title: UKN1timecourse_ND_6h_Exp1

source_name: hESCs have been incubated with culturing medium for 6h


title: UKN1timecourse_ND_144h_Exp1

status: Public on Oct 26 2020

type: RNA

city: Berlin

first: Johannes

last: Meisig

address: Chariteplatz 1

department: Institut für Pathologie

country: Germany

institute: Charite Universitätsmedizin

description: Gene expression data from H9 human embryonic stem cells

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: Microarrays were analyzed using RMA (Robust Multi-array Analysis) as available in the bioconductor R  package oligo

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: hESCs have been incubated with culturing medium for 144h

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

growth_protocol: According to Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

extract_protocol: Total RNA has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: H9 hESCs were differentiated for up to 6 days in the presence and absence of valproic acid into neuroepithelia progenitors (NEP)  (Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).

tag: gender

value: female

tag: state

value: differentiated state

tag: tissue

value: H9 human embryonic stem cells


title: UKN1timecourse_ND_d-3_Exp2

source_name: hESC maintenance culture

value: undifferentiated


title: UKN1timecourse_0h_Exp1

source_name: hESCs have been incubated with culturing medium for 0h


title: UKN1timecourse_ND_d-3_Exp1


title: UKN1timecourse_ND_60h_Exp1

source_name: hESCs have been incubated with culturing medium for 60h


title: Input_GS

type: SRA

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2.
For peak calling for mePontin, we used Homer (v4.7.2).  mePontin upon glucose starvation was compared against control input.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including mePontin peak information

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblast(MEF)

extract_protocol:
For ChIP experiments, cell lysates were clarified from sonicated nuclei and IP with mePontin antibody.
The sequencing library is prepared by random fragmentation of the DNA, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

tag: cell type

value: Mouse embryonic fibroblast(MEF)

tag: chip antibody

value: Input

tag: media

value: Glucose starvation


title: Input_CTL

value: Normal


title: mePontin_CTL

value: mePontin


title: mePontin_GS


title: WT_2_Ribo

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

country: USA

institute: The Jackson Laboratory

description: Ribosome protected RNA fragments

library_source: transcriptomic

data_processing:
Cerebellum RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM20 transcript reference.
Cerebellum ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Cerebellum ribosome profiling reads were counted at the gene-level using featureCounts for reads overlapping CDS features.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts ribosome profiling samples.

molecule: polyA RNA

source_name: Cerebellum

extract_protocol:
Cerebella from various strains were isolated from 3-week-old mice and immediately frozen in liquid nitrogen.
RNA-Seq libraries were prepared using the TruSeq v2 mRNA kit (Illumina). Briefly, total cerebellar RNA was isolated and RNA quality was assessed on Agilent TapeStation. mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. After fragmentation of mRNA, libraries were prepared according to manufacturer’s instructions. Paired end reads (2x100bp) were obtained using the HiSeq 4000 (Illumina). Ribosome profiling libraries were generated as previously described (Ingolia et al., 2012; Ishimura et al., 2014) and sequenced on an Illumina HiSeq 4000.

tag: strain

value: Cerebellum

tag: age

value: 3 weeks old

tag: genotype

value: Wildtype

tag: batch

value: Batch 2


title: WT_1_Ribo

description: Ribosome protected RNA fragments


title: WT_3_Ribo

description: Ribosome protected RNA fragments


title: UC organoid#4 RNA1

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

country: Japan

institute: Tokyo medical and dental university

description: Gene expression of UC organoids #4

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent)

source_name: UC derived organoid #4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human colonic organoids were maintained in DMEM-based culture medium (Advanced-DMEM, Invitrogen Corporation, Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated using an RNeasy Micro Kit (Qiagen, Venlo, Netherlands) according to the manufacturer's instructions.

treatment_protocol: The mixture of 100 ng/mL of flagellin (Invitrogen Corporation, Carlsbad, CA, USA), 10 ng/mL of human IL-1β (PeproTech, Rocky Hill, NJ, USA) and 100 ng/mL of human tumor necrosis factor (TNF)-α (PeproTech)  was added to media every other day and cultured for 60weeks

tag: sample type

value: Organoids derived from colonic mucosa with active UC

value: Organoids derived from colonic mucosa

value: male


title: Gtpbp2_3_Ribo

description: Ribosome protected RNA fragments

value: Gtpbp2 -/-


title: UC organoid#4 RNA2

description: Gene expression of UC organoids #4


title: UC organoid#4 RNA3

description: Gene expression of UC organoids #4


title: H.colon organoid#2 Inf(+)

description: Gene expression of long-term inflammed organoids #2

source_name: Long-term inflammed organoid #2

value: Inflammed for 60weeks (derive from normal organoids#2)


title: UPEC injected 5 day old embryo cells

city: Indianapolis

first: Andrew

last: Schwaderer

state: IN

address: 1044 West Walnut Street

department: Pediatric Nephrology

institute: Indiana University School of Medicine

data_processing:
CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer.
CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files
The FASTQ files were then aligned to the zebrafish reference genome Danio_rerio.GRCz11 with RNAseq aligner STAR
The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell.The filtered feature-cell barcode matrices generated by CellRanger were used for further analysis.
Genome_build: GRCz11-3.1.0
Supplementary_files_format_and_content: Tab delimited text file containing count matrix for each gene and cell

organism: Danio rerio

source_name: 5 day old embryo

extract_protocol:
The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL (Sigma) containing DNAse I (Sigma) in DMEM using gentleMACS (Miltenyi Biotec) in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear, DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead (Miltenyi Biotec) with MS column. Live cells were then centrifuged and resuspended in DPBS (without Ca2+ or Mg2+) and processed for single cell RNA sequencing on 10x genomics platform.
Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1.

treatment_protocol: Zebrafish were injected with red fluorescent protein (RFP) expressing UPEC. After 24 hours, the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for ~4 days post fertilization (dpf) in a 28.5°C incubator in egg water-filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above, phenol red, and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C.

tag: tissue preparation

value: Single cell suspension

value: embryo

value: 5 days

tag: treatment

value: UPEC


title: Saline injected 5 day old embryo cells

value: Saline


title: H.colon organoid#1 Inf(+) RNA1

description: Gene expression of long-term inflammed organoids #1

source_name: Long-term inflammed organoid #1

value: Inflammed for 60weeks (derive from normal organoids#1)


title: H.colon organoid#1 Inf(-) RNA3

description: Gene expression of normal organoids #1

source_name: Normal organoid #1

value: Normal


title: H.colon organoid#2 Inf(R)

description: Gene expression of inflammation removed organoids #2

source_name: Inflammation-removed organoid #2

value: After 10weeks from the removal of 60weeks inflammation (derive from normal organoids#2)


title: H.colon organoid#1 Inf(+) RNA2


title: H.colon organoid#1 Inf(+) RNA3


title: Gtpbp2_1_Ribo

description: Ribosome protected RNA fragments

value: Cerebellum


title: H.colon organoid#1 Inf(R) RNA1

description: Gene expression of inflammation removed organoids #1

source_name: Inflammation-removed organoid #1

value: After 10weeks from the removal of 60weeks inflammation (derive from normal organoids#1)


title: Gtpbp1_2_Ribo

description: Ribosome protected RNA fragments

value: 3 weeks old

value: Gtpbp1 -/-


title: H.colon organoid#2 Inf(-)

description: Gene expression of normal organoids #2

source_name: Normal organoid #2


title: H.colon organoid#1 Inf(-) RNA1

description: Gene expression of normal organoids #1


title: Gtpbp1_3_Ribo

description: Ribosome protected RNA fragments

value: Batch 2


title: H.colon organoid#1 Inf(-) RNA2

description: Gene expression of normal organoids #1

value: Organoids derived from colonic mucosa


title: H.colon organoid#1 Inf(R) RNA2

value: male


title: H.colon organoid#1 Inf(R) RNA3


title: Gtpbp1_1_Ribo

description: Ribosome protected RNA fragments


title: WT_3_RNA

description: poly(A) selected RNA

value: Wildtype

value: Batch 1


title: WT_1_RNA

description: poly(A) selected RNA


title: WT_2_RNA

description: poly(A) selected RNA


title: Gtpbp2_3_RNA

description: poly(A) selected RNA

value: Gtpbp2 -/-


title: BG532_Gata3_Hoxb8FL

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: ChIP-Seq from Gata3 -/- Hoxb8-FL cells grown under self-renewal conditions, background control, repeat2

data_processing:
Reads aligned to mm10 using Bowtie2.
bedGraphs created using bedtools.
bigWigs created using UCSC utilities.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig density profiles

source_name: Hoxb8-FL cell line

growth_protocol: Hoxb8-FL cells were grown in: DMEM with 10% FCS, 5% Flt3L-conditioned medium, 50 uM 2-Mercaptoethanol, 1% Penicillin + Streptomycin, 1% Glutamine solution, 1 uM β-Estradiol, unless otherwise indicated

extract_protocol:
Cells were fixed in 1% formaldehyde, isolated chromatin was fragment and immunoprecipitated using the indicated antisera.
ChIP followed by Illumina TruSeq library generation. Please see the accompanying publication for a detailed protocol.

treatment_protocol: No treatment

value: bone marrow

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing, Gata3-/-

value: Not treated

tag: antibody


title: Gtpbp2_2_RNA

description: poly(A) selected RNA


title: Gtpbp1_3_RNA

description: poly(A) selected RNA


title: Gtpbp2_1_RNA

description: poly(A) selected RNA


title: Gtpbp1_1_RNA

description: poly(A) selected RNA


title: Gtpbp1_2_RNA

description: poly(A) selected RNA


title: BG531_Gata3_Hoxb8FL

description: ChIP-Seq from Gata3 -/- Hoxb8-FL cells grown under self-renewal conditions, background control, repeat1


title: RBG24133_Plate18_E12_Cbfb_sg3

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
TFnet_exon_counts.csv
TFnet_intron_counts.csv

data_processing:
sequencing reads alignment with STAR (default settings)
Counting of reads to exons or introns, summarised per gene - featureCounts. Ensembl v93 genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with either total number of reads mapping to exonic or intronic regions, summed per gene.

extract_protocol:
375 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

treatment_protocol: Cells were transduced with constructs carrying sgRNAs expression cassetes (Perturb-Seq GBC library backbone) targeting indicated genes.

value: Cas9 expressing, Hoxb8 expressing

value: Treated with Cbfb_sg3

tag: day


title: RBG24135_Plate18_G12_Cbfb_sg3


title: RBG24136_Plate18_H12_Cbfb_sg3


title: RBG24134_Plate18_F12_Cbfb_sg3


title: RBG24132_Plate18_D12_Cbfb_sg3


title: RBG24131_Plate18_C12_Cbfb_sg3


title: RBG24130_Plate18_B12_Cbfb_sg3


title: RBG24126_Plate18_F11_Cbfb_sg2

value: Treated with Cbfb_sg2


title: RBG24128_Plate18_H11_Cbfb_sg2


title: RBG24123_Plate18_C11_Cbfb_sg2


title: RBG24124_Plate18_D11_Cbfb_sg2


title: RBG24127_Plate18_G11_Cbfb_sg2


title: RBG24125_Plate18_E11_Cbfb_sg2


title: RBG24122_Plate18_B11_Cbfb_sg2


title: RBG24129_Plate18_A12_Cbfb_sg3


title: RBG24120_Plate18_H10_Cbfb_sg1

value: Treated with Cbfb_sg1


title: RBG24121_Plate18_A11_Cbfb_sg2


title: RBG24119_Plate18_G10_Cbfb_sg1


title: BG356_IgG_Hoxb8FL

description: ChIP-Seq from Hoxb8-FL cells grown under self-renewal conditions, background control

value: IgG


title: RBG24118_Plate18_F10_Cbfb_sg1


title: RBG24114_Plate18_B10_Cbfb_sg1


title: RBG24117_Plate18_E10_Cbfb_sg1


title: RBG24115_Plate18_C10_Cbfb_sg1


title: RBG24116_Plate18_D10_Cbfb_sg1


title: RBG24113_Plate18_A10_Cbfb_sg1


title: RBG24111_Plate18_G9_R26

value: Treated with controlR26


title: RBG24107_Plate18_C9_R26


title: RBG24110_Plate18_F9_R26


title: RBG24108_Plate18_D9_R26


title: RBG24106_Plate18_B9_R26


title: RBG24101_Plate18_E8_Runx2_sg3

value: Treated with Runx2_sg3


title: RBG24098_Plate18_B8_Runx2_sg3


title: RBG24104_Plate18_H8_Runx2_sg3


title: RBG24103_Plate18_G8_Runx2_sg3


title: RBG24100_Plate18_D8_Runx2_sg3


title: RBG24097_Plate18_A8_Runx2_sg3


title: RBG24099_Plate18_C8_Runx2_sg3


title: RBG24105_Plate18_A9_R26


title: RBG24096_Plate18_H7_Runx2_sg2

value: Treated with Runx2_sg2


title: RBG24095_Plate18_G7_Runx2_sg2


title: RBG24094_Plate18_F7_Runx2_sg2


title: RBG24112_Plate18_H9_R26


title: RBG24092_Plate18_D7_Runx2_sg2


title: RBG24093_Plate18_E7_Runx2_sg2


title: RBG24109_Plate18_E9_R26


title: RBG24090_Plate18_B7_Runx2_sg2


title: RBG24084_Plate18_D6_Runx2_sg1

value: Treated with Runx2_sg1


title: RBG24088_Plate18_H6_Runx2_sg1


title: RBG24085_Plate18_E6_Runx2_sg1


title: RBG24087_Plate18_G6_Runx2_sg1


title: RBG24083_Plate18_C6_Runx2_sg1


title: RBG24102_Plate18_F8_Runx2_sg3


title: RBG24077_Plate18_E5_emptyV_b2a

value: Treated with controlNT_b2a


title: RBG24081_Plate18_A6_Runx2_sg1


title: RBG24080_Plate18_H5_emptyV_b2a


title: RBG24078_Plate18_F5_emptyV_b2a


title: RBG24076_Plate18_D5_emptyV_b2a


title: RBG24075_Plate18_C5_emptyV_b2a


title: RBG24073_Plate18_A5_emptyV_b2a


title: RBG24072_Plate18_H4_Zbtb17_sg3

value: Treated with Zbtb17_sg3


title: RBG24071_Plate18_G4_Zbtb17_sg3


title: RBG24069_Plate18_E4_Zbtb17_sg3


title: RBG24086_Plate18_F6_Runx2_sg1


title: RBG24068_Plate18_D4_Zbtb17_sg3


title: RBG24091_Plate18_C7_Runx2_sg2


title: RBG24067_Plate18_C4_Zbtb17_sg3


title: RBG24089_Plate18_A7_Runx2_sg2


title: RBG24070_Plate18_F4_Zbtb17_sg3


title: RBG24082_Plate18_B6_Runx2_sg1


title: RBG24064_Plate18_H3_Zbtb17_sg2

value: Treated with Zbtb17_sg2


title: RBG24063_Plate18_G3_Zbtb17_sg2


title: RBG24065_Plate18_A4_Zbtb17_sg3


title: RBG24061_Plate18_E3_Zbtb17_sg2


title: RBG24062_Plate18_F3_Zbtb17_sg2


title: RBG24079_Plate18_G5_emptyV_b2a


title: RBG24060_Plate18_D3_Zbtb17_sg2


title: RBG24059_Plate18_C3_Zbtb17_sg2


title: RBG24057_Plate18_A3_Zbtb17_sg2


title: RBG24074_Plate18_B5_emptyV_b2a


title: RBG24056_Plate18_H2_Zbtb17_sg1

value: Treated with Zbtb17_sg1


title: RBG24058_Plate18_B3_Zbtb17_sg2

value: bone marrow


title: RBG24055_Plate18_G2_Zbtb17_sg1

value: early hematopoietic progenitor cells


title: RBG24054_Plate18_F2_Zbtb17_sg1


title: SEM_Input_MED12

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling and annotation using Homer v4.7

