title: WG17009_G07-W02


title: WG17009_G06-W28

status: Public on Aug 22 2018

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped  to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability. For the human samples all reads mapping anywhere within the whole locus, defined as the region (including actual introns) from the start of the 100 base 5'end extension of the first exon up to the end of the last exon, were counted as exon-derived.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

molecule: polyA RNA

organism: Mus musculus

source_name: striatum

growth_protocol: Mice were housed on a standard 12+12 light/dark cycle with 2-5 mice per cage

extract_protocol:
Dorso-lateral striatum (bregma, AP: 1.42 to -0.58 mm) from Lhx6Cre:RFP, Pvcre:TdT and Htr3aEGFP mice was dissociated into a single cell suspension as described in Zeisel et al., Science vol. 347  p.1138 (2015) . Dissociated cells were FACS sorted based on fluorescence (RFP+ and EGFP+) and positive cells were sorted using BD FACSAria II SORP into a 9600 multiwell array (2400 cells/plate) prefilled with 50 nl lysis buffer (500nM STRT-P1-T31, 4.5nM dNTP, 2% Triton-X-100, 20mM DTT, 1.5U/μl TaKaRa RNase Inhibitor), followed by 3min lysis at 72°C.
85nl reverse transcription (RT) mix (2.1X SuperScript II First-Strand Buffer, 12.6mM MgCl2, 1.79M betaine, 14.7U/μl SuperScript II, 1.58U/μl TaKaRa RNase Inhibitor, 10.5μM P1B-UMI-RNA-TSO) were dispensed and RT carried out 42°C for 90 minutes. 96 Transposome stocks were assembled (6.25μM barcoded adapter (STRT-Tn5-Idx[1-96]), 6.25μM Tn5 transposase, 40% glycerol), 37°C 1h.  Tn5 reactions were assembled with 3μl transposome and 2μl amplified cDNA, in a total 20μl 1x CutSmart buffer (NEB), and incubated at 55°C 20min.

tag: strain

tag: Sex

value: male

tag: postnatal days

tag: cell type

value: Migrating


title: WG17009_G07-W26


title: WG17009_G07-W18


title: 1772094153_A05

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: text table of total number of detected mRNA molecules from each gene in each cell

molecule: total RNA

growth_protocol: Two mouse transgenic lines on CD1 background were used in order to enrich the interneuron populations. The Lhx6-Cre  RFP, a BAC transgenic mouse that express Cre under transcriptional  control of Lim homeobox 6, together with the expression of the tandem-dimer red  fluorescent protein (tdRFP) (ubiquitously expressed under the ROSA26 locus. And  the BAC transgenic mouse 5HT3a-EGFP, where EGFP is expressed under the control of  the Htr3a promoter. The mice were between postnatal day 22-28  and comprised both sexes.

extract_protocol:
Mice were deeply anesthetized, and the brain was quickly dissected and sectioned on a  vibratome (VT1200 S, Leica) in 300 micrometer thick slices. The dorso-lateral striatum (bregma, AP: 1.42 to -0.58 mm) was  dissected from each slice, and the tissue was dissociated using the Papain dissociation  system (Worthington). The cell suspension obtained was filtered with 20 micrometer  filter (Partec). RFP+ or EGFP+ cells were immediately FACS sorted using a BD FACSAria III Cell Sorter B5/R3/V3 system.   7 microliter of both the fluorescent and non-fluorescent populations at 600-1000 cells/microliter had 4 microliter of C1 Cell Suspension Reagent added, and loaded on a C1  Single-Cell AutoPrep IFC microfluidic chip designed for 10-17-micrometer cells  (Fluidigm Inc.).
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip.  The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR.  The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected.   To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

tag: tissue

value: brain

tag: brain region

value: dorsolateral striatum

value: ASTRO

tag: gfp fluorescence

tag: rfp fluorescence

tag: age (days)

