title: Day 21 c15b

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_d7c15b

value: Naproxen sodium


title: Day 21 c16b

status: Public on Sep 08 2015

type: SRA

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

country: USA

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_d7c16b

library_source: transcriptomic

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)

molecule: total RNA

organism: Homo sapiens

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: DMSO


title: KASUMI-1 2h JQ1 200 nM

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

description:
Sample 33
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_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

source_name: Cell line

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: treatment

value: 2h JQ1 200 nM

tag: diagnosis

value: Leukemia


title: KASUMI-1 24h JQ1 200 nM

description:
Sample 34
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c18a

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_d7c18a

value: Cefepime


title: Day 21 c14b

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_d7c14b

value: ficoll 401


title: MOLM-13 24h JQ1 200 nM

description:
Sample 31
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: KASUMI-1 DMSO

description:
Sample 32
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c13b

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_d7c13b

value: aspirin


title: MOLM-13 DMSO

description:
Sample 29
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 c15a

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_d7c15a


title: Day 21 c11a

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_d7c11a

value: glycerol


title: Day 21 c10b

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_d7c10b

value: ibuprofen


title: Day 21 c11b

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_d7c11b


title: Day 21 c12a

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_d7c12a

value: glucosamine


title: Day 21 c10a

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_d7c10a


title: Day 21 b9a

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_d7b9a

value: Oleic acid


title: Day 21 b9b

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_d7b9b


title: Day 21 c13a

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_d7c13a


title: Day 21 b8b

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_d7b8b

value: PenStrep (1x)


title: Day 21 b7b

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_d7b7b

value: maltose


title: Day 21 b7a

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_d7b7a


title: Day 21 b8a

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_d7b8a


title: Day 21 b6b

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_d7b6b

value: lactose


title: Day 21 b5b

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_d7b5b

value: Ouabain


title: Day 21 b6a

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_d7b6a


title: Day 21 c12b

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_d7c12b


title: Day 21 b3b

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_d7b3b


title: Day 21 b4a

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_d7b4a


title: Day 21 b5a

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_d7b5a


title: Day 21 c14a

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_d7c14a

value: ficoll 400


title: Day 21 b4b

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_d7b4b


title: Day 21 b2b

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_d7b2b


title: MOLM-13 2h JQ1 200 nM

description:
Sample 30
processed_data file: human_JQ1_timeseries_counts.tsv
processed_data file: human_JQ1_timeseries_RPKMs.tsv


title: Day 21 b3a

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_d7b3a


title: Day 21 b2a

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_d7b2a


title: Day 21 b1a

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_d7b1a

value: cyclopamine


title: Day 21 b10b

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_d7b10b

value: arabinose


title: Day 21 b10a

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_d7b10a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2un2b

value: untreated control


title: Day 16 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 16.
140304_multiplexing_Lanes123456_d2t13a_reprep

value: Arsenic


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2un2a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2un1b


title: Day 16 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 16.
140304_multiplexing_Lanes123456_d2t11a_reprep

value: Cytosine β-D-arabinofuranoside


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t9b

value: propylthiouracil


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2un1a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t9a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t7b

value: permethrin


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t8b

value: L-phenylalanine


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t7a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t6b

value: monosodium glutamate


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t8a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t4b

value: hydroxyurea


title: Day 21 b1b

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_d7b1b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t5a

value: maneb


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t35a

value: kainate


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t5b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t3a

value: diazinon


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t34a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t33b

value: BMAA


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t34b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t35b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t3b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t33a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t32b

value: amprolium


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t6a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t32a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t2a

value: bioallethrin


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t30b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t29b

value: Dexamethasone


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t30a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t2b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t29a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t28b


title: Day 16 t4a

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 16.
140218_multiplexing_Lanes123456_d2t4a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t27b

value: Vincristine


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t26a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t24b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t24a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t23b

value: Bis-I


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t22a

value: lead acetate


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t23a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t22b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t21a

value: Isotretinoin


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t25a

value: Okadaic acid


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t21b


title: Day 21 c16a

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_d7c16a

value: DMSO


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t19b

value: Amiodarone


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t19a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t1b

value: benzene


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t20a

value: Carbamazepine


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t18b

value: Thalidomide


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t17b

value: (trans) Retinoic acid


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t20b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t17a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t28a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t16b