source_name: ChIP seq Input for MED12 in SEM cells

growth_protocol: Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (EZH2). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

tag: cell line

value: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

value: input


title: RBG24052_Plate18_D2_Zbtb17_sg1

value: Cas9 expressing, Hoxb8 expressing


title: RBG24053_Plate18_E2_Zbtb17_sg1


title: RBG24066_Plate18_B4_Zbtb17_sg3


title: RBG24045_Plate18_E1_emptyV

value: Treated with controlNT


title: RBG24049_Plate18_A2_Zbtb17_sg1


title: RBG24046_Plate18_F1_emptyV


title: UKN1timecourse_ND_3h_Exp1

source_name: hESCs have been incubated with culturing medium for 3h

value: female

value: differentiated state

value: H9 human embryonic stem cells


title: RBG24050_Plate18_B2_Zbtb17_sg1


title: RBG24048_Plate18_H1_emptyV


title: RBG24044_Plate18_D1_emptyV


title: RBG24047_Plate18_G1_emptyV


title: RBG24043_Plate18_C1_emptyV


title: RBG24042_Plate18_B1_emptyV


title: RBG24040_Plate17_H12_Fli1_sg3

value: Treated with Fli1_sg3


title: RBG24041_Plate18_A1_emptyV


title: RBG24039_Plate17_G12_Fli1_sg3


title: RBG24036_Plate17_D12_Fli1_sg3


title: RBG24035_Plate17_C12_Fli1_sg3


title: RBG24034_Plate17_B12_Fli1_sg3


title: RBG24030_Plate17_F11_Fli1_sg2

value: Treated with Fli1_sg2


title: RBG24032_Plate17_H11_Fli1_sg2


title: RBG24033_Plate17_A12_Fli1_sg3


title: RBG24051_Plate18_C2_Zbtb17_sg1


title: RBG24029_Plate17_E11_Fli1_sg2


title: RBG24031_Plate17_G11_Fli1_sg2


title: RBG24028_Plate17_D11_Fli1_sg2


title: RBG24037_Plate17_E12_Fli1_sg3


title: UKN1timecourse_ND_16h_Exp1

source_name: hESCs have been incubated with culturing medium for 16h


title: UKN1timecourse_ND_10h_Exp1

source_name: hESCs have been incubated with culturing medium for 10h


title: RBG24027_Plate17_C11_Fli1_sg2


title: RBG24026_Plate17_B11_Fli1_sg2


title: RBG24023_Plate17_G10_Fli1_sg1

value: Treated with Fli1_sg1


title: RBG24024_Plate17_H10_Fli1_sg1


title: RBG24018_Plate17_B10_Fli1_sg1


title: RBG24017_Plate17_A10_Fli1_sg1


title: RBG24021_Plate17_E10_Fli1_sg1


title: RBG24016_Plate17_H9_R26

value: Treated with controlR26


title: RBG24022_Plate17_F10_Fli1_sg1


title: RBG24014_Plate17_F9_R26


title: RBG24015_Plate17_G9_R26


title: RBG24019_Plate17_C10_Fli1_sg1


title: RBG24025_Plate17_A11_Fli1_sg2


title: RBG24038_Plate17_F12_Fli1_sg3


title: RBG24013_Plate17_E9_R26


title: RBG24012_Plate17_D9_R26


title: RBG24011_Plate17_C9_R26


title: RBG24009_Plate17_A9_R26


title: RBG24008_Plate17_H8_Foxo1_sg3

value: Treated with Foxo1_sg3


title: RBG24007_Plate17_G8_Foxo1_sg3


title: RBG24005_Plate17_E8_Foxo1_sg3


title: RBG24006_Plate17_F8_Foxo1_sg3


title: RBG24003_Plate17_C8_Foxo1_sg3


title: RBG24002_Plate17_B8_Foxo1_sg3


title: RBG24001_Plate17_A8_Foxo1_sg3


title: RBG24020_Plate17_D10_Fli1_sg1


title: RBG24000_Plate17_H7_Foxo1_sg2

value: Treated with Foxo1_sg2


title: RBG23999_Plate17_G7_Foxo1_sg2


title: RBG23998_Plate17_F7_Foxo1_sg2


title: RBG23997_Plate17_E7_Foxo1_sg2


title: RBG23995_Plate17_C7_Foxo1_sg2


title: RBG23996_Plate17_D7_Foxo1_sg2


title: RBG23994_Plate17_B7_Foxo1_sg2


title: RBG23992_Plate17_H6_Foxo1_sg1

value: Treated with Foxo1_sg1


title: RBG23989_Plate17_E6_Foxo1_sg1

value: bone marrow


title: RBG23993_Plate17_A7_Foxo1_sg2

value: early hematopoietic progenitor cells


title: RBG23990_Plate17_F6_Foxo1_sg1


title: RBG23987_Plate17_C6_Foxo1_sg1


title: RBG23988_Plate17_D6_Foxo1_sg1


title: RBG23986_Plate17_B6_Foxo1_sg1


title: RBG23991_Plate17_G6_Foxo1_sg1


title: RBG23985_Plate17_A6_Foxo1_sg1


title: RBG23983_Plate17_G5_emptyV_b2a

value: Treated with controlNT_b2a


title: RBG24010_Plate17_B9_R26


title: RBG23981_Plate17_E5_emptyV_b2a


title: RBG23980_Plate17_D5_emptyV_b2a


title: RBG24004_Plate17_D8_Foxo1_sg3


title: RBG23982_Plate17_F5_emptyV_b2a


title: RBG23978_Plate17_B5_emptyV_b2a


title: RBG23977_Plate17_A5_emptyV_b2a


title: RBG23975_Plate17_G4_Klf6_sg3

value: Treated with Klf6_sg3


title: RBG23973_Plate17_E4_Klf6_sg3


title: RBG23972_Plate17_D4_Klf6_sg3


title: RBG23976_Plate17_H4_Klf6_sg3


title: RBG23971_Plate17_C4_Klf6_sg3


title: RBG23974_Plate17_F4_Klf6_sg3


title: RBG23967_Plate17_G3_Klf6_sg2

value: Treated with Klf6_sg2


title: RBG23969_Plate17_A4_Klf6_sg3

value: Cas9 expressing, Hoxb8 expressing


title: RBG23968_Plate17_H3_Klf6_sg2


title: RBG23965_Plate17_E3_Klf6_sg2


title: RBG23960_Plate17_H2_Klf6_sg1

value: Treated with Klf6_sg1


title: RBG23984_Plate17_H5_emptyV_b2a


title: RBG23966_Plate17_F3_Klf6_sg2


title: RBG23963_Plate17_C3_Klf6_sg2


title: RBG23964_Plate17_D3_Klf6_sg2


title: RBG23958_Plate17_F2_Klf6_sg1


title: RBG23959_Plate17_G2_Klf6_sg1


title: RBG23957_Plate17_E2_Klf6_sg1


title: RBG23962_Plate17_B3_Klf6_sg2


title: RBG23961_Plate17_A3_Klf6_sg2


title: RBG23979_Plate17_C5_emptyV_b2a


title: RBG23955_Plate17_C2_Klf6_sg1


title: RBG23952_Plate17_H1_emptyV

value: Treated with controlNT


title: RBG23953_Plate17_A2_Klf6_sg1


title: RBG23951_Plate17_G1_emptyV


title: RBG23950_Plate17_F1_emptyV


title: RBG23948_Plate17_D1_emptyV


title: RBG23947_Plate17_C1_emptyV


title: RBG23946_Plate17_B1_emptyV


title: RBG23970_Plate17_B4_Klf6_sg3


title: RBG23949_Plate17_E1_emptyV


title: RBG23944_Plate16_H12_Crtc1_sg3

value: Treated with Crtc1_sg3


title: RBG23943_Plate16_G12_Crtc1_sg3


title: RBG23940_Plate16_D12_Crtc1_sg3


title: RBG23939_Plate16_C12_Crtc1_sg3


title: RBG23938_Plate16_B12_Crtc1_sg3


title: RBG23956_Plate17_D2_Klf6_sg1


title: RBG23937_Plate16_A12_Crtc1_sg3


title: RBG23933_Plate16_E11_Crtc1_sg2

value: Treated with Crtc1_sg2


title: RBG23935_Plate16_G11_Crtc1_sg2


title: RBG23954_Plate17_B2_Klf6_sg1


title: RBG23931_Plate16_C11_Crtc1_sg2


title: RBG23930_Plate16_B11_Crtc1_sg2


title: RBG23929_Plate16_A11_Crtc1_sg2


title: RBG23941_Plate16_E12_Crtc1_sg3


title: RBG23932_Plate16_D11_Crtc1_sg2


title: RBG23925_Plate16_E10_Crtc1_sg1

value: Treated with Crtc1_sg1


title: RBG23926_Plate16_F10_Crtc1_sg1


title: RBG23927_Plate16_G10_Crtc1_sg1


title: RBG23936_Plate16_H11_Crtc1_sg2


title: RBG23924_Plate16_D10_Crtc1_sg1


title: RBG23923_Plate16_C10_Crtc1_sg1


title: RBG23945_Plate17_A1_emptyV


title: RBG23919_Plate16_G9_R26


title: RBG23928_Plate16_H10_Crtc1_sg1


title: RBG23918_Plate16_F9_R26


title: RBG23922_Plate16_B10_Crtc1_sg1


title: RBG23920_Plate16_H9_R26


title: RBG23921_Plate16_A10_Crtc1_sg1


title: RBG23917_Plate16_E9_R26


title: RBG23942_Plate16_F12_Crtc1_sg3


title: RBG23916_Plate16_D9_R26


title: RBG23934_Plate16_F11_Crtc1_sg2


title: RBG23913_Plate16_A9_R26


title: RBG23911_Plate16_G8_Ebf1_sg3

value: Treated with Ebf1_sg3


title: RBG23912_Plate16_H8_Ebf1_sg3


title: RBG23909_Plate16_E8_Ebf1_sg3


title: RBG23910_Plate16_F8_Ebf1_sg3


title: RBG23907_Plate16_C8_Ebf1_sg3


title: RBG23914_Plate16_B9_R26


title: RBG23903_Plate16_G7_Ebf1_sg2

value: Treated with Ebf1_sg2


title: RBG23915_Plate16_C9_R26

value: Treated with controlR26


title: RBG23902_Plate16_F7_Ebf1_sg2


title: RBG23906_Plate16_B8_Ebf1_sg3


title: RBG23900_Plate16_D7_Ebf1_sg2


title: RBG23905_Plate16_A8_Ebf1_sg3


title: RBG23899_Plate16_C7_Ebf1_sg2


title: RBG23908_Plate16_D8_Ebf1_sg3


title: RBG23898_Plate16_B7_Ebf1_sg2


title: RBG23901_Plate16_E7_Ebf1_sg2


title: RBG23897_Plate16_A7_Ebf1_sg2


title: RBG23896_Plate16_H6_Ebf1_sg1

value: Treated with Ebf1_sg1


title: RBG23894_Plate16_F6_Ebf1_sg1


title: RBG23893_Plate16_E6_Ebf1_sg1


title: RBG23891_Plate16_C6_Ebf1_sg1


title: RBG23889_Plate16_A6_Ebf1_sg1


title: RBG23892_Plate16_D6_Ebf1_sg1


title: RBG23890_Plate16_B6_Ebf1_sg1


title: RBG23895_Plate16_G6_Ebf1_sg1


title: RBG23887_Plate16_G5_emptyV_b2a


title: RBG23888_Plate16_H5_emptyV_b2a


title: RBG23886_Plate16_F5_emptyV_b2a


title: RBG23884_Plate16_D5_emptyV_b2a


title: RBG23904_Plate16_H7_Ebf1_sg2


title: RBG23883_Plate16_C5_emptyV_b2a


title: RBG23882_Plate16_B5_emptyV_b2a


title: RBG23880_Plate16_H4_Cebpb_sg3

value: Treated with Cebpb_sg3


title: RBG23881_Plate16_A5_emptyV_b2a


title: RBG23879_Plate16_G4_Cebpb_sg3


title: RBG23877_Plate16_E4_Cebpb_sg3


title: RBG23874_Plate16_B4_Cebpb_sg3


title: RBG23871_Plate16_G3_Cebpb_sg2

value: Treated with Cebpb_sg2


title: RBG23870_Plate16_F3_Cebpb_sg2

value: bone marrow


title: RBG23878_Plate16_F4_Cebpb_sg3

value: early hematopoietic progenitor cells


title: RBG23873_Plate16_A4_Cebpb_sg3


title: RBG23875_Plate16_C4_Cebpb_sg3


title: RBG23868_Plate16_D3_Cebpb_sg2


title: RBG23872_Plate16_H3_Cebpb_sg2


title: RBG23869_Plate16_E3_Cebpb_sg2


title: RBG23865_Plate16_A3_Cebpb_sg2


title: RBG23867_Plate16_C3_Cebpb_sg2


title: RBG23866_Plate16_B3_Cebpb_sg2


title: RBG23862_Plate16_F2_Cebpb_sg1

value: Treated with Cebpb_sg1


title: RBG23858_Plate16_B2_Cebpb_sg1


title: RBG23860_Plate16_D2_Cebpb_sg1


title: RBG23857_Plate16_A2_Cebpb_sg1


title: RBG23861_Plate16_E2_Cebpb_sg1


title: RBG23859_Plate16_C2_Cebpb_sg1


title: RBG23885_Plate16_E5_emptyV_b2a

value: Treated with controlNT_b2a


title: RBG23855_Plate16_G1_emptyV


title: RBG23854_Plate16_F1_emptyV


title: RBG23849_Plate16_A1_emptyV


title: RBG23853_Plate16_E1_emptyV


title: RBG23850_Plate16_B1_emptyV


title: RBG23852_Plate16_D1_emptyV


title: RBG21299_Plate15_H12_noB

value: Cas9 expressing, Hoxb8 expression switched off for 16h

value: Hoxb8 expression switched off for 16h


title: RBG23876_Plate16_D4_Cebpb_sg3

value: Cas9 expressing, Hoxb8 expressing


title: RBG21295_Plate15_D12_noB


title: RBG21294_Plate15_C12_noB


title: RBG21293_Plate15_B12_noB


title: RBG21298_Plate15_G12_noB


title: RBG21292_Plate15_A12_noB


title: RBG21297_Plate15_F12_noB


