title: Prdm16s-Bulk_3

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were mapped to mm10 using STAR, version 2.5.3a, with settings: “alignSJoverhangMin” 8; “alignSJDBoverhangMin” 1; “outFilterMismatchNmax” 999; “alignIntronMin” 20; “alignIntronMax” 1000000; “alignMatesGapMax” 1000000; “twopassMode” Basic; “sjdbOverhang” 100.
FPKM and differential gene expression were calculated with DESeq2 (version 1.18.1) and Ensembl 84 as the reference.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (TSV) file containing a matrix of FPKM values for all samples

source_name: Prdm16s GFP+ bone marrow cells

extract_protocol:
Cell were sorted into Trizol and RNA were extracted using RNeasy MiniElute Cleanup kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
cDNA libraries were generated using the Smart-seq2 protocol as described previously. Sequencing libraries were generated from 250 pg of amplified cDNA using Nextera XT kit according to the manufacturer's instructions. Barcoded libraries were purified and sequenced on a HiSeq2500 platform.

treatment_protocol: L-MEP and GFP+ leukemic cells were isolated from leukemic recipient mice. WT MEPs and whole bone marrow cells were isolated from wild-type mice.

value: Prdm16s GFP+ bone marrow cells


title: Ctrl-Bulk_3

status: Public on Mar 01 2019

type: SRA

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Ctrl bone marrow cells

tag: strain

tag: genotype

value: wild type

tag: cell type

value: bone marrow cells


title: Input_Ctrl-MEP_3

library_source: genomic

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Enhancer and super-enhancer prediction was performed using HOMER (version 4.10)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

molecule: genomic DNA

source_name: Ctrl MEP cells

growth_protocol: We transduced wild-type murine MEP cells with retroviral vectors encoding Prdm16s and transplanted them into syngeneic recipient mice. L-MEPs were sorted in mice the developed leukemia for library preparation.

extract_protocol:
10,000 L-MEP and normal MEP were sorted and treated with Mnase, histone-DNA complexes were isolated with antibody
ChIP DNA was purified for end repair, adapter ligation, and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England BioLabs, Ipswich, MA)

tag: chip antibody

value: megakaryocyte-erythroid progenitor (MEP) cells


title: Input_L-MEP_3

source_name: Prdm16s Leukemic-MEP cells

value: leukemic megakaryocyte-erythroid progenitor (MEP) cells


title: Prdm16s-Bulk_1


title: Ctrl-Bulk_2


title: Prdm16s-Bulk_2


title: Ctrl-Bulk_1


title: L-MEP_2


title: Ctrl-MEP_3


title: L-MEP_1


title: Ctrl-MEP_2


title: Ctrl-MEP_1


title: H3K4me3_Ctrl-MