title: 54Dp1_F03_smart-seq


title: 54Dp1_E03_smart-seq

status: Public on Sep 30 2016

type: SRA

city: Seattle

first: Zizhen

last: yao

state: WA

department: MAT

country: USA

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Read were aligned transcriptome by RSEM to RefSeq gene annotation (April 23, 2013), and unmapped reads were aligned to genome by Bowtie. The remaining reads were aligned to ERCC.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM TPM gene expression matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: cultured embryonic stem cells

growth_protocol: hESCs were seeded for a 12-day cortical induction phase in NIM media with SMAD inhibitors and cyclopamine; reseeded for the progenitor expansion phase at D12 and D19 in neural stem cell culture media with EGF and bFGF, and finally at D26 for neural differentiation with neurogenic/neurotrophic factors BDNF, GDNF, NT3, and cAMP.  The protocol was ended at D54.

extract_protocol:
To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase  (ThermoFisher)  at  37°C.    Light  trituration  using  a P1000  pipette  was  done  every  5  min  until  nearly  all clumps  had  been  dissociated  (up  to  1  h).    Cell  suspension  was  washed  and  filtered  through  a  40  μm  cell  strainer.  Cells were washed in PBS with 1% FBS and stained with 0.5-1 μg/mL DAPI.  Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  μm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy.
SmartSeq2 protocol. After  reverse  transcription  and  template  switching,  we amplified  cDNA  with  KAPA  HotStart  HIFI  2×  ReadyMix  (Kapa  Biosystems)  for  22  cycles  for  RNA  from  single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay   Kit  (Thermo  Fisher)  on  an  Enspire  plate  reader  (PerkinElmer).  We  used  1  ng  of  cDNA  to  generate  RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads

tag: days in culture

tag: cre line

value: DCX+

tag: differentiation#

tag: control

value: FALSE


title: 54Dp1_E04_smart-seq


title: 54Dp1_E10_smart-seq


title: 54Dp1_F05_smart-seq


title: 54Dp1_E07_smart-seq


title: 54Dp1_E09_smart-seq


title: 54Dp1_E01_smart-seq


title: 54Dp1_E08_smart-seq


title: 54Dp1_E05_smart-seq


title: 54Dp1_E02_smart-seq


title: 54Dp1_D11_smart-seq


title: 54Dp1_E11_smart-seq


title: 54Dp1_G01_smart-seq


title: 54Dp1_F04_smart-seq


title: 54Dp1_D10_smart-seq


title: 54Dp1_D05_smart-seq


title: 54Dp1_D09_smart-seq


title: 54Dp1_D04_smart-seq


title: 54Dp1_F09_smart-seq


title: 54Dp1_D06_smart-seq


title: 54Dp1_D08_smart-seq


title: 54Dp1_D02_smart-seq


title: 54Dp1_D03_smart-seq


title: 54Dp1_D07_smart-seq


title: 54Dp1_D01_smart-seq


title: 54Dp1_C09_smart-seq


title: 54Dp1_C08_smart-seq


title: 54Dp1_C11_smart-seq


title: 54Dp1_C06_smart-seq


title: 54Dp1_C10_smart-seq


title: 54Dp1_C03_smart-seq


title: 54Dp1_C04_smart-seq


title: 54Dp1_B10_smart-seq


title: 54Dp1_C05_smart-seq


title: 54Dp1_B05_smart-seq


title: 54Dp1_B08_smart-seq


title: 54Dp1_C02_smart-seq


title: 54Dp1_B11_smart-seq


title: 54Dp1_B03_smart-seq


title: 54Dp1_A11_smart-seq


title: 54Dp1_A07_smart-seq


title: 54Dp1_B02_smart-seq


title: 54Dp1_A06_smart-seq


title: 54Dp1_B04_smart-seq


title: 54Dp1_B09_smart-seq


title: 54Dp1_C07_smart-seq


title: 54Dp1_A05_smart-seq


title: 54Dp1_A10_smart-seq


title: 54Dp1_A09_smart-seq


title: 54Dp1_B01_smart-seq


title: 54Dp1_B06_smart-seq


title: 54Dp1_C01_smart-seq


title: 54Dp1_B07_smart-seq


title: 54Dp1_A04_smart-seq


title: 54Dp1_A08_smart-seq


title: 54Dp1_A03_smart-seq


title: 54Dp1_A02_smart-seq


title: 26Dn1_H10_smart-seq

value: DCX-


title: 54Dp1_A01_smart-seq


title: 26Dn1_H08_smart-seq


title: 26Dn1_H06_smart-seq


title: 26Dn1_H09_smart-seq


title: 26Dn1_H04_smart-seq


title: 26Dn1_H03_smart-seq


title: 26Dn1_H02_smart-seq


title: 26Dn1_G07_smart-seq


title: 26Dn1_H05_smart-seq


title: 26Dn1_G09_smart-seq


title: 26Dn1_H01_smart-seq


title: 26Dn1_G06_smart-seq


title: 26Dn1_G04_smart-seq


title: 26Dn1_H07_smart-seq


title: 26Dn1_G03_smart-seq


title: 26Dn1_G05_smart-seq


title: 26Dn1_G10_smart-seq


title: 26Dn1_F10_smart-seq


title: 26Dn1_G02_smart-seq


title: 26Dn1_F11_smart-seq


title: 26Dn1_G01_smart-seq


title: 26Dn1_G11_smart-seq


title: 26Dn1_G08_smart-seq


title: 26Dn1_F07_smart-seq


title: 26Dn1_F09_smart-seq


title: 26Dn1_F08_smart-seq


title: 26Dn1_H11_smart-seq


title: 26Dn1_F03_smart-seq


title: 26Dn1_F04_smart-seq


title: 26Dn1_F02_smart-seq


title: 26Dn1_E10_smart-seq


title: 26Dn1_F01_smart-seq


title: 26Dn1_E11_smart-seq


title: 26Dn1_E04_smart-seq


title: 26Dn1_E06_smart-seq


title: 26Dn1_E08_smart-seq


title: 26Dn1_E05_smart-seq


title: 26Dn1_E03_smart-seq


title: 26Dn1_D09_smart-seq


title: 26Dn1_E07_smart-seq


title: 26Dn1_D11_smart-seq


title: 26Dn1_E09_smart-seq


title: 26Dn1_D10_smart-seq


title: 26Dn1_D05_smart-seq


title: 26Dn1_D04_smart-seq


title: 26Dn1_D03_smart-seq


title: 26Dn1_E02_smart-seq


title: 26Dn1_C11_smart-seq


title: 26Dn1_F05_smart-seq


title: 26Dn1_D01_smart-seq


title: 26Dn1_D07_smart-seq


title: 26Dn1_D02_smart-seq


title: 26Dn1_F06_smart-seq


title: 26Dn1_E01_smart-seq


title: 26Dn1_D06_smart-seq


title: 26Dn1_C09_smart-seq


title: 26Dn1_C10_smart-seq


title: 26Dn1_C08_smart-seq


title: 26Dn1_C07_smart-seq


title: 26Dn1_C06_smart-seq


title: 26Dn1_C04_smart-seq


title: 26Dn1_C05_smart-seq


title: 26Dn1_D08_smart-seq


title: 26Dn1_B09_smart-seq


title: 26Dn1_C01_smart-seq


title: 26Dn1_B11_smart-seq


title: 26Dn1_B07_smart-seq


title: 26Dn1_B05_smart-seq


title: 26Dn1_B08_smart-seq


title: 26Dn1_C02_smart-seq


title: 26Dn1_C03_smart-seq


title: 26Dn1_A11_smart-seq


title: 26Dn1_B03_smart-seq


title: 26Dn1_B04_smart-seq


title: 26Dn1_A09_smart-seq


title: 26Dn1_B01_smart-seq


title: 26Dn1_A07_smart-seq


title: 26Dn1_A06_smart-seq


title: 26Dn1_A08_smart-seq


title: 26Dn1_A05_smart-seq


title: 26Dn1_A04_smart-seq


title: 26Dn1_A10_smart-seq


title: 26Dn1_A02_smart-seq


title: 26Dn1_A01_smart-seq


title: 26Dp1_H11_smart-seq


title: 26Dp1_H10_smart-seq


title: 26Dn1_B10_smart-seq


title: 26Dp1_H09_smart-seq


title: 26Dp1_H06_smart-seq


title: 26Dn1_B06_smart-seq


title: 26Dp1_H05_smart-seq


title: 26Dp1_G11_smart-seq


title: 26Dp1_H02_smart-seq


title: 26Dp1_G10_smart-seq


title: 26Dp1_G09_smart-seq


title: 26Dn1_B02_smart-seq


title: 26Dp1_H01_smart-seq


title: 26Dp1_H04_smart-seq


title: 26Dp1_G07_smart-seq


title: 26Dp1_G06_smart-seq


title: 26Dp1_G04_smart-seq


title: 26Dp1_G05_smart-seq


title: 26Dp1_G03_smart-seq


title: 26Dn1_A03_smart-seq


title: 26Dp1_G01_smart-seq


title: 26Dp1_G02_smart-seq


title: 26Dp1_F10_smart-seq


title: 26Dp1_F09_smart-seq


title: 26Dp1_H08_smart-seq


title: 26Dp1_F08_smart-seq


title: 26Dp1_F07_smart-seq


title: 26Dp1_F04_smart-seq


title: 26Dp1_F02_smart-seq


title: 26Dp1_F01_smart-seq


title: 26Dp1_H03_smart-seq


title: 26Dp1_E11_smart-seq


title: 26Dp1_E08_smart-seq


title: 26Dp1_G08_smart-seq


title: 26Dp1_E09_smart-seq


title: 26Dp1_E10_smart-seq


title: 26Dp1_E07_smart-seq


title: 26Dp1_E06_smart-seq


title: 26Dp1_F11_smart-seq


title: 26Dp1_E01_smart-seq


title: 26Dp1_E03_smart-seq


title: 26Dp1_D10_smart-seq


title: 26Dp1_E02_smart-seq


title: 26Dp1_E04_smart-seq


title: 26Dp1_E05_smart-seq


title: 26Dp1_D11_smart-seq


title: 26Dp1_D09_smart-seq


title: 26Dp1_F06_smart-seq


title: 26Dp1_D06_smart-seq


title: 26Dp1_F05_smart-seq


title: 26Dp1_D07_smart-seq


title: 26Dp1_F03_smart-seq


title: 26Dp1_D08_smart-seq


title: 26Dp1_D04_smart-seq


title: 26Dp1_D05_smart-seq


title: 26Dp1_D03_smart-seq


title: 26Dp1_C11_smart-seq


title: 26Dp1_D01_smart-seq


title: 26Dp1_C10_smart-seq


title: 26Dp1_C09_smart-seq


title: 26Dp1_C08_smart-seq


title: 26Dp1_C07_smart-seq


title: 26Dp1_C06_smart-seq


title: 26Dp1_C04_smart-seq


title: 26Dp1_C05_smart-seq


title: 26Dp1_C03_smart-seq


title: 26Dp1_C02_smart-seq


title: 26Dp1_C01_smart-seq


title: 26Dp1_B11_smart-seq


title: 26Dp1_B10_smart-seq


title: 26Dp1_B09_smart-seq


title: 26Dp1_B08_smart-seq


title: 26Dp1_B03_smart-seq


title: 26Dp1_B05_smart-seq


title: 26Dp1_D02_smart-seq


title: 26Dp1_B02_smart-seq


title: 26Dp1_A11_smart-seq


title: 26Dp1_A09_smart-seq


title: 26Dp1_A08_smart-seq


title: 26Dp1_B01_smart-seq


title: 26Dp1_A05_smart-seq


title: 26Dp1_A07_smart-seq


title: 26Dp1_A06_smart-seq


title: 26Dp1_A03_smart-seq


title: 26Dp1_A10_smart-seq


title: 26Dp1_A01_smart-seq


title: 26Dp1_A04_smart-seq


title: H9-D54-2_bulk

molecule: total RNA

extract_protocol:
Total RNA was purified from cell using a Qiagen RNeasy Kit
Library construction was carried out using the Illumina True Seq kit at the company Expression Analysis