title: RBG21291_Plate15_H11_R26


title: RBG21296_Plate15_E12_noB


title: RBG21286_Plate15_C11_R26


title: RBG21288_Plate15_E11_R26


title: RBG21287_Plate15_D11_R26


title: RBG21289_Plate15_F11_R26


title: RBG23863_Plate16_G2_Cebpb_sg1


title: RBG21284_Plate15_A11_R26


title: RBG21285_Plate15_B11_R26


title: RBG21290_Plate15_G11_R26


title: RBG21281_Plate15_F10_emptyV

value: Treated with controlNT


title: RBG21280_Plate15_E10_emptyV


title: RBG21282_Plate15_G10_emptyV


title: RBG21279_Plate15_D10_emptyV


title: RBG23851_Plate16_C1_emptyV


title: RBG21278_Plate15_C10_emptyV


title: RBG21277_Plate15_B10_emptyV


title: RBG21273_Plate15_F9_Nfic_sg3

value: Treated with Nfic_sg3


title: RBG21276_Plate15_A10_emptyV


title: RBG21272_Plate15_E9_Nfic_sg3


title: RBG21275_Plate15_H9_Nfic_sg3


title: RBG21274_Plate15_G9_Nfic_sg3


title: RBG21270_Plate15_C9_Nfic_sg3


title: RBG21271_Plate15_D9_Nfic_sg3


title: RBG21269_Plate15_B9_Nfic_sg3


title: RBG21267_Plate15_H8_Nfic_sg2

value: Treated with Nfic_sg2


title: RBG21266_Plate15_G8_Nfic_sg2


title: RBG21264_Plate15_E8_Nfic_sg2


title: RBG21263_Plate15_D8_Nfic_sg2


title: RBG21260_Plate15_A8_Nfic_sg2


title: RBG21265_Plate15_F8_Nfic_sg2


title: RBG21262_Plate15_C8_Nfic_sg2


title: RBG21261_Plate15_B8_Nfic_sg2


title: RBG21259_Plate15_H7_Nfic_sg1

value: Treated with Nfic_sg1


title: RBG21283_Plate15_H10_emptyV


title: RBG21255_Plate15_D7_Nfic_sg1


title: RBG21256_Plate15_E7_Nfic_sg1


title: RBG21258_Plate15_G7_Nfic_sg1


title: RBG21253_Plate15_B7_Nfic_sg1


title: RBG21257_Plate15_F7_Nfic_sg1


title: RBG21251_Plate15_H6_Ikzf1_sg3

value: Treated with Ikzf1_sg3


title: RBG21250_Plate15_G6_Ikzf1_sg3


title: RBG21252_Plate15_A7_Nfic_sg1


title: RBG21248_Plate15_E6_Ikzf1_sg3


title: RBG21247_Plate15_D6_Ikzf1_sg3


title: RBG21268_Plate15_A9_Nfic_sg3


title: RBG21246_Plate15_C6_Ikzf1_sg3


title: RBG21244_Plate15_A6_Ikzf1_sg3


title: RBG21243_Plate15_H5_Ikzf1_sg2

value: Treated with Ikzf1_sg2


title: RBG21241_Plate15_F5_Ikzf1_sg2


title: RBG21239_Plate15_D5_Ikzf1_sg2


title: RBG21240_Plate15_E5_Ikzf1_sg2


title: RBG21237_Plate15_B5_Ikzf1_sg2


title: RBG21236_Plate15_A5_Ikzf1_sg2


title: RBG21235_Plate15_H4_Ikzf1_sg1

value: Treated with Ikzf1_sg1


title: RBG21234_Plate15_G4_Ikzf1_sg1


title: RBG21254_Plate15_C7_Nfic_sg1


title: RBG21233_Plate15_F4_Ikzf1_sg1


title: RBG21232_Plate15_E4_Ikzf1_sg1


title: RBG21231_Plate15_D4_Ikzf1_sg1


title: RBG21249_Plate15_F6_Ikzf1_sg3


title: RBG21230_Plate15_C4_Ikzf1_sg1


title: RBG21227_Plate15_H3_Gfi1_sg3

value: Treated with Gfi1_sg3


title: RBG21226_Plate15_G3_Gfi1_sg3


title: RBG21224_Plate15_E3_Gfi1_sg3


title: RBG21245_Plate15_B6_Ikzf1_sg3


title: RBG21225_Plate15_F3_Gfi1_sg3


title: RBG21223_Plate15_D3_Gfi1_sg3


title: RBG21222_Plate15_C3_Gfi1_sg3


title: RBG21221_Plate15_B3_Gfi1_sg3


title: RBG21220_Plate15_A3_Gfi1_sg3


title: RBG21242_Plate15_G5_Ikzf1_sg2


title: RBG21217_Plate15_F2_Gfi1_sg2

value: Treated with Gfi1_sg2


title: RBG21238_Plate15_C5_Ikzf1_sg2


title: RBG21216_Plate15_E2_Gfi1_sg2


title: RBG21215_Plate15_D2_Gfi1_sg2


title: RBG21212_Plate15_A2_Gfi1_sg2


title: RBG21209_Plate15_F1_Gfi1_sg1

value: Treated with Gfi1_sg1


title: RBG21219_Plate15_H2_Gfi1_sg2

value: bone marrow


title: RBG21211_Plate15_H1_Gfi1_sg1

value: early hematopoietic progenitor cells


title: RBG21207_Plate15_D1_Gfi1_sg1


title: RBG21229_Plate15_B4_Ikzf1_sg1


title: RBG21208_Plate15_E1_Gfi1_sg1


title: RBG21205_Plate15_B1_Gfi1_sg1


title: RBG21204_Plate15_A1_Gfi1_sg1


title: RBG21228_Plate15_A4_Ikzf1_sg1


title: RBG21210_Plate15_G1_Gfi1_sg1


title: RBG21195_Plate13_H11_R26

value: Treated with controlR26


title: RBG21213_Plate15_B2_Gfi1_sg2


title: RBG21193_Plate13_F11_R26


title: RBG21192_Plate13_E11_R26


title: RBG21194_Plate13_G11_R26


title: RBG21191_Plate13_D11_R26


title: RBG21188_Plate13_A11_R26


title: RBG21218_Plate15_G2_Gfi1_sg2


title: RBG21187_Plate13_H10_emptyV


title: RBG21185_Plate13_F10_emptyV


title: RBG21186_Plate13_G10_emptyV


title: RBG21214_Plate15_C2_Gfi1_sg2


title: RBG21184_Plate13_E10_emptyV


title: RBG21183_Plate13_D10_emptyV


title: RBG21181_Plate13_B10_emptyV


title: RBG21182_Plate13_C10_emptyV


title: RBG21179_Plate13_H9_Runx1_sg3

value: Treated with Runx1_sg3


title: RBG21206_Plate15_C1_Gfi1_sg1


title: RBG21190_Plate13_C11_R26


title: RBG21189_Plate13_B11_R26


title: RBG21176_Plate13_E9_Runx1_sg3


title: RBG21173_Plate13_B9_Runx1_sg3


title: RBG21172_Plate13_A9_Runx1_sg3


title: RBG21174_Plate13_C9_Runx1_sg3


title: RBG21170_Plate13_G8_Runx1_sg2

value: Treated with Runx1_sg2


title: RBG21166_Plate13_C8_Runx1_sg2


title: RBG21167_Plate13_D8_Runx1_sg2


title: RBG21165_Plate13_B8_Runx1_sg2


title: RBG21177_Plate13_F9_Runx1_sg3


title: RBG21164_Plate13_A8_Runx1_sg2


title: RBG21178_Plate13_G9_Runx1_sg3


title: RBG21171_Plate13_H8_Runx1_sg2


title: RBG21169_Plate13_F8_Runx1_sg2


title: RBG21161_Plate13_F7_Runx1_sg1

value: Treated with Runx1_sg1


title: RBG21180_Plate13_A10_emptyV

value: Cas9 expressing, Hoxb8 expressing


title: RBG21160_Plate13_E7_Runx1_sg1


title: RBG21155_Plate13_H6_Meis1_sg3

value: Treated with Meis1_sg3


title: RBG21159_Plate13_D7_Runx1_sg1


title: RBG21156_Plate13_A7_Runx1_sg1


title: RBG21158_Plate13_C7_Runx1_sg1


title: RBG21157_Plate13_B7_Runx1_sg1


title: RBG21175_Plate13_D9_Runx1_sg3


title: RBG21153_Plate13_F6_Meis1_sg3


title: RBG21152_Plate13_E6_Meis1_sg3


title: RBG21163_Plate13_H7_Runx1_sg1


title: RBG21162_Plate13_G7_Runx1_sg1


title: RBG21151_Plate13_D6_Meis1_sg3


title: RBG21150_Plate13_C6_Meis1_sg3


title: RBG21146_Plate13_G5_Meis1_sg2

value: Treated with Meis1_sg2


title: RBG21147_Plate13_H5_Meis1_sg2


title: RBG21145_Plate13_F5_Meis1_sg2


title: RBG21148_Plate13_A6_Meis1_sg3


title: RBG21144_Plate13_E5_Meis1_sg2


title: RBG21168_Plate13_E8_Runx1_sg2


title: RBG21141_Plate13_B5_Meis1_sg2


title: RBG21140_Plate13_A5_Meis1_sg2


title: RBG21149_Plate13_B6_Meis1_sg3


title: RBG21143_Plate13_D5_Meis1_sg2


title: RBG21139_Plate13_H4_Meis1_sg1

value: Treated with Meis1_sg1


title: RBG21137_Plate13_F4_Meis1_sg1


title: RBG21138_Plate13_G4_Meis1_sg1


title: RBG21142_Plate13_C5_Meis1_sg2


title: RBG21136_Plate13_E4_Meis1_sg1


title: RBG21154_Plate13_G6_Meis1_sg3


title: RBG21135_Plate13_D4_Meis1_sg1


title: RBG21134_Plate13_C4_Meis1_sg1


title: RBG21115_Plate9_H11_R26


title: RBG21114_Plate9_G11_R26


title: RBG21113_Plate9_F11_R26


title: RBG21133_Plate13_B4_Meis1_sg1


title: RBG21132_Plate13_A4_Meis1_sg1


title: RBG21112_Plate9_E11_R26


title: RBG21110_Plate9_C11_R26


title: RBG21109_Plate9_B11_R26


title: RBG21108_Plate9_A11_R26


title: RBG21107_Plate9_H10_emptyV

value: Treated with controlNT


title: RBG21106_Plate9_G10_emptyV


title: RBG21103_Plate9_D10_emptyV


title: RBG21105_Plate9_F10_emptyV


title: RBG21098_Plate9_G9_Max_sg3

value: Treated with Max_sg3


title: RBG21101_Plate9_B10_emptyV


title: RBG21100_Plate9_A10_emptyV


title: RBG21099_Plate9_H9_Max_sg3


title: RBG21104_Plate9_E10_emptyV


title: RBG21095_Plate9_D9_Max_sg3


title: RBG21097_Plate9_F9_Max_sg3


title: RBG21096_Plate9_E9_Max_sg3


title: RBG21093_Plate9_B9_Max_sg3


title: RBG21090_Plate9_G8_Max_sg2

value: Treated with Max_sg2


title: RBG21092_Plate9_A9_Max_sg3


title: RBG21089_Plate9_F8_Max_sg2


title: RBG21111_Plate9_D11_R26


title: RBG21086_Plate9_C8_Max_sg2


title: RBG21087_Plate9_D8_Max_sg2


title: RBG21085_Plate9_B8_Max_sg2


title: RBG21084_Plate9_A8_Max_sg2


title: RBG21082_Plate9_G7_Max_sg1

value: Treated with Max_sg1


title: RBG21081_Plate9_F7_Max_sg1


title: RBG21080_Plate9_E7_Max_sg1


title: RBG21088_Plate9_E8_Max_sg2


title: RBG21079_Plate9_D7_Max_sg1


title: RBG21078_Plate9_C7_Max_sg1


title: RBG21083_Plate9_H7_Max_sg1


title: RBG21094_Plate9_C9_Max_sg3


title: RBG21076_Plate9_A7_Max_sg1


title: RBG21071_Plate9_D6_Fos_sg3

value: Treated with Fos_sg3


title: RBG21073_Plate9_F6_Fos_sg3


title: RBG21075_Plate9_H6_Fos_sg3


title: RBG21072_Plate9_E6_Fos_sg3


title: RBG21070_Plate9_C6_Fos_sg3


title: RBG21077_Plate9_B7_Max_sg1


title: RBG21066_Plate9_G5_Fos_sg2

value: Treated with Fos_sg2


title: RBG21069_Plate9_B6_Fos_sg3


title: RBG21074_Plate9_G6_Fos_sg3


title: RBG21102_Plate9_C10_emptyV


title: RBG21091_Plate9_H8_Max_sg2


title: RBG21064_Plate9_E5_Fos_sg2


title: RBG21065_Plate9_F5_Fos_sg2


title: RBG21063_Plate9_D5_Fos_sg2


title: RBG21062_Plate9_C5_Fos_sg2


title: RBG21061_Plate9_B5_Fos_sg2


title: RBG21060_Plate9_A5_Fos_sg2


title: RBG21059_Plate9_H4_Fos_sg1

value: Treated with Fos_sg1


title: RBG21057_Plate9_F4_Fos_sg1

value: bone marrow


title: RBG21056_Plate9_E4_Fos_sg1

value: early hematopoietic progenitor cells


title: RBG21055_Plate9_D4_Fos_sg1


title: RBG21053_Plate9_B4_Fos_sg1


title: RBG21052_Plate9_A4_Fos_sg1


title: RBG21058_Plate9_G4_Fos_sg1


title: RBG21054_Plate9_C4_Fos_sg1


title: RBG21068_Plate9_A6_Fos_sg3


title: RBG21050_Plate9_G3_Jun_sg3

value: Treated with Jun_sg3


title: RBG21067_Plate9_H5_Fos_sg2


title: RBG21041_Plate9_F2_Jun_sg2

value: Treated with Jun_sg2


title: RBG21045_Plate9_B3_Jun_sg3


title: RBG21042_Plate9_G2_Jun_sg2


title: RBG21047_Plate9_D3_Jun_sg3


title: RBG21043_Plate9_H2_Jun_sg2


title: RBG21046_Plate9_C3_Jun_sg3


title: RBG21038_Plate9_C2_Jun_sg2


title: RBG21036_Plate9_A2_Jun_sg2


title: RBG21040_Plate9_E2_Jun_sg2


title: RBG21035_Plate9_H1_Jun_sg1

value: Treated with Jun_sg1


title: RBG21037_Plate9_B2_Jun_sg2


title: RBG21039_Plate9_D2_Jun_sg2


title: RBG21034_Plate9_G1_Jun_sg1


title: RBG21033_Plate9_F1_Jun_sg1


title: RBG21032_Plate9_E1_Jun_sg1