value: female


title: 1772094153_A03


title: 1772094153_A11

value: VSM


title: 1772094153_B06


title: 1772094153_B09

value: OLIGOS


title: 1772094152_H04


title: WG17009_G06-W19


title: 1772094153_C01


title: 1772094152_H02


title: WG17009_G06-W18


title: 1772094152_G06


title: 1772094152_G05


title: WG17009_G06-W14


title: 1772094152_H10


title: WG17009_G06-W13


title: 1772094153_A09

value: ENDO


title: 1772094152_F06


title: 1772094152_F04


title: WG17009_G06-W12


title: WG17009_G06-W11


title: 1772094152_E11


title: WG17009_G06-W25


title: 1772094152_E06


title: WG17009_G06-W26


title: 1772094152_E04


title: WG17009_G06-W09

value: Cycling


title: 1772094152_G10


title: WG17009_G06-W16


title: WG17009_G06-W07


title: 1772094152_D05


title: 1772094152_D04


title: 1772094152_C12


title: WG17009_G06-W03


title: WG17009_G06-W01

value: Th


title: 1772094152_C08


title: WG17009_G06-W02


title: WG17009_G05-W28


title: WG17009_G05-W26


title: WG17009_G05-W25


title: 1772094152_B11


title: 1772094152_B12


title: 1772094152_D08


title: WG17009_G06-W08


title: WG17009_G05-W19

value: Pthlh


title: WG17009_G05-W20


title: WG17009_G06-W04


title: 1772094152_A12


title: WG17009_G06-W05


title: 1772094152_B06


title: WG17009_G05-W15


title: WG17009_G05-W17


title: WG17009_G05-W18


title: 1772094152_C11


title: 1772094152_C07


title: 1772094148_G03

value: MICROGLIA


title: 1772094148_E12


title: WG17009_G10-W06


title: WG17009_G05-W14


title: WG17009_G05-W13


title: 1772094147_H12


title: 1772094147_H06


title: WG17009_G05-W10


title: WG17009_G05-W12


title: 1772094152_B10


title: WG17009_G05-W21


title: 1772094152_B05


title: WG17009_G05-W07


title: 1772094147_G05


title: WG17009_G05-W06


title: 1772094147_G06


title: 1772094148_C02


title: 1772094147_F06


title: WG17009_G05-W04


title: WG17009_G05-W05


title: WG17009_G05-W02


title: 1772094147_F02


title: 1772094147_F12


title: 1772094147_H07

value: OPC


title: WG17009_G05-W03


title: 1772094147_E01


title: 1772094147_E10


title: 1772094147_E04


title: WG17009_G05-W01


title: WG17009_G04-W25


title: 1772094147_C10


title: 1772094147_D04


title: 1772094147_G11


title: WG17009_G04-W26


title: WG17009_G05-W09


title: 1772094147_C06


title: 1772094147_E02


title: 1772094147_C08


title: WG17009_G04-W28


title: 1772094147_C05


title: WG17009_G04-W19


title: WG17009_G04-W21


title: 1772094147_A05


title: 1772094147_B11


title: WG17009_G04-W20


title: WG17009_G04-W11


title: 1772094147_C04


title: 1772094147_C03


title: 1772094147_C01


title: WG17009_G04-W15


title: WG17009_G04-W13


title: WG17009_G04-W18


title: WG17009_G04-W12


title: 1772094147_A04


title: WG17009_G04-W10


title: 1772092318_H06


title: WG17009_G04-W08


title: WG17009_G04-W05


title: WG17009_G04-W09


title: 1772092318_G08


title: WG17009_G04-W16


title: 1772092318_H04


title: WG17009_G04-W04


title: WG17009_G04-W06


title: 1772092318_G05


title: 1772092318_G04

value: Sst


title: 1772092318_F12

value: Pvalb


title: 1772092318_G06


title: WG17009_G04-W01


title: WG17009_G03-W27


title: 1772092318_F11


title: 1772092318_F07


title: 1772092318_F09


title: 1772092318_F06


title: WG17009_G03-W18


title: WG17009_G03-W09


title: WG17009_G03-W05


title: WG17009_G03-W17


title: WG17009_G03-W11


title: WG17009_G03-W07


title: WG17009_G03-W10


title: WG17009_G03-W15


title: WG17009_G03-W02


title: WG17009_G03-W12


title: 1772092318_F04


title: WG17009_G04-W03

value: Cck


title: 1772092318_F02

value: male


title: WG17009_G03-W01

value: Migrating


title: WG17009_G03-W04


title: 1772092318_F01

value: brain


title: 1772092318_E11

value: dorsolateral striatum


title: 1772092318_E08


title: 1772092318_D06


title: 1772092318_E06


title: 1772092318_D12


title: 1772092318_D11


title: 1772092318_E07


title: 1772092318_C10


title: 1772092318_D05


title: 1772092318_C11


title: WG17009_G02-W19


title: WG17009_G02-W10


title: WG17009_G02-W08


title: 1772092318_C09


title: WG17009_G03-W25


title: WG17009_G01-W26


title: 1772092318_C07


title: WG17009_G01-W20


title: WG17009_G01-W25


title: 1772092318_B10


title: 1772092318_B07


title: 1772092318_C06


title: WG17009_G01-W11


title: WG17009_G01-W17


title: WG17009_G01-W13


title: 1772092318_B05


title: WG17009_G01-W03


title: WG17009_G01-W10


title: WG17009_G01-W09


title: 1772092318_B03


title: WG17009_F11-W26


title: WG17009_F11-W18


title: 1772092318_A12


title: WG17009_F11-W17


title: 1772092318_B02


title: 1772092318_A11


title: 1772092318_A10


title: WG17009_F11-W16


title: 1772092318_A09


title: 1772092318_A04


title: 1772092318_A05


title: WG17009_F11-W08


title: 1772092318_A02


title: WG17009_F11-W07


title: 1772092315_H07


title: 1772092315_H10


title: WG17009_G01-W07


title: WG17009_F10-W15


title: WG17009_F09-W28


title: 1772092315_H04


title: WG17009_F09-W27


title: 1772092315_H06

value: ASTRO


title: WG17009_F09-W26


title: 1772092315_G10

value: female


title: 1772092315_G09


title: 1772092315_G07


title: WG17009_F11-W02


title: 1772092315_G06


title: 1772092315_G02

value: VSM


title: 1772092315_F11

value: OLIGOS


title: 1772092315_G01


title: 1772092315_F12


title: WG17009_F09-W18


title: WG17009_F09-W16


title: 1772092315_F10


title: WG17009_F09-W19


title: 1772092315_F09

value: ENDO


title: WG17009_F09-W17


title: 1772092315_F04


title: WG17009_F09-W12


title: WG17009_F09-W10


title: WG17009_F09-W11


title: 1772092315_G12


title: WG17009_F10-W07


title: 1772092315_F03


title: WG17009_F09-W09


title: 1772092315_E10


title: WG17009_F09-W08


title: WG17009_F09-W04


title: WG17009_F09-W03


title: WG17009_F09-W07


title: 1772092315_E02


title: 1772092315_E06


title: WG17009_F09-W14


title: 1772092315_E05


title: WG17009_F09-W02


title: WG17009_F08-W28


title: WG17009_F08-W27


title: WG17009_F08-W25


title: WG17009_F08-W20


title: 1772092315_D05


title: WG17009_F08-W18


title: WG17009_F08-W14


title: 1772092315_C04


title: 1772092315_D03


title: 1772092315_B05


title: WG17009_F08-W17


title: 1772092315_B04


title: 1772092315_C07

value: CHAT


title: 1772092315_A12


title: 1772092315_C05


title: 1772092315_A06


title: WG17009_F08-W12


title: 1772092315_B01


title: 1772092315_A04


title: 1772092315_A02


title: 1772092315_A01


title: WG17009_F08-W02

value: Cycling


title: WG17009_F08-W11


title: 1772092312_H02


title: 1772092315_C11


title: WG17009_F08-W01


title: WG17009_F07-W28


title: WG17009_F08-W16


title: WG17009_F07-W27


title: 1772092312_H01


title: 1772092312_G10


title: WG17009_F07-W26


title: WG17009_F07-W20

value: Cck+Vip+


title: WG17009_F07-W25

value: Th


title: WG17009_F07-W17


title: 1772092312_F08


title: 1772092312_E08


title: 1772092312_F03


title: WG17009_F08-W04


title: WG17009_F08-W09


title: WG17009_F07-W15


title: WG17009_F07-W13


title: WG17009_F07-W14


title: WG17009_F07-W16


title: 1772092312_E07


title: 1772092312_E06


title: 1772092312_D12


title: 1772092312_D09


title: WG17009_F07-W12


title: WG17009_F07-W11


title: 1772092312_D02


title: 1772092312_D05


title: 1772092312_G04


title: WG17009_F07-W09


title: 1772092312_C06

value: MICROGLIA


title: 1772092312_C04

value: CYCLING


title: 1772092312_C03


title: 1772092312_C02


title: WG17009_F07-W06


title: WG17009_F07-W07


title: WG17009_F07-W08


title: WG17009_F07-W04


title: 1772092312_B09


title: WG17009_F07-W02


title: WG17009_F07-W03


title: 1772092312_B12


title: 1772092312_B03


title: 1772092312_A03


title: WG17009_F06-W13


title: WG17009_F06-W14

value: Pthlh


title: WG17009_F06-W16


title: 1772092312_A02


title: 1772092311_H04


title: WG17009_F06-W15


title: WG17009_F06-W12


title: WG17009_F07-W01


title: 1772092311_G10


title: 1772092312_B05

value: Sst


title: WG17009_F06-W11

value: male


title: 1772092311_G12


title: WG17009_F06-W10


title: WG17009_F06-W07


title: 1772092311_F05


title: 1772092311_F08


title: WG17009_F06-W04


title: WG17009_F06-W05


title: 1772092311_E05


title: 1772092311_F04


title: 1772092312_A08


title: WG17009_F05-W26


title: 1772092311_E02


title: WG17009_F05-W25


title: WG17009_F05-W18

value: Migrating


title: 1772092311_D12

value: brain


title: 1772092311_E01

value: dorsolateral striatum


title: WG17009_F05-W12


title: 1772092311_D08


title: WG17009_F05-W13


title: 1772092311_D05


title: WG17009_F05-W11


title: WG17009_F05-W09


title: WG17009_F05-W08


title: WG17009_F05-W28


title: WG17009_F05-W06


title: WG17009_F05-W27


title: 1772092311_D04

value: ASTRO


title: 1772092311_C10


title: WG17009_F05-W05


title: 1772092311_F11


title: 1772092311_D03


title: 1772092311_C11


title: WG17009_F05-W07


title: 1772092311_C09


title: WG17009_F05-W14


title: 1772092311_D11


title: 1772092311_D06


title: WG17009_F05-W03

value: female


title: 1772092311_C06

value: VSM


title: WG17009_F05-W02


title: WG17009_F05-W01


title: WG17009_F04-W27


title: 1772092311_B10

value: OLIGOS


title: WG17009_F04-W26


title: 1772092311_B06


title: WG17009_F04-W15


title: WG17009_F04-W16


title: 1772092311_A12


title: WG17009_F05-W04


title: 1772092311_A11


title: WG17009_F04-W07


title: 1772092311_A05

value: OPC


title: 1772092311_C05


title: 1772092309_H06


title: 1772092311_A03


title: WG17009_F04-W03


title: 1772092311_B12


title: WG17009_F04-W05


title: 1772092311_B09


title: WG17009_F03-W28


title: WG17009_F03-W27


title: 1772092309_G04


title: 1772092309_F08


title: WG17009_F04-W21


title: 1772092311_B05


title: WG17009_F04-W11


title: WG17009_F03-W25


title: 1772092311_A04


title: WG17009_F04-W08


title: WG17009_F09-W15


title: WG17009_F03-W19


title: 1772092309_E04


title: 1772092309_E02


title: 1772092309_G01


title: 1772092309_E01


title: WG17009_F03-W16


title: WG17009_F03-W18


title: WG17009_F03-W15


title: 1772092309_D12


title: WG17009_F03-W13


title: WG17009_F03-W26


title: WG17009_F03-W12


title: 1772092309_D01

value: Pvalb


title: 1772092309_D03


title: WG17009_F03-W11


title: 1772092309_D10


title: 1772092309_C10


title: 1772092309_F06


title: 1772092309_C03


title: WG17009_F03-W20

value: Cck


title: 1772092309_E06


title: WG17009_F03-W14


title: WG17009_F03-W09


title: WG17009_F03-W08


title: WG17009_F03-W07


title: 1772092309_B10