title: 26Dp1_A02_smart-seq


title: H9-D54-1_bulk


title: H9-D26-2_bulk


title: H9-D26-1_bulk


title: H9-D19-2_bulk


title: H9-D19-1_bulk


title: 26Dp1_B06_smart-seq


title: 26Dp1_B04_smart-seq


title: H9-D12-2_bulk


title: H9-D12-1_bulk


title: H9-D9-2_bulk


title: H9-D9-1_bulk


title: H9-D6-1_bulk


title: H1-D54-2_bulk


title: H9-D0-2_bulk


title: H9-D0-1_bulk


title: H1-D54-1_bulk


title: H1-D26-2_bulk


title: H1-D19-1_bulk


title: H1-D12-1_bulk


title: H1-D26-1_bulk


title: H1-D9-2_bulk


title: H1-D0-3_bulk


title: H1-D9-1_bulk


title: H1-D0-2_bulk


title: H1-D6-2_bulk


title: H1-D0-1_bulk


title: H1-D6-1_bulk


title: 54Dn4_H09

data_processing:
Reads  were  de-multiplexed  by  CelSeq  index,  allowing  for  one  sequence mismatch.
The  transcript  reads  for  each  cell  were  aligned  to  the  RefSeq  transcriptome  (downloaded  March  2013) using Tophat with default parameters
Unaligned reads were then aligned to the genome using Bowtie (Langmead et al., 2009), followed by alignment to the ERCC spike-in controls.
Remaining unaligned  reads  were mapped  to  the  genome  again  using  GSNAP
Reads mapping  to  exons of  the  same  gene  were  collapsed  by  their  Unique  Molecular Identifier  (UMI)
Reads mapped within 1kb of the 3′ end of a gene in the proper orientation are ascribed to that gene
Cells with fewer than 20,000 total cellular UMIs were discarded, and data for all remaining cells was randomly subsampled to 20,000 total cellular UMIs.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_20K.2684.csv: UMI gene counts (subsampled to 20K)
Supplementary_files_format_and_content: UMI.2684.csv: UMI gene counts

extract_protocol:
To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase  (ThermoFisher)  at  37°C.    Light  trituration  using  a P1000  pipette  was  done  every  5  min  until  nearly  all clumps  had  been  dissociated  (up  to  1  h).    Cell  suspension  was  washed  and  filtered  through  a  40  μm  cell  strainer.  Cells were washed in PBS with 1% FBS and stained with 0.5-1 μg/mL DAPI.  Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  μm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy.
CelSeq protocol with a few modifications. Single cells were sorted with a FACSAria (BD) into 96-well plates containing 1.2 μL 2× CellsDirect Buffer (Thermo Fisher) with 0.1 μL of External RNA Controls Consortium (ERCC) control RNAs diluted to 1 × 10-6 molecules (Thermo Fisher). After sorting, plates were then frozen and stored at -80C. For library preparation, plates were thawed on ice. mRNA was reverse transcribed using 1.25 pmol or 0.15625 pmol of oligoT  primer  carrying  a  cell-specific  8  NT  barcode  and  a  5  NT  unique  molecular  identifier  (UMI)  (Islam  et  al., 2014) (see Table S4). Barcode design ensured at least three nucleotide differences from any other barcode. Samples were  incubated  in a  PCR  machine  (Tetrad,  BioRad)  at  70  °C  with a  70 °C  heated  lid  for  3  min,  spun,  and heated again for two more minutes. Samples were reverse transcribed using Superscript III (Thermo Fisher) for two hours at 50 °C with a 52 °C lid and subsequently treated with 1 μL of ExoSAP-IT (Affymetrix). Samples were cooled on ice  for  second  strand  synthesis,  where  Second  Strand  Synthesis  Buffer,  dNTPs,  DNA  Polymerase,  and  RNAse  H (NEB) were added to the samples for a 10 μL total volume and incubated at 16 °C for 2 h. Single cells were pooled by 24 wells per library, with each library containing a water-only well and an ERCC-only well. Single cell pools or population  RNA  libraries  were  purified  with  an  equal  volume  of RNA  Clean  Beads  (Beckman  Coulter),  linearly amplified at 37 C for 15 h using the HiScribe T7 High Yield RNA Synthesis kit (NEB), and treated with DNAse I (Thermo Fisher). RNA  was fragmented using the NEBNext RNA Fragmentation Module (NEB), purified using an equal volume of RNA Clean Beads, and visualized (RNA Pico Kit, Bioanalyzer 2100, Agilent). The RNA fragments were repaired by treating with Antarctic Phosphatase and Polynucleotide Kinase (NEB)  and purified with an equal volume of  RNA Clean Beads. cDNA libraries were made using the NEBNext Small Library Prep Kit according to the  manufacturer’s  protocol,  except  Superscript  III  was  used  for  the  RT  step. Index  primers  were  used  in  PCR amplification.  Libraries  were  purified  using  an  equal  volume  of  RNA  Clean  Beads  and  were  quantified  on  the Bioanalyzer using the DNA High Sensitivity Kit (Agilent). Approximately 160-200 nmol of a pool of libraries were size  selected  to  exclude  species  <180  bp  on  a  2%  Dye-Free  cassette  on  the  Pippin  Prep  (Sage)  and  Speed  Vac concentrated    to    approximately    14    μL.    Libraries    were    then quantified    by    qRT-PCR    using    p5    (5’-AATGATACGGCGACCACCGAGA-3’) and  p7   (5’-CAAGCAGAAGACGGCATACGAGAT-3’)   primers   and visualized (DNA High Sensitivity Kit, Bioanalyzer 2100). Library pools were then sequenced on an Illumina HiSeq  using a custom read1 primer (5’-TCTACACGTTCAGAGTTCTACAGTCCGACGATC-3’) and the Illumina primer HP10. Standard Illumina primers HP12 and HP11 were used for the index read and the transcript read, respectively. PE50 kits (Illumina) were used for sequencing with read lengths of 25 nt, 6 nt, and 47 nt for read1, index, and read2, respectively.