value: Busulfan


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t27a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t26b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t16a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t25b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t15b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t18a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t15a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t14a

value: Cadmium


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t1a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t13b

value: Arsenic


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t12b

value: Dioxin


title: BxPC3 #3

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: HPAF-II #2

value: HPAF-II


title: HPAF-II #3


title: HPAF-II #1


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t10a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t12a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t10b


title: CFPAC-1 #3


title: BxPC3 #1


title: BxPC3 #2


title: CFPAC-1 #1


title: Capan-2 #3


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c9b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t14b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c8b

value: PVP


title: CFPAC-1 #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c7b

value: fructose


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c9a


title: Panc10.05 #3


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c7a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c8a


title: Panc10.05 #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c6b

value: sucrose


title: Capan-2 #1


title: Panc10.05 #1


title: AsPC1 #3


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c5b

value: sorbitol


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c6a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c5a


title: AsPC1 #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2t11b

value: Cytosine β-D-arabinofuranoside


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c4b

value: saccharin


title: Panc05.04 #3

tag: sf3b1 mutation


title: AsPC1 #1


title: Panc05.04 #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c4a


title: Capan-2 #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c3b

value: glyphosate


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c3a


title: Nalm-6 H662Q #3

source_name: B-cell precursor


title: Nalm-6 H662Q #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c2a

value: amoxicillin


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c2b


title: Panc05.04 #1


title: Nalm-6 H662Q #1


title: Nalm-6 K666N #3


title: Nalm-6 K666N #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c26b

value: hCG


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c26a


title: Nalm-6 K666N #1


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c25b

value: 18 beta-estradiol


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c24b


title: Nalm-6 K700E + CHX #3

value: CHX


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c25a

value: 17 beta-estradiol


title: Nalm-6 K700E + CHX #2


title: Nalm-6 K700E + CHX #1


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c23b

value: tamoxifen


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c24a


title: Nalm-6 WT + CHX #3


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c23a


title: Nalm-6 WT + CHX #2


title: Nalm-6 WT + CHX #1


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c22a

value: Carbenicillin


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c22b


title: Nalm-6 K700E #3


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c21a

value: Doxycycline


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c21b


title: Nalm-6 K700E #2


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c20b

value: Meropenem


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c20a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c1a

value: Acetaminophen


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c1b


title: Nalm-6 WT #2


title: Nalm-6 WT #1


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c19b

value: glycogen


title: 863P-R

source_name: Bone Marrow

tag: disease state

value: MDS


title: 826P-R


title: 712P-R


title: Day 16 c18a

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 16.
140218_multiplexing_Lanes123456_d2c18a

value: Cefepime


title: 703P-R


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c18b


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c19a


title: Day 16 c16b

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 16.
140218_multiplexing_Lanes123456_d2c16b

value: DMSO


title: 404P-R


title: 411P-R


title: 403P-R


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c17a

value: Resveratrol


title: Nalm-6 K700E #1


title: Day 16 c16a

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 16.
140218_multiplexing_Lanes123456_d2c16a


title: Day 16 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 16.
140218_multiplexing_Lanes123456_d2c17b


title: Nalm-6 WT #3


title: 401P-R


title: Day 16 c15b

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 16.
140218_multiplexing_Lanes123456_d2c15b

value: Naproxen sodium


title: Day 16 c14b

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 16.
140218_multiplexing_Lanes123456_d2c14b

value: ficoll 401


title: Day 16 c15a

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 16.
140218_multiplexing_Lanes123456_d2c15a


title: 417P-R


title: 400P-R


title: 399P-R


title: 302P-R


title: Day 16 c14a

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 16.
140218_multiplexing_Lanes123456_d2c14a

value: ficoll 400


title: 390P-R


title: Day 16 c13b

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 16.
140218_multiplexing_Lanes123456_d2c13b

value: aspirin


title: 1116P-R


title: NIH-3T3 K700E #2

organism: Mus musculus

source_name: Stroma


title: Day 16 c13a

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 16.
140218_multiplexing_Lanes123456_d2c13a


title: NIH-3T3 K700E #1


title: CLL320-DMSO

value: CLL


title: NIH-3T3 WT #3


title: Day 16 c12a

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 16.
140218_multiplexing_Lanes123456_d2c12a