title: RBG21030_Plate9_C1_Jun_sg1


title: RBG21031_Plate9_D1_Jun_sg1


title: RBG21029_Plate9_B1_Jun_sg1


title: RBG21051_Plate9_H3_Jun_sg3


title: RBG20829_Plate12_H11_R26

value: Treated with controlR26


title: RBG20826_Plate12_E11_R26

value: Cas9 expressing, Hoxb8 expressing


title: RBG20825_Plate12_D11_R26


title: RBG20824_Plate12_C11_R26


title: RBG20823_Plate12_B11_R26


title: RBG20827_Plate12_F11_R26


title: RBG20828_Plate12_G11_R26


title: RBG21048_Plate9_E3_Jun_sg3


title: RBG21049_Plate9_F3_Jun_sg3


title: RBG20821_Plate12_H10_emptyV


title: RBG20820_Plate12_G10_emptyV


title: RBG20819_Plate12_F10_emptyV


title: RBG20822_Plate12_A11_R26


title: RBG20817_Plate12_D10_emptyV


title: RBG20818_Plate12_E10_emptyV


title: RBG20813_Plate12_H9_Hoxa9_sg3

value: Treated with Hoxa9_sg3


title: RBG20812_Plate12_G9_Hoxa9_sg3


title: RBG20810_Plate12_E9_Hoxa9_sg3


title: RBG20811_Plate12_F9_Hoxa9_sg3


title: RBG20815_Plate12_B10_emptyV


title: RBG20809_Plate12_D9_Hoxa9_sg3


title: RBG20808_Plate12_C9_Hoxa9_sg3


title: RBG20814_Plate12_A10_emptyV


title: RBG20816_Plate12_C10_emptyV


title: RBG20805_Plate12_H8_Hoxa9_sg2

value: Treated with Hoxa9_sg2


title: RBG20804_Plate12_G8_Hoxa9_sg2


title: RBG21028_Plate9_A1_Jun_sg1


title: RBG20802_Plate12_E8_Hoxa9_sg2


title: RBG20807_Plate12_B9_Hoxa9_sg3


title: RBG20801_Plate12_D8_Hoxa9_sg2


title: RBG20799_Plate12_B8_Hoxa9_sg2


title: RBG20798_Plate12_A8_Hoxa9_sg2


title: RBG20796_Plate12_G7_Hoxa9_sg1

value: Treated with Hoxa9_sg1


title: RBG20797_Plate12_H7_Hoxa9_sg1


title: RBG20795_Plate12_F7_Hoxa9_sg1


title: RBG20803_Plate12_F8_Hoxa9_sg2


title: RBG20793_Plate12_D7_Hoxa9_sg1


title: RBG20794_Plate12_E7_Hoxa9_sg1


title: RBG20790_Plate12_A7_Hoxa9_sg1


title: RBG20792_Plate12_C7_Hoxa9_sg1


title: RBG20789_Plate12_H6_Zfpm1_sg3

value: Treated with Zfpm1_sg3


title: RBG20788_Plate12_G6_Zfpm1_sg3


title: RBG20786_Plate12_E6_Zfpm1_sg3


title: RBG20787_Plate12_F6_Zfpm1_sg3


title: RBG20785_Plate12_D6_Zfpm1_sg3


title: RBG20784_Plate12_C6_Zfpm1_sg3


title: RBG21044_Plate9_A3_Jun_sg3


title: RBG20806_Plate12_A9_Hoxa9_sg3


title: RBG20783_Plate12_B6_Zfpm1_sg3


title: RBG20781_Plate12_H5_Zfpm1_sg2

value: Treated with Zfpm1_sg2


title: RBG20782_Plate12_A6_Zfpm1_sg3


title: RBG20780_Plate12_G5_Zfpm1_sg2


title: RBG20779_Plate12_F5_Zfpm1_sg2


title: RBG20778_Plate12_E5_Zfpm1_sg2


title: RBG20777_Plate12_D5_Zfpm1_sg2


title: RBG20775_Plate12_B5_Zfpm1_sg2


title: RBG20776_Plate12_C5_Zfpm1_sg2


title: RBG20773_Plate12_H4_Zfpm1_sg1

value: Treated with Zfpm1_sg1


title: RBG20772_Plate12_G4_Zfpm1_sg1


title: RBG20770_Plate12_E4_Zfpm1_sg1


title: RBG20774_Plate12_A5_Zfpm1_sg2


title: RBG20771_Plate12_F4_Zfpm1_sg1


title: RBG20791_Plate12_B7_Hoxa9_sg1


title: RBG20767_Plate12_B4_Zfpm1_sg1


title: RBG20766_Plate12_A4_Zfpm1_sg1


title: RBG20765_Plate12_H3_Mitf_sg3

value: Treated with Mitf_sg3


title: RBG20764_Plate12_G3_Mitf_sg3


title: RBG20768_Plate12_C4_Zfpm1_sg1


title: RBG20761_Plate12_D3_Mitf_sg3


title: RBG20760_Plate12_C3_Mitf_sg3


title: RBG20762_Plate12_E3_Mitf_sg3


title: RBG20756_Plate12_G2_Mitf_sg2

value: Treated with Mitf_sg2


title: RBG20757_Plate12_H2_Mitf_sg2


title: RBG20758_Plate12_A3_Mitf_sg3


title: RBG20754_Plate12_E2_Mitf_sg2


title: RBG20751_Plate12_B2_Mitf_sg2


title: RBG20752_Plate12_C2_Mitf_sg2


title: RBG20753_Plate12_D2_Mitf_sg2


title: RBG20750_Plate12_A2_Mitf_sg2


title: RBG20749_Plate12_H1_Mitf_sg1

value: Treated with Mitf_sg1


title: RBG20748_Plate12_G1_Mitf_sg1


title: RBG20747_Plate12_F1_Mitf_sg1


title: RBG20769_Plate12_D4_Zfpm1_sg1


title: RBG20745_Plate12_D1_Mitf_sg1


title: RBG20746_Plate12_E1_Mitf_sg1


title: RBG20744_Plate12_C1_Mitf_sg1


title: RBG20645_Plate4_H11_R26


title: RBG20643_Plate4_F11_R26


title: RBG20743_Plate12_B1_Mitf_sg1


title: RBG20642_Plate4_E11_R26


title: RBG20641_Plate4_D11_R26


title: RBG20644_Plate4_G11_R26


title: RBG20742_Plate12_A1_Mitf_sg1


title: RBG20637_Plate4_H10_emptyV

value: Treated with controlNT


title: RBG20759_Plate12_B3_Mitf_sg3

value: bone marrow


title: RBG20636_Plate4_G10_emptyV

value: early hematopoietic progenitor cells


title: RBG20640_Plate4_C11_R26


title: RBG20755_Plate12_F2_Mitf_sg2


title: RBG20638_Plate4_A11_R26


title: RBG20639_Plate4_B11_R26


title: RBG20635_Plate4_F10_emptyV


title: RBG20634_Plate4_E10_emptyV


title: RBG20632_Plate4_C10_emptyV


title: RBG20630_Plate4_A10_emptyV


title: RBG20631_Plate4_B10_emptyV


title: RBG20629_Plate4_H9_Erg_sg3

value: Treated with Erg_sg3


title: RBG20633_Plate4_D10_emptyV


title: RBG20626_Plate4_E9_Erg_sg3


title: RBG20627_Plate4_F9_Erg_sg3


title: RBG20628_Plate4_G9_Erg_sg3


title: RBG20625_Plate4_D9_Erg_sg3


title: RBG20624_Plate4_C9_Erg_sg3


title: RBG20623_Plate4_B9_Erg_sg3


title: RBG20622_Plate4_A9_Erg_sg3


title: RBG20621_Plate4_H8_Erg_sg2

value: Treated with Erg_sg2


title: RBG20620_Plate4_G8_Erg_sg2


title: RBG20617_Plate4_D8_Erg_sg2


title: RBG20616_Plate4_C8_Erg_sg2


title: RBG20615_Plate4_B8_Erg_sg2


title: RBG20619_Plate4_F8_Erg_sg2


title: RBG20618_Plate4_E8_Erg_sg2


title: RBG20614_Plate4_A8_Erg_sg2


title: RBG20613_Plate4_H7_Erg_sg1

value: Treated with Erg_sg1


title: RBG20610_Plate4_E7_Erg_sg1


title: RBG20608_Plate4_C7_Erg_sg1


title: RBG20609_Plate4_D7_Erg_sg1


title: RBG20607_Plate4_B7_Erg_sg1


title: RBG20605_Plate4_H6_Elf1_sg3

value: Treated with Elf1_sg3


title: RBG20611_Plate4_F7_Erg_sg1

value: Cas9 expressing, Hoxb8 expressing


title: RBG20603_Plate4_F6_Elf1_sg3


title: RBG20604_Plate4_G6_Elf1_sg3


title: RBG20601_Plate4_D6_Elf1_sg3


title: RBG20602_Plate4_E6_Elf1_sg3


title: RBG20599_Plate4_B6_Elf1_sg3


title: RBG20598_Plate4_A6_Elf1_sg3


title: RBG20596_Plate4_G5_Elf1_sg2

value: Treated with Elf1_sg2


title: RBG20594_Plate4_E5_Elf1_sg2


title: RBG20595_Plate4_F5_Elf1_sg2


title: RBG20593_Plate4_D5_Elf1_sg2


title: RBG20592_Plate4_C5_Elf1_sg2


title: RBG20612_Plate4_G7_Erg_sg1


title: RBG20586_Plate4_E4_Elf1_sg1

value: Treated with Elf1_sg1


title: RBG20584_Plate4_C4_Elf1_sg1


title: RBG20585_Plate4_D4_Elf1_sg1


title: RBG20583_Plate4_B4_Elf1_sg1


title: RBG20587_Plate4_F4_Elf1_sg1


title: RBG20606_Plate4_A7_Erg_sg1


title: RBG20588_Plate4_G4_Elf1_sg1


title: RBG20579_Plate4_F3_Spi1_sg3

value: Treated with Spi1_sg3


title: RBG20580_Plate4_G3_Spi1_sg3


title: RBG20581_Plate4_H3_Spi1_sg3


title: RBG20575_Plate4_B3_Spi1_sg3


title: RBG20574_Plate4_A3_Spi1_sg3


title: RBG20577_Plate4_D3_Spi1_sg3


title: RBG20576_Plate4_C3_Spi1_sg3


title: RBG20572_Plate4_G2_Spi1_sg2

value: Treated with Spi1_sg2


title: RBG20590_Plate4_A5_Elf1_sg2


title: RBG20600_Plate4_C6_Elf1_sg3


title: RBG20571_Plate4_F2_Spi1_sg2


title: RBG20569_Plate4_D2_Spi1_sg2


title: RBG20597_Plate4_H5_Elf1_sg2


title: RBG20582_Plate4_A4_Elf1_sg1


title: RBG20591_Plate4_B5_Elf1_sg2


title: RBG20567_Plate4_B2_Spi1_sg2


title: RBG20570_Plate4_E2_Spi1_sg2


title: RBG20566_Plate4_A2_Spi1_sg2


title: RBG20565_Plate4_H1_Spi1_sg1

value: Treated with Spi1_sg1


title: RBG20563_Plate4_F1_Spi1_sg1


title: RBG20562_Plate4_E1_Spi1_sg1


title: RBG20578_Plate4_E3_Spi1_sg3


title: RBG20559_Plate4_B1_Spi1_sg1


title: RBG20560_Plate4_C1_Spi1_sg1


title: RBG20557_Plate3_H11_R26

value: Treated with controlR26


title: RBG20573_Plate4_H2_Spi1_sg2


title: RBG20556_Plate3_G11_R26


title: RBG20555_Plate3_F11_R26


title: RBG20554_Plate3_E11_R26


title: RBG20553_Plate3_D11_R26


title: RBG20568_Plate4_C2_Spi1_sg2


title: RBG20552_Plate3_C11_R26


title: RBG20550_Plate3_A11_R26


title: RBG20549_Plate3_H10_emptyV


title: RBG20546_Plate3_E10_emptyV


title: RBG20548_Plate3_G10_emptyV


title: RBG20547_Plate3_F10_emptyV


title: RBG20542_Plate3_A10_emptyV


title: RBG20545_Plate3_D10_emptyV


title: RBG20543_Plate3_B10_emptyV


title: RBG20541_Plate3_H9_E2F4_sg3

value: Treated with E2F4_sg3


title: RBG20540_Plate3_G9_E2F4_sg3


title: RBG20564_Plate4_G1_Spi1_sg1


title: RBG20539_Plate3_F9_E2F4_sg3


title: RBG20558_Plate4_A1_Spi1_sg1


title: RBG20561_Plate4_D1_Spi1_sg1


title: RBG20538_Plate3_E9_E2F4_sg3


title: RBG20537_Plate3_D9_E2F4_sg3


title: RBG20535_Plate3_B9_E2F4_sg3


title: RBG20536_Plate3_C9_E2F4_sg3


title: RBG20533_Plate3_H8_E2F4_sg2

value: Treated with E2F4_sg2


title: RBG20532_Plate3_G8_E2F4_sg2


title: RBG20551_Plate3_B11_R26


title: RBG20531_Plate3_F8_E2F4_sg2


title: RBG20530_Plate3_E8_E2F4_sg2


title: RBG20529_Plate3_D8_E2F4_sg2


title: RBG20527_Plate3_B8_E2F4_sg2


title: RBG20544_Plate3_C10_emptyV


title: RBG20528_Plate3_C8_E2F4_sg2


title: RBG20526_Plate3_A8_E2F4_sg2


title: RBG20522_Plate3_E7_E2F4_sg1

value: Treated with E2F4_sg1


title: RBG20525_Plate3_H7_E2F4_sg1


title: RBG20524_Plate3_G7_E2F4_sg1


title: RBG20520_Plate3_C7_E2F4_sg1


title: RBG20523_Plate3_F7_E2F4_sg1


title: RBG20519_Plate3_B7_E2F4_sg1


title: RBG20521_Plate3_D7_E2F4_sg1


title: RBG20518_Plate3_A7_E2F4_sg1


title: RBG20516_Plate3_G6_Tal1_sg3

value: Treated with Tal1_sg3


title: RBG20515_Plate3_F6_Tal1_sg3

value: bone marrow


title: RBG20513_Plate3_D6_Tal1_sg3

value: early hematopoietic progenitor cells


title: RBG20512_Plate3_C6_Tal1_sg3


title: RBG20534_Plate3_A9_E2F4_sg3


title: RBG20510_Plate3_A6_Tal1_sg3


title: RBG20508_Plate3_G5_Tal1_sg2

value: Treated with Tal1_sg2


title: RBG20509_Plate3_H5_Tal1_sg2


title: RBG20511_Plate3_B6_Tal1_sg3


title: RBG20514_Plate3_E6_Tal1_sg3


title: RBG20507_Plate3_F5_Tal1_sg2


title: RBG20505_Plate3_D5_Tal1_sg2


title: RBG20506_Plate3_E5_Tal1_sg2


title: RBG20503_Plate3_B5_Tal1_sg2


title: RBG20502_Plate3_A5_Tal1_sg2


title: RBG20504_Plate3_C5_Tal1_sg2


title: RBG20500_Plate3_G4_Tal1_sg1