title: 1772092309_C02


title: 1772092309_B07


title: WG17009_F03-W06


title: 1772092309_B06


title: WG17009_F03-W05


title: WG17009_F03-W03


title: 1772092309_B04


title: 1772092309_B02


title: WG17009_F02-W28


title: WG17009_F03-W02


title: 1772092309_A11

value: NPY-NGC


title: 1772092309_A07


title: 1772092309_A04


title: WG17009_F02-W20


title: WG17009_F02-W17


title: 1772092309_A01


title: WG17009_F02-W15


title: WG17009_F02-W18

value: Th


title: 1772092308_H06


title: WG17009_F02-W08


title: 1772092308_G10


title: 1772092308_G02


title: 1772092308_G03


title: WG17009_F02-W05


title: 1772092308_F12


title: WG17009_F02-W12


title: WG17009_F01-W25


title: 1772092308_F11


title: WG17009_F01-W13


title: 1772092308_F10


title: WG17009_F01-W12


title: WG17009_F01-W07


title: 1772092308_F02


title: 1772092308_F09

value: MICROGLIA


title: 1772092308_E05


title: 1772092308_F05


title: WG17009_F01-W08


title: WG17009_F01-W06


title: 1772092308_D09


title: 1772092308_D11


title: WG17009_E11-W13


title: WG17009_E11-W08


title: 1772092308_E02


title: WG17009_E10-W28


title: WG17009_E10-W19


title: WG17009_E10-W27


title: WG17009_F01-W10


title: WG17009_F01-W02


title: 1772092308_D06


title: 1772092308_D04


title: WG17009_E10-W06


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value: Npy-Mia


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value: Pthlh


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title: 1772092287_G08


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title: WG17009_C05-W20


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title: 1772092287_E04


title: 1772092287_D10


title: 1772092287_D12


title: WG17009_C05-W01


title: WG17009_C04-W20

value: Th


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title: WG17009_C04-W19


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title: 1772092286_B05


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title: 1772092286_A09


title: 1772092286_A11


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title: 1772092286_A07


title: WG17009_C03-W08


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title: 1772092265_F04


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title: WG17009_C02-W14


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title: WG17009_C02-W02


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title: WG17009_C01-W15


title: 1772092265_D06


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title: 1772092265_D01


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title: WG17009_B07-W25


title: 1772092265_C10


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title: 1772092265_C03


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title: WG17009_B05-W17


title: 1772092265_C02


title: 1772092265_C01


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title: WG17009_B05-W16


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title: 1772092265_B07


title: 1772092265_B08


title: WG17009_B05-W12


title: WG17009_B05-W10


title: WG17009_B05-W09


title: 1772092265_B05


title: WG17009_B05-W08


title: 1772092265_B02


title: 1772092265_A11


title: 1772092265_B01


title: WG17009_B05-W25


title: WG17009_B05-W07


title: 1772092265_A09


title: 1772092265_A05


title: 1772092265_A06


title: 1772092265_A02


title: WG17009_B05-W04


title: WG17009_B04-W04


title: 1772092264_H11


title: 1772092264_H08


title: 1772092265_B09


title: 1772092264_H06


title: WG17009_B05-W02


title: WG17009_B04-W03


title: 1772092264_H04


title: 1772092264_H02


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title: 1772092264_G07


title: WG17009_B03-W27


title: 1772092264_G09


title: 1772092264_G06


title: 1772092264_F11


title: WG17009_B03-W20


title: 1772092264_G01


title: 1772092264_F08


title: 1772092264_F06


title: WG17009_B03-W18

value: Cck


title: WG17009_B03-W15


title: 1772092264_F05


title: WG17009_B05-W06


title: 1772092264_H05


title: 1772092264_E11


title: WG17009_B03-W13


title: 1772092264_F04


title: WG17009_B03-W12

value: Cycling


title: 1772092264_E09


title: WG17009_B03-W11


title: 1772092264_E10


title: WG17009_B03-W08


title: 1772092264_E04


title: 1772092264_E06


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title: 1772092264_E02


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title: 1772092264_B12


title: 1772092264_A09


title: 1772092264_A05


title: 1772092264_A04


title: 1772092264_A06


title: WG17009_B01-W28


title: WG17009_B03-W04


title: 1772092263_H12

value: ENDO


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title: 1772092263_H09


title: 1772092264_C08


title: 1772092263_H08


title: WG17009_B01-W13


title: 1772092263_H02


title: 1772092264_C01


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value: Pthlh


title: 1772092263_H01


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value: Migrating


title: 1772094153_E06

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value: dorsolateral striatum


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title: WG17009_A04-W10


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title: 1772078108_F04


title: 1772078108_E11


title: WG17009_A04-W03


title: WG17009_A04-W07


title: 1772078108_F03


title: 1772078108_E10


title: 1772078108_E08


title: WG17009_A03-W28


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title: 1772078108_E05


title: 1772078108_E07


title: 1772078108_E09


title: WG17009_A03-W27


title: 1772078108_E04


title: 1772078108_E02


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title: 1772078108_D08


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title: 1772078108_D05


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title: 1772078108_C09


title: WG17009_A03-W16


title: 1772078108_C12


title: 1772078108_C06


title: 1772078108_C02


title: 1772078108_C04


title: WG17009_A03-W14


title: 1772078108_B10


title: WG17009_A03-W13


title: 1772078108_C01


title: 1772078108_B09


title: WG17009_A03-W11


title: 1772078108_A11


title: WG17009_A03-W09


title: 1772078108_B03


title: 1772078108_B02


title: 1772078108_B01


title: 1772078108_A10


title: WG17009_A03-W10


title: 1772078108_A08


title: 1772078108_A07


title: WG17009_A03-W07


title: 1772078108_A05


title: 1772078108_A03


title: 1772078108_A02


title: 1772078108_A01


title: WG17009_A03-W05


title: 1772078033_H12


title: 1772078033_H11


title: 1772078033_H06


title: 1772078033_H03

value: ASTRO


title: WG17009_A03-W17


title: 1772078033_H02


title: WG17009_A03-W04


title: WG17009_A03-W01


title: 1772078033_H01


title: WG17009_A03-W12


title: 1772078108_A09

value: female


title: 1772078033_G10


title: 1772078033_G02


title: WG17009_A03-W06

value: Cck+Vip+


title: 1772078033_G03

value: OLIGOS


title: 1772078033_G06

value: VSM


title: WG17009_A02-W25


title: 1772078033_G04


title: WG17009_A03-W08


title: WG17009_A02-W09


title: WG17009_A02-W05


title: WG17009_A02-W15


title: WG17009_A02-W17


title: WG17009_A01-W27


title: WG17009_A02-W12


title: WG17009_A02-W06


title: WG17009_A02-W21


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title: 1772078033_F04


title: 1772078033_F11


title: 1772078033_F09


title: 1772078033_F12


title: WG17009_A01-W25


title: 1772078033_F03


title: 1772078033_E10


title: 1772078033_F01


title: WG17009_A01-W21


title: 1772078033_E08


title: WG17009_A01-W18


title: WG17009_A01-W20


title: 1772078033_E06


title: WG17009_A01-W16


title: 1772078033_E03


title: WG17009_A01-W15


title: 1772078033_D10


title: WG17009_A01-W13


title: 1772078033_D05


title: 1772078033_D12


title: 1772078033_D07


title: WG17009_A01-W05


title: 1772078033_E04


title: WG17009_A01-W07


title: 1772078033_D02


title: WG17009_A01-W08


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title: WG17009_A01-W12


title: 1772078033_D01


title: WG17009_A01-W04


title: 1772078033_C06


title: WG17009_A01-W17


title: 1772078033_C04


title: 1772078033_C05

value: MICROGLIA


title: WG17009_A01-W14

value: male


title: 1772078033_C03


title: 1772078033_B12


title: WG17009_A02-W04


title: 1772078033_F02


title: 1772078033_B11


title: WG17009_A01-W02


title: WG17009_A01-W03


title: 1772078033_C11


title: 1772078033_B09


title: 1772078033_B06


title: 1772078033_B10


title: 1772078033_B07


title: 1772078033_A11


title: 1772078033_A10


title: 1772078033_A07


title: 1772078033_A08


title: 1772078033_A04


title: 1772078033_H10


title: 1772078033_A05


title: 1772078033_A01


title: WG17009_A03-W15


title: +/+ replicate 1

city: Cold Spring Harbor

first: Dong-Woo

last: Hwang

state: NY

address: 1 Bungtown Rd

department: Cancer Center

country: USA

institute: Cold Spring Harbor Laboratory

data_processing:
Build Bowtie2 (version 2.2.3) index file using mm10 UCSC genome and known transcriptome.
Mapping reads to the index with command line options  “-q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 --nofw -p 8 -k 200”.
Using RSEM (version 1.2.20) to estimate relative gene expression levels with default settings on the alignments generated by Bowtie2.
Genome_build: mm10 ucsc transcriptome
Supplementary_files_format_and_content: Estimated relative gene expression levels for all samples presented as a matrix of transcripts per million (TPM). The file is in txt format.

source_name: Primary neural stem/progenitor cells (NSCs)

growth_protocol: Primary NSCs were generated by dissociation of periventricular region of the brain (including the ventricular zone (VZ) and the subventricular zone (SVZ)) from individual neonatal (postnatal day 1, P1). NSCs were cultured in NSC proliferation medium (DMEM/F-12 1:1 mix (HyClone), 1x N-2 media supplement (Gibco), 0.1% bovine serum albumin (BSA) fraction V (Sigma), and 0.5% penicillin-streptomycin, 20 ng/ml epidermal growth factor (Pepro Tech), and 20ng fibroblast growth factor 2 (Pepro Tech)).

extract_protocol:
Total RNA was isolated from NSCs using a column-based RNA isolation kit (RNeasy Mini Kit, Qiagen), and RNA was treated with DNase I (Qiagen). RNA quality of each sample was evaluated by an electrophoresis-based assay (Bioanalyzer 2100, Agilent).
mRNA (cDNA) sequencing libraries were prepared using a commercially available library preparation kit (TruSeq® Stranded mRNA Sample Preparation Kit, Illumina).