value: glucosamine


title: CLL292-DMSO


title: NIH-3T3 WT #2


title: CLL230-DMSO


title: NIH-3T3 WT #1


title: Day 16 c11a

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 16.
140218_multiplexing_Lanes123456_d2c11a

value: glycerol


title: Day 16 c10b

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 16.
140218_multiplexing_Lanes123456_d2c10b

value: ibuprofen


title: Day 16 c10a

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 16.
140218_multiplexing_Lanes123456_d2c10a


title: WT control MECs, replicate 2

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

data_processing:
RNA-Seq NGS reads were mapped using STAR RNASeq aligner (version 2.3.0)
Paired read count tabulations generated for each transcript based on overlap with transcript start and stop
count tabulations were performed with HTSeq (version 0.3.1)
Genome_build: mm9
Supplementary_files_format_and_content: forGEO_mm9.txt generated by HTSeq v0.3.1

source_name: Primary mammary epithelial cells

extract_protocol:
Primary mammary epithelial cells were extracted and purified using FACS sorting.  Cells were collected, spun down to remove media and flash frozen in liquid nitrogen as pellets. Total RNA was isolated using Qiagen's miRNeasy kit according to the manufacture's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

value: 129X1/SvJ, C57BL/6, and Swiss Webster

tag: age

value: Nine weeks

tag: Sex

value: Female

tag: developmental stage

value: Adult

tag: genotype/variation

value: mT-mG/SmoM2;+ (wild type)

tag: cell type

value: MEC


title: WT control MECs, replicate 4


title: WT control MECs, replicate 3


title: Day 16 b9b

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 16.
140218_multiplexing_Lanes123456_d2b9b

value: Oleic acid


title: WT control MECs, replicate 1


title: Day 16 c11b

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 16.
140218_multiplexing_Lanes123456_d2c11b


title: NIH-3T3 K700E #3


title: CLL221-DMSO


title: CLL391


title: Day 16 b9a

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 16.
140218_multiplexing_Lanes123456_d2b9a


title: CLL371


title: CLL368


title: Unrecombined SmoM2- MECs, replicate 4

value: mT-mG/SmoM2;MMTV-Cre (SmoM2 negative)


title: Unrecombined SmoM2- MECs, replicate 3


title: CLL037-DMSO


title: Day 16 c12b

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 16.
140218_multiplexing_Lanes123456_d2c12b


title: Unrecombined SmoM2- MECs, replicate 2


title: CLL290


title: Day 16 b7b

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 16.
140218_multiplexing_Lanes123456_d2b7b

value: maltose


title: Unrecombined SmoM2- MECs, replicate 1


title: CLL172-DMSO


title: CLL203


title: Recombined SmoM2+ MECs, replicate 4

value: mT-mG/SmoM2;MMTV-Cre (SmoM2 positive)


title: Recombined SmoM2+ MECs, replicate 3


title: Day 16 b7a

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 16.
140218_multiplexing_Lanes123456_d2b7a


title: CLL179


title: Recombined SmoM2+ MECs, replicate 2


title: STARRSeq_JQ1

description:
polyA+ RNA; PCR amplified cDNA (STARR-seq transcript)
Sample 108

data_processing:
Library strategy: STARR-Seq
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

extract_protocol: BAC DNA was fragmented using a Covaris sonicator. Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector. The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.

value: Leukemia


title: Day 16 b8b

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 16.
140218_multiplexing_Lanes123456_d2b8b

value: PenStrep (1x)


title: Day 16 b8a

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 16.
140218_multiplexing_Lanes123456_d2b8a


title: Day 16 b6a

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 16.
140218_multiplexing_Lanes123456_d2b6a

value: lactose


title: Recombined SmoM2+ MECs, replicate 1


title: STARRSeq_Input

description:
whole genome library (in STARR-seq vector); plasmid DNA (containing genomic DNA fragments); PCR amplified cDNA (STARR-seq transcript)
Sample 109

library_source: genomic

molecule: genomic DNA


title: Day 16 b4b

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 16.
140218_multiplexing_Lanes123456_d2b4b


title: STARRSeq_DMSO

description:
polyA+ RNA; PCR amplified cDNA (STARR-seq transcript)
Sample 107

value: DMSO, 24h


title: Day 16 b4a

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 16.
140218_multiplexing_Lanes123456_d2b4a


title: IP Ig on involved psoriatic skin sample

city: Montpellier

first: Geneviève

last: Garcin

address: UM2. Place Eugene Bataillon. Bat 24.