tag: library prep#


title: 54Dn5a_A09


title: 54Dn4_D08


title: 54Dn4_C03


title: 54Dn4_B11


title: 54Dn4_E07


title: 54Dn7_C05


title: 54Dp6c_G08


title: 54Dn7_A11


title: 54Dn7_D11


title: 54Dn4_G07


title: 54Dn7_C01


title: 54Dp6c_H11


title: 54Dn4_H04


title: 54Dn5a_C06


title: 54Dn4_C06


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title: 54Dn5a_D10


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title: 54Dn4_G02


title: 54Dn6_B04


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title: 54Dn4_D11


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title: 54Dn6_C07


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title: 54Dn4_H05


title: 54Dp6c_D10


title: 54Dn7_D08


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title: 54Dn6_C05


title: 54Dp6c_F02


title: 54Dn6_B10


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title: 54Dn6_C09


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title: 54Dn4_A03


title: 54Dn7_B01


title: 54Dn4_B08


title: 54Dn5a_A08


title: 54Dn4_A07


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title: 54Dn6_D11


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title: 54Dn7_D07


title: 54Dn7_D03


title: 54Dn7_D04


title: 54Dn5a_C09


title: 54Dp6c_E03


title: 54Dn4_C07


title: 54Dn4_H10


title: 54Dp6c_E04


title: 54Dn5a_C12


title: 54Dp6c_H04


title: 54Dp6c_D03


title: 54Dn7_D09


title: 54Dn4_A09


title: 54Dn4_F05


title: 54Dn6_A04


title: 54Dn4_D01


title: 54Dn4_B04


title: 54Dn6_C02


title: 54Dn7_A05


title: 54Dn7_D10


title: 54Dn4_E03


title: 54Dn4_A02


title: 54Dn4_B09


title: 54Dp6c_F05


title: 54Dn4_A11


title: 54Dn4_C10


title: 54Dn5a_C02


title: 54Dn7_A08


title: 54Dn5a_C07


title: 54Dn5a_C03


title: 54Dn7_A06


title: 54Dn7_B03


title: 54Dp6c_E05


title: 54Dp6c_G10


title: 54Dp6c_G05


title: 54Dn4_H03


title: 54Dn1b_C07


title: 54Dn6_A06


title: 54Dn4_B10


title: 54Dn6_B06


title: 54Dn5a_D02


title: 54Dn5a_A11


title: 54Dn5a_B05


title: 54Dp6c_H01


title: 54Dn4_A10


title: 54Dn4_D02


title: 54Dp6c_G09


title: 54Dn6_B09


title: 54Dn7_C02


title: 54Dn4_D07


title: 54Dn5a_A06


title: 54Dn4_F01


title: 54Dn4_D10


title: 54Dn4_D03


title: 54Dn4_C01


title: 54Dn4_D04


title: 54Dn4_C09


title: 54Dn5a_B01


title: 54Dn6_C03


title: 54Dn4_F09


title: 54Dn4_A04


title: 54Dp2b_E02


title: 54Dp6c_G11


title: 54Dp2b_F05


title: 54Dn1b_C12


title: 54Dp7b_G11


title: 54Dn1b_D02


title: 54Dn5a_B06


title: 54Dp7b_F04


title: 54Dn5a_A03


title: 54Dn4_F11


title: 54Dn5a_A07


title: 54Dn6_D10


title: 54Dn5a_A10


title: 54Dn7_C07


title: 54Dn4_A06


title: 54Dn6_D07


title: 54Dn6_A08


title: 54Dn6_D09


title: 54Dn7_A09


title: 54Dp6c_B11


title: 54Dn7_C11


title: 54Dp7b_E10


title: 54Dp6c_F07


title: 54Dn6_C04


title: 54Dn4_B05


title: 54Dn5a_B02


title: 54Dn4_F10


title: 54Dn5a_A04


title: 54Dn5a_A05


title: 54Dn5a_D03


title: 54Dn4_C11


title: 54Dn4_H02


title: 54Dn6_D04


title: 54Dn5a_B10


title: 54Dp6c_B04


title: 54Dn5a_C05


title: 54Dp6c_F06


title: 54Dp6c_B01


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title: 26Sp3b_G01


title: 26Sp3b_D02


title: 26Sp3b_C03


title: 26Sp3b_F02


title: 26Sp3b_A03


title: 26Sp3b_F03


title: 26Sp3b_D05


title: 26Sp3a_B10


title: 26Sp3b_H09


title: 26Sp3b_E06


title: 26Sp3b_B06


title: 26Sp3b_C05


title: 26Sp3b_A09


title: 26Sp3b_E07


title: 26Sp3b_F01


title: 26Sp3b_G09


title: 26Sp3b_E08


title: 26Sp3b_F11


title: 26Sp3b_H11


title: 26Sp3b_G11


title: 26Sp2c_A06


title: 26Sp2e_B11


title: 26Sp2c_A11


title: 26Sp1b_A04


title: 26Sp3b_G10


title: 26Sp3a_A08


title: 26Sp3b_B10


title: 26Sp2d_C01


title: 26Sp3b_A05


title: 26Sp3b_A10


title: 26Sp1f_C01


title: 26Sp3b_C09


title: 26Sp2e_A09


title: 26Sp2c_B02


title: 26Dn2_A10


title: 26Sp2c_B08


title: 26Sp2h_C05


title: 26Sp3b_E09


title: 26Sp3b_H05


title: 26Sp3b_C04


title: 26Sp2b_C11


title: 26Sp2g_A08


title: 26Sp2c_B04


title: 26Sp3b_C08


title: 26Sp1e_B11


title: 26Sp3a_E06


title: 26Sp2c_B07


title: 26Sp3b_D09


title: 26Sp3a_C12


title: 26Sp2g_A01


title: 26Sp2b_C05


title: 26Sn3a_E11


title: 26Sp2b_D09


title: 26Sp2b_D05


title: 26Sp3b_A06


title: 26Sp3b_B11


title: 26Sp2f_D11


title: 26Sp2c_B05


title: 26Sp3a_F07


title: 26Sp3b_C07


title: 26Sp2g_B02


title: 26Sp2a_A01


title: 26Sp2c_B11


title: 26Sp2f_C03


title: 26Sp1e_A11


title: 26Sp2c_A02


title: 26Sp2f_D04


title: 26Sp2g_A05


title: 26Sp1b_B05


title: 26Sp2b_C09


title: 26Sp1e_A01


title: 26Sp2a_B04


title: 26Sp3b_F09


title: 26Sp2a_C01


title: 26Sp2g_B08


title: 26Sp3b_C10


title: 26Sp3b_A11


title: 26Dn2_B08


title: 26Dn2_C05


title: 26Sp1a_D02


title: 26Dn1a_B03


title: 26Sp1a_D09


title: 26Sp1d_B03


title: 26Sp2a_B12


title: 26Dn2_A02


title: 26Sp1b_A09


title: 26Sp1c_A05


title: 26Sp1c_B07


title: 26Sp1f_C11


title: 26Sp1c_B03


title: 26Sp1g_C08


title: 26Dn1a_A05


title: 26Sp1d_A09


title: 26Dn2d_C09


title: 26Sp1g_C10


title: 26Sp2b_D08


title: 26Sp2a_A03


title: 26Sp2a_B05


title: 26Sp1a_D08


title: 26Sp1d_A11


title: 26Sp2a_B07


title: 26Sp1h_C10


title: 26Sp2f_D01


title: 26Sp2d_D04


title: 26Sp1h_D02


title: 26Sp2b_C08


title: 26Sp2f_D09


title: 26Sp2e_B01


title: 26Sp2f_C11


title: 26Sp2h_C02


title: 26Sp2g_A09


title: 26Sp1h_C05


title: 26Sp2h_C08


title: 26Sp2g_A06


title: 26Sp3a_H05


title: 26Sp3a_B01


title: 26Sp3a_H09


title: 26Sp2h_C12


title: 26Sp3a_G07


title: 26Sp2f_D07


title: 26Sp3a_E09


title: 26Sp2f_D08


title: 26Sp3a_E08


title: 26Sp3b_E02


title: 26Sp3b_H02


title: 26Sp3a_D09


title: 26Sp3b_A01


title: 26Sp3b_G02


title: 26Sp3b_F06


title: 26Sp3b_D04


title: 26Sp3a_D07


title: 26Sp3b_A08


title: 26Sp3b_E05


title: 26Sp3b_F07


title: 26Sp3b_H04


title: 26Sp3a_A10


title: 26Sp3a_A03


title: 26Dn1a_D07


title: 26Sp2c_B12


title: 26Sp1d_B06


title: 26Sp2c_A08


title: 26Sp2c_B06


title: 26Sp2f_D10


title: 26Sp2f_C02


title: 26Sp2f_C09


title: 26Sp3a_C05


title: 26Sp2f_C04


title: 26Sp3a_D02


title: 26Sp2e_B03


title: 26Sp3a_A09


title: 26Sp3b_B07


title: 26Sp2h_D03


title: 26Sp3b_B04


title: 26Sp2g_A10


title: 26Dn1a_D04


title: 26Dn2_B01


title: 26Dn2_C03


title: 26Sp2g_B09


title: 26Dn1a_C03


title: 26Dn1a_A09


title: 26Sp1b_A01


title: 26Sp1b_A03


title: 26Dn2_C07


title: 26Sp1a_D03


title: 26Sp1h_C01


title: 26Sp1b_B07


title: 26Sp1e_B02


title: 26Sp2a_A08


title: 26Dn1a_B07


title: 26Sp2g_A12


title: 26Sp2g_B10


title: 26Sp2g_B06


title: 26Sp1b_B12


title: 26Sp1c_B04


title: 26Dn2_C08


title: 26Sp2b_D07


title: 26Sp1e_B03


title: 26Sp2c_A12


title: 26Sp2b_D03


title: 26Dn1a_B11


title: 26Sp2g_A11


title: 26Sp3a_C01


title: 26Sp1h_D01


title: 26Sp2h_D04


title: 26Sp2e_B07


title: 26Sp2g_B11


title: 26Sp3a_A05


title: 26Sp3a_E04


title: 26Sp2f_C12


title: 26Sp1a_D07


title: 26Sp3a_B03


title: 26Dn2_C04


title: 26Sp1h_C04


title: 26Sp2e_B06


title: 26Sp2f_D03


title: 26Sp2a_B03


title: 26Sp3a_E03


title: 26Dn1a_C11


title: 26Sp3b_E10


title: 26Sp3a_F06


title: 26Sp2g_A04


title: 26Sp2a_B01


title: 26Sn3a_A03


title: 26Sn3a_C04


title: 26Sp2a_B06


title: 26Sp1f_C10


title: 26Sn3a_H11


title: 26Sp1d_B07


title: 26Sp3b_D07


title: 26Sn3a_D03


title: 26Sp3b_B03


title: 26Sp2f_C08


title: 26Sp2b_D02


title: 26Sp1a_C08


title: 26Sp3a_G03


title: 26Sn3a_E09


title: 26Sn3a_H03


title: 26Dn2_C11


title: 26Sn3a_A08


title: 26Sp1b_B06


title: 26Sp3b_B01


title: 26Sn3a_D06


title: 26Sp3b_C06


title: 26Sn3a_B07


title: 26Sn3a_E03


title: 26Sn3a_A07


title: 26Sn3a_H04


title: 26Sp3a_E05


title: 26Sp2c_C01


title: 26Dn2_D05


title: 26Sp3b_H10


title: 26Dp2b_D09


title: 26Sn3a_B11