value: Treated with Tal1_sg1


title: RBG20501_Plate3_H4_Tal1_sg1


title: RBG20499_Plate3_F4_Tal1_sg1


title: RBG20498_Plate3_E4_Tal1_sg1


title: RBG20517_Plate3_H6_Tal1_sg3


title: RBG20497_Plate3_D4_Tal1_sg1


title: RBG20493_Plate3_H3_Cbfa2t3_sg3

value: Treated with Cbfa2t3_sg3


title: RBG20491_Plate3_F3_Cbfa2t3_sg3


title: RBG20494_Plate3_A4_Tal1_sg1


title: RBG20495_Plate3_B4_Tal1_sg1


title: RBG20490_Plate3_E3_Cbfa2t3_sg3


title: RBG20492_Plate3_G3_Cbfa2t3_sg3


title: RBG20489_Plate3_D3_Cbfa2t3_sg3


title: RBG20488_Plate3_C3_Cbfa2t3_sg3


title: RBG20487_Plate3_B3_Cbfa2t3_sg3


title: RBG20485_Plate3_H2_Cbfa2t3_sg2

value: Treated with Cbfa2t3_sg2


title: RBG20486_Plate3_A3_Cbfa2t3_sg3

value: Cas9 expressing, Hoxb8 expressing


title: RBG20484_Plate3_G2_Cbfa2t3_sg2


title: RBG20483_Plate3_F2_Cbfa2t3_sg2


title: RBG20482_Plate3_E2_Cbfa2t3_sg2


title: RBG20479_Plate3_B2_Cbfa2t3_sg2


title: RBG20480_Plate3_C2_Cbfa2t3_sg2


title: RBG20481_Plate3_D2_Cbfa2t3_sg2


title: RBG20478_Plate3_A2_Cbfa2t3_sg2


title: RBG20477_Plate3_H1_Cbfa2t3_sg1

value: Treated with Cbfa2t3_sg1


title: RBG20476_Plate3_G1_Cbfa2t3_sg1


title: RBG20474_Plate3_E1_Cbfa2t3_sg1


title: RBG20473_Plate3_D1_Cbfa2t3_sg1


title: RBG20472_Plate3_C1_Cbfa2t3_sg1


title: RBG20496_Plate3_C4_Tal1_sg1


title: RBG20470_Plate3_A1_Cbfa2t3_sg1


title: RBG20471_Plate3_B1_Cbfa2t3_sg1


title: RBG18695_Plate8_G11_R26


title: RBG18696_Plate8_H11_R26


title: RBG18694_Plate8_F11_R26


title: RBG18691_Plate8_C11_R26


title: RBG18692_Plate8_D11_R26


title: RBG18689_Plate8_A11_R26


title: RBG18690_Plate8_B11_R26


title: RBG18688_Plate8_H10_emptyV

value: Treated with controlNT


title: RBG18685_Plate8_E10_emptyV


title: RBG18687_Plate8_G10_emptyV


title: RBG18684_Plate8_D10_emptyV


title: RBG18686_Plate8_F10_emptyV


title: RBG18680_Plate8_H9_Myc_sg3

value: Treated with Myc_sg3


title: RBG18679_Plate8_G9_Myc_sg3


title: RBG18681_Plate8_A10_emptyV


title: RBG18682_Plate8_B10_emptyV


title: RBG18683_Plate8_C10_emptyV


title: RBG20475_Plate3_F1_Cbfa2t3_sg1


title: RBG18693_Plate8_E11_R26


title: RBG18676_Plate8_D9_Myc_sg3


title: RBG18675_Plate8_C9_Myc_sg3


title: RBG18673_Plate8_A9_Myc_sg3


title: RBG18672_Plate8_H8_Myc_sg2

value: Treated with Myc_sg2


title: RBG18674_Plate8_B9_Myc_sg3


title: RBG18677_Plate8_E9_Myc_sg3


title: RBG18669_Plate8_E8_Myc_sg2


title: RBG18670_Plate8_F8_Myc_sg2


title: RBG18671_Plate8_G8_Myc_sg2


title: RBG18667_Plate8_C8_Myc_sg2


title: RBG18668_Plate8_D8_Myc_sg2


title: RBG18663_Plate8_G7_Myc_sg1

value: Treated with Myc_sg1


title: RBG18664_Plate8_H7_Myc_sg1


title: RBG18662_Plate8_F7_Myc_sg1


title: RBG18660_Plate8_D7_Myc_sg1


title: RBG18659_Plate8_C7_Myc_sg1


title: RBG18658_Plate8_B7_Myc_sg1


title: RBG18661_Plate8_E7_Myc_sg1


title: RBG18678_Plate8_F9_Myc_sg3


title: RBG18657_Plate8_A7_Myc_sg1


title: RBG18655_Plate8_G6_Rad21_sg3

value: Treated with Rad21_sg3


title: RBG18652_Plate8_D6_Rad21_sg3


title: RBG18654_Plate8_F6_Rad21_sg3


title: RBG18651_Plate8_C6_Rad21_sg3


title: RBG18650_Plate8_B6_Rad21_sg3


title: RBG18649_Plate8_A6_Rad21_sg3


title: RBG18666_Plate8_B8_Myc_sg2


title: RBG18644_Plate8_D5_Rad21_sg2

value: Treated with Rad21_sg2


title: RBG18643_Plate8_C5_Rad21_sg2


title: RBG18647_Plate8_G5_Rad21_sg2


title: RBG18646_Plate8_F5_Rad21_sg2


title: RBG18640_Plate8_H4_Rad21_sg1

value: Treated with Rad21_sg1


title: RBG18648_Plate8_H5_Rad21_sg2


title: RBG18665_Plate8_A8_Myc_sg2


title: RBG18639_Plate8_G4_Rad21_sg1


title: RBG18641_Plate8_A5_Rad21_sg2


title: RBG18642_Plate8_B5_Rad21_sg2


title: RBG18637_Plate8_E4_Rad21_sg1


title: RBG18638_Plate8_F4_Rad21_sg1


title: RBG18636_Plate8_D4_Rad21_sg1


title: RBG18635_Plate8_C4_Rad21_sg1


title: RBG18634_Plate8_B4_Rad21_sg1


title: RBG18633_Plate8_A4_Rad21_sg1


title: RBG18656_Plate8_H6_Rad21_sg3


title: RBG18631_Plate8_G3_Myb_sg3

value: Treated with Myb_sg3


title: RBG18630_Plate8_F3_Myb_sg3


title: RBG18629_Plate8_E3_Myb_sg3


title: RBG18627_Plate8_C3_Myb_sg3


title: RBG18628_Plate8_D3_Myb_sg3


title: RBG18626_Plate8_B3_Myb_sg3


title: RBG18645_Plate8_E5_Rad21_sg2


title: RBG20589_Plate4_H4_Elf1_sg1

value: Treated with Elf1_sg1


title: RBG18624_Plate8_H2_Myb_sg2

value: bone marrow

value: Treated with Myb_sg2


title: RBG18625_Plate8_A3_Myb_sg3

value: early hematopoietic progenitor cells


title: RBG18623_Plate8_G2_Myb_sg2


title: RBG18622_Plate8_F2_Myb_sg2


title: RBG18653_Plate8_E6_Rad21_sg3


title: RBG18619_Plate8_C2_Myb_sg2


title: RBG18618_Plate8_B2_Myb_sg2


title: RBG18614_Plate8_F1_Myb_sg1

value: Treated with Myb_sg1


title: RBG18613_Plate8_E1_Myb_sg1


title: RBG18607_Plate7_G11_R26

value: Treated with controlR26


title: RBG18603_Plate7_C11_R26


title: RBG18632_Plate8_H3_Myb_sg3


title: RBG18606_Plate7_F11_R26


title: RBG18616_Plate8_H1_Myb_sg1


title: RBG18620_Plate8_D2_Myb_sg2


title: RBG18602_Plate7_B11_R26


title: RBG18608_Plate7_H11_R26


title: RBG18609_Plate8_A1_Myb_sg1


title: RBG18615_Plate8_G1_Myb_sg1


title: RBG18600_Plate7_H10_emptyV


title: RBG18617_Plate8_A2_Myb_sg2


title: RBG18611_Plate8_C1_Myb_sg1


title: RBG18610_Plate8_B1_Myb_sg1


title: RBG18604_Plate7_D11_R26


title: RBG18612_Plate8_D1_Myb_sg1


title: RBG18598_Plate7_F10_emptyV


title: RBG18596_Plate7_D10_emptyV


title: RBG18605_Plate7_E11_R26


title: RBG18595_Plate7_C10_emptyV


title: RBG18599_Plate7_G10_emptyV


title: RBG18597_Plate7_E10_emptyV


title: RBG18594_Plate7_B10_emptyV


title: RBG18621_Plate8_E2_Myb_sg2


title: RBG18593_Plate7_A10_emptyV


title: RBG18601_Plate7_A11_R26


title: RBG18592_Plate7_H9_Lmo2_sg3

value: Treated with Lmo2_sg3


title: RBG18589_Plate7_E9_Lmo2_sg3

value: Cas9 expressing, Hoxb8 expressing


title: RBG18585_Plate7_A9_Lmo2_sg3


title: RBG18581_Plate7_E8_Lmo2_sg2

value: Treated with Lmo2_sg2


title: RBG18588_Plate7_D9_Lmo2_sg3


title: RBG18582_Plate7_F8_Lmo2_sg2


title: RBG18590_Plate7_F9_Lmo2_sg3


title: RBG18577_Plate7_A8_Lmo2_sg2


title: RBG18580_Plate7_D8_Lmo2_sg2


title: RBG18579_Plate7_C8_Lmo2_sg2


title: RBG18584_Plate7_H8_Lmo2_sg2


title: RBG18587_Plate7_C9_Lmo2_sg3


title: RBG18578_Plate7_B8_Lmo2_sg2


title: RBG18571_Plate7_C7_Lmo2_sg1

value: Treated with Lmo2_sg1


title: RBG18575_Plate7_G7_Lmo2_sg1


title: RBG18569_Plate7_A7_Lmo2_sg1


title: RBG18574_Plate7_F7_Lmo2_sg1


title: RBG18591_Plate7_G9_Lmo2_sg3


title: RBG18576_Plate7_H7_Lmo2_sg1


title: RBG18570_Plate7_B7_Lmo2_sg1


title: RBG18567_Plate7_G6_Ldb1_sg3

value: Treated with Ldb1_sg3


title: RBG18568_Plate7_H6_Ldb1_sg3


title: RBG18566_Plate7_F6_Ldb1_sg3


title: RBG18583_Plate7_G8_Lmo2_sg2


title: RBG18565_Plate7_E6_Ldb1_sg3


title: RBG18564_Plate7_D6_Ldb1_sg3


title: RBG18563_Plate7_C6_Ldb1_sg3


title: RBG18562_Plate7_B6_Ldb1_sg3


title: RBG18573_Plate7_E7_Lmo2_sg1


title: RBG18557_Plate7_E5_Ldb1_sg2

value: Treated with Ldb1_sg2


title: RBG18560_Plate7_H5_Ldb1_sg2


title: RBG18559_Plate7_G5_Ldb1_sg2


title: RBG18556_Plate7_D5_Ldb1_sg2


title: RBG18558_Plate7_F5_Ldb1_sg2


title: RBG18553_Plate7_A5_Ldb1_sg2


title: RBG18552_Plate7_H4_Ldb1_sg1

value: Treated with Ldb1_sg1


title: RBG18549_Plate7_E4_Ldb1_sg1


title: RBG18546_Plate7_B4_Ldb1_sg1


title: RBG18550_Plate7_F4_Ldb1_sg1


title: RBG18548_Plate7_D4_Ldb1_sg1


title: RBG18544_Plate7_H3_Cebpa_sg3

value: Treated with Cebpa_sg3


title: RBG18551_Plate7_G4_Ldb1_sg1


title: RBG18542_Plate7_F3_Cebpa_sg3


title: RBG18554_Plate7_B5_Ldb1_sg2


title: RBG18547_Plate7_C4_Ldb1_sg1


title: RBG18543_Plate7_G3_Cebpa_sg3


title: RBG18541_Plate7_E3_Cebpa_sg3


title: RBG18545_Plate7_A4_Ldb1_sg1


title: RBG18539_Plate7_C3_Cebpa_sg3


title: RBG18540_Plate7_D3_Cebpa_sg3


title: RBG18538_Plate7_B3_Cebpa_sg3


title: RBG18537_Plate7_A3_Cebpa_sg3


title: RBG18536_Plate7_H2_Cebpa_sg2

value: Treated with Cebpa_sg2


title: RBG18535_Plate7_G2_Cebpa_sg2


title: RBG18561_Plate7_A6_Ldb1_sg3


title: RBG18555_Plate7_C5_Ldb1_sg2


title: RBG18531_Plate7_C2_Cebpa_sg2


title: RBG18532_Plate7_D2_Cebpa_sg2


title: RBG18534_Plate7_F2_Cebpa_sg2


title: RBG18530_Plate7_B2_Cebpa_sg2


title: RBG18529_Plate7_A2_Cebpa_sg2


title: RBG18523_Plate7_C1_Cebpa_sg1

value: Treated with Cebpa_sg1


title: RBG18526_Plate7_F1_Cebpa_sg1


title: RBG18522_Plate7_B1_Cebpa_sg1


title: RBG18527_Plate7_G1_Cebpa_sg1


title: RBG18525_Plate7_E1_Cebpa_sg1


title: RBG18524_Plate7_D1_Cebpa_sg1


title: RBG18520_Plate6_H11_R26


title: RBG18528_Plate7_H1_Cebpa_sg1


title: RBG18519_Plate6_G11_R26


title: RBG18517_Plate6_E11_R26


title: RBG18514_Plate6_B11_R26


title: RBG18518_Plate6_F11_R26


title: RBG18516_Plate6_D11_R26


title: RBG18515_Plate6_C11_R26


title: RBG18513_Plate6_A11_R26


title: RBG18511_Plate6_G10_emptyV

value: Treated with controlNT


title: RBG18533_Plate7_E2_Cebpa_sg2


title: RBG18509_Plate6_E10_emptyV


title: RBG18512_Plate6_H10_emptyV


title: RBG18510_Plate6_F10_emptyV


title: RBG18507_Plate6_C10_emptyV


title: RBG18508_Plate6_D10_emptyV


title: RBG18504_Plate6_H9_Egr1_sg3

value: Treated with Egr1_sg3


title: RBG18506_Plate6_B10_emptyV

value: bone marrow


title: RBG18521_Plate7_A1_Cebpa_sg1


title: RBG18505_Plate6_A10_emptyV


title: Fat-H-2

city: Karaj

first: Abolfazl

last: Bahrami

address: Daneshgah

department: Biology

country: Iran

institute: University of Tehran

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to bostau8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: bosTau8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Fat

extract_protocol:
Tissues were removed, flash frozen on dry 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

value: Fat

tag: fertility

value: high