value: Brain

tag: age

value: Postnatal day 1

tag: genotype


title: 1772078032_H04


title: Chd5-/- replicate 1

value: Postnatal day 3


title: +/+ replicate 2

value: Postnatal day 2


title: 1772078032_G12


title: 1772078032_G11

value: Pvalb


title: 1772078033_B04


title: 1772078032_G10

value: ENDO


title: 1772078033_A06


title: 1772078032_G07

value: CHAT


title: 1772078032_G04


title: 1772078033_D04


title: 1772078033_A02

value: OPC


title: 1772078032_E12

value: brain


title: 1772078032_G05

value: dorsolateral striatum

value: Sst


title: Chd5-/- replicate 2

value: Postnatal day 4


title: 1772078032_D10

value: Pthlh


title: 1772078032_D05


title: 1772078032_F04


title: 1772078032_H08


title: 1772078032_C06

value: Th


title: 1772078032_C05


title: 1772078032_C09


title: 1772078032_B09


title: 1772078032_C04


title: 1772078032_H01


title: 1772078032_B06


title: 1772078032_B05


title: 1772078032_B04


title: 1772078024_H06


title: 1772078032_A01


title: 1772078032_E10


title: 1772078024_H02

value: OLIGOS


title: 1772078024_H03


title: 1772078024_G12


title: 1772078032_E06


title: 1772078024_G07


title: 1772078024_G09


title: 1772078024_G05


title: 1772078024_G06


title: 1772078024_G04


title: 1772078024_F07


title: 1772078024_F06


title: 1772078024_E11


title: 1772078024_F03


title: 1772078024_E12


title: 1772078024_D11


title: 1772078024_F05


title: 1772078032_G03


title: 1772078024_E06


title: 1772078024_D04


title: 1772078024_D05


title: 1772078024_E04


title: 1772078024_B12


title: 1772078024_B10


title: 1772078024_B04


title: 1772078024_B03


title: 1772078024_C08


title: 1772078032_A05


title: 1772078024_F11


title: 1772078024_A11


title: 1772078024_A09


title: 1772078024_A01


title: 1772078024_A04


title: 1772072239_H03


title: 1772072239_F07


title: 1772072239_G02


title: 1772072239_E05


title: 1772072239_E01


title: 1772072239_A02


title: 1772072239_A01


title: 1772072239_E03


title: 1772072239_D09


title: 1772072239_A06


title: 1772072238_H11


title: 1772072238_H06


title: 1772072238_H02


title: 1772072238_H01


title: 1772078024_B06


title: 1772072238_G08


title: 1772072238_F12


title: 1772078024_A07


title: 1772078024_A05


title: 1772072238_G04


title: 1772072238_F11


title: 1772072239_G09


title: 1772072238_F01


title: 1772072238_E09


title: 1772072238_E08


title: 1772072238_E06


title: 1772072238_D09


title: 1772072239_E07


title: 1772072238_E02


title: 1772072238_D02


title: 1772072238_H08


title: 1772072238_C10


title: 1772072238_B10


title: 1772072238_C03


title: 1772072238_G10


title: 1772072238_B06


title: 1772072238_C05


title: 1772072238_B03


title: 1772072238_A09


title: 1772072238_A12


title: 1772072238_A10


title: 1772072238_B09


title: 1772072238_G07


title: 1772072238_A04


title: 1772071019_H06

value: female


title: 1772072238_A05

value: male


title: 1772071019_H04


title: 1772071019_G12


title: 1772071019_G02


title: 1772071019_H02


title: 1772071019_F09


title: 1772071019_E02

value: NPY-NGC


title: 1772071019_E09


title: 1772072238_C08


title: 1772071019_F02


title: 1772071019_C09


title: 1772071019_D11


title: 1772071019_C02


title: 1772072238_A07


title: 1772071019_C01


title: 1772071019_B09


title: 1772071019_A08


title: 1772071019_A10


title: 1772067077_H08

value: unknown


title: 1772071019_A04


title: 1772072238_C06


title: 1772067077_F07


title: 1772067077_F06


title: 1772067077_F05


title: 1772067077_E08


title: 1772067077_H03


title: 1772067077_G02


title: 1772067077_F03


title: 1772067077_F10


title: 1772067077_E04


title: 1772067077_G09


title: 1772067077_D10


title: 1772067077_D08


title: 1772067077_C12


title: 1772067077_E07


title: 1772067077_B09


title: 1772067077_C07


title: 1772067077_B03


title: 1772067077_B07


title: 1772067077_A04


title: 1772067077_A01


title: 1772063072_H06


title: 1772071019_B06


title: 1772063072_H05


title: 1772063072_F06


title: 1772063072_F09


title: 1772063072_G06


title: 1772063072_F08


title: 1772063072_F12


title: 1772063072_H03


title: 1772063072_E11


title: 1772063072_E09


title: 1772063072_D12


title: 1772063072_F01


title: 1772063072_E08


title: 1772063072_D07


title: 1772063072_D04


title: 1772063072_D10


title: 1772063072_E05


title: 1772063072_C12


title: 1772063072_D08


title: 1772063072_C07


title: 1772063072_C02


title: 1772063072_C05


title: 1772063072_D01


title: 1772063072_B10


title: 1772063072_B11


title: 1772063072_B09


title: 1772063072_C01


title: 1772063072_B07


title: 1772063072_E12


title: 1772063072_B05


title: 1772063072_D09


title: 1772063072_B01


title: 1772063072_B02


title: 1772063072_A09


title: 1772063072_A07


title: 1772063072_A05


title: 1772062117_H12


title: 1772063072_A03


title: 1772063072_A11


title: 1772062117_H04

value: CYCLING


title: 1772062117_H07


title: 1772062117_H10


title: 1772062117_H03


title: 1772062117_H01


title: 1772062117_H08


title: 1772062117_G12


title: 1772062117_G11


title: 1772062117_G10


title: 1772062117_G09


title: 1772062117_G08


title: 1772062117_G07


title: 1772063072_D03


title: 1772062117_G05


title: 1772062117_G06


title: 1772062117_G04


title: 1772062117_G03


title: 1772062117_G02


title: 1772062117_G01


title: 1772063072_A01


title: 1772062117_F11


title: 1772062117_F09


title: 1772062117_F08


title: 22Rv1DR_si2_2

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Data preprocessing and transcript abundance calculation (FPKM: fragments per kilo bases of exons for million mapped reads) were performed using TopHat and Cufflinks software using the human reference genome (hg19). The FPKM values were floored by 1 and log2 transformed.
Genome_build: mm10
Supplementary_files_format_and_content: gct file include normalized expression values for each sample

organism: Homo sapiens

source_name: Cell line

growth_protocol: DU145 and 22Rv1 prostate cancer cell lines were obtained from ATCC, and aggressive sublines, DU145-DR and 22Rv1-DR cells, were generated as previously described (Cancer Cell 22:373-388,2012).  The cells were maintained in RPMI media (Gibco) supplemented with 10% FBS and 1 % penicillin/streptomycin (Gibco) at 37C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini kit (Qiagen), and cDNA was synthesized using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen) following manufacturer’s instructions.
Poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol.
Poly A-selected RNA for RNA-Seq

treatment_protocol: Treated with either of commercially available POM121-targeting siRNA construct 1 (s59623) and 2 (s19145) (Silencer Select siRNA, life technologies) following manufacturer’s instructions.

tag: cell line

tag: condition

value: Knockout

tag: transduced construct

value: siPOM121, construct 2


title: 1772062117_E02


title: 1772062117_D11


title: 1772062117_E04


title: 1772062117_D12


title: 22Rv1DR_si2_1


title: 1772062117_F01


title: 1772062117_E05


title: 1772062117_F04


title: 1772062117_E03


title: 1772062117_E09


title: 1772062117_E08


title: 22Rv1DR_si2_4


title: 1772062117_E01


title: 1772062117_E07


title: 1772062117_D09


title: 1772062117_E06


title: 22Rv1DR_si1_4

value: siPOM121, construct 1


title: 1772062117_D08


title: 22Rv1DR_si1_3


title: 1772062117_F07


title: 22Rv1DR_si1_2


title: 22Rv1DR_si1_1


title: 1772062117_D04


title: 1772062117_D05


title: 1772062117_E11

value: ENDO


title: 1772062117_D02


title: 1772062117_D01


title: 22Rv1DR_control_3

value: Control


title: 22Rv1DR_control_2


title: 22Rv1DR_control_1


title: 1772062117_C12

value: brain


title: 1772062117_C11

value: dorsolateral striatum


title: 1772062117_C07


title: DU145DR_si2_2


title: 22Rv1DR_control_4


title: DU145DR_si1_2


title: 1772062117_C06


title: DU145DR_si1_1


title: 1772062117_C02


title: 1772062117_C05


title: 1772062117_C01


title: DU145DR_si2_4


title: 1772062117_B12


title: DU145DR_control_4


title: DU145DR_si2_3


title: DU145DR_si2_1


title: 1772062117_B11


title: 1772062117_C04


title: DU145DR_control_2


title: 1772062117_B10


title: 1772062117_B07


title: DU145DR_si1_4


title: 1772062117_B08


title: 1772062117_B06


title: 22Rv1DR_si2_3


title: OVCAR8_OTX015_24h_2

city: Montreal

first: Michael

last: Witcher

state: QC

address: 3755 Chemin de la Cote Ste-Catherine

country: Canada

institute: Lady Davis Institut

data_processing:
Using Trimmomatic, low quality bases and adapters were removed, and only reads with a minimum length of 35 bases, and in pairs, were kept for the next step.
Clean paired sequences were aligned using “Star” then the number of reads per gene using UCSC hg19 annotation and “featureCount” was obtained and used for differential expression analysis with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing matrix of normalized counts generated by DESeq2 only from exonic region, annotation UCSC.hg19

growth_protocol: SCCOHT1 and OVCAR8 cell lines were cultured in RPMI-1640 1x medium supplemented with 10% FBS. The cell lines were maintained at 37C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using Gene Elute Mammalian Total RNA kit (Sigma, #RTN350) according manufactured procedure. 1ug of RNA by replicate was sent to the sequencing.
mRNA stranded library preparation was carried out using Illumina TruSeq rRNA-depleted stranded library preparation followed by paired-end 100bp sequencing with a HiSeq 2500.

