv

value: eyes closed


title: closed batch B


title: S_15

description: iliac crest needle biopsies


title: S_23

description: iliac crest needle biopsies


title: S_17

description: iliac crest needle biopsies


title: S_20

description: iliac crest needle biopsies


title: S_50

description: iliac crest needle biopsies


title: Smooth.24.2

data_processing:
Basecalls were performed using Illumina CASAVA v1.8.2
Adapters were trimmed from the 3' ends of sequenced reads using Fastx-toolkit
Reads were aligned to the human reference genome using bowtie v1.1.2 using the mapper.pl script from miRdeep2, with the -d -n -e -h -j and -m flags
Read counts for miRNAs were obtained using the miRDeep2.pl script from miRdeep2, with mature and precursor human miRNA sequences from miRBase
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of the numbers of reads mapped to all miRNAs from miRBase

extract_protocol:
At 1, 4 and 24 hours post-infection, infected macrophages were washed twice with PBS and homogenized by adding Trizol reagent (Sigma). All the aliquots were stored at -80°C until required for RNA extraction. RNA extraction was performed by adding 200uL of chloroform (Sigma) to each sample and mixing by vortexing for 60 sec. The solution was then centrifuged for 15 min at 12000xg at 4°C. The aqueous phase was removed, transferred to a separate tube containing 500uL of isopropanol (Sigma), gently mixed and centrifuged 10 min at 12000xg at 4°C. The supernatant was discarded, the RNA pellet was resuspended in 1mL of 75% Ethanol, mixed by vortexing and centrifuged 5 min at 7500xg at 4°C. After discarding all the supernatants, the RNA was transferred to a miRNeasy mini kit column (Qiagen, Ldt.) and further purification steps were conducted according to the manufacturer’s instructions. In addition, the RNA was subjected to an on-column DNase treatment step (Qiagen Ltd.) to remove any DNA residues that could affect the downstream reaction. RNA quantity and quality was assessed using a NanoDrop TM 1000 spectrophotometer (Thermo Fisher Scientific Inc.) and on an Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Ltd.). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers (RIN) greater than 7,5.
Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Sample Preparation Kit according to the manufacturer’s protocol using 1ug of total RNA (extracted from not-infected and infected samples not bead-beaten). Briefly, RNA adapters were ligated to the 5’ and 3’ ends of the small RNA molecules, followed by reverse transcription and 11 cycles of PCR amplification by using indexed primers. The libraries were size-selected on a 6% polyacrylamide gel for the desired size of 147-157 bp and then purified from the gel. The molarity and size of finished miRNA-seq libraries were quantified on an Agilent 2100 Bioanalyzer using an Agilent High Sensitivity DNA chip (Agilent technologies). Libraires were loaded at a concentration of 10pM onto the flowcell and were single-end sequenced on Illumina HiSeq 2000 or Illumina MiSeq.

value: M. abscessus Smooth (MAB-S)-infected


title: S_11

description: iliac crest needle biopsies

value: Female


title: Smooth.4.1


title: Smooth.1.1


title: closed batch C


title: Smooth.4.2


title: Rough.4.2

value: M. abscessus Rough (MAB-R)-infected


title: Rough.24.1


title: S_26

description: iliac crest needle biopsies

value: bone


title: Rough.24.2


title: Mac.4.3

value: Uninfected control


title: Rough.1.2


title: Mac.4.2


title: Rough.4.1


title: Smooth.24.1


title: Mac.4.1


title: Mac.24.1


title: Mac.1.2


title: Mac.24.2


title: Smooth.24.3 [mRNA]


title: Mac.1.3


title: Smooth.24.4


title: Smooth.24.3


title: Smooth.1.2


title: Rough.24.4


title: Rough.1.1


title: wild type

city: Durham

first: Adam

middle: Lee

last: Mefferd

address: 408 Andrews Road

department: Molecular Genetics and Microbiology

institute: Duke University

description: common transformed embryonic kidney cell line

data_processing:
Bioinformatic analyses were completed as follows. Reads were first processed with the FASTX-Toolkit and Bowtie as described previously (Flores et al. 2014). Briefly, reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33 | fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15  | fastx_collapser. Note that reads with and without the 3' adaptor were retained. All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al. 2009) with the following options: –k 1 (default) –v 1 --best --strata –m 25. The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins, (Kozomara and Griffiths-Jones 2014), and finally the human functional RNA database version 3.4 (Mituyama et al. 2009). Reads aligning to the fRNAdb were further filtered with in-house Perl scripts. All reads greater than 25 nt aligning to all tRNAs in the fRNAdb were assigned unambiguously to an amino acid group and then summed. These read totals were then normalized both to total reads aligning to the fRNAdb to assess tRNA pool sizes and internally to assess relative pool stoichiometry. As a scaling factor, it was assumed there are 2X106 tRNA molecules per cell
The processed data column headings are as follows:

Column A: Sequence ID in Functional RNA database (fRNAdb)

Column B: Sequence start position

Column C: Sequence end position

Column D: Reads per million

Column E: strand polarity

source_name: wild type HEK-293T cells

growth_protocol: DMEM supplmented with 10% FBS and 1 ug/ml puromycin (samples 2 and 3)

extract_protocol:
Small RNA was harvested using miRvana isolation kit (ambion) and small RNAs between 50 and 140 nucletodes isolated by PAGE
To ensure the presence of a single 5’ phosphate, the isolated RNAs were dephosphorylated using recombinant shrimp alkaline phosphatase (NEB) in NEB cutsmart buffer. The reaction was heated at 65°C for 5 min and then the RNA molecules were phosphorylated using T4 polynucleotide kinase (NEB) in NEB Ligase Buffer. The reaction was then incubated at 65°C for 20 min. The isolated small RNAs were then processed using a TruSeq Small RNA Sample Preparation Kit (Illumina). cDNA was generated as previously described (Flores et al. 2014). Briefly, adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices. cDNA molecules corresponding to a length of ~170 - ~240 bp were then isolated by gel electrophoresis and sequenced on an Illumina HiSeq 2000 using a 50-bp single end protocol.

tag: cell type


title: E6 Gln

source_name: HEK-293T cells expressing Cas9 and an sgRNA from Glutamine tRNA


title: E6 U6

source_name: HEK-293T cells expressing Cas9 and an sgRNA from U6 polIII promoter


title: Rough.24.3


title: Mac.24.3


title: 293 PARN KD

status: Public on Sep 08 2015

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
Alignment to transcriptome with HISAT 0.1.6.
Transcript quantification using Salmon 0.3.2.
Gene-level summarization.
Natural log transform (plus one pseudocount)
Genome_build: GRCh38

source_name: HEK 293

growth_protocol: iPS cells were maintained in Essential 8 medium on hES-qualified matrigel matrix and were routinely passaged with accutase (typically 200,000 to 300,000 cells/well onto 6 well plate). HEK 293 and fibroblast cells were maintained in DMEM (10-15% FBS) and passaged with 0.05% trypsin.

extract_protocol:
From plates of cells at 90-100% confluence, 1ml of Trizol was added directly onto cells after a PBS wash and scraped into eppendorf tubes for extraction according to protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEK 293

tag: parn mutational status

tag: parn knock down

value: Knock down


title: Patient 2 cl1 iPS

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells

value: mut


title: 293 control KD

value: control


title: Patient 1 cl2 iPS


title: WT2 iPS

value: wild type


title: WT1 iPS


title: Patient 1 FIB

source_name: fibroblast

value: fibroblast


title: Mac.1.1


title: WT2 FIB


title: WT1 FIB


title: Molm13_Input

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

country: Germany

institute: University Stuttgart

description:
input
Sample 100

data_processing:
Adaptors of the single-read fragments were removed using cutadapt v1.4.25 and reads with a length of less than 18bp in any read of the pair were discarded.
The remaining reads were aligned to the genome (mouse: mm10, human: hg19) using Bowtie v1.0.0
Reads with same start and end position on the same strand were removed from the alignment
Remaining reads were normalized to total mapped reads.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: ChIP-Seq bigWig-files for each individual IP
Read processing was performed as described in Arnold et al., Science 2013, PMID: 23328393
Genome_build: hg19
Supplementary_files_format_and_content: STARR-Seq bigWig-files were generated for each STARR-Seq sample

source_name: Cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: diagnosis

value: Leukemia


title: Molm13_H3K27ac

description:
H3K27ac antibody (Abcam, 4729)
Sample 99


title: K562_Input

description:
input
Sample 98


title: K562_H3K27ac

description:
H3K27ac antibody (Abcam, 4729)
Sample 97


title: Day 21 t4a

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t4a

data_processing:
Basecalls performed using CASAVA version 1.8.2
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment.
Genome Reference: hg19
Supplementary_files_format_and_content: RSEM TPMs (Gene expression levels)

source_name: H1 human embryonic stem cell derived neural progenitor cells, endothelial cells, mesenchymal stem cells, and microglia/macrophage precursors

extract_protocol:
Qiagen Rneasy mini kit with RLT lysis buffer
TruSeq and custom library prep

tag: screening chemicals

value: hydroxyurea


title: Day 21 t8b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t8b

value: L-phenylalanine


title: Day 21 t3a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t3a

value: diazinon


title: Day 21 t7b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t7b

value: permethrin


title: Day 21 t9b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t9b

value: propylthiouracil


title: Day 21 t8a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t8a


title: Day 21 un2b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7un2b

value: untreated control


title: Day 21 t3b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t3b


title: Day 21 t5b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t5b

value: maneb


title: Day 21 t35b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t35b

value: kainate


title: Day 21 t4b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t4b


title: Day 21 t5a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t5a


title: Day 21 un1b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7un1b


title: Day 21 t6a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t6a

value: monosodium glutamate


title: Day 21 un2a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7un2a


title: Day 21 t7a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t7a


title: Day 21 un1a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7un1a


title: Day 21 t6b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t6b


title: Day 21 t9a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t9a


title: Day 21 t30a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t30a


title: Day 21 t32b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t32b

value: amprolium


title: Day 21 t34b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t34b


title: Day 21 t30b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t30b


title: Day 21 t33b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t33b

value: BMAA


title: Day 21 t35a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t35a


title: Day 21 t33a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t33a


title: Day 21 t32a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t32a


title: Day 21 t34a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t34a


title: S_14

description: iliac crest needle biopsies

value: Female

value: bone

tag: age

value: old


title: Day 21 t29b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t29b

value: Dexamethasone


title: Day 21 t28a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t28a


title: Day 21 t26b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t26b


title: Day 21 t29a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t29a


title: Day 21 t27b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t27b

value: Vincristine


title: Day 21 t2b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t2b

value: bioallethrin


title: Day 21 t27a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t27a


title: Day 21 t2a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t2a


title: Day 21 t28b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t28b


title: Day 21 t21b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t21b

value: Isotretinoin


title: Day 21 t25a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t25a

value: Okadaic acid


title: Day 21 t26a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t26a


title: Day 21 t24a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t24a


title: Day 21 t23b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t23b

value: Bis-I


title: Day 21 t24b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t24b


title: Day 21 t22b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t22b

value: lead acetate


title: Day 21 t22a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t22a


title: Day 21 t18b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t18b

value: Thalidomide


title: Day 21 t20a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t20a

value: Carbamazepine


title: Day 21 t20b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t20b


title: Day 21 t18a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t18a


title: Day 21 t19a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t19a

value: Amiodarone


title: Day 21 t21a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t21a


title: Day 21 t1b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t1b

value: benzene


title: Day 21 t19b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t19b


title: Day 21 t17b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t17b

value: (trans) Retinoic acid


title: Day 21 t23a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t23a


title: Day 21 t1a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t1a


title: MOLM-13 BRD2.1638

description:
Sample 88
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv

data_processing:
The paired-end and single-read fragments were trimmed on their 5' end (6 cycles PE100, 2 cycles SR50 NEB RNA sample prep protocol)
Adaptors were removed using cutadapt v1.4.2 and reads with a length of less than 18bp in any read of the pair were discarded. (Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, Read2: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT)
The trimmed and adaptor free reads were aligned against rDNA of the respective organism using bowtie2 v2.0.2 for paired-end and bowtie v0.12.5 for single-end reads. (100PE: bowtie2 (v2.0.2) --sensitive-local, 50SR: bowtie v0.12.5 -v 3 -k 1 --tryhard --chunkmbs 256)
The rRNA cleaned paired-end reads were aligned against the transcriptome to estimate the fragment size and the standard deviation of the fragment size using bwa v0.6.2. ( -N 1 -n 1 -a 1000)
The rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-Seq reads using splice junction guidance of a GTF annotation file (mouse: mm10, RefSeq from UCSC, 2012/5/23, human: hg19, RefSeq 2012/11/30) (--segment-mismatches 1 --max-multihits 20 --library-type fr-firststrand --initial-read-mismatches 2, 100PE: --segment-length 25 --mate-inner-dist value from transcriptome alignment --mate-std-dev value from transcriptome alignment; SR50: --segment-length 24)
The uniquely aligning reads were used for counting per gene with htseq-count v 0.6.1p with the overlap-resolution mode option set to 'union' using the processed RefSeq-annotated gene database (supplementary files refseq.hg19.2014_0110.imp.merged.uniq.exons.fulltable.gtf and refseq.mm10.2014_3006.imp.merged.uniq.exons.fulltable.gtf)
genome build: hg19 / mm10
processed data files format and content: Tab-delimited text files containing raw counts and RPKMs for given samples

extract_protocol:
Cells were harvested, flash frozen on dry ice, and RNA was extracted using RLT plus buffer (Qiagen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA

value: Leukemia


title: MOLM-13 BRD3.3235

description:
Sample 89
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: Day 21 t16b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t16b

value: Busulfan


title: Day 21 t15b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t15b


title: K-562 BRD3.3235

description:
Sample 85
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: Day 21 t16a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t16a


title: K-562 BRD4.1817

description:
Sample 86
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: Day 21 t25b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t25b


title: Day 21 t14b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t14b

value: Cadmium


title: SU-8686 2h JQ1 200 nM

description:
Sample 81
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

tag: treatment

value: 2h JQ1 200 nM

value: PDAC


title: K-562 BRD2.1638

description:
Sample 84
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: Day 21 t15a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t15a


title: MIAPACA-2 2h JQ1 200 nM

description:
Sample 78
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: SU-8686 24h JQ1 200 nM

description:
Sample 82
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MIAPACA-2 24h JQ1 200 nM

description:
Sample 79
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 t17a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t17a


title: MOLM-13 BRD4.1817

description:
Sample 90
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: MIAPACA-2 DMSO

description:
Sample 77
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

value: DMSO


title: HUPT-4 24h JQ1 200 nM

description:
Sample 76
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: HUPT-4 2h JQ1 200 nM

description:
Sample 75
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MOLM-13 Ren.713

description:
Sample 87
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: Day 21 t10a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t10a


title: Day 21 t11b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t11b

value: Cytosine β-D-arabinofuranoside


title: Day 21 t10b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t10b


title: Day 21 t11a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t11a


title: Day 21 t12a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t12a

value: Dioxin


title: Day 21 t12b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t12b


title: Day 21 t13b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t13b

value: Arsenic


title: Day 21 t13a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t13a


title: HUPT-4 DMSO

description:
Sample 74
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: CAPAN-2 2h JQ1 200 nM

description:
Sample 72
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c9b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c9b


title: K-562 Ren.713

description:
Sample 83
processed_data file: BRD_KD_counts.tsv
processed_data file: BRD_KD_RPKMs.tsv


title: CAPAN-2 24h JQ1 200 nM

description:
Sample 73
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 t14a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7t14a


title: Day 21 c8b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c8b

value: PVP


title: Day 21 c9a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c9a


title: SU-8686 DMSO

description:
Sample 80
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: CAPAN-2 DMSO

description:
Sample 71
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: HPAF-1 24h JQ1 200 nM

description:
Sample 70
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: HPAF-1 2h JQ1 200 nM

description:
Sample 69
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c7b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c7b

value: fructose


title: Day 21 c8a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c8a


title: HPAF-1 DMSO

description:
Sample 68
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c6b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c6b

value: sucrose


title: ASPC-1 24h JQ1 200 nM

description:
Sample 67
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c6a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c6a


title: ASPC-1 2h JQ1 200 nM

description:
Sample 66
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: ASPC-1 DMSO

description:
Sample 65
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c5b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c5b

value: sorbitol


title: SHP-77 2h JQ1 200 nM

description:
Sample 63
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

value: SCLC


title: SHP-77 24h JQ1 200 nM

description:
Sample 64
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c5a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c5a


title: Day 21 c3b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c3b

value: glyphosate


title: DMS-53 24h JQ1 200 nM

description:
Sample 61
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: SHP-77 DMSO

description:
Sample 62
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c4b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c4b

value: saccharin


title: DMS-53 2h JQ1 200 nM

description:
Sample 60
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c2a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c2a

value: amoxicillin


title: DMS-273 24h JQ1 200 nM

description:
Sample 58
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: DMS-273 2h JQ1 200 nM

description:
Sample 57
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: DMS-53 DMSO

description:
Sample 59
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c26b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c26b

value: hCG


title: DMS-273 DMSO

description:
Sample 56
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c25b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c25b

value: 18 beta-estradiol


title: Day 21 c25a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c25a

value: 17 beta-estradiol


title: Day 21 c7a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c7a


title: NCIH-82 2h JQ1 200 nM

description:
Sample 54
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

value: 2h JQ1 200 nM


title: Day 21 c24b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c24b


title: NCIH-82 DMSO

description:
Sample 53
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c23b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c23b

value: tamoxifen


title: NCIH-69 24h JQ1 200 nM

description:
Sample 52
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: NCIH-69 2h JQ1 200 nM

description:
Sample 51
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c2b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c2b


title: Day 21 c4a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c4a


title: Day 21 c22b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c22b

value: Carbenicillin


title: NCIH-1048 2h JQ1 200 nM

description:
Sample 48
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: NCIH-1048 DMSO

description:
Sample 47
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

value: DMSO


title: NCIH-1048 24h JQ1 200 nM

description:
Sample 49
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c26a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c26a


title: Day 21 c20b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c20b

value: Meropenem


title: K-562 24h JQ1 200 nM

description:
Sample 46
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv

value: Leukemia


title: K-562 2h JQ1 200 nM

description:
Sample 45
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c20a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c20a


title: Day 21 c21b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c21b

value: Doxycycline


title: NCIH-82 24h JQ1 200 nM

description:
Sample 55
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MOLT-3 24h JQ1 200 nM

description:
Sample 43
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MOLT-3 2h JQ1 200 nM

description:
Sample 42
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c3a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c3a


title: K-562 DMSO

description:
Sample 44
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c1a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c1a

value: Acetaminophen


title: Day 21 c24a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c24a


title: Day 21 c19b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c19b

value: glycogen


title: MOLT-3 DMSO

description:
Sample 41
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: NCIH-69 DMSO

description:
Sample 50
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c18b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c18b

value: Cefepime


title: Day 21 c19a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c19a


title: Day 21 c22a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c22a


title: Day 21 c23a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c23a


title: MEG-1 24h JQ1 200 nM

description:
Sample 40
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MEG-1 2h JQ1 200 nM

description:
Sample 39
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MEG-1 DMSO

description:
Sample 38
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c17a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c17a

value: Resveratrol


title: MV4-11 24h JQ1 200 nM

description:
Sample 37
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: MV4-11 2h JQ1 200 nM

description:
Sample 36
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c17b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c17b


title: Day 21 c21a

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c21a


title: MV4-11 DMSO

description:
Sample 35
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c1b

description:
Human neural progenitor cells were cultured on PEG hydrogel in N2B27F2 media, endothelial cells and mesenchymal cells were then seeded on top of the NPC on day 9. Microglia/macrophage progenitors were seeded on day 13. Chemicals exposure started on day 14. Cells were lysed for RNA purification on day 21.
140304_multiplexing_Lanes123456_d7c1b