title: 26Sn3a_H06


title: 26Sn3a_H05


title: 26Sn3a_H01


title: 26Dp4_B07


title: 26Dp4_H02


title: 26Dp4_H06


title: 26Sn3a_D04


title: 26Sn3a_G03


title: 26Sn3a_D07


title: 26Dp4_A11


title: 26Sn3a_E01


title: 26Sn3a_C05


title: 26Sn3a_H02


title: 26Sn3a_D01


title: 26Sn3a_G02


title: 26Sn3a_G01


title: 26Sn3a_C08


title: 26Sn3a_G06


title: 26Sn3a_C06


title: 26Sn3a_C09


title: 26Sn3a_D08


title: 26Sn3a_H10


title: 26Sn3a_G07


title: 26Sn3a_H09


title: 26Sn3a_D09


title: 26Sn3a_C07


title: 26Sn3a_D11


title: 26Sn3a_C01


title: 26Sn3a_C10


title: 26Sn3a_C11


title: 26Sn3a_G11


title: 26Sn3a_D10


title: 26Sn3a_G10


title: 26Dp1a_A06


title: 26Dp1a_A04


title: 26Dp1a_A07


title: 26Dp1a_A01


title: 26Dp1a_B03


title: 26Sn3a_H07


title: 26Sn3a_G04


title: 26Dp1a_D06


title: 26Dp1a_B04


title: 26Dp1a_B09


title: 26Dp1a_B05


title: 26Dp1a_A08


title: 26Dp1a_D05


title: 26Dp1a_C07


title: 26Dp1a_B06


title: 26Dp1a_C08


title: 26Dp1a_C06


title: 26Dp1a_C05


title: 26Dp1a_A09


title: 26Dp1a_B08


title: 26Dp1a_B07


title: 26Dp1a_A11


title: 26Dp1a_C09


title: 26Dp1a_D08


title: 26Dp1a_D09


title: 26Dp1a_C10


title: 26Dp1a_A02


title: 26Dp1a_B10


title: 19Dp2b_B02


title: 26Dp1a_B11


title: 19Dp2b_D02


title: 26Dp1a_C11


title: 26Dp1a_A05


title: 19Dp1a_C11


title: 19Dp1b_B06


title: 19Dp1b_D07


title: 26Dp1a_A03


title: 26Dp1a_A10


title: 19Dp1b_D03


title: 19Dp1b_A07


title: 19Dp1a_A05


title: 19Dp1b_D08


title: 26Dp1a_D10


title: 19Dp1a_D10


title: 19Dp1b_A01


title: 19Dp1b_C03


title: 19Dp2a_B09


title: 19Dp2b_D08


title: 19Dp2b_B06


title: 19Dp2b_B04


title: 19Dp2a_C03


title: 19Dp2a_D04


title: 26Dp1a_D11


title: 19Dp2b_A05


title: 19Dp2a_C07


title: 19Dp2a_C11


title: 19Dp2a_D06


title: 19Dp2a_C01


title: 19Dp2a_C05


title: 19Dp2b_A02


title: 19Dp2a_D01


title: 19Dp2a_D11


title: 19Dp2b_A08


title: 19Dp2a_C09


title: 19Dp2b_A06


title: 19Dp2b_D06


title: 19Dp2b_A10


title: 19Dp1a_B01


title: 19Dp1a_D02


title: 19Dp1a_B02


title: 19Dp1a_B03


title: 19Dp1a_C02


title: 19Dp1a_D03


title: 19Dp1a_A01


title: 19Dp1a_A03


title: 19Dp1b_D06


title: 19Dp1a_B04


title: 19Dp1a_D07


title: 19Dp1a_B05


title: 19Dp1a_D05


title: 19Dp1a_C04


title: 19Dp1a_D04


title: 19Dp2a_D05


title: 19Dp2b_C10


title: 19Dp1a_B06


title: 19Dp1b_C11


title: 19Dp1a_C05


title: 19Dp1a_A06


title: 19Dp1a_C06


title: 19Dp1a_C03


title: 19Dp1a_C09


title: 19Dp1a_B07


title: 19Dp1a_A02


title: 19Dp1a_B08


title: 19Dp1a_C07


title: 19Dp1a_C08


title: 19Dp1a_C10


title: 19Dp1a_A08


title: 19Dp1a_A09


title: 19Dp1a_A10


title: 19Dp1a_B10


title: 19Dp1b_B01


title: 19Dp1b_C02


title: 19Dp1a_B11


title: 19Dp1b_A03


title: 19Dp1b_B02


title: 19Dp2a_A02


title: 19Dp1a_D08


title: 19Dp2a_D07


title: 19Dp1b_D04


title: 19Dp1b_C04


title: 19Dp1b_B03


title: 19Dp1b_B05


title: 19Dp1b_A04


title: 19Dp1b_A06


title: 19Dp1b_A02


title: 19Dp1b_B08


title: 19Dp1b_A05


title: 19Dp1a_A11


title: 19Dp1b_B09


title: 19Dp1b_B04


title: 19Dp1b_A08


title: 19Dp1b_A09


title: 4dpi_Input

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

library_source: genomic

data_processing:
Reads were mapped to mm9 genome using STAR aligner software. Reads mapping to more than one locus and/or having more than three mismatches were filtered out.
Peaks were detected using the findPeaks script of HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Binding site of 4dpi Lmo2 in bed format

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts 4 days post SLHR induction

growth_protocol: tdTomato+ MEFs were derived from E12.5-E13.5 embryos of the membrane-targeted tdTomato (mT) reporter mice strain (mT/mG, JAX mice stock No: 007676). Fibroblasts were prepared, cultured and transduced as described 68-70. Fibroblasts were purified through removing of any cells that positive stained with a cocktail of hematopoietic surface makers (FITC for Sca1 and APC for c-kit, CD150, CD48, AA4.1, CD45, CD19, B220, CD3, CD4, CD8, Gr-1, CD11b, F4/80, Ter119, CD41, CD42d) by sorting (FACSAria llu SORP cell sorter, Becton Dickinson). Hematopoietic cell-free fibroblasts transduced with hematopoietic factors were co-cultured with inactivated OP9 stromal cells and maintained in IMDM medium supplemented with 10% FBS and cytokine cocktail (SCF, IL3, TPO, FLT3L, 10ng/ml each, R&D Systems), and dox (4µg/ml, for inducible vectors) for observation of appearance of 'cobblestone' colonies and generation of iHPs for FACS, molecular and functional analysis.

extract_protocol: 10 million cells were crosslinked using 1% formaldehyde for 10 min at room temperature followed by quenching by using 200 mM glycine. After that, cell were lysed using a lysis buffer consisting of 10 mM Tris-Cl (pH 8), 100 mM NaCl, 10 mM EDTA, 0.25% Triton X-100 and protease inhibitor cocktail (Roche). Cells were then resuspended in 1% SDS lysis buffer composed of 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC and protease inhibitor cocktail. The suspension was nutated for 15 mins at cold room before spinning down to collect the chromatin pellet. The pellet was then washed two times with 0.1% SDS lysis buffer containing 50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.1% SDS, 2 mM EDTA, 1% Triton X-100, 0.1% NaDOC, 1 mM PMSF and protease inhibitor cocktail. Chromatin was then fragmented by sonication which was conducted with cells on ice with 11 cycles, power amplitude of 35% and 30 sec pulses on with 59.9 s pulses off (Branson Sonifier 250). The chromatin solution was clarified by centrifugation at 20,000 g at 4°C for 45 mins and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hrs at 4°C. The pre-cleared chromatin sample was incubated with 50 μl of Dynabeads protein A loaded with 5 µg antibody overnight at 4°C. The beads were washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8), 1 mM EDTA, 0.5% NP40, 0.25 LiCl, 0.5% NaDOC, and once with TE buffer (PH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 min at 68°C in 50 mM TrisCl (pH 7.5), 10 mM EDTA, 1% SDS. Reverse crosslinking was carried out by incubating the samples with 1.5 μg/ml Pronase at 42°C for 2 hr followed by a 6 hours incubation at 67°C. DNA was then purified using MinElute PCR Purification kit (Qiagen).

tag: antibody


title: 19Dp1b_A10


title: 19Dp2a_B01


title: 19Dp1b_A11


title: 4dpi_Lmo2

value: anti- hLmo2, AF2726, R&D Systems


title: 19Dp2a_B02


title: 19Dp2a_D02


title: E12.5 RET NULL GUT REP1

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
Broad Institute’s Picard Pipeline was used for de-multiplexing and data aggregation
The resultant BAM files were sorted and conveted to fastq files for each paierd end using bam2fastq-1.1.0
The files were thenmapped to the mouse genome mm10 index file uisng Tophat2 with the following attributes --library-type fr-unstranded -G (unstranded and pair end)
Successfully mapped reads were used to assemble transcripts and estimate their abundances ((FPKM) using Cufflinks
assembled transcripts  for replicates for each genotype were merged using cuffmerge and differential expression test was done using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output file in txt format showing FPKM values for each gene at both genotypes plus test statistics, fold change and significance

source_name: Gut

extract_protocol:
Guts were dissected out in cold leibovitz medium and RNA was extracted and cleaned using a Trizol Rneasy column hybrid method
cDNA  was prepared  by oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template as part of the Illumina Tru Seq™ RNA Sample Preparation protocol. The resultant cDNA then was used for library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using standard Illumina protocols.