title: Fat-L-3

value: low


title: Fat-L-2


title: Fat-H-3


title: Fat-L-1


title: RBG18501_Plate6_E9_Egr1_sg3

value: early hematopoietic progenitor cells


title: RBG18499_Plate6_C9_Egr1_sg3


title: RBG18498_Plate6_B9_Egr1_sg3


title: RBG18497_Plate6_A9_Egr1_sg3


title: RL 2

city: Rochester

first: Joe

last: Chakkalakal

state: NY

address: 601 Elmwood Avenue, Box 711

institute: University of Rochester

data_processing:
See Bachman et al, iScience 2020- Materials and Methods "NGS data processing and allignment" for details
Genome_build: Mus musculus (GRCm38.p5)
Supplementary_files_format_and_content: Processed data includes the following DeSeq2 comparisons: CTL vs CL, CL vs RL, and CTL vs RL. Reads, Normalized reads, and r(log) normalized counts are provided

source_name: gastrocnemius muscle

extract_protocol:
Gastrocnemius muscles were dissected and flash frozen on dry ice in Trizol. RNA was isolated using Rneasy Plus Mini Kit (Qiagen).
Library construction was performed by UR Genomics Research Center using TruSeq Tital Stranded RNA Sample Preperation Kit.

value: ~ 8 weeks old

value: gastrocnemius muscle

value: Irradiated gastroc (3 weeks post)


title: RL 1


title: CL 3

value: contralateral gastroc of mouse that received radiation, (3 weeks post)


title: CL 2


title: RBG18495_Plate6_G8_Egr1_sg2

value: Cas9 expressing, Hoxb8 expressing

value: Treated with Egr1_sg2


title: RBG18496_Plate6_H8_Egr1_sg2


title: RBG18494_Plate6_F8_Egr1_sg2


title: CTL 3

value: 0 Gy CTL (no radiation)


title: CTL 2


title: RBG18493_Plate6_E8_Egr1_sg2


title: RBG18491_Plate6_C8_Egr1_sg2


title: RBG18503_Plate6_G9_Egr1_sg3


title: RBG18502_Plate6_F9_Egr1_sg3


title: RBG18500_Plate6_D9_Egr1_sg3


title: RL 3


title: RBG18489_Plate6_A8_Egr1_sg2


title: RBG18488_Plate6_H7_Egr1_sg1

value: Treated with Egr1_sg1


title: RBG18490_Plate6_B8_Egr1_sg2


title: RBG18487_Plate6_G7_Egr1_sg1


title: RBG18486_Plate6_F7_Egr1_sg1


title: RBG18485_Plate6_E7_Egr1_sg1


title: EO771_Treg_ablated_rep1

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
FastQC v.0.11.5 49 was used for quality control at all stages of RNA-seq preprocessing. The Mouse GRCm38/mm10 reference genome was obtained from UCSC Genome Browser Gateway (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz), and the corresponding gene annotation file was obtained from Ensemble (ftp://ftp.ensembl.org/pub/release-83/gtf/mus_musculus/Mus_musculus.GRCm38.83.gtf.gz) on 02/20/2016. Only autosomes, mitochondrial, and sex chromosomes were used.
Reads were trimmed with Trimmomatic v.0.33 50 and aligned to the indexed reference genome using Subread v1.6.2 51. Read counting on a transcript reference file was performed using Subread’s “featureCounts” algorithm.
Genes with a read count of zero for all samples were removed prior to identifying differentially expressed genes using the DESeq2 R package v.1.16.1 54.  Genes are considered significantly differentially expressed if the Benjamini-Hochberg adjusted p-value is <= 0.05 and the absolute value of the Log2 Fold Change is >= 1.4.
Genome_build: mm10
Supplementary_files_format_and_content: gzipped tab-delimited files containing featurecounts counts for each sample

source_name: Tumor assotiated macrophages (defined as CD45+ CD11B+ Ly6G- F4/80+ cells) sorted from EO771 orthotopic breast tumors 4 days after Treg cell ablation, as described

extract_protocol:
TAMs (defined as CD45+ CD11B+ Ly6G- F4/80+ cells) were sorted from EO771 orthotopic breast tumors as described, and collected into TrizolLS (Thermo Fisher) for subsequent RNA isolation. RNA isolation was performed following manufacturer’s protocols. Initial quality control was performed using an Agilent Bioanalizer System through the Pathology Tissue and Data Acquisition and Analysis Core (TDAAC). All samples were sent to the Brigham Young University DNA sequencing core for further library construction and sequencing.
KAPA Stranded mRNA-Seq Kit was used for library preparation. Samples were sequenced on the Illumina Hi-Seq 2500 according to Illumina’s sequencing-by-synthesis protocol. 125bp paired-end reads were generated, yielding on average 87M reads per sample.

treatment_protocol: EO771 orthotopic mammary tumors were treated with two doses of 50ug/kg of diphteria toxin to ablate Treg cells, and TAMs were sorted 4 days after treatment. Control tumors were left untreated.

value: freshly sorted TAMs

value: Treg cell ablated


title: EO771_control_rep2

source_name: Tumor assotiated macrophages (defined as CD45+ CD11B+ Ly6G- F4/80+ cells) sorted from EO771 orthotopic breast control tumors

value: Control


title: EO771_control_rep1


title: EO771_control_rep3


title: RBG17276_Exp1_TC_F10_Gata3sg2_12d

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
exp1_exon_counts.csv
exp1_intron_counts.csv

extract_protocol:
75 BFP+/7AAD (live) cells were sorted using flow cytometry into Smart-Seq2 lysis plates.
small-scale bulk RNA-Seq was performed using a modified version of Smart-Seq2 (Picelli et al. Nature Protocols 2014). Please see the accompanying publication for a detailed protocol.

value: Treated with Gata3_sg2


title: RBG17277_Exp1_TC_G10_Gata3sg2_12d

value: bone marrow


title: RBG17278_Exp1_TC_H10_Gata3sg2_12d


title: RBG17275_Exp1_TC_E10_Gata3sg2_12d


title: RBG18482_Plate6_B7_Egr1_sg1


title: RBG18492_Plate6_D8_Egr1_sg2


title: RBG17274_Exp1_TC_D10_Gata3sg2_12d


title: RBG18481_Plate6_A7_Egr1_sg1


title: CL 1


title: CTL 1


title: RBG18480_Plate6_H6_Gfi1b_sg3

value: Treated with Gfi1b_sg3


title: EO771_Treg_ablated_rep2


title: RBG18479_Plate6_G6_Gfi1b_sg3


title: RBG18477_Plate6_E6_Gfi1b_sg3


title: RBG18478_Plate6_F6_Gfi1b_sg3


title: mC_forebrain_zebrafish

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
CASAVA v1.8.2
Adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.8 before methylation quantification with CGmaptools
Genome_build: Monodelphis domestica we used ENSEMBL Monodelphis_domestica.BROADO5.dna.toplevel.fa
Genome_build: Ornithorhynchus anatinus we used ENSEMBL Ornithorhynchus_anatinus.OANA5.dna.toplevel.fa
Genome_build: Gallus gallus we used ENSEMBL Gallus_gallus.Galgal4.dna.toplevel.fa
Genome_build: Callorhinchus milii we used calMil1 (GCA_000165045.2)
Genome_build: Lethenteron camtschaticum we used LetJap1.0 (GCA_000466285.1)
Genome_build: Apis mellifera we used ENSEMBL Apis_mellifera.GCA_000002195.1.31.dna.genome.fa
Genome_build: Octopus bimaculoides we used ENSEMBL Octopus_bimaculoides.PRJNA270931.dna.toplevel.fa
Genome_build: Branchiostoma lanceolatum we used ENSEMBL Branchiostoma_lanceolatum.BraLan2.dna.toplevel.fa
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2/CGmaptools (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).

source_name: forebrain

extract_protocol:
DNeasy Blood & Tissue kit (Qiagen)
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

tag: source

value: Mix AB/Tubingen


title: RBG18476_Plate6_D6_Gfi1b_sg3


title: RBG18484_Plate6_D7_Egr1_sg1


title: BT474m1_300nMlapatinib_300nMJQ1_48h

first: Steven

middle: P

last: Angus

address: 1044 W Walnut St

department: Pediatrics

data_processing:
Reads were aligned to the human reference genome hg19_M_rCRS using MapSplice v2.1.4; alignment profile was determined by Picard Tools v1.88.
Aligned reads were sorted and indexed using SAMtools v1.2 and translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics Utilities v1.2.
Transcript abundance estimates were determined using RSEM and upper-quartile normalized.
For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: RSEM gene-level expected read counts were imported into R version 3.2.2. and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and post-treatment conditions.  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain normalized transcript abundance estimates, organized by official gene symbol and gene ID.

source_name: BT474m1 HER2+ breast carcinoma cell line

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
4 µg total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

treatment_protocol: RPMI supplemented with 10% FBS

value: BT474m1 HER2+

value: treated with 300nM lapatinib and 300nM JQ1 for 48h

tag: library preparation kit

value: Illumina TruSeq RNA library kit v2


title: BT474m1_300nMJQ1_48h

value: treated with 300nM JQ1 for 48h


title: BT474m1_300nMlapatinib_48h

value: treated with 300nM lapatinib for 48h


title: RBG18483_Plate6_C7_Egr1_sg1

tag: tissue

value: early hematopoietic progenitor cells


title: RBG18474_Plate6_B6_Gfi1b_sg3

tag: cell type

value: Cas9 expressing, Hoxb8 expressing


title: RBG18473_Plate6_A6_Gfi1b_sg3


title: SKBR3_DMSO_48h

source_name: SKBR-3 HER2+ breast carcinoma cell line

value: SKBR-3 HER2+

value: treated with DMSO for 48h


title: RBG18472_Plate6_H5_Gfi1b_sg2

value: Treated with Gfi1b_sg2


title: SKBR3_300nMJQ1_48h


title: SKBR3_300nMlapatinib_48h


title: RBG18471_Plate6_G5_Gfi1b_sg2


title: RBG18470_Plate6_F5_Gfi1b_sg2


title: SKBR3_siFOXA1_300nM_lapatinib_24h_rep3

data_processing: For DESeq differential expression analysis comparing pre-treatment and post-treatment patient tumors: RSEM gene-level expected read counts were imported into R version 3.2.2. and were analyzed using DESeq2 v1.12.3 to detect genes that were differentially expressed between pre-treatment and post-treatment conditions.  Default DESeq2 parameters were used for the analysis, specifying sample ID in addition to pre and post treatment status to account for pairing between samples in the specification of the model design matrix.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus kit.
4 ug total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.