treatment_protocol: Cells were exposed to 0.01% DMSO or 100nM OTX015 for 4 and 24 hours

value: OVCAR8 ovarian cancer cell line

value: SMARCA4 WT

tag: treatment

tag: time


title: 1772062117_B09

value: Pthlh


title: 1772062117_B03


title: OVCAR8_OTX015_4h_2


title: 1772062117_B05


title: OVCAR8_OTX015_4h_1


title: OVCAR8_DMSO_2

value: control


title: 1772062117_A11


title: OVCAR8_DMSO_1


title: DU145DR_control_1


title: SCCOHT1_OTX015_4h_2

value: SCCOHT1 ovarian cancer cell line

value: SMARCA4 loss of function mutation


title: SCCOHT1_OTX015_24h_1


title: 1772062117_B02

value: male


title: 1772062117_A06


title: C57BL/6_delMYRF_OPC_72hrPostT3

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Output FASTQ files were aligned to the mm9 genome using Tophat (Version 2.0.8) with default settings.
Fragments per kilobase per million reads (FPKM) were calculated for known RefSeq genes using Cufflinks (Version 2.0.2).
Genome_build: mm9
Supplementary_files_format_and_content: Standard cufflinks output (genes.fpkm_tracking)

source_name: ESC derived OPCs 72-hrs post T3 differentiation treatment

growth_protocol: Cultures of iPSC and mESC derived OPCs were maintained and expanded on Nunclon-Δ wells coated with poly(L-ornithine) followed by laminin in neural medium which consisted of DMEM/F12 (Invitrogen) supplemented with 1x N2 (R&D Systems), 1x B-27 without vitamin A (Invitrogen), and 2 mM glutamax (Invitrogen) supplemented with 200 ng/ml SHH, 20 ng/ml PDGF-AA, 100 ng/ml noggin, 100 ng/ml IFG-1 (R&D Systems), 10 µM cyclic AMP (Sigma), and 10 ng/ml NT3 (R&D Systems).

extract_protocol:
Cells were lysed directly in 1 ml of TRIzol (Invitrogen) and stored at -80°C. Once all samples were collected, samples were thawed on ice and RNA was separated with chloroform using Phase Lock Gel tubes (5prime). RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacture’s protocol.
One microgram of each sample was then subject to ribosome depletion, fragmented, and library prepared using the TruSeq Stranded Total RNA Kit with Ribo Zero Gold (Illumina) according to the manufacturer’s protocol and indexed using TruSeq adapters. One hundred base pair paired-end reads were generated for each sample on the Illumina HISeq 2500 (Case Western Reserve University Sequencing Core; Cleveland, OH).

treatment_protocol: OPCs were seeded at 2-2.6 x104 cells/cm2 on Nunclon-Δ wells coated with poly(L-ornithine) followed by laminin in supplemented neural medium which consisted of DMEM/F12 (Invitrogen) supplemented with 1x N2 (R&D Systems), 1x B-27 without vitamin A (Invitrogen), and 2 mM glutamax (Invitrogen) for 2 days. On day 3 media was aspirated and cells were washed with 1x PBS and cultured in neural medium supplemented with 200 ng/ml SHH, 100 ng/ml noggin, 100 ng/ml IGF-1, 10 µM cyclic AMP, and 10 ng/ml NT3, and 40 ng/ml T3 for 1 day (24 hr), 2 days (48 hr) or 3 days (72 hr).

value: Embryonic Stem Cell-Derived Oligodendrocyte Progenitors

tag: mutation status

value: Homozygous deletion of Exon 1 of mouse MYRF


title: C57BL/6_OPC_24hrPostT3

source_name: ESC derived OPCs 24-hrs post T3 differentiation treatment

tag: strain

value: normal male


title: C57BL/6_OPC_72hrPostT3


title: SCCOHT1_OTX015_24h_2


title: C57BL/6_OPC

source_name: ESC derived OPCs


title: SCCOHT1_OTX015_4h_1


title: C57BL/6_OPC_48hrPostT3

source_name: ESC derived OPCs 48-hrs post T3 differentiation treatment


title: 1772063072_A04

tag: Sex


title: Shiverer_OPC_72hrPostT3

source_name: iPSC derived OPCs 72-hrs post T3 differentiation treatment

value: Induced Pluripotent Stem Cell-Derived Oligodendrocyte Progenitors

value: Homozygous deletion of Exons 3-7 of mouse MBP


title: OVCAR8_OTX015_24h_1


title: DU145DR_control_3


title: 1772062117_C03

value: Th


title: DU145DR_si1_3

value: Knockout

value: siPOM121, construct 1


title: 1772062117_A12

value: brain


title: SCCOHT1_DMSO_2


title: 129_OPC_72hrPostT3


title: 129_OPC_48hrPostT3


title: 1772062117_A02

value: dorsolateral striatum


title: 1772062117_A08


title: 129_OPC_24hrPostT3


title: 1772062117_A01


title: 1772062117_A07


title: 129_OPC


title: 1772062117_A03


title: CBA/Ca_OPC_72hrPostT3

value: CBA/Ca


title: SCCOHT1_DMSO_1


title: CBA/Ca_OPC_48hrPostT3


title: CBA/Ca_OPC_24hrPostT3


title: PO_OPC

value: PO


title: PO_OPC_24hrPostT3


title: PO_OPC_72hrPostT3diff


title: RNA-seq GFP rep 2

status: Public on Aug 21 2018

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Academic Medical Center, University of Amsterdam

data_processing:
Raw sequencing reads were filtered for low complexity or repetitive sequences and aligned to the Mus musculus genome (assembly mm10, Dec. 2011) using TopHat 2.1 (Trapnell et al., 2009).
The number of uniquely mapping read counts per gene was determined using HTSeq (Anders et al., 2015).
Differential expression analysis between GFP and HA-NUR77 overexpressing cells was performed using DESeq2 (Love et al., 2014), wherein genes with a false discovery rate (FDR)-adjusted p-value < 0.05 and a log2(fold-change) < -0.3 or > 0.3 were considered to be differentially regulated.
Genome_build: mm10
Supplementary_files_format_and_content: .txt files contain HTSeq counts of sequencing reads for each ENSEMBL transcript.

source_name: pINDUCER20b-GFP RAW264.7 macrophages

growth_protocol: RAW264.7 macrophage stable cell lines with Dox-inducible overexpression of GFP or HA-NUR77 were seeded in one 10-cm dish per replicate in DMEM medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine.

extract_protocol:
Cells were lysed directly in plates and total RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer's instructions.
Strand-specific libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Polyadenylated RNA from 1000 ng intact total RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen). Second strand synthesis was performed using Polymerase I and RNase H with replacement of dTTP for dUTP. The generated cDNA fragments were 3' end adenylated and ligated to Illumina Paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent), diluted, and pooled in equimolar ratio into a 13-plex, 10 nM sequencing pool.

treatment_protocol: 24 hours after seeding, cells were treated with 1 µg/mL Doxycycline (Dox) for 18 hours.

tag: transgene

value: 1 µg/mL Dox for 18 hours

tag: number of cells


title: ChIP-seq HA-NUR77 rep 3

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the Mus musculus genome (assembly mm9, July 2007) using Burrow-Wheeler Aligner 0.7.10 (Li and Durbin, 2009). Reads that aligned poorly or mapped to multiple locations were discarded and only reads with a mapping quality score (MAPQ) over 20 were used for peak calling.
Raw input sequencing data for RAW264.7 cells was obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (accession numbers GSM1232949 and GSM1559473) and aligned and filtered as described above.
High-confidence Nur77 binding sites were identified by comparing aligned input and Nur77 ChIP-seq data using two peak calling algorithms, MACS (Zhang et al., 2008) and DFilter (Kumar et al., 2013). For MACS, default settings were used except for a p-value cut-off of 10^-7. For DFilter, the settings bs = 50, ks = 30, refine, and nonzero were used with a p-value cut-off of 10^-6.
Nur77 binding sites identified by both peak callers and present in at least two of the three biological replicates were used for further analyses.
Genome_build: mm9
Supplementary_files_format_and_content: .wig files contain genome-wide fragment pile-up data generated by MACS for each sample; .bed files contain consensus peak calls from MACS and DFilter for each Nur77 ChIP-seq sample.
Input control processed data files are linked at the foot of the Series record.

molecule: genomic DNA

growth_protocol: RAW264.7 macrophage stable cell line with Dox-inducible overexpression of HA-NUR77 were seeded in six 15-cm dishes per replicate in DMEM medium supplemented with 10% fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine.