tag: strain

tag: age

tag: genotype

value: Ret null


title: E12.5 WT GUT REP3

value: Wildtype


title: E12.5 RET NULL GUT REP3


title: E12.5 RET NULL GUT REP2


title: 19Dp2a_B03


title: 19Dp2a_C02


title: 19Dp2a_A03


title: E12.5 WT GUT REP2


title: E12.5 WT GUT REP1


title: E11.5 RET NULL GUT REP2


title: E11.5 RET NULL GUT REP3


title: 19Dp2a_A04


title: 19Dp1b_B10


title: 19Dp1b_B11


title: 19Dp2a_C04


title: E11.5 RET NULL GUT REP1


title: 19Dp2a_A01


title: E11.5 WT GUT REP2


title: E11.5 WT GUT REP1


title: 19Dp2a_A06


title: 19Dp2a_B07


title: 19Dp2a_C06


title: 19Dp2a_B08


title: 19Dp2a_A07


title: 19Dp2a_A08


title: 19Dp2a_D08


title: 19Dp2a_B04


title: 19Dp2a_D09


title: 19Dp2a_A09


title: 19Dp2a_A11


title: 19Dp2a_D10


title: 19Dp2a_B10


title: E11.5 WT GUT REP3


title: 19Dp2b_C01


title: 19Dp2a_A05


title: 19Dp2a_B11


title: 19Dp2b_B01


title: 19Dp2b_C02


title: 19Dp2a_C10


title: 19Dp2b_A07


title: 19Dp2b_A01


title: 19Dp2b_B03


title: 19Dp2a_B06


title: 19Dp2b_C03


title: 19Dp2b_D03


title: 19Dp2b_D04


title: 19Dp2b_A03


title: 19Dp2b_A04


title: 19Dp2b_D05


title: 19Dp2b_C04


title: 19Dp2b_D07


title: 19Dp2b_B05


title: 19Dp2b_C06


title: 19Dp2b_B07


title: 19Dp2b_B09


title: 19Dp2a_B05


title: 19Dp2b_A09


title: 19Dp2b_C08


title: 19Dp2b_C07


title: 19Dp2b_B10


title: 19Dp2b_C11


title: 19Dp1b_C01


title: 19Dp1b_C07


title: 19Dp2b_D10


title: 19Dp2b_D11


title: 19Dp2b_B11


title: 19Dp1b_C05


title: 19Dp2b_C09


title: 19Dp1b_C06


title: 19Dp1a_C01


title: 19Dp1b_C08


title: 19Dp1b_D01


title: 19Dp1b_D02


title: 19Dp1b_D11


title: 19Dp1b_C10


title: 19Dp1b_D05


title: 19Dp2a_D03


title: 19Dp2b_C05


title: 19Dp2a_C08


title: 19Dp2b_B08


title: 19Dp1b_D10


title: 19Dp1b_D09


title: 19Dp2b_A11


title: 19Dp1a_B09


title: 19Dp1b_B07


title: 19Dn1_A01


title: 19Dp1a_A04


title: 19Dn1_C01


title: 19Dn1_B02


title: 19Dn1_A07


title: 19Dn1_D02


title: 19Dn1_B01


title: 19Dn1_C02


title: 19Dn1_D01


title: 19Dn1_A02


title: 19Dn1_C03


title: 19Dn1_B03


title: 19Dn1_A03


title: 19Dn1_D04


title: 19Dn1_D03


title: 19Dn1_B04


title: 19Dn1_A04


title: 19Dn1_D07


title: 19Dn1_C04


title: 19Dn1_B05


title: 19Dn1_A06


title: 19Dn1_C05


title: 19Dn1_C06


title: 19Dp1b_C09


title: 19Dn1_B07


title: 19Dn1_C08


title: 19Dn1_C09


title: 19Dn1_B08


title: 19Dn1_B09


title: 19Dn1_A08


title: 19Dn1_D08


title: 19Dn1_A11


title: 19Dn1_D09


title: 19Dn1_C10


title: 19Dn1_B10


title: 19Dn2a_B01


title: 19Dn1_D10


title: 19Dn1_C11


title: 19Dn1_D11


title: 19Dn1_D05


title: 19Dn1_A09


title: 19Dn2a_B02


title: 19Dn2a_A01


title: 19Dn2a_B03


title: 19Dn2a_C02


title: 19Dn2a_D01


title: 19Dn1_C07


title: 19Dn2a_C04


title: 19Dn1_A10


title: 19Dn2a_D03


title: 19Dn1_B11


title: 19Dn2a_A02


title: 19Dn2a_C06


title: 19Dn2a_C07


title: 19Dn2a_C03


title: 19Dn2a_C09


title: 19Dn2a_C01


title: 19Dn2a_A11


title: 19Dn2a_B09


title: 19Dn2a_B11


title: 19Dn2b_D01


title: 19Dn2a_B10


title: 19Dn2a_A10


title: 19Dn2a_A09


title: 19Dn2b_D02


title: 19Dn2b_C01


title: 19Dn2a_C11


title: 19Dn2a_A07


title: 19Dn2b_B03


title: 19Dn2a_C10


title: 19Dn2a_D11


title: 19Dn2a_C08


title: 19Dn2b_A01


title: 19Dn2a_D09


title: 19Dn2b_A07


title: 19Dn2b_C02


title: 19Dn2b_B01


title: 19Dn2b_D05


title: 19Dn2b_A03


title: 19Dn2b_B04


title: 19Dn2b_D03


title: 19Dn2b_C03


title: 19Dn2b_A02


title: 19Dn2b_B05


title: 19Dn2b_A04


title: 19Dn2b_D04


title: 19Dn2b_D06


title: 19Dn2b_A05


title: 19Dn2b_C07


title: 19Dn2b_B07


title: 19Dn2b_C06


title: 19Dn2b_C08


title: 19Dn2b_B08


title: 19Dn2b_A09


title: 19Dn2b_B09


title: 19Dn2b_A10


title: 19Dn2b_D07


title: 19Dn2b_D09


title: 19Dn2b_D10


title: 19Dn2b_B06


title: 19Dn2b_C11


title: 19Dn2b_A06


title: 19Dn2b_C05


title: 19Dn2b_B10


title: 19Dn2b_C09


title: 19Dn2b_A08


title: 19Dn2b_A11


title: 19Dn2b_C04


title: 12Dn1b_C06


title: 19Dn2b_D08


title: 19Dn2b_B11


title: 19Dn2b_D11


title: 12Dn4_F06


title: 12Dn3_D05


title: 12Dn4_A10


title: 12Dn3_H04


title: 12Dn1b_C07


title: 12Dn3_C07


title: 12Dn3_B06


title: 12Dn4_D06


title: 12Dn4_C07


title: 12Dn1b_A07


title: 12Dn1b_C01


title: 12Dn2_D11


title: 12Dn3_D04


title: 12Dn4_A07


title: 12Dn3_D03


title: 12Dn3_E02


title: 12Dn4_D08


title: 12Dn1a_A01


title: 12Dn3_D07


title: 12Dn3_F09


title: 12Dn1a_B02


title: 12Dn1a_C01


title: 12Dn1a_D01


title: 12Dn1a_B01


title: 12Dn1a_D02


title: 12Dn1b_D07


title: 12Dn1b_D04


title: 12Dn1a_A02


title: 12Dn1a_A07


title: 12Dn1a_C02


title: 12Dn1a_D03


title: 12Dn1a_D04


title: 12Dn3_C11


title: 12Dn1a_A03


title: 12Dn1a_A04


title: 12Dn1a_B04


title: 12Dn1a_C04


title: 12Dn1a_B05


title: 12Dn1a_D06


title: 12Dn1a_D05


title: 12Dn1a_A06


title: 12Dn1a_B06


title: 12Dn1a_C05


title: 12Dn1a_C07


title: 12Dn1a_C06


title: 12Dn1a_B08


title: 12Dn1a_B09


title: 12Dn1a_A08


title: 12Dn1a_A09


title: 12Dn1a_C08


title: 12Dn1a_D08


title: 12Dn1a_C10


title: 12Dn1a_C03


title: 12Dn1a_D10


title: 12Dn1a_D07


title: 12Dn1a_B10


title: 12Dn1a_D11


title: 12Dn1b_B03


title: 12Dn1a_B11


title: 12Dn1a_C09


title: 12Dn1b_D01


title: 12Dn1b_B02


title: 12Dn1b_C03


title: 12Dn1b_A02


title: 12Dn1a_A11


title: 12Dn1b_A04


title: 12Dn1b_B04


title: 12Dn1b_B05


title: 12Dn1b_A06


title: 12Dn1b_C05


title: 12Dn1a_C11


title: 12Dn1b_B06


title: 12Dn1b_D06


title: 12Dn1b_B07


title: 12Dn1b_C09


title: 12Dn1b_B01


title: 12Dn1b_C08


title: 12Dn1a_B03


title: 12Dn1b_A01


title: 12Dn1b_B08


title: 12Dn1b_D03


title: 12Dn1b_B09


title: 12Dn1b_A08


title: 12Dn1b_C10


title: 12Dn1b_A09


title: 12Dn1b_A11


title: 12Dn1b_A10


title: 12Dn1b_B10


title: 12Dn1b_D10


title: 12Dn1b_A03


title: 12Dn2_B02


title: 12Dn1b_B11


title: 12Dn2_C01


title: 12Dn2_A01


title: 12Dn2_B03


title: 12Dn2_C02


title: 12Dn2_A07


title: 12Dn2_D02


title: 12Dn2_D05


title: 12Dn2_B04


title: 12Dn2_D03


title: 12Dn2_C04


title: 12Dn2_D06


title: 12Dn2_C05


title: 12Dn2_B06


title: 12Dn2_D07


title: 12Dn2_C07


title: 12Dn1a_A10


title: 12Dn2_A09


title: 12Dn2_B01


title: 12Dn2_B09


title: 19Dn2b_C10


title: 12Dn2_C08


title: 12Dn2_B08


title: 12Dn2_A06


title: 12Dn2_C06


title: 12Dn2_D09


title: 12Dn2_A11


title: 12Dn2_D10


title: 12Dn2_A08


title: 12Dn3_E04


title: 12Dn3_A07


title: 12Dn3_H02


title: 12Dn3_H03


title: 12Dn3_D02


title: 12Dn3_A03


title: 12Dn3_C01


title: 12Dn2_C09


title: 12Dn3_B04


title: 12Dn3_A02


title: 12Dn3_A04


title: 12Dn3_C03


title: 12Dn3_F04


title: 12Dn3_H06


title: 12Dn3_G04


title: 12Dn3_B01


title: 12Dn2_C11


title: 12Dn3_A01


title: 12Dn3_A05


title: 12Dn3_E05


title: 12Dn3_C06


title: 12Dn3_C05


title: 12Dn3_F06


title: 12Dn3_B07


title: 12Dn3_B03


title: 12Dn3_A06


title: 12Dn3_B05


title: 12Dn3_C08


title: 12Dn3_H10


title: 12Dn3_C09


title: 12Dn3_G07


title: 12Dn3_H09


title: 12Dn3_A08


title: 12Dn3_B08


title: 12Dn3_E08


title: 12Dn3_A09


title: 12Dn3_B09


title: 12Dn3_A10


title: 12Dn3_E09


title: 12Dn3_A11


title: 12Dn3_F08


title: 12Dn3_G05


title: 12Dn3_D09


title: 12Dn3_E11


title: 12Dn3_D08


title: 12Dn3_F05


title: 12Dn3_C10


title: 12Dn3_E10


title: 12Dn3_F11


title: 12Dn3_B10


title: 12Dn3_D11


title: 12Dn4_F01


title: 12Dn3_G10


title: 12Dn4_A01


title: 12Dn3_B11


title: 12Dn4_B02


title: 12Dn4_G02


title: 12Dn4_H02


title: 12Dn4_D05


title: 12Dn4_C01


title: 12Dn4_B06


title: 12Dn4_A03


title: 12Dn4_A05


title: 12Dn4_F04


title: 12Dn4_B05


title: 12Dn4_B07


title: 12Dn4_B04


title: 12Dn4_C08


title: 12Dn4_A06


title: 12Dn4_E07


title: 12Dn4_B08


title: 12Dn4_E09


title: 12Dn4_F08


title: 12Dn4_B09


title: 12Dn4_A08


title: 12Dn4_A11


title: 12Dn4_H11


title: 12Dn4_D09


title: 12Dn4_F10


title: 12Dn4_B11


title: 12Dn4_C11


title: 12Dn4_D10


title: 12Dn4_G11


title: 12Dn4_F11


title: 12Dn2_B05


title: 12Dn3_H11


title: 12Dn4_E11


title: 12Dn3_E07


title: 12Dn3_D01


title: 12Dn3_F07


title: 12Dn3_E03


title: 12Dn3_G06


title: 12Dn2_B07


title: 12Dn4_A04


title: 12Dn4_F07


title: 12Dn2_A10


title: 12Dn3_B02


title: 12Dn4_C09


title: 12Dn4_C04


title: 12Dn4_A02


title: 12Dn1b_D02


title: 12Dn1b_C11


title: 12Dn1b_C04


title: 12Dn4_B10


title: 12Dn4_E08


title: 12Dn4_C06


title: 12Dn3_E01


title: 12Dn1b_D11


title: 12Dn1b_D09


title: 12Dn4_C05


title: 12Dn4_B01


title: 12Dn1b_D05


title: 12Dn3_G11


title: 12Dn4_D03


title: 12Dn1b_C02


title: 12Dp1a_D09


title: 12Dn2_C10


title: 12Dp1a_D07


title: 12Dp1a_C05


title: 12Dp1a_D06


title: 12Dp1a_D11


title: 12Dp1a_D01


title: 12Dp2c_A09


title: 12Dp1a_D03


title: 12Dp1a_D04


title: 12Dn1a_B07


title: 12Dp1a_C03


title: 12Dp1a_A01


title: 12Dp4_F07


title: 12Dn1b_D08


title: 12Dp1a_B02


title: 12Dp1a_C01


title: 12Dn4_C02


title: 12Dp1a_B03


title: 12Dp1a_D02


title: 12Dp1a_A07


title: 12Dp1a_A02


title: 12Dn2_D01


title: 12Dp1a_A03


title: 12Dn3_C04


title: 12Dp1a_D10


title: 12Dp1a_B06


title: 12Dp1a_A09


title: 12Dp1a_B05


title: 12Dp1a_C07


title: 12Dp1a_C04


title: 12Dp1a_B08