value: FOXA1 siRNA pool  for 48h, then treated with 300nM lapatinib for 24h


title: SKBR3_siFOXA1_300nM_lapatinib_24h_rep1


title: SKBR3_siFOXA1_300nM_lapatinib_24h_rep2


title: RBG18469_Plate6_E5_Gfi1b_sg2


title: SKBR3_siFOXA1_DMSO_24h_rep3

value: FOXA1 siRNA pool  for 48h, then treated with DMSO for 24h


title: RBG18468_Plate6_D5_Gfi1b_sg2


title: BT474m1_DMSO_48h


title: SKBR3_siFOXA1_DMSO_24h_rep1


title: RBG18466_Plate6_B5_Gfi1b_sg2


title: SKBR3_siFOXA1_DMSO_24h_rep2


title: RBG18475_Plate6_C6_Gfi1b_sg3


title: SKBR3_siNT_300nM_lapatinib_24h_rep3

value: non-targeting (NT) siRNA control pool  for 48h, then treated with 300nM lapatinib for 24h


title: RBG18464_Plate6_H4_Gfi1b_sg1

value: Treated with Gfi1b_sg1


title: RBG18463_Plate6_G4_Gfi1b_sg1

value: bone marrow


title: SKBR3_siNT_300nM_lapatinib_24h_rep2


title: SKBR3_siNT_DMSO_24h_rep3

value: non-targeting (NT) siRNA control pool  for 48h, then treated with DMSO for 24h


title: RBG18462_Plate6_F4_Gfi1b_sg1


title: RBG18465_Plate6_A5_Gfi1b_sg2


title: SKBR3_siNT_DMSO_24h_rep2


title: SKBR3_siNT_DMSO_24h_rep1


title: SKBR3_siNT_300nM_lapatinib_24h_rep1


description:
SEM_BRD4_peaks_IBET_annotated.txt.gz
ChIP seq Input for BRD4 in IBET-treated SEM cells

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19, dm3
Peak calling, normalization and annotation using Homer v4.7

source_name: Leukemia cell line (SEM)

extract_protocol:
Cells were washed with PBS and fixed in 2mM DSG for 30 minutes and 1% FA for 30 minutes. Fixed Drosophila S2 cells were added at a 1:4 ratio (Dm:Hs) to allow reference normalization. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBNext Ultra II DNA library preparation kit for Illumina

treatment_protocol: See sample table

value: IBET-151 at 1uM for 90 min

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: RBG18459_Plate6_C4_Gfi1b_sg1


title: BRD4 ChIP-seq in IBET-treated SEM cells

description:
SEM_BRD4_peaks_IBET_annotated.txt.gz
BRD4 ChIP-seq in IBET-treated SEM cells

tag: chip antibody

value: Bethyl A301-985A


title: SEM_Input_BRD4_DMSO90

description:
SEM_BRD4_peaks_IBET_annotated.txt.gz
ChIP seq Input for BRD4 in DMSO-treated SEM cells

value: DMSO for 90 min


title: SEM_BRD4_DMSO90

description:
SEM_BRD4_peaks_IBET_annotated.txt.gz
BRD4 ChIP-seq in DMSO-treated SEM cells


title: RBG18460_Plate6_D4_Gfi1b_sg1


title: RBG18458_Plate6_B4_Gfi1b_sg1


title: RBG18457_Plate6_A4_Gfi1b_sg1


title: RBG18456_Plate6_H3_Tcf3_sg3

value: Treated with Tcf3_sg3


title: SEM_Input_BRD4_MED1_Hexanediol

description:
SEM_BRD4_peaks_Hexanediol_annotated.txt.gz
SEM_MED1_peaks_Hexanediol_annotated.txt.gz
ChIP seq Input for BRD4/MED1 in hexanediol-treated SEM cells

value: Hexanediol at 1.5% for 30 min


title: RBG18455_Plate6_G3_Tcf3_sg3

value: early hematopoietic progenitor cells


title: RBG18454_Plate6_F3_Tcf3_sg3

value: Cas9 expressing, Hoxb8 expressing


title: SEM_Input_BRD4_MED1_Untreated

description:
SEM_BRD4_peaks_Hexanediol_annotated.txt.gz
SEM_MED1_peaks_Hexanediol_annotated.txt.gz
ChIP seq Input for BRD4/MED1 in untreated SEM cells

value: Untreated (control for hexanediol)


title: SEM_BRD4_Hexanediol

description:
SEM_BRD4_peaks_Hexanediol_annotated.txt.gz
BRD4 ChIP-seq in hexanediol-treated SEM cells


title: RBG18461_Plate6_E4_Gfi1b_sg1


title: RBG18452_Plate6_D3_Tcf3_sg3


title: RBG18451_Plate6_C3_Tcf3_sg3


title: RBG18453_Plate6_E3_Tcf3_sg3


title: RBG18450_Plate6_B3_Tcf3_sg3


title: RBG18449_Plate6_A3_Tcf3_sg3


title: SEM_BRD4_Untreated

description:
SEM_BRD4_peaks_Hexanediol_annotated.txt.gz
BRD4 ChIP-seq in untreated SEM cells


title: RBG18448_Plate6_H2_Tcf3_sg2

value: Treated with Tcf3_sg2


title: SEM_Input_BRD4_MED1_AT1

description:
SEM_BRD4_peaks_AT1_annotated.txt.gz
SEM_MED1_peaks_AT1_annotated.txt.gz
ChIP seq Input for BRD4/MED1 in IBET-treated SEM cells

value: AT1 at 1uM for 24h


title: SEM_BRD4_AT1

description:
SEM_BRD4_peaks_AT1_annotated.txt.gz
BRD4 ChIP-seq in AT1-treated SEM cells


title: SEM_MED1_AT1

description:
SEM_MED1_peaks_AT1_annotated.txt.gz
MED1 ChIP-seq in AT1-treated SEM cells

value: Bethyl A300-793A


title: RBG18447_Plate6_G2_Tcf3_sg2


title: SEM_Input_BRD4_MED1_DMSO24h

description:
SEM_BRD4_peaks_AT1_annotated.txt.gz
SEM_MED1_peaks_AT1_annotated.txt.gz
ChIP seq Input for BRD4/MED1 in DMSO-treated SEM cells

value: DMSO for 24h


title: RBG18446_Plate6_F2_Tcf3_sg2


title: RBG18444_Plate6_D2_Tcf3_sg2


title: SEM_BRD4_DMSO24h

description:
SEM_BRD4_peaks_AT1_annotated.txt.gz
BRD4 ChIP-seq in DMSO-treated SEM cells


title: SEM_MED1_Hexanediol

description:
SEM_MED1_peaks_Hexanediol_annotated.txt.gz
MED1 ChIP-seq in hexanediol-treated SEM cells


title: Capture-C in 24h AT1-treated SEM cells rep3

description:
3C library preparation followed by double oligonucleotide capture
Capture-C in 24h AT1-treated SEM cells
SEM_AT1_CapC_combined.gfc.gz

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: hg19
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

extract_protocol:
Cells fixed with 2% formaldehyde and lysed using dounce homogenisation
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde, quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNase. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. 5 ug DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina NextSeq (150bp paired end reads) platform.

treatment_protocol: see sample table

tag: genes analysed

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: RBG18443_Plate6_C2_Tcf3_sg2

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
TFnet_exon_counts.csv
TFnet_intron_counts.csv


title: Capture-C in 24h AT1-treated SEM cells rep2


title: RBG18442_Plate6_B2_Tcf3_sg2


title: Capture-C in 24h AT1-treated SEM cells rep1


title: RBG18467_Plate6_C5_Gfi1b_sg2

value: Treated with Gfi1b_sg2


title: SEM_MED1_DMSO24h

description:
SEM_MED1_peaks_AT1_annotated.txt.gz
MED1 ChIP-seq in DMSO-treated SEM cells


title: SEM_MED1_Untreated

description:
SEM_MED1_peaks_Hexanediol_annotated.txt.gz
MED1 ChIP-seq in untreated SEM cells


title: SKBR3_300nMlapatinib_300nMJQ1_48h

value: SKBR-3 HER2+

value: treated with 300nM lapatinib and 300nM JQ1 for 48h

value: Illumina TruSeq RNA library kit v2


title: Capture-C in DMSO-treated SEM cells (control for AT1 24h) rep2

description:
3C library preparation followed by double oligonucleotide capture
Capture-C in DMSO-treated SEM cells (control for AT1 24h)
SEM_AT1_CapC_combined.gfc.gz


title: Capture-C in DMSO-treated SEM cells (control for AT1 24h) rep3


title: RBG18440_Plate6_H1_Tcf3_sg1

value: bone marrow

value: Treated with Tcf3_sg1


title: RBG18441_Plate6_A2_Tcf3_sg2


title: RBG18439_Plate6_G1_Tcf3_sg1


title: Capture-C in DMSO-treated SEM cells (control for AT1 24h) rep1


title: RBG18438_Plate6_F1_Tcf3_sg1


title: RBG18436_Plate6_D1_Tcf3_sg1


title: AW_N2_D195N_Rep2

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description: Chromatin-associated RNA isolated from WT-BAC VhsD195N infected HFF at 8h p.i.

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: gene read counts

source_name: Chromatin-associated RNA, WT-BAC VhsD195N, 8h p.i., Rep 2

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells around passage 15 were infected with HSV-1 strain 17, its vhs-null mutant, WT-BAC or WT-BAC VhsD195N at an MOI of 10

extract_protocol:
Subcellular RNA fractions were prepared combinig the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina)  with Ribo-Zero Human/Mouse/Rat.
NextSeq 500 sequencing 75bp single-end reads

treatment_protocol: Cells were infected for 1hr min using an MOI of 10.  After infection (time point 1h), cell culture media was replaced with fresh media. Cells were harvested prior to infection or at 8h p.i. Chromatin-associated RNA was prepared and subjected to standard RNA-seq including rRNA deplation

value: human foreskin fibroblasts

tag: time post infection

value: WT-BAC VhsD195N 8h p.i.

tag: replicate

value: Replicate 2

tag: molecule subtype

value: Chromatin-associated RNA


title: RBG18437_Plate6_E1_Tcf3_sg1

value: early hematopoietic progenitor cells

tag: genotype

value: Cas9 expressing, Hoxb8 expressing


title: AW_N1_D195N_Rep1

source_name: Chromatin-associated RNA, WT-BAC VhsD195N, 8h p.i., Rep 1

value: Replicate 1


title: RBG18445_Plate6_E2_Tcf3_sg2

value: Treated with Tcf3_sg2


title: RBG18435_Plate6_C1_Tcf3_sg1


title: RBG18434_Plate6_B1_Tcf3_sg1


title: AW_B1_WTBAC_Rep1

description: Chromatin-associated RNA isolated from WT-BAC infected HFF at 8h p.i.

source_name: Chromatin-associated RNA, WT-BAC, 8h p.i., Rep 1

value: WT BAC 8h p.i.


title: AW_V2_dVHS_Rep2

description: Chromatin-associated RNA isolated from delta-Vhs infected HFF at 8h p.i.

source_name: Chromatin-associated RNA, delta-Vhs, 8h p.i., Rep 2

value: delta-Vhs 8h p.i.


title: RBG18433_Plate6_A1_Tcf3_sg1

source_name: Hoxb8-FL cell line


title: RBG18432_Plate5_H11_R26

value: Treated with controlR26


title: AW_V1_dVHS_Rep1

source_name: Chromatin-associated RNA, delta-Vhs, 8h p.i., Rep 1


title: RBG18430_Plate5_F11_R26


title: AW_M2_Mock_Rep2

description: Chromatin-associated RNA isolated from mock infected HFF

source_name: Chromatin-associated RNA, Mock, Rep 2

value: Mock


title: AW_W2_WT_Rep2

description: Chromatin-associated RNA isolated from HSV-1 strain 17 infected HFF at 8h p.i.

source_name: Chromatin-associated RNA, HSV-1 strain 17 8h p.i., Rep 2

value: HSV-1 strain 17 8h p.i.


title: AW_M1_Mock_Rep1

source_name: Chromatin-associated RNA, Mock, Rep 1


title: RBG18431_Plate5_G11_R26


title: RBG18429_Plate5_E11_R26


title: RBG18428_Plate5_D11_R26


title: Nascent_RNA_Hexanediol_replicate_2

description:
Nascent RNA
SEM_RNA_Hexanediol_hg19_featuresCounted.txt.gz
SEM_RNA_Hexanediol_hg19_contrast_cpm.txt.gz

data_processing:
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Genome_build: hg19

source_name: Nascent RNA-seq in 30 min Hexanediol-treated SEM cells

extract_protocol:
108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
DNA libraries were prepared using the NEB Next Ultra Directional RNA library preparation kit for Illumina (E7765).