extract_protocol:
Cells were washed with PBS and dual crosslinked directly in culture plates with 2 mM Di(N-succinimidyl) glutarate (Sigma) in PBS for 45 minutes at room temperature, followed by 1% formaldehyde (Sigma) for 15 minutes at room temperature. Crosslinking reactions were quenched by addition of glycine to 0.125 M final concentration and incubation for 5 minutes at room temperature. Crosslinked cells were washed with ice-cold PBS and collected by scraping in ice-cold PBS followed by centrifugation for 5 minutes at 500 x g. Cell pellets were resuspended  in resuspension buffer L1A (10 mM HEPES-KOH pH 7.9, 85 mM KCl, 1 mM EDTA). Cell membranes were lysed by diluting samples 1:1 with lysis buffer L1B (L1A plus 1% IGEPAL CA-630) and incubating 10 minutes on ice. Cells were subsequently centrifuged 5 minutes at 700 x g and pellets were resuspended in lysis buffer L2 (50 mM Tris-HCl pH 7.4, 1% SDS, 10 mM EDTA). Nuclei were ruptured and chromatin was sonicated into approximately 200 bp fragments using a Bioruptor Pico (Diagenode) for 20 cycles of 30 seconds on and 30 seconds off. Fragment length was confirmed by running an aliquot of reverse crosslinked chromatin on a 1.2% agarose gel. Sonicated chromatin samples were centrifuged for 10 minutes at 16,000 x g to pellet cell debris. Supernatants were transferred to DNA LoBind tubes (Sigma) and diluted 1:1.5 with dilution buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 2 mM EDTA, 0.5% Triton X-100). Per ChIP reaction, 30 µL Protein G Dynabeads (Novex) were washed twice with 0.5% bovine serum albumin (BSA) in PBS and incubated with 2 µg anti-HA antibody (Diagenode) for 3 hours at 4°C. Dynabead-antibody complexes were added to each diluted chromatin sample (18 ChIPs total) and incubated overnight at 4°C to immunoprecipitate chromatin-linked HA-NUR77 protein. Immunoprecipitates were washed four times with wash buffer 1 (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), four times with wash buffer 2 (10 mM Tris-HCl pH 7.4, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% sodium deoxycholate, 1 mM EDTA), twice with wash buffer 3 (10 mM Tris-HCl pH 7.4, 0.2% Triton X-100, 1 mM EDTA), and twice with wash buffer 4 (10 mM Tris-HCl pH 7.4, 50 mM NaCl, 1 mM EDTA). Samples were transferred to fresh DNA LoBind tubes after the first and second to last wash steps to reduce background. Chromatin was eluted from Dynabeads by incubating in elution buffer (10 mM Tris-HCl pH 7.4, 2% SDS, 1 mM EDTA) for 20 minutes at 37°C. Crosslinks were reversed by addition of NaCl to a final concentration of 300 mM and incubating overnight at 65°C. DNA was purified by incubating samples with 0.33 mg/mL RNase A for 1 hour at 37°C, followed by 0.5 mg/mL Proteinase K for 1 hour at 50°C, and extraction of DNA by phenol:chloroform:isoamylalcohol precipitation. Precipitated DNA was dissolved in ultrapure water and DNA from 6 separate ChIP reactions was pooled to create one biological replicate, resulting in three biological replicates total.
ChIP DNA libraries were prepared as previously described (Schmidt et al., 2009; PMID: 19275939).

tag: chip antibody

value: Mouse anti-HA tag (Diagenode, catalog# C15200190, lot# 001)


title: RNA-seq GFP rep 3


title: ChIP-seq HA-NUR77 rep 1


title: ChIP-seq HA-NUR77 rep 2


title: Cardiosphere derived cells (normoxia)

city: Los angeles

first: Xiangming

last: Ding

state: CA

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

description: N

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
mirDeep2 was used to calculate the count of each human miRNA and PRM (reads per million) was used for normalization
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for all Samples

source_name: Cardiosphere derived cells (normoxia)

growth_protocol: Cardiosphere derived cells culture under hypoxia and normoxia

extract_protocol:
Ultracentrifugation
RNA libraries were prepared for sequencing using sNEBNext® Small RNA Library Prep Set for Illumina®

tag: cell type

value: exosomes

tag: passage


title: Cardiosphere derived cells (hypoxia)

description: H

source_name: Cardiosphere derived cells (hypoxia)


title: RNA-seq HA-NUR77 rep 3


title: PO_OPC_48hrPostT3


title: RNA-seq HA-NUR77 rep 1


title: RNA-seq GFP rep 1


title: RNA-seq HA-NUR77 rep 2


title: CBA/Ca_OPC


title: WT1-H3K27me3_PE

city: Hong Kong

first: Siu Yuen

last: Chan

address: 21 Sassoon Road

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

description: PE and SE raw data was pooled to generate processed data

data_processing:
Basecalls performed using CASAVA (version 1.8.2).
Fastq files were filtered using the following specifications: Minimum Quality:20 and Maximum number of bases allowed outside of quality range: half of the read length.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9-r16 with default parameters. Reads with MAPQ no less than 30 were used for downstream analysis.
Average fragment size was esitmated from paired mapped tags. Reads 1 of paired-end reads were pooled with single-end reads of the same BioSample for downstream analysis.
Tags pileups (bedgraph files) were generated using MASC 2.0 with the following setting: -g mm --to-large --broad -f BED --nomodel --extsize 175 --buffer-size 30000000 -B --SPMR
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using data2wig.pl from Bio-ToolBox-1.32; Scores represent tag counts per 1 million mappable reads.

source_name: Hippocampal primary neurons

growth_protocol: Mouse hippocampi from embryos 16.5 days post coitum (E16.5) were dissected in cold HBSS and disassociated by adding warm 0.25 % trypsin. One tenth of the trypsin volume of FBS was added to neutralize trypsin. Cells were collected by centrifugation at 200 RCF for 5 minutes and were resuspended and then cultured in Neurobasal Medium (NBM) with 1 % FBS, 1 % P/S, and 1x B27 supplement (all from Invitrogen). Seeding density is 1000 cells/mm2. Primary cells were cultured at 37°C with 5 % CO2 for 14 days before collected.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB). Library fragments between 175 – 225 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

value: Hippocampal primary neurons

tag: development stage

tag: days in vitro

value: H3K27me3 (Diagenode, pAb-069-052)


title: KO1_H3K27me3_PE

value: H3K27me3 (Diagenode, pAb-069-050)


title: KO2-H3K27me3_PE

value: H3K27me3 (Diagenode, pAb-069-056)


title: WT1-input_PE

description: PE and SE WT input raw data was pooled to generate processed data


title: WT2-input_PE


title: KO1-input_PE

description: PE and SE KO input raw data was pooled to generate processed data


title: CAF_48

city: Singapore

first: Tannistha

last: Nandi

address: 60 Biopolis Street, Genome, #02-01

department: Cancer Therapeutics & Stratified Oncology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Sequencing reads were  mapped against human genome reference hg19 using Tophat2.
Transcript abundances were estimated by cufflinks-2.2.0 suite and the expression was reported in Fragments per Kilo base of exon per Million fragments mapped (FPKM)
Genome_build: hg19

source_name: cancer fibroblast

growth_protocol: NFs or CAFs cells were cultured in RPMI 1640 containing 10% fetal bovine serum.

extract_protocol:
Total RNA were extracted from NFs or CAFs cells using an miRNeasy Mini Kit (Qiagen).
Two micrograms  of total RNA was used to create libraries with illumina TruSeq RNA Sample Prep Kit v2 (illumina, San Diego, California, USA) according to manufacturer’s instructions. Samples successfully meeting the size and concentration criteria were pooled at equimolar concentrations. Two samples with unique index-tag adapter sequences were combined for multiplex NGS in each lane on the illumina HiSeq 2000 (Illumina, San Diego, California, USA).

tag: gender

value: male

tag: borrman classification

value: type 2

value: CAF

tag: tissue

value: stomach


title: CAF_76

value: IIc

tag: cell line


title: CAF_79

value: type 3


title: CAF_47

value: female

value: type 4


title: CAF_37


title: NF_76

source_name: normal fibrobalst

value: NF


title: NF_54

value: 0‐Ⅲ


title: CAF_58


title: CAF_45


title: NF_47


title: CAF_33


title: CAF_38


title: NF_79


title: CAF_54


title: NF_45


title: NF_44


title: NF_48


title: WT2-H3K27me3_PE

value: H3K27me3 (Diagenode, pAb-069-054)


title: NF_33


title: CAF_44


title: NF_58


title: KO2-input_SE


title: H3K27ac juvenile acinar (EA39)