title: 12Dp1a_B10


title: 12Dp1b_B01


title: 12Dp1a_B04


title: 12Dp1a_A04


title: 12Dp4_F04


title: 12Dp1a_A06


title: 12Dp1a_B09


title: 12Dp1a_C06


title: 12Dp1a_A08


title: 12Dp1a_A05


title: 12Dp1a_C09


title: 12Dp1a_A11


title: 12Dp1b_D02


title: 12Dp1b_B02


title: 12Dp1a_C10


title: 12Dp1b_B03


title: 12Dp1b_D01


title: 12Dp1b_A02


title: 12Dp1a_B01


title: 12Dp1b_A07


title: 12Dp1b_A01


title: 12Dp1b_C01


title: 12Dp1a_A10


title: 12Dp1b_C02


title: 12Dp1b_C03


title: 12Dp1b_D05


title: 12Dp1b_B06


title: 12Dp1b_D04


title: 12Dp1b_D06


title: 12Dp1b_C04


title: 12Dp1b_D07


title: 12Dp1b_C09


title: 12Dp1b_B04


title: 12Dp1b_A04


title: 12Dp1b_B07


title: 12Dp1b_A06


title: 12Dp1b_D08


title: 12Dp1b_C06


title: 12Dp1b_C10


title: 12Dp1b_A09


title: 12Dp1b_C05


title: 12Dp1b_C11


title: 12Dp1b_B09


title: 12Dp1b_B11


title: 12Dp1b_A10


title: 12Dp1b_C07


title: 12Dp1b_A11


title: 12Dp1b_D09


title: 12Dp1b_D10


title: 12Dp1b_D11


title: 12Dp1b_A03


title: 12Dp1c_B01


title: 12Dp1b_A05


title: 12Dp1c_C01


title: 12Dp1c_D02


title: 12Dp1c_D01


title: 12Dp1c_B03


title: 12Dp1c_A07


title: 12Dp1c_A02


title: 12Dp1c_A03


title: 12Dp1c_C02


title: 12Dp1c_C03


title: 12Dp1c_B05


title: 12Dp1c_B06


title: 12Dp1c_D07


title: 12Dp1c_A04


title: 12Dp1c_D06


title: 12Dp1c_A05


title: 12Dp1c_D04


title: 12Dp1c_D05


title: 12Dp1c_B04


title: 12Dp1c_B07


title: 12Dp1c_C05


title: 12Dp1c_C06


title: 12Dp1c_C07


title: 12Dp1c_A01


title: 12Dp1c_B08


title: 12Dp1c_B02


title: 12Dp1c_C08


title: 12Dp1c_B09


title: 12Dp1c_C09


title: 12Dp1c_A08


title: 12Dp1c_D03


title: 12Dp1c_A10


title: 12Dp1c_A09


title: 12Dp1c_D08


title: 12Dp1c_A06


title: 12Dp1c_D09


title: dLBSLBR input

city: Pasadena

first: Chun-Kan

last: Chen

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

data_processing:
Base-calling was performed using Illumina software
Sequenced paired-end reads were aligned to mm9 genome with Bowtie2 using the following parameters: -k 1 -p 12 --very-sensitive-local --maxins 2000 --fr --no-discordant --no-mixed –no-unal
We identified protein binding sites on the Xist RNA by identifying regions that were enriched relative to the same region in the input control (“differential enrichment”) and also was enriched relative to all other regions on the remainder of the Xist RNA (“local enrichment”).
To compute significant enrichment, we computed the differential enrichment as IP/Input for each window (window size=100 nucleotides). We computed the local enrichment for each region by taking the normalized number of reads for each region (IP) and dividing it by the normalized number of reads over the entire Xist RNA.
To make these rates comparable, we divided each number by their respective region length prior to taking the ratio. We then generated 1,000 random permutations of the reads in the IP samples and paired input samples across the Xist RNA. For each permutation, we computed the differential and local enrichments and generated an empirical distribution of the maximum value observed for each permutation.
We assigned a multiple-testing corrected p-value to each region by comparing the observed differential and local enrichment values to these permutation distributions. We identified significant windows that had a differential p-value <0.01 and a local p-value<0.01.
We computed the enrichment for the Xist region by normalizing the number of reads upon immunoprecipitation with a specific protein relative to the number of reads in its input control (input sample). Specifically, we counted the total number of reads overlapping the Xist RNA region (negative strand in genomic alignments) in either the immunoprecipitation sample or the input control. To account for differences in read coverage between samples, each of these numbers was normalized to the total number of reads within the same experiment. This generates a normalized score, per region, within each sample. We then computed an enrichment metric by taking the ratio of these normalized values (IP/Input).
Genome_build: mm9
Supplementary_files_format_and_content: .bed files showing identified binding sites of SHARP, LBR, and PTBP1 on Xist transcript.

source_name: mouse ES cells

extract_protocol:
We crosslinked 6 hour doxycycline-induced pSM33 mouse male ES cells with 0.4 J/cm2 of UV254. Cells were lysed and RNA was digested with RNase I to achieve a size range of 100-500 nucleotides in length. For each CLIP sample, target proteins were immunoprecipitated from 20 million cells with antibody pre-coupled with Protein G beads. Samples were then washed and RNAs were eluted with NLS elution buffer with 100 mM DTT. Samples were then run through a standard SDS-PAGE gel and transferred to a nitrocellulose membrane, and a region 75 kDa above the molecular size of the protein of interest was isolated and treated with protease followed by phenol/chloroform/isoamyl alcohol extraction to isolate the RNAs.
The purified RNA in each sample was dephosphorylated and ligated to a mixture of barcoded adapters in which each adapter had a unique barcode identifier and Illumina sequencing libraries were generated according to our Massively Multiplexed RNA Sequencing method.

tag: binding sites

tag: treatment

value: doxycycline-induced

tag: cell lline


title: 12Dp1c_A11


title: 12Dp1c_D10


title: 12Dp1c_B11


title: 12Dp1c_C10


title: dLBSLBR CLIP

value: dLBS


title: 12Dp1c_C11


title: 12Dp1c_B10


title: 12Dp1d_B02


title: 12Dp1d_B01


title: 12Dp1d_C01


title: 12Dp1d_A01


title: 12Dp1c_D11


title: 12Dp1d_C02


title: 12Dp1d_D02


title: 12Dp1d_A02


title: 12Dp1d_D03


title: 12Dp1d_C03


title: 12Dp1d_A07


title: 12Dp1d_A03


title: 12Dp1d_B03


title: 12Dp1d_D04


title: 12Dp1d_C04


title: dALBR CLIP

value: dA-Wutz


title: 12Dp1d_A05


title: 12Dp1d_B04


title: 12Dp1d_A04


title: 12Dp1d_D01


title: 12Dp1d_D06


title: 12Dp1d_D07


title: 12Dp1d_B05


title: 12Dp1d_C05


title: 12Dp1d_B07


title: 12Dp1d_C09


title: 12Dp1d_C08


title: 12Dp1d_C06


title: 12Dp1d_C07


title: 12Dp1d_A10


title: 12Dp1d_D08


title: 12Dp1d_D09


title: 12Dp1d_D10


title: 12Dp1d_A09


title: 12Dp1d_C10


title: 12Dp1d_B10


title: 12Dp1d_D05


title: 12Dp1d_C11


title: 12Dp1d_B11


title: 12Dp2b_C10


title: 12Dp1d_D11


title: 12Dp2c_B07


title: 12Dp2c_A11


title: 12Dp2c_B10


title: 12Dp1d_B06


title: 12Dp2b_C11


title: 12Dp2c_B09


title: 12Dp3_B01


title: 12Dp2c_B11


title: 12Dp1d_B08


title: 12Dp3_B02


title: 12Dp1d_A06


title: 12Dp3_B03


title: 12Dp3_D01


title: 12Dp1d_A08


title: 12Dp1d_A11


title: 12Dp3_A01


title: 12Dp3_A07


title: 12Dp3_A04


title: 12Dp3_A05


title: 12Dp3_D06


title: 12Dp3_D07


title: 12Dp3_D04


title: 12Dp3_D05


title: 12Dp3_B05


title: 12Dp3_B06


title: 12Dp3_C08


title: 12Dp3_B09


title: 12Dp3_C06


title: 12Dp3_A08


title: 12Dp3_B07


title: 12Dp3_C07


title: 12Dp3_D08


title: 12Dp3_A11


title: 12Dp3_A09


title: 12Dp3_C09


title: 12Dp3_A03


title: 12Dp3_F07


title: 12Dp3_A10


title: 12Dp3_C11


title: 12Dp3_C10


title: 12Dp3_B11


title: 12Dp3_G10


title: 12Dp4_C01


title: 12Dp4_B01


title: 12Dp4_D01


title: 12Dp3_C05


title: 12Dp3_G11


title: 12Dp4_A07


title: 12Dp4_B02


title: 12Dp4_A02


title: 12Dp4_H04


title: 12Dp4_F03


title: 12Dp4_B04


title: 12Dp4_F02


title: 12Dp4_G03


title: 12Dp3_D09


title: 12Dp4_G02


title: 12Dp3_D10


title: 12Dp4_C04


title: 12Dp4_D05


title: 12Dp3_E10


title: 12Dp4_G04


title: 12Dp4_E05


title: 12Dp4_D06


title: 12Dp4_D04


title: 12Dp4_H06


title: 12Dp4_G05


title: 12Dp4_F05


title: 12Dp4_F06


title: 12Dp4_C02


title: 12Dp4_B05


title: 12Dp4_C05


title: 12Dp4_B07


title: 12Dp4_C06


title: 12Dp4_A06


title: 12Dp4_H07


title: 12Dp4_H08


title: 12Dp4_G07


title: 12Dp4_C08


title: 12Dp4_G08


title: 12Dp4_A05


title: 12Dp4_H09


title: 12Dp4_C09


title: 12Dp4_B09


title: 12Dp4_E07


title: 12Dp4_A08


title: 12Dp4_H10


title: 12Dp4_E11


title: 12Dp4_C10


title: 12Dp4_A10


title: 12Dp4_D08


title: 12Dp4_D10


title: 12Dp4_B10


title: 12Dp4_D09


title: 12Dp4_C11


title: 12Dp1b_B05


title: 12Dp1b_D03


title: 12Dp4_B11


title: 12Dp1b_B10


title: 12Dp1a_D08


title: 0b_C10


title: 0b_D12


title: 0b_C12


title: 0b_C11


title: 0b_D08


title: 0b_D09


title: 0b_C09


title: 0b_C08


title: 0b_C06


title: 0b_D11


title: 0b_D07


title: 0b_C05


title: 0b_C04


title: 0b_D06


title: 0b_D04


title: 12Dp4_G06


title: 0b_C03


title: 0b_D01


title: 12Dp4_C07


title: 0b_D05


title: 0b_D02


title: 0b_D03


title: 0b_C01


title: 0a_C12


title: 0a_D12


title: 0a_D11


title: 0a_D08


title: 0a_C07


title: 0a_C06


title: 0a_C09


title: 0a_C04


title: 0b_C02


title: 0a_C05


title: 0a_D05


title: 0a_D07


title: 0a_C03


title: 0a_C10


title: 0a_C02


title: 0a_D02


title: 0a_D01


title: 0a_D04


title: 12Dp1d_B09


title: HCC78_sgRNA-GFP_Cas9_3

city: New York

first: Harold

last: Varmus

state: NY

address: 1300 York Ave

department: Department of Medicine

institute: Weill Cornell Medicine

description:
HCC78 cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Clonal.
CCR17390_HCC78_P127_3