country: France

institute: CNRS UMR5235

description:
Mix of 5 biopsies from 5 patients.
IgG-binding RNA.

data_processing:
Library strategy: RIP-Seq
Image analyses and basecalling were performed using the HiSeq Control Software (HCS 1.4.8) and Real-Time Analysis component (RTA 1.12.4.0).
Demultiplexing, alignments and RNA counting were performed using CASAVA 1.8.1 (Illumina).
Alignment was made with eland_rna on the UCSC hg19 version of the human genome and on several contaminants (the ribosomal RNA sequences RN28S1, RN18S1 and RN5S1, the mitochondrial chromosome, the PhiX genome and the Illumina adaptors).
The transcript annotation ("exonic") was retrieved from UCSC (refFlat file) on January 22, 2012. Sequences were also aligned on intronic regions (downloaded from UCSC, refGene table).
Genome_build: GRCh37
Supplementary_files_format_and_content: Exonic.xls: Tab-delimited text file of HuR mature RNAs binding for uninvolved and involved psoriatic skin HuR RIP-Seq. 'HuR IP involved' and 'HuR IP uninvolved' are normalized counts. Transcripts with less than 10 reads in both uninvolved and involved skin HuR IPs were filtered and thus removed from the analysis. Transcripts with a ratio (HuR IP)/(mock IP) inferior to 0.5 log2 were also excluded. To avoid contamination of mature RNA transcripts with pre-mature RNA, values represent an "exonic relative read". Both in the 'HuR IP involved' and 'Hur IP uninvolved' columns, "exonic relative read" is calculated as follows: "exonic relative count"  = (("exonic count" divided by "mRNA length") minus ("intronic count" divided by ("gene length" minus "mRNA length")) multiplied by "mRNA length", where "gene length" was as indicated in the UCSC table and "mRNA length" was as  given in the RPKM formulation. We kept transcripts in the exonic listing when the ratio between "exonic relative count" and "intronic count" was superior or equal to 2 log2.
Supplementary_files_format_and_content: Intronic.txt: Tab-delimited text file of HuR pre-mature RNAs binding for uninvolved and involved psoriatic skin HuR RIP-Seq. 'HuR IP involved' and 'HuR IP uninvolved' are normalized counts. Transcripts with less than 10 reads in both uninvolved and involved skin HuR IPs were filtered and thus removed from the analysis. Transcripts with a ratio (HuR IP)/(mock IP) inferior to 0.5 log2 were also excluded.

source_name: involved psoriatic skin biopsies, IgG IP

growth_protocol: Five different patients were used for both uninvolved and involved psoriatic skin.

extract_protocol:
Frozen skin biopsies were disrupted using the MagNA Pure Instrument (Roche). Immunoprecipitations of endogenous RNA-protein complexes for involved and uninvolved psoriatic skin were carried out as previously described (Peritz T et al. Nat Protoc. 2006 (PMID     17406284 )) using protein-A-agarose that had been pre-coated with anti-HuR (clone 3A2, Santa Cruz Biotechnology, catalog number sc-5261, Lot# F1710)  or with isotype control (mock; clone G3A1, Cell Signaling, catalog number 5415, Lot# 1) antibodies.
Illumina TruSeq RNA Sample Prep Kit (RS-122-1001) was used with 10 ng of each RNA sample for the construction of sequencing libraries, as per manufacturer's recommendations.

tag: tissue

value: skin

tag: disease status

value: psoriasis

tag: ip antibody

value: mouse IgG1 isotype control


title: IP HuR on uninvolved psoriatic skin sample

description:
Mix of 5 biopsies from 5 patients.
HuR-binding RNA.