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Reads were mapped to hg19 using ATAC-Seq pipeline.
Peaks were called using the ZINBA algorithm
Tags were counted using the HOMER software and normalized using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample

source_name: pancreas

extract_protocol:
Nextera Tagmentation (Buenrostro et al 2013. PMID:24097267)
Illumina HiSeq/TruSeq

value: acinar

tag: age

value: juvenile

tag: antibody

value: pancreas


title: Tn5 juvenile beta (Tn5_EA14)

data_processing:
Library strategy: ATAC-Seq
Reads were mapped to hg19 using ATAC-Seq pipeline.
Peaks were called using the ZINBA algorithm
Tags were counted using the HOMER software and normalized using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample

value: beta


title: H3K27ac juvenile duct (EA33)

value: duct


title: Tn5 adult alpha (Tn5_EA28)

value: alpha

value: adult


title: H3K27ac adult duct (EA29)


title: H3K27ac adult endocrine (EA65)

value: endocrine


title: H3K4me3 adult endocrine (EA67)


title: H3K27ac adult acinar (EA61)


title: NF_38


title: Tn5 juvenile duct (Tn5_EA43)


title: H3K4me3 juvenile duct (EA35)


title: H3K4me3 juvenile endocrine (EA47)


title: H3K4me3 juvenile acinar (EA41)


title: Tn5 adult beta (Tn5_EA29)


title: Tn5 juvenile duct (Tn5_EA10)


title: H3K4me3 adult acinar (EA63)


title: Tn5 juvenile duct (Tn5_EA44)


title: WT2-input_SE

value: Hippocampal primary neurons


title: H3K4me3 juvenile endocrine (EA71)


title: NF_37

value: male

value: stomach


title: KO1-input_SE

description:
PE and SE KO input raw data was pooled to generate processed data
koinput_nomodel_SPMR_control_lambda.wig.gz


title: Tn5 juvenile alpha (Tn5_EA7)


title: H3K4me3 adult duct (EA31)


title: Tn5 juvenile acinar (Tn5_EA9)


title: Tn5 adult acinar (Tn5_EA27)


title: Tn5 juvenile beta (Tn5_EA8)


title: Tn5 adult acinar (Tn5_EA6)


title: Tn5 adult duct (Tn5_EA11)


title: WT1-input_SE

description:
PE and SE WT input raw data was pooled to generate processed data
wtinput_nomodel_SPMR_control_lambda.wig.gz


title: Tn5 adult alpha (Tn5_EA4)


title: Control_3

status: Public on Aug 20 2018

city: Basel

first: Tommy

middle: Beat

last: Schlumpf

state: Basel-Stadt

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH Zürich

description:
wild type eye discs, transplanted into the adult abdomen and take out one day after the transplantation
Ctrl_3

data_processing:
Short read alignment was performed with TopHat 2.0.12 and Bowtie 2.2.3 using --b2-very-sensitive -g 1. For samples 1 to 9 single end and for samples 10-12 paired end alignment was used.
mRNA expression was quantified in R 3.3.1 with counts per million reads located in exonic ranges for each gene normalized to library size using edgeR 3.16.5. The annotations from Ensembl were used.
Genome_build: dm6
Supplementary_files_format_and_content: Abundance of mRNA transcripts in counts per million of library normalized reads

organism: Drosophila melanogaster

source_name: wild type eye discs

growth_protocol: Flies were raised at 25˚C on standard medium

extract_protocol:
Arcturus PicoPure RNA Isolation kit
SMARTSeq2 NexteraXT

value: wild type eye discs late 3rd instar


title: bMSC(31Y)-5

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome (hg19) using TopHat v2.0.12.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0.Fragment per kilobases per million mapped reads were calculated by Cufflinks(v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: "counts.csv" containes gene counts;"fpkm.csv" contains gene fpkm values.

source_name: bone mesenchymal stem cell

growth_protocol: Human fibroblast cells and fibroblast-derived cells till 15 days were routinely maintained in DMEM (Hyclone) with 10% fetal bovine serum(BI), bone mesenchymal stem cell and MSC-LC were cultured in MSC medium(MSC medium (Cyagen, HUXMA-90011) for expansion.

extract_protocol:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) according to the instruction manual.

treatment_protocol: Fibroblasts were treated by small molecule cocktail for 12 days,and treated for 5 days were denoted as fibroblast induced D5, for 12 days denoted as fibroblast induced D12, and on day 15 denoted as mesenchymal stem cell-LC D15.

value: bone mesenchymal stem cell


title: D5(39Y)-3

source_name: fibroblast induced D5

value: fibroblast induced D5


title: WT2-H3K27me3_SE

description:
PE and SE raw data was pooled to generate processed data
wt2chip_VS_wtinput_nomodel_SPMR_treat_pileup.wig.gz

value: H3K27me3 (Diagenode, pAb-069-053)


title: WT1-H3K27me3_SE

description:
PE and SE raw data was pooled to generate processed data
wt1chip_VS_wtinput_nomodel_SPMR_treat_pileup.wig.gz

value: H3K27me3 (Diagenode, pAb-069-051)


title: KO2-H3K27me3_SE

description:
PE and SE raw data was pooled to generate processed data
ko2chip_VS_koinput_nomodel_SPMR_treat_pileup.wig.gz

value: H3K27me3 (Diagenode, pAb-069-055)


title: D5(38Y)-2


title: Tn5 adult beta (Tn5_EA5)


title: D15(MSC-LC-62Y)-2

source_name: mesenchymal stem cell-LC D15

value: mesenchymal stem cell-LC D15


title: Sph_1

description:
Metamorphed cells replicate 1
Sph_1

source_name: ph505 clone in the adult stage

value: non tumorigenic adult ph505 clone


title: D0(Fib-62Y)-2

source_name: fibroblast

value: fibroblast


title: bMSC(33Y)-3


title: Control_1

description:
wild type eye discs, transplanted into the adult abdomen and take out one day after the transplantation
Ctrl_1


title: bMSC(33Y)-4


title: Sph_2

description:
Metamorphed cells replicate 2
Sph_2


title: Control_2

description:
wild type eye discs, transplanted into the adult abdomen and take out one day after the transplantation
Ctrl_2


title: KO1_H3K27me3_SE

description:
PE and SE raw data was pooled to generate processed data
ko1chip_VS_koinput_nomodel_SPMR_treat_pileup.wig.gz

value: H3K27me3 (Diagenode, pAb-069-050)


title: bMSC(36Y)-3


title: D0(Fib-39Y)-4


title: D12(62Y)-1

source_name: fibroblast induced D12

value: fibroblast induced D12


title: D12(62Y)-2


title: bMSC(36Y)-4


title: D15(MSC-LC-62Y)-1


title: D5(62Y)-2


title: D0(Fib-62Y)-1


title: Sph_3

description:
Metamorphed cells replicate 3
Sph_3


title: D5(62Y)-3


title: KO2-input_PE


title: D15(MSC-LC-39Y)-7


title: D15(MSC-LC-39Y)-5


title: D5(62Y)-1


title: D5(39Y)-2


title: D12(38Y)-2


title: D12(38Y)-3


title: D12(39Y)-3


title: D15(MSC-LC-38Y)-4


title: D12(39Y)-2


title: D12(39Y)-4


title: D15(MSC-LC-39Y)-3


title: D5(39Y)-1


title: D15(MSC-LC-38Y)-3


title: D15(MSC-LC-39Y)-4


title: D15(MSC-LC-38Y)-2


title: D5(38Y)-1


title: D15(MSC-LC-39Y)-1


title: D15(MSC-LC-39Y)-2


title: D15(MSC-LC-38Y)-1


title: D0(Fib-39Y)-2


title: D15(MSC-LC-39Y)-6


title: bMSC(33Y)-2


title: bMSC(31Y)-2


title: bMSC(36Y)-1


title: D15(MSC-LC-38Y)-5


title: bMSC(31Y)-1


title: bMSC(33Y)-1


title: D12(38Y)-1


title: D0(Fib-38Y)-2


title: D0(Fib-39Y)-3


title: D12(39Y)-1


title: D0(Fib-38Y)-4


title: POS92

city: Clayton

first: Sebastian

last: Scheer

address: 15 Innovation Walk

country: Australia

institute: Monash University

data_processing:
Used RNAsik pipeline to bam, counts and gather different metrics on RNAseq data https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
Used Degust  to analysis table of counts, output form RNAsik. Degust is a webapp that uses either edgeR or limma-voom for differential gene analysis http://degust.erc.monash.edu
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: raw counts file was generated by featureCounts, which than was uploaded to Degust

source_name: sorted YFP-pos CD4+ T cells after Th1 polarization in the presence of SGC0946

growth_protocol: Cells were preeinriched from the spleen and peripheral lymph nodes of IFN-g-YFP reporter mice

extract_protocol:
RNA was extracted using the Macherey & Nagel Nucleospin RNA kit according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells of spleen and peripheral lymph nodes of IFNg-YFP reporter mice were enriched for CD4+ T cells and cultured for 4 days under Th1 polarizing conditions (plate boud anti-CD3 and anti-CD28 [1 µg/ml each], 10 ng/ml IL-2, 10 ng/ml IL-12 and 10 µg/ml anti-IL4) and either SGC0946 (NEG91-3 and POS91-3) or SGC0649 (NEG61-3 and POS61-3) and FACS sorted for either CD4+ YFP+ (POS) or CD4+ YFP- (NEG) cells

tag: strain background

tag: genotype/variation

value: IFN-g-YFP reporter

value: spleen and peripheral lymph nodes


title: bMSC(31Y)-3


title: POS62

source_name: sorted YFP-pos CD4+ T cells after Th1 polarization in the presence of SGC0649


title: POS93

value: sorted YFP-pos CD4+ T cells after Th1 polarization in the presence of SGC0946


title: bMSC(33Y)-5


title: D0(Fib-39Y)-1


title: D0(Fib-38Y)-3


title: POS91


title: POS63

value: sorted YFP-pos CD4+ T cells after Th1 polarization in the presence of SGC0649


title: NEG61

source_name: sorted YFP-neg CD4+ T cells after Th1 polarization in the presence of SGC0649


title: NEG93

source_name: sorted YFP-neg CD4+ T cells after Th1 polarization in the presence of SGC0946


title: NEG92

value: sorted YFP-neg CD4+ T cells after Th1 polarization in the presence of SGC0946


title: NEG91


title: NEG62

value: sorted YFP-neg CD4+ T cells after Th1 polarization in the presence of SGC0649


title: POS61


title: NAIVE1

source_name: sorted naïve CD4+ T cells

treatment_protocol: Cells of spleen and peripheral lymph nodes of IFNg-YFP reporter mice were FACS sorted for CD4+ CD44- CD62L+

value: sorted naive CD4+ T cells


title: NAIVE3


title: NC-HUVEC

city: ShangHai

first: Yuan

last: Tianyou

address: No.1239,SiPing road,YangPu District

institute: tongji university

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
mapping to reference genome using hisat2
count counting
Genome_build: GRCh38、rnor6

source_name: Umbilical Vein

growth_protocol: All cells were grown  in DMEM supplemented with 10%FBS, 100 U/ml penicillin, 100 μg/ml streptomycin.