data_processing:
Reads were first mapped to these transcripts using RSEM [PMCID: PMC3163565]. Remaining unaligned reads were then mapped to a database of possible junctions between all 5' and 3' splice sites of those transcripts, and then subsequently to the GRCh37 human genome assembly, using TopHat [PMID: 19289445]
Differentially spliced events were identified using MISO v2.0 to quantify reads supporting distinct isoforms and/or junction-spanning reads [PMID: 21057496].
These read counts were then subjected to Wagenmakers’s Bayesian alternative to the binomial proportion test [PMID: 20064637].
Differentially spliced events were defined as those that exhibited a difference in absolute isoform ratio of at least 10% with an associated Bayes factor of at least 5, and with at least 20 relevant reads in the samples being compared.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel tables. Each row of the table corresponds to an isoform of a splicing event that is differentially spliced in at least one of the indicated comparisons between cell lines that do or do not express U2AF1 S34F. In each case, the isoform for which information is given is as follows: the inclusion isoform for cassette exons (type “se”), the intron-proximal isoform for competing 5' or 3' splice site events (types “a5ss” or “a3ss”), inclusion of the upstream exon for mutually exclusive exon events (type “mxe”), splicing of retained introns annotated as alternative (type “ri”) or constitutive (type “ci”), or canonical splicing of an annotated constitutive junction (type “cj”). The columns specify relevant annotations for each event as follows: “coords” specifies the genomic coordinates of the event; “gene” specifies the Ensembl gene ID; “geneName” specifies the gene name; “geneDescription” is a description of the gene as given by Ensembl; “type” specifies the type of splicing event; “nmdTarget” specifies whether the isoform is a predicted substrate for degradation by NMD (NA indicates that either all or no isoforms of the event are predicted NMD substrates). The columns prefixed by “deltaPsi_” give the absolute difference in isoform ratio (Percent Spliced In or “PSI” value) for the indicated comparisons. Table is restricted to events that are differentially spliced in at least one comparison.

source_name: Lung adenocarcinoma cell line

growth_protocol: HBEC3kt-derived cell lines were grown in Keratinocyte serum-free media supplemented with epidermal growth factor and bovine pituitary extract (Invitrogen); H441- and HCC78-derived cell lines were grown in RPMI1640 supplemented with 10% fetal bovine serum and Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted by trizol, followed by a RNA cleanup step using the RNeasy mini-column (Qiagen)
Poly A selection followed by library construction using the TruSeq V3 chemistry (Illumina)

treatment_protocol: The U2AF1 S34F mutation was created in the endogenous U2AF1 locus in HBEC3kt cells through gene editing using a method described previously (PMID 24071911); the wild-type or S34F mutant U2AF1 alleles were also selectively disrupted in the indicated cells by transducing them with CRISPR/Cas9 and a single-guide RNA (sgRNA) targeting either the wild-type or S34F U2AF1 allele.

value: U2AF1 allele-specific disruption

tag: u2af1 status

value: wild-type and S34F mutation

tag: parental cells


title: HCC78_sgRNA-S34F_Cas9_6

description:
HCC78 cells were transduced to express a CRISPR-Cas9 and a sgRNA against the U2AF1 S34F mutant allele. Clonal.
CCR17388_HCC78_P131_6

value: wild-type


title: H441_sgRNA-S34F_Cas9_1

description:
H441 cells were transduced to express a CRISPR-Cas9 and a sgRNA against the U2AF1 S34F mutant allele. Clonal.
CCR17393_H441_P131_1


title: HCC78_sgRNA-GFP_Cas9_2

description:
HCC78 cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Clonal.
CCR17391_HCC78_P127_2


title: H441_sgRNA-GFP_Cas9_p

description:
H441 cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Polyclonal.
CCR17386_H441_P127poly


title: MUT1a_sgRNA-WT_Cas9_p

description:
MUT1a cells were transduced to express CRISPR-Cas9 and a sgRNA against the wild-type U2AF1 allele. Polyclonal.
CCR17635_MUT1_P133_2

source_name: Immortalized lung epithelial cell line

value: S34F mutation (wild-type-depleted)


title: WT1_sgRNA-WT_Cas9_p

description:
WT1 cells were transduced to express CRISPR-Cas9 and a sgRNA against the wild-type U2AF1 allele. Polyclonal.
CCR17637_WT1_p133_2

value: wild-type-depleted


title: WT1_sgRNA-GFP_Cas9_p

description:
WT1 cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Polyclonal.
CCR17636_WT1_P127_2


title: MUT1a_sgRNA-GFP_Cas9_p

description:
MUT1a cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Polyclonal.
CCR17634_MUT1_P127_2


title: MUT1a

description:
MUT1a cells carry both the wild-type and S34F mutant U2AF1 alleles. Clonal.
CCR102462_CCR15366_MUT1

value: gene editing


title: MUT1b

description:
MUT1b cells carry both the wild-type and S34F mutant U2AF1 alleles. Clonal.
CCR102462_CCR15367_MUT2


title: shH1.0-2 NT biological replicate 2 [FAIRE-Seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: FAIRE-seq

data_processing:
Alignments were performed using BWA in paired-end mode, allowing three mismatches across a seed length of the full 101bp sequence
Reads were filtered for proper-pairing and non-PCR duplication using Samtools, and non-overlap of ENCODE blacklisted regions using Bamutils
Nucleosome depleted regions were identified using MACS (v2.0.10) without input sample
Genome_build: hg19
Supplementary_files_format_and_content: MACS output peak files

source_name: in vitro transformed human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing  15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
FAIRE DNA was purified by phenol-chloroform extraction follwing the protocol decribed in Simon et al. Nat Protocols, 2012.
Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification. Sequenced was performed on an Illumina HiSeq 2500 at The Crick Institute, London.

treatment_protocol: SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibrobalsts derived from hTERT-immortalized skin fribroblasts. Cells were infected with lentiviral constructs expressing shRNAs targeting H1F0 under a doxycycline-inducible promoter

tag: cell line

value: SSEA1+ CSCs

value: No treatment

tag: genotype/variation

value: wildtype


title: shH1.0-2 DOX biological replicate 2 [FAIRE-Seq]

description: FAIRE-seq

value: Plus doxycycline

value: doxycycline induced histone linker H1.0 knockdown


title: shH1.0-2 DOX biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-2 Input biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq

value: Input


title: shH1.0-1 DOX biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-1 Input biological replicate 2 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-1 NT biological replicate 2 [FAIRE-Seq]

description: FAIRE-seq


title: H441_sgRNA-GFP_Cas9_1

description:
H441 cells were transduced to express a CRISPR-Cas9 and a control sgRNA. Clonal.
CCR17387_H441_P127_1


title: H441_sgRNA-S34F_Cas9_p

description:
H441 cells were transduced to express a CRISPR-Cas9 and a sgRNA against the U2AF1 S34F mutant allele. Polyclonal.
CCR17392_H441_P131poly

value: wild-type (S34F-depleted)


title: shH1.0-1 NT biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-2 NT biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-1 Input biological replicate 1 [FAIRE-Seq]

description: FAIRE-seq


title: HCC78_sgRNA-S34F_Cas9_4

description:
HCC78 cells were transduced to express a CRISPR-Cas9 and a sgRNA against the U2AF1 S34F mutant allele. Clonal.
CCR17389_HCC78_P131_4


title: shH1.0-2 DOX H3K27me3 biological replicate 2

extract_protocol:
ChIP was performed as detailed by Sailaja et al PNAS 109:E3687-3695 2012
Paired end libraries were constructed using standard Illumina protocols, with some modifications. Agencourt AMPure XP (Beckman Coulter) at 0.8x ratio were used to size select out adapter dimers. The Illumina Phusion enzyme was replaced by Kapa HiFi HotStart ready mix (Kapa Biosystems). An Invitrogen SizeSelect R-gel system (Life Technologies) was used to size select following PCR amplification. Sequenced was performed on an Illumina HiSeq 2500 at The Crick Institute, London.


title: shH1.0-2 DOX H3K27me3 biological replicate 1


title: shH1.0-2 NT H3K27me3 biological replicate 1


title: shH1.0-1 DOX H3K27me3 biological replicate 2


title: 0a_C11


title: shH1.0-1 NT H3K27me3 biological replicate 2


title: shH1.0-2 DOX H3K27ac biological replicate 2


title: shH1.0-2 NT H3K27ac biological replicate 2


title: shH1.0-1 DOX H3K27me3 biological replicate 1


title: shH1.0-1 NT H3K27me3 biological replicate 1


title: shH1.0-2 Input biological replicate 2


title: shH1.0-2 DOX H3K27ac biological replicate 1


title: shH1.0-2 NT H3K27ac biological replicate 1


title: shH1.0-1 DOX biological replicate 2 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-2 Input biological replicate 1


title: shH1.0-2 Input biological replicate 2 [FAIRE-Seq]

description: FAIRE-seq


title: shH1.0-2 NT H3K27me3 biological replicate 2


title: shH1.0-1 DOX H3K27ac biological replicate 2


title: shH1.0-1 Input biological replicate 2


title: shH1.0-1 NT H3K27ac biological replicate 2


title: shH1.0-1 Input biological replicate 1


title: shH1.0-1 DOX H3K27ac biological replicate 1


title: WT1

description:
WT1 cells only carry the wild-type U2AF1 allele. Clonal.
CCR102462_CCR15364_WT1


title: ΔyonO mitomycin rep2

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

data_processing:
Basecalling by standard Illumina pipeline (RTA2 for base calling and filtering, bcl2fastq v2 for producing FASTQ files).
Pre-processing using FASTX-toolkit by adaptor removal (fastx_clipper -l 10 -n) and trimming to a maximum length of 45 nt (fastx_trimmer -l 45), before trimming of the low quality sequence from the 3’ end (fastq_quality_filter -q 20 -p 80 -l 10)
Genome alignment by Bowtie 1.1.2, allowing only unique alignments with up to three mismatches (-a -n 3 -m 1).
Gene coverage was calculated using the Rsubread package
Differentially expressed genes were identified using the EdgeR exact test. Genes were considered significant at a fold change of 2 and a p-value threshold of 0.05, following correction using Benjamini-Hochberg false discovery rate.
Genome_build: NC_000964
Supplementary_files_format_and_content: text files of integer counts per gene

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: bacteria

growth_protocol: A single colony was inoculated into MMB medium (1% bacto-tryptone, 0.5% bacto-yeast extract, 1% NaCl, 5 mM MgCl2 and 0.1 mM MnCl2) and grown overnight at 30 ᵒC. The overnight culture was used to inoculate fresh MMB medium to a starting OD600 of 0.02.