source_name: uninvolved psoriatic skin biopsies, HuR IP

value: no psoriasis

value: anti-HuR mouse monoclonal antibody


title: WT, rep2

city: Los Angeles

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description: WT-5; Wildtype Esrp1 and Esrp2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then mm10 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped pairs.
Genome_build: mm10
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample

source_name: Esrp1 WT/Esrp2 WT_E18.5 embryo

extract_protocol:
RNA from purified total epidermis (basal keratinocyte layer to cornified layer) of E18.5 mouse embryos were harvested by Trizol extraction. (Esrp1+/+, Esrp2-/- (n=2), Esrp1-/-, Esrp2+/+ (n=3), Esrp1-/-, Esrp2+/- (n=2), and Esrp1-/-, Esrp2-/- (n=2). 1 ug of total RNA was used for  for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed; C57BL6/129Sv (with back-crossed F4 generation into C57BL6/6)

value: Esrp1 WT/Esrp2 WT

value: Epidermis


title: WT, rep1

description: WT-1; Wildtype Esrp1 and Esrp2


title: IP HuR on involved psoriatic skin sample

source_name: involved psoriatic skin biopsies, HuR IP


title: KO, rep3

description: KO-4; Esrp1 KO, Wildtype Esrp2

source_name: Esrp1 KO/Esrp2 WT_E18.5 embryo

value: Esrp1 KO/Esrp2 WT


title: KO, rep2

description: KO-2; Esrp1 KO, Wildtype Esrp2


title: Day 16 b3a

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 16.
140218_multiplexing_Lanes123456_d2b3a


title: H3K27ac_LT_Off_Input

description:
input
Sample 106

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

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: shRNA

value: Longterm JQ1, 4 days drug withdrawal


title: KO, rep1

description: KO-1; Esrp1 KO, Wildtype Esrp2


title: H3K27ac_LT_Off

description:
H3K27ac antibody (Abcam, 4729)
Sample 105


title: Day 16 b2b

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 16.
140218_multiplexing_Lanes123456_d2b2b

tag: screening chemicals


title: KH, rep2

description: KH-2; Esrp1 KO, het Esrp2

source_name: Esrp1 KO/Esrp2 Het_E18.5 embryo

value: Esrp1 KO/Esrp2 Het


title: H3K27ac_LT_Input

description:
input
Sample 104

tag: treatment

value: Longterm JQ1


title: KH, rep1

description: KH-1; Esrp1 KO, het Esrp2


title: Day 16 b2a

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 16.
140218_multiplexing_Lanes123456_d2b2a


title: Day 16 b5a

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 16.
140218_multiplexing_Lanes123456_d2b5a

value: Ouabain


title: DKO, rep2

description: DKO-3; both Esrp1 and Esrp2 KO

source_name: Esrp1 KO/Esrp2 KO_E18.5 embryo

value: Esrp1 KO/Esrp2 KO


title: Day 16 b1b

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 16.
140218_multiplexing_Lanes123456_d2b1b

value: cyclopamine


title: Day 16 b5b

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 16.
140218_multiplexing_Lanes123456_d2b5b


title: H3K27ac_LT

description:
H3K27ac antibody (Abcam, 4729)
Sample 103

tag: diagnosis

value: Leukemia


title: Day 16 b1a

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 16.
140218_multiplexing_Lanes123456_d2b1a


title: H3K27ac_Renilla

description:
H3K27ac antibody (Abcam, 4729)
Sample 101

tag: cell line


title: Day 16 b10b

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 16.
140218_multiplexing_Lanes123456_d2b10b

value: arabinose


title: DMSO_Input

description:
Sample 28
processed_data file: mouse_DMSO_Input.bw

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) 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: mm10
processed data files format and content: bigWig files were generated for each individual IP.


title: Day 16 b3b

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 16.
140218_multiplexing_Lanes123456_d2b3b


title: DMSO_H3K27me3

description:
Sample 27
processed_data file: mouse_DMSO_H3K27me3.bw


title: Day 21 NPC + EC + MSC + MG Plate 2 s2

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. Cells were lysed for RNA purification on day21.
131227_multiplexing_Lanes7_E2_NPC_100KplusMSCinPeriplusECplusMG_D21_2


title: JQ1_Input

description:
Sample 25
processed_data file: mouse_JQ1_Input.bw

value: 3d JQ1 25 nM


title: p00satb_107

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
paired-end map to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
paired-end map (repeat-filtered reads) to mm9 with tophat
convert mappings to coverage of mm9 UCSC Known Genes
differential expression analysis with DESeq on per-gene, per-sample read counts, 3 replicates per condition
use DESeq sizeFactors to report per-sample normalized read counts for significant genes
Genome_build: mm9
Supplementary_files_format_and_content: for each significant gene, the read counts, normalized by DESeq sizeFactors, are shown for all replicates.

source_name: cortex

growth_protocol: Satb2+/- mice were bred with each other. P0 Satb2+/+ and Satb2-/- pups were used for the study.

extract_protocol:
Qiagen RNAeasy protocol was followed to isolate total RNAs from the dissected cortices.
Illumina TruSeq RNA sample preparation protocol
pairend sequencing, 50nt per end

treatment_protocol: Cerebral cortex was dissected out from 3 P0 Satb2+/+ and 3 Satb2-/- mice. Total RNAs from each brain were isolated using Qiagen RNAeasy kit. The sequencing libraries were generated following Illumina RNA TruSeq protocol. The libraries were sequenced on an Illumina Genome Analyzer II platform. DESeq was used to identify genes differentially expressed in Satb2-/- cortices.

value: cortex

value: post-natal day 0

tag: genotype

value: satb2 cKO

tag: litter


title: p00wild_110

value: wild type


title: Day 21 NPC + EC + MSC + MG Plate 1 s2

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. Cells were lysed for RNA purification on day21.
131227_multiplexing_Lanes7_E2_NPC_100KplusMSCinMSCplusECplusMG_D21_2


title: Day 21 NPC + EC + MSC + MG Plate 2 s1

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. Cells were lysed for RNA purification on day21.
131227_multiplexing_Lanes7_E2_NPC_100KplusMSCinPeriplusECplusMG_D21_1


title: p00wild_062


title: p00satb_106


title: CLL307

tag: disease state

value: CLL

tag: sf3b1 mutation


title: DKO, rep1

description: DKO-2; both Esrp1 and Esrp2 KO

value: mixed; C57BL6/129Sv (with back-crossed F4 generation into C57BL6/6)

tag: age


title: H3K27ac_Renilla_Input

description:
input
Sample 102


title: Day 16 b6b

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 16.
140218_multiplexing_Lanes123456_d2b6b

value: lactose


title: p00satb_105


title: H1  Human Embryonic Stem Cells Sample 4

description:
Human embrynoic stem cell H1 were cultured in E8 media and harvested for RNA.
131227_multiplexing_Lanes3_Sample_38463_000192

source_name: H1 human embryonic stem cells


title: satb2_36

data_processing:
The raw 100x100bp pairedEnd reads were trimmed to 75x75bp by discarding 5bp from the 5' end and 20bp from the 3'end of both read1 and read2.
The trimmed reads were paired-end mapped to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
The (repeat-filtered) reads were paired-end mapped to mm9 with bowtie
The mapped paired-end reads were used to estimate the MACS shiftsize parameter
The read1 mappings were input to MACS for peak calling, using the input sample as a control for the ChIP sample.
Genome_build: mm9
Supplementary_files_format_and_content: MACS peaks are in bed format. Score is -10log10 of pval

growth_protocol: timed pregnant CD1 mice were ordered from Charles River Laboratory

extract_protocol:
Lysate from sonicaed cortices were cleared after centrifugation. Satb2-DNA complexes were isolated using a Satb2 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
ChIP-Seq library was sequenced for pair-end sequencing (100 nt per end) on an Illumina Genome Analyzer II platform

treatment_protocol: Cerebral cortex were dissected out from E15 embryos, fixed in 1% formadehyde, neutralized using 2% glycine,  and processed for chromatin IP using Satb2 antibody.

tag: strain

value: embryonic day 15

tag: chip antibody

value: SATB2 antibody


title: input_38


title: p00wild_064


title: H1  Human Embryonic Stem Cells Sample 3

description:
Human embrynoic stem cell H1 were cultured in E8 media and harvested for RNA.
131227_multiplexing_Lanes3_Sample_38460_000189


title: H1  Human Embryonic Stem Cells Sample 2

description:
Human embrynoic stem cell H1 were cultured in E8 media and harvested for RNA.
131227_multiplexing_Lanes3_Sample_38459_000188


title: RN2 Empty vector

description:
Sample 17
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv

value: Empty vector


title: RN2 Ren.713

description:
Sample 16
processed_data file: mouse_KD_counts.tsv
processed_data file: mouse_KD_RPKMs.tsv


title: Day 16 b10a

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 16.
140218_multiplexing_Lanes123456_d2b10a


title: H1  Human Embryonic Stem Cells Sample 1

description:
Human embrynoic stem cell H1 were cultured in E8 media and harvested for RNA.
131227_multiplexing_Lanes3_Sample_38458_000187