extract_protocol:
All cells were washed once by cold PBS  on ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Negative control siRNA and LRP6-targeted siRNA were transfected into the cells corresponding for 72 hours.

value: HUVEC

tag: transfection

value: negative control siRNA

tag: induced time

value: 72 hour


title: LRP6 KD-HUVEC

value: LRP6-targeted siRNA


title: NAIVE2


title: LRP6 KD-HeLa

source_name: Cervical cancer

value: HeLa


title: NC-HeLa


title: D0(Fib-38Y)-1


title: CFPAC-1 AZA a

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

description: 5-AZA-Dc treated cells for 4 days

data_processing:
base-calling: Sequence reads were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python. Low quality nucleotides and adapter sequences were trimmed off during analysis QC.
Read alignment: Sequence reads were aligned back to the reference genome using Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/), an aligner optimized for bisulfite sequence data and methylation calling (Krueger & Andrews, Bioinformatics, 2011). Paired-end alignment was used as default thus requiring both read 1 and read 2 be aligned within a certain distance, otherwise both read 1 and read 2 were discarded.
methylation calling: Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Nucleotides in primers were trimmed off from amplicons during methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: UCSC hg19 reference genome
Supplementary_files_format_and_content: The processed data file called: zr1157_all_count_10_onesheet  is tab-delimited text format and represents a detailed description of the chromosomal position of each CpG of interest and the corresponding methylation ratio( ratio of methylated-probe signal to total locus signal intensity) and total CpG count for each sample.

source_name: epithelial cells derivef from pancreatic ductal adenocarcinoma

growth_protocol: Healthy pancreatic cancer cells were trypsinized and plated in 30% confluence.

extract_protocol:
Isolation of genomic DNA using QIAamp DNA Mini Kit (Qiagen).
Samples were bisulfite converted using the EZ DNA Methylation-LightningTM Kit (www.zymoresearch.com - catalog number D5030) according to the manufacturer’s instructions. Multiplex amplification of all samples using ROI specific primer pairs and the Fluidigm Access ArrayTM System was performed according the to the manufacturer’s instructions. The resulting amplicons were pooled for harvesting and subsequent barcoding according to the Fluidigm instrument’s guidelines. After barcoding, samples were purified (ZR-96 DNA Clean & Concentrator™ - ZR, Cat#D4023) and then prepared for massively parallel sequencing using a MiSeq V2 300bp Reagent Kit and paired-end sequencing protocol according to the manufacturer’s guidelines.

treatment_protocol: The culture media has been replaced every 24 h with fresh media containing 5-AZA-Dc (1μM) for 4 days in total.

value: CFPAC-1 pancreatic cancer cell line


title: CFPAC-1 AZA c

description: 5-AZA-Dc treated cells for 4 days


title: Zy-unmeth_total_CpG_count

description: DKO cell line that has been enzymatically methylated using a CpG methylase (positive control)

source_name: HCT116 DKO cell line

value: HCT116 cancer cell line


title: CFPAC-1 con c

description: untreated cells


title: CFPAC-1 AZA b

description: 5-AZA-Dc treated cells for 4 days


title: Zy-meth_total_CpG_count

description: double knockout cell line for DNMT1 and DNMT3b (negative control)


title: CAPAN-1 AZA c

description: 5-AZA-Dc treated cells for 4 days

source_name: epithelial cells derivef from pancreatic adenocarcinoma

value: CAPAN-1 pancreatic cancer cell line


title: CAPAN-1 AZA b

description: 5-AZA-Dc treated cells for 4 days


title: CFPAC-1 con a

description: untreated cells


title: CAPAN-1 con c

description: untreated cells


title: Bx-PC-3 AZA c

description: 5-AZA-Dc treated cells for 4 days

value: Bx-PC-3 pancreatic cancer cell line


title: Bx-PC-3 con b

description: untreated cells


title: CAPAN-1 con b

description: untreated cells


title: Bx-PC-3 AZA b

description: 5-AZA-Dc treated cells for 4 days


title: Bx-PC-3 con a

description: untreated cells


title: AsPC-1 AZA a

description: 5-AZA-Dc treated cells for 4 days

value: AsPC-1 pancreatic cancer cell line


title: Bx-PC-3 AZA a

description: 5-AZA-Dc treated cells for 4 days


title: CFPAC-1 con b

description: untreated cells


title: AsPC-1 con c

description: untreated cells


title: AsPC-1 AZA c

description: 5-AZA-Dc treated cells for 4 days


title: AsPC-1 AZA b

description: 5-AZA-Dc treated cells for 4 days


title: AsPC-1 con b

description: untreated cells


title: AsPC-1 con a

description: untreated cells


title: MIA AZA c

description: 5-AZA-Dc treated cells for 4 days

source_name: epithelial cells derivef from pancreatic carcinoma

value: MIA PaCa-2 pancreatic cancer cell line


title: MIA AZA a

description: 5-AZA-Dc treated cells for 4 days


title: MIA con c

description: untreated cells


title: MIA con b

description: untreated cells


title: MIA AZA b

description: 5-AZA-Dc treated cells for 4 days


title: CAPAN-1 con a

description: untreated cells


title: CAPAN-1 AZA a

description: 5-AZA-Dc treated cells for 4 days


title: MIA con a

description: untreated cells


title: CS0-2

city: Shenyang

first: Zhiyong

last: Liu

institute: Shenyang Agriculture University

data_processing:
Libraries were sequenced on an Illumina Hiseq platform (San Diego, CA, USA)
The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12.
Gene expression levels were calculated based on reads per kb per million reads. Differential expression analysis of eight samples (three biological replicates per condition) was performed using DESeq R package v.1.10.1. The false discovery rate (FDR) method was used to determine the threshold P value in multiple tests to identify DEGs; an adjusted log2 ratio ≥ 5 and FDR ≤ 0.001 were set as the threshold for differential expression.
Genome_build: the genome website （http://cucurbitgenomics.org/）
Supplementary_files_format_and_content: DESeq output

organism: Cucumis sativus

source_name: leaves

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
In total, of 3 μg RNA per sample from four time points each with three independent biological replicates were used to construct 12 cDNA libraries designated as CS0, CS0-1, CS0-2, CS1, CS1-1, CS1-2, CS2, CS2-1, CS2-2, CS3, CS3-1, and CS3-2.

tag: strain

value: leaves

tag: developmental stage

value: trifoliate

tag: treatment

value: untreated


title: CS2-2

value: exposed to an air temperature of 6°C for 6 h


title: CS3-1

value: exposed to an air temperature of 6°C for 12 h


title: bMSC(36Y)-2

source_name: bone mesenchymal stem cell

tag: cell type

value: bone mesenchymal stem cell


title: MYC RNAP II ChIP-seq

city: Lebanon

middle: David

last: Cole

state: NH

address: One Medical Center Drive

department: Genetics

institute: Geisel School of Medicine at Dartmouth

description:
ChIP-Seq for RNA Pol II in mouse embryonic fibroblasts transfected with MYC vector
MEF_MYC_RNA_POL2

data_processing:
Reads were aligned to the mm9 genome build using Bowtie version 1.0 with the following command: "bowtie -e 70 -k 1 -m1 -n 2 -p 4 -l 50 --best --sam "
enriched regions were defined using macs1.4.2 with a p-value cutoff of 1e-9
.wig files were produced from macs1.4.2 --wig option
mapped .txt files were produced using a custom script https://github.com/BradnerLab/pipeline/blob/master/bamToGFF_turbo.py that quantifies extended read density at regions in units of reads per base pair per million mapped reads. bamToGFF_turbo.py was called using flags -e 200 -m 1 -r
Genome_build: mm9
Supplementary_files_format_and_content: .wig files of read pile up genome wide. .txt mapped read density at promoters and gene bodies in units of reads per base pair per million mapped reads

source_name: immortalized MEF cells

growth_protocol: Immortalized mouse embryonic fibroblasts grown in DMEM 10% FBS

extract_protocol:
Harvest by Millipore ChIP Lysis Buffer followed by chromatin immunoprecipitation and phenol/chloroform extraction
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Cells containing empty vector (PBMN), Myc, or MycN were passaged equivalently before harvest for ChIP

value: Immortalized mouse embryonic fibroblasts (MEFs)

value: expressing C-Myc

tag: chip antibody

value: RNA pol II (Abcam ab5408)


title: Bx-PC-3 con c

description: untreated cells