extract_protocol:
For cell lysis, the FastRNA Pro Blue kit (MP Bio) was used whilst RNA was isolated and cleaned up using the Total RNA Purification Plus kit (Norgen). Cell pellets were resuspended in 1ml of the phenol based lysis solution and added to the supplied bead matrix. The samples were disrupted twice for 20 seconds using the Precellys 24 homogeniser (Bertin Technologies). After centrifugation, the supernatant (750 μl) was added to 300 μl of chloroform. After a 5 minute incubation at room temperature, the samples were centrifuged at full speed at 4 ᵒC. The resultant aqueous phase was added to an equal volume of the Norgen lysis buffer and the RNA was purified as per the exact instructions supplied with the Total RNA Purification Plus kit. The quality and concentration of the total RNA was determined an Agilent Bioanalyser 2100 using the RNA 6000 Nano kit. Sequencing was performed by Vertis Biotechnologie AG (Germany).
From the total RNA samples, ribosomal RNA molecules were depleted using Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). RNA samples were fragmented using RNaseIII. The samples were then poly(A)-tailed using poly(A) polymerase. The samples were then treated with RNA 5' Polyphosphatase (+5'PP, Epicentre) in order to convert 5'PPP structures into 5' monophosphate ends. Afterwards, an RNA adapter was ligated to the 5'-monophosphate of the RNA. First- strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase.

treatment_protocol: The cultures were grown at 37 ᵒC with vigorous shaking until an OD600 of 0.4 – 0.5 was reached. The culture was divided and to one half, mitomycin C (dissolved in 50% ethanol) was added to a final concentration of 0.5 μg/ml. This culture was incubated with shaking for a further 60 minutes after which 1.4ml of culture was harvested and flash frozen in liquid nitrogen.

tag: mitomycin

value: 0.5 ug/ml

value: delta-yonO


title: WT2

description:
WT2 cells only carry the wild-type U2AF1 allele. Clonal.
CCR102462_CCR15365_WT2


title: ΔyonO mitomycin rep3


title: RNA-Seq HCT116 Daunorubicin Replicate #1

city: Sherbrooke

first: Jean-Francois

last: Lucier

state: Quebec

address: 2500, boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

data_processing:
We used the RNA-seq pipeline version 1.4 developed by MUGQIC (https://bitbucket.org/mugqic/mugqic_pipelines) to analyze our data. Briefly, the raw reads were trimmed using Trimmomatic 0.32 [1] to remove from the 3’-end the bases with a Phred quality score below 30, and remove the trimmed reads shorter than 32 bp. The trimmed reads were then aligned onto the human reference genome hg19 using TopHat 2.0.11 [2] and Bowtie 2.2.2 [3] with default parameters except --library-type fr-firststrand -G transcripts_ensembl.gtf (GRCh37.68), then MarkDuplicates from Picard 1.118 (ref) was applied. Finally FPKM values were calculated for each gene using Cufflinks 2.1.1 [4] with default parameters except -G transcripts_ensembl.gtf (GRCh37.68).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: RNA-Seq HCT116 Daunorubicin

growth_protocol: HCT116 were collected in exponential growth phase

extract_protocol:
Total RNA was extracted from HCT116 p53+/+ cells using GenElute (Sigma) and treated with DNaseI (Ambion)
Illumina’s TruSeq Stranded mRNA LT Kit

treatment_protocol: 250 nM daunorubicin 8h or vehicle for non-treated

tag: cell type

value: Colon carcinoma cells

tag: growth phase

value: exponential growth phase

tag: treated with

value: 250 nM daunorubicin for 8hrs


title: Rad21-ChIP-seq-HCT_NT-Rep#2

data_processing:
We based the analyses of Rad21 ChIP-Seq data on the ChIP-seq pipeline version 1.4 developed by MUGQIC. Briefly the raw reads were trimmed as for RNA-Seq reads, then aligned onto hg19 using BWA 0.7.5a with default parameters, then filtered on alignment quality using Samtools 0.1.19  with the settings view -F4 -q 20 [5]. The two biological replicates per condition were then combined using makeTagDirectory from Homer 4.1 [6]. The signal density files in BedGraph were generated using Homer 4.1 and the default settings of the command makeUCSCfile [6]. Narrow peak summits were determined using MACS2 version 2.0.10 [7] with default parameters except --fix-bimodal -f BAMPE.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

extract_protocol:
ChIP were performed as described in Gevry N, Chan HM, Laflamme L, Livingston DM, Gaudreau L. p21 transcription is regulated by differential localization of histone H2A.Z. Genes & development. 2007;21(15):1869-81. PubMed PMID: 17671089 except for the following steps. For each treatment conditions six immuno-precipitations were performed. Immuno-precipitations were performed using Dynabeads coupled to protein A (Life Technologies) without pre-clearing.
The libraries for deep-sequencing were prepared from 10 ng ChIPed DNA using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol

value: vehicle for 8hrs

tag: chip antibody

value: Rad21 (AbCam 992)


title: RNA-Seq HCT116 Non-Treated Replicate #2

source_name: RNA-Seq HCT116 Non-Treated


title: RNA-Seq HCT116 Daunorubicin Replicate #2


title: Rad21-ChIP-seq-HCT_NT-Rep#1


title: Rad21-ChIP-seq-HCT_DAU-Rep#1


title: Rad21-ChIP-seq-HCT_DAU-Rep#2


title: ΔyonO mitomycin rep1


title: WT mitomycin rep2

value: WT


title: RNA-Seq HCT116 Non-Treated Replicate #1


title: ΔyonO rep3

treatment_protocol: The cultures were grown at 37 ᵒC with vigorous shaking until an OD600 of 1.6 was reached. 1.4ml of culture was harvested and flash frozen in liquid nitrogen.

value: 0 ug/ml


title: WT rep2


title: shH1.0-1 NT H3K27ac biological replicate 1


title: WT mitomycin rep1


title: WT mitomycin rep3


title: WT rep3


title: ΔyonO rep2


title: WT rep1


title: Tibialis_DM1_54

status: Public on Sep 29 2016

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Used standard Hiseq 2000 software.
Reads were mapped using Hisat2.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] Alternative splicing events were quantitated using MISO software.

source_name: Tibialis anterior muscle

extract_protocol:
Frozen tissue samples were lysed using a homogenizer in Trizol. Chloroform was added and mixed, and the aqueous layer was added to isopropanol to precipitate RNA. The RNA was then cleaned up on RNeasy columns (Qiagen) with on column DNase treatment.
Strand-specific libraries (using dUTP incorporation during reverse transcription, and USER treatment prior to PCR) were prepared using standard protocols. RNA was first fragmented, and then ribosomal RNA was subtracted using ribo-zero beads from Epicentre Biotechnologies. Reverse transcription was performed using random primers, followed by 2nd strand cDNA synthesis, end repair, adenylation, and ligation of adapters. Products were run on agarose, size selected, and then subjected to 14-18 cycles of PCR.

treatment_protocol: Autopsy and biopsy samples were frozen at -80 until RNA extraction.

tag: source

value: biopsy

tag: anonymized patient identifier

tag: anonymized center identifier

value: A

tag: disease classification

value: myotonic dystrophy type 1

tag: tissue

value: Tibialis anterior muscle


title: ΔyonO rep1

tag: genotype

tag: strain


title: Tibialis_DM1_55


title: Tibialis_DM1_56


title: Tibialis_Duchenne_58

value: autopsy

value: C

value: Duchenne muscular dystrophy


title: Tibialis_DM1_53


title: Tricep_Control_1

source_name: Tricep muscle

value: Tricep muscle


title: Tibialis_DM1_51


title: Tibialis_DM1_52


title: Tibialis_DM1_49


title: Tibialis_DM1_48


title: Tibialis_DM1_47


title: Tibialis_DM1_41


title: Tibialis_DM1_42


title: Tibialis_DM1_46


title: Tibialis_DM1_44


title: Tibialis_DM1_50


title: Tibialis_DM1_40


title: Tibialis_DM1_45


title: Tibialis_DM1_43


title: Tibialis_DM1_37


title: Tibialis_DM1_39


title: Tibialis_DM1_34


title: Tibialis_DM1_38


title: Tibialis_DM1_36


title: Tibialis_DM1_57


title: Tibialis_DM1_32


title: Tibialis_DM1_30


title: Tibialis_DM1_29


title: Tibialis_DM1_27


title: Tibialis_DM1_26


title: Tibialis_DM1_28


title: Tibialis_DM1_24


title: Tibialis_DM1_25


title: Tibialis_DM1_33


title: Tibialis_DM1_22


title: Tibialis_DM1_21


title: Tibialis_DM1_20


title: Tibialis_DM1_35


title: Tibialis_DM1_15


title: Tibialis_DM1_31


title: Tibialis_DM1_19


title: Tibialis_Control_9


title: Tibialis_Control_3


title: Tibialis_Control_8


title: Tibialis_DM1_18


title: Tibialis_DM1_16


title: Tibialis_DM1_12


title: Tibialis_DM1_13


title: Tibialis_Control_2


title: Tibialis_DM1_14


title: Tibialis_Control_7


title: Tibialis_Control_11


title: Tibialis_Control_5


title: Tibialis_Control_1


title: Tibialis_Control_4


title: Tibialis_DM1_23


title: Soleus_DM1_1

source_name: Soleus muscle

value: Soleus muscle


title: Tibialis_Control_10


title: Rectus_Femoris_DM1_1

source_name: Rectus femoris muscle

value: Rectus femoris muscle


title: Tibialis_Control_6


title: Skeletal_Muscle_DM1_1

source_name: Muscle

value: Muscle


title: Quad_Duchenne_28

source_name: Quadriceps muscle

value: Quadriceps muscle


title: Quad_DM2_5

value: D


title: Quad_DM1_27

value: B


title: Quad_DM1_4


title: Tibialis_DM1_17


title: Quad_DM1_3


title: Quad_DM1_26


title: Quad_DM1_25


title: Quad_DM1_22


title: Quad_DM1_20


title: Quad_DM1_2


title: Quad_DM1_24


title: Quad_DM1_23


title: Quad_DM1_18


title: Quad_DM1_15


title: Quad_DM1_21


title: Quad_DM1_13


title: Quad_Control_8


title: Quad_DM1_19


title: Quad_Control_5


title: Quad_DM1_16


title: Quad_DM1_17


title: Quad_DM1_1


title: Quad_DM1_14


title: Quad_Control_9


title: Quad_Control_3


title: Quad_Control_7


title: Quad_Control_1


title: Pectoral_DM2_1

source_name: Pectoral muscle

value: myotonic dystrophy type 2

value: Pectoral muscle


title: Quad_Control_10


title: Quad_Control_11


title: Quad_Control_6