value: Leukemia cell line (SEM)

value: Hexanediol at 1.5% for 30 min

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: RBG18427_Plate5_C11_R26

value: bone marrow


title: Nascent_RNA_Hexanediol_replicate_1


title: AW_B2_WTBAC_Rep2

source_name: Chromatin-associated RNA, WT-BAC, 8h p.i., Rep 2

value: human foreskin fibroblasts


title: Nascent_RNA_Untreated_replicate_2

source_name: Nascent RNA-seq in SEM cells (control for Hexanediol)

value: Untreated


title: RBG18426_Plate5_B11_R26


title: Nascent_RNA_Hexanediol_replicate_3


title: RBG18424_Plate5_H10_emptyV

value: Treated with controlNT


title: RBG18423_Plate5_G10_emptyV


title: RBG18422_Plate5_F10_emptyV


title: Nascent_RNA_Untreated_replicate_3


title: RBG18421_Plate5_E10_emptyV


title: Nascent_RNA_IBET24h_replicate_1

description:
Nascent RNA
SEM_RNA_IBET24h_hg19_featuresCounted.txt.gz
SEM_RNA_IBET24h_hg19_contrast_cpm.txt.gz

source_name: Nascent RNA-seq in 24h IBET-treated SEM cells

value: IBET-151 at 1uM for 24h


title: AW_W1_WT_Rep1

source_name: Chromatin-associated RNA, HSV-1 strain 17 8h p.i., Rep 1

value: Chromatin-associated RNA


title: Nascent_RNA_IBET24h_replicate_3


title: RBG18420_Plate5_D10_emptyV

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: Nascent_RNA_DMSO24h_replicate_3

source_name: Nascent RNA-seq in DMSO-treated SEM cells (control for IBET24h)

value: DMSO for 24h


title: RBG18419_Plate5_C10_emptyV


title: RBG18418_Plate5_B10_emptyV


title: Nascent_RNA_IBET24h_replicate_2


title: RBG18425_Plate5_A11_R26


title: Nascent_RNA_DMSO24h_replicate_1


title: RBG18416_Plate5_H9_Nfe2_sg3

value: Treated with Nfe2_sg3


title: Nascent_RNA_DMSO24h_replicate_2


title: RBG18417_Plate5_A10_emptyV


title: Nascent_RNA_IBET90_replicate_3

description:
Nascent RNA
SEM_RNA_IBET90_hg19_featuresCounted.txt.gz
SEM_RNA_IBET90_hg19_contrast_cpm.txt.gz

source_name: Nascent RNA-seq in 90 min IBET-treated SEM cells

value: IBET-151 at 1uM for 90 min


title: RBG18415_Plate5_G9_Nfe2_sg3


title: Nascent_RNA_IBET90_replicate_1


title: Nascent_RNA_Untreated_replicate_1


title: Nascent_RNA_IBET90_replicate_2


title: RBG18414_Plate5_F9_Nfe2_sg3


title: RBG18413_Plate5_E9_Nfe2_sg3


title: Nascent_RNA_DMSO90_replicate_3

source_name: Nascent RNA-seq in DMSO-treated SEM cells (control for IBET90)

value: DMSO for 90 min


title: RBG18412_Plate5_D9_Nfe2_sg3


title: RBG18410_Plate5_B9_Nfe2_sg3


title: Nascent_RNA_DMSO90_replicate_1


title: Nascent_RNA_DMSO90_replicate_2


title: RBG18411_Plate5_C9_Nfe2_sg3


title: SEM_Input_BRD4_IBET

source_name: ChIP seq Input for BRD4 in IBET-treated SEM cells

value: input


title: RBG18409_Plate5_A9_Nfe2_sg3


title: RBG18407_Plate5_G8_Nfe2_sg2

value: Treated with Nfe2_sg2


title: RBG18406_Plate5_F8_Nfe2_sg2


title: RBG18408_Plate5_H8_Nfe2_sg2


title: SEM_RAD21

source_name: RAD21 ChIP-seq in SEM cells

value: Leukemia cell line (SEM)


title: Capture-C_Hexanediol_replicate_3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
SEM_Hexanediol_CapC_combined.gfc.gz

data_processing:
Library strategy: Capture-C-Seq
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: hg19
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Capture-C in Hexanediol-treated SEM cells

value: Hexanediol at 1.5% for 30 min

value: ARID1B, ASH2L, BAZ2B, BCL11A, BCL2, CDK6, ELL2, EP300, EZH2, FLT3, FOS, FUT10, GADD45A, JARID1A, JMJD1C, JUN, LMO4, MBNL1, MED13, MSL3, MYC, OGT, SMYD2, SPI1, SUPT3H, SUZ12, TAPT1, TET2


title: RBG18405_Plate5_E8_Nfe2_sg2

value: bone marrow


title: RBG18404_Plate5_D8_Nfe2_sg2


title: RBG18403_Plate5_C8_Nfe2_sg2


title: Capture-C_Hexanediol_replicate_2


title: RBG18402_Plate5_B8_Nfe2_sg2


title: Capture-C_Hexanediol_replicate_1


title: RBG18400_Plate5_H7_Nfe2_sg1

value: Treated with Nfe2_sg1


title: RBG18399_Plate5_G7_Nfe2_sg1


title: Capture-C_Untreated_replicate_1

source_name: Capture-C in SEM cells (control for Hexanediol)

value: Untreated


title: RBG18401_Plate5_A8_Nfe2_sg2

source_name: Hoxb8-FL cell line


title: Capture-C_JQ1_IBET90_replicate_3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
SEM_JQ1_CapC_combined.gfc.gz

source_name: Capture-C in 90 min JQ1-treated SEM cells

value: JQ1 at 1uM for 90 min


title: RBG18397_Plate5_E7_Nfe2_sg1


title: RBG18396_Plate5_D7_Nfe2_sg1


title: SEM_BRD4_IBET

source_name: BRD4 ChIP-seq in IBET-treated SEM cells

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: Capture-C_Untreated_replicate_3


title: RBG18398_Plate5_F7_Nfe2_sg1


title: Capture-C_JQ1_90_replicate_1


title: Capture-C_JQ1_IBET90_replicate_2


title: Capture-C_DMSO90_(JQ1)_replicate_3

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
SEM_IBET90_CapC_combined.gfc.gz

source_name: Capture-C in DMSO-treated SEM cells (control for JQ1)


title: SEM_Input_RAD21

source_name: ChIP seq Input for RAD21 in SEM cells


title: RBG18394_Plate5_B7_Nfe2_sg1


title: RBG18395_Plate5_C7_Nfe2_sg1


title: RBG18393_Plate5_A7_Nfe2_sg1


title: Capture-C_IBET24h_replicate_2

description:
Next generation Capture-C products
3C library preparation followed by double oligonucleotide capture
SEM_IBET24h_CapC_combined.gfc.gz

source_name: Capture-C in 24h IBET-treated SEM cells

value: IBET-151 at 1uM for 24h


title: Capture-C_DMSO90_(JQ1)_replicate_1


title: Capture-C_IBET24h_replicate_3


title: Capture-C_DMSO90_(JQ1)_replicate_2


title: Capture-C_Untreated_replicate_2


title: RBG18392_Plate5_H6_Gata2_sg3

value: early hematopoietic progenitor cells

value: Treated with Gata2_sg3


title: RBG18391_Plate5_G6_Gata2_sg3

value: Cas9 expressing, Hoxb8 expressing


title: Capture-C_IBET24h_replicate_1


title: Capture-C_DMSO24h_replicate_3

source_name: Capture-C in DMSO-treated SEM cells (control for IBET24h)

value: DMSO for 24h


title: RBG18390_Plate5_F6_Gata2_sg3


title: Capture-C_DMSO24h_replicate_2


title: RBG18389_Plate5_E6_Gata2_sg3


title: Capture-C_DMSO24h_replicate_1


title: RBG18387_Plate5_C6_Gata2_sg3


title: RBG18388_Plate5_D6_Gata2_sg3


title: Capture-C_IBET90_replicate_2

source_name: Capture-C in 90 min IBET-treated SEM cells

value: IBET-151 at 1uM for 90 min

value: ADAM10, AKT3, ARID1B, ASAP2, ASH2L, BAZ2B, BCL11A, BCL2, BRD4, BTK, CD109, CDK6, EGLN1, ELL2, EP300, ERG, EZH2, FLI1, FLT3, FOS, FOXO3, FUT10, GADD45A, GNAI1, GNAQ, HIVEP2, HMGA2, INPP5B, INTS3, JARID1A, JMJD1C, JUN, LIPC, LMO4, MBNL1, MED13, MEIS1, MSL3, MTCH1, MYC, OGT, PARP1, PBX3, PTMA, PXDN, RAD18, RUNX1, SKI, SMYD2, SPI1, STIM2, SUPT3H, SUZ12, TAPT1, TEAD4, TET2, TGFBR2, TRAM2, VCAN, ZNRF1


title: Capture-C_IBET90_replicate_3


title: Capture-C_DMSO90_replicate_3

source_name: Capture-C in DMSO-treated SEM cells (control for IBET90)

value: DMSO for 90 min


title: RBG18385_Plate5_A6_Gata2_sg3


title: Capture-C_IBET90_replicate_1


title: RBG18384_Plate5_H5_Gata2_sg2

value: Treated with Gata2_sg2


title: Capture-C_DMSO90_replicate_1

value: Leukemia cell line (SEM)


title: RBG18382_Plate5_F5_Gata2_sg2


title: Capture-C_DMSO90_replicate_2


title: RBG18383_Plate5_G5_Gata2_sg2


title: H3K4me3 ChIPmentation mock Rep 2

description: H3K4me3 ChIPmentation from mock infected HFF

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Enriched H3K4me3 regions were identified using F-Seq v1.85
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed files with identified H3K4me3 regions

source_name: human FETAL foreskin fibroblasts (HFFF)s

growth_protocol: Human fetal foreskin fibroblasts were cultured in DMEM supplements with 10% FBS, 1% MEM NEAA  and P/S. Cells at passage 14 were infected with HSV-1 strain 17 at an MOI of 10.

extract_protocol:
Samples were processed according to the ChIPmentation protocol (ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors, Christian Schmidl et al, Nature Methods 2015)
See Christian Schmidl et al, Nature Methods 2015
NextSeq 500 sequencing 36bp paired-end reads

treatment_protocol: Cells were infected with wildtype HSV-1 for 15min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Samples were harvested at the indicated time points and all samples were processed according to the ChIPmentation protocol.

value: Mock

value: Replicate 2


title: RBG18379_Plate5_C5_Gata2_sg2

description:
RNA-Seq from Hoxb8-FL cells treated as indicated
TFnet_exon_counts.csv
TFnet_intron_counts.csv

value: bone marrow


title: H3K4me3 ChIPmentation 8hpi Rep 1

description: H3K4me3 ChIPmentation from HSV-1 infected HFF at 8h p.i.

value: human FETAL foreskin fibroblasts (HFFF)s

value: HSV-1 8h p.i.

value: Replicate 1


title: RBG18380_Plate5_D5_Gata2_sg2


title: H3K4me3 ChIPmentation mock Rep 1


title: 4sU-RNA - 7-8 hpi Rep 2

description:
newly transcribed RNA (4sU-RNA)
Purified from total RNA using 4sU-tagging

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 13 were infected at 60% confluency 24h after the last split.

extract_protocol:
Total RNA was prepared using Trizol. Newly transcribed RNA was purified as described in Rädle et al., JoVE 2013.
TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (only for total RNA). No rRNA depletion was performed for the 4sU-RNA samples!

treatment_protocol: Cells were infected for 15 min with HSV-1 strain 17 at an MOI of 10 followed by PBS wash and media replacement. 500µM 4-thiouridine was added to the cell culture at the indicated time points.

value: human foreskin fibroblasts

value: 60 min 500 uM 4sU at 7-8 h p.i.

tag: infection with

value: vhs-null mutant of herpes simplex virus 1, strain 17


title: RBG18377_Plate5_A5_Gata2_sg2

value: early hematopoietic progenitor cells


title: 4sU-RNA - 6-7 hpi Rep 2

value: 60 min 500 uM 4sU at 6-7 h p.i.


title: RBG18376_Plate5_H4_Gata2_sg1

value: Cas9 expressing, Hoxb8 expressing

value: Treated with Gata2_sg1


title: 4sU-RNA - 5-6 hpi Rep 2

value: 60 min 500 uM 4sU at 5-6 h p.i.


title: RBG18386_Plate5_B6_Gata2_sg3

value: Treated with Gata2_sg3


title: RBG18375_Plate5_G4_Gata2_sg1


title: RBG18374_Plate5_F4_Gata2_sg1


title: 4sU-RNA - 4-5 hpi Rep 2

value: 60 min 500 uM 4sU at 4-5 h p.i.


title: 4sU-RNA - 2-3 hpi Rep 2

value: 60 min 500 uM 4sU at 2-3 h p.i.


title: RBG18373_Plate5_E4_Gata2_sg1


title: RBG18381_Plate5_E5_Gata2_sg2

value: Treated with Gata2_sg2


title: RBG18371_Plate5_C4_Gata2_sg1


title: H3K4me3 ChIPmentation 8hpi Rep 2

value: Replicate 2


title: 4sU-RNA - 1-2 hpi Rep 2

value: 60 min 500 uM 4sU at 1-2 h p.i.


title: 4sU-RNA - 0-1 hpi Rep 2

value: 60 min 500 uM 4sU at 0-1 h p.i.


title: RBG18370_Plate5_B4_Gata2_sg1

value: bone marrow


title: RBG18372_Plate5_D4_Gata2_sg1


title: RBG18368_Plate5_H3_Gata3_sg3

value: Treated with Gata3_sg3


title: 4sU-RNA - 3-4 hpi Rep 2

value: human foreskin fibroblasts

value: 60 min 500 uM 4sU at 3-4 h p.i.


title: RBG18369_Plate5_A4_Gata2_sg1


title: Total RNA - 4hpi Rep 2

description:
total RNA
Total RNA prepared using Trizol

source_name: Total RNA

value: 4 h p.i.

value: vhs-null mutant of herpes simplex virus 1, strain 17


title: Total RNA - 8hpi Rep 2

value: 8 h p.i.


title: RBG18366_Plate5_F3_Gata3_sg3

value: early hematopoietic progenitor cells

value: Cas9 expressing, Hoxb8 expressing


title: RBG18378_Plate5_B5_Gata2_sg2


title: Total RNA - mock Rep 2

value: mock


title: Total RNA - 2hpi Rep 2

value: 2 h p.i.


title: RBG18365_Plate5_E3_Gata3_sg3


title: 4sU-RNA - mock Rep 2

value: 60 min 500 uM 4sU prior to infection


title: RBG18364_Plate5_D3_Gata3_sg3


title: 4sU-RNA - 7-8 hpi Rep 1

value: 60 min 500 uM 4sU at 7-8 h p.i.


title: 4sU-RNA - 6-7 hpi Rep 1

value: 60 min 500 uM 4sU at 6-7 h p.i.


title: RBG18363_Plate5_C3_Gata3_sg3


title: RBG18362_Plate5_B3_Gata3_sg3


title: 4sU-RNA - 5-6 hpi Rep 1

value: 60 min 500 uM 4sU at 5-6 h p.i.


title: RBG18361_Plate5_A3_Gata3_sg3


title: 4sU-RNA - 3-4 hpi Rep 1


title: 4sU-RNA - 4-5 hpi Rep 1

value: 60 min 500 uM 4sU at 4-5 h p.i.


title: Total RNA - 6hpi Rep 2

value: 6 h p.i.


title: RBG18359_Plate5_G2_Gata3_sg2

value: bone marrow

value: Treated with Gata3_sg2


title: RBG18358_Plate5_F2_Gata3_sg2


title: RBG18367_Plate5_G3_Gata3_sg3

value: Treated with Gata3_sg3


title: RBG18360_Plate5_H2_Gata3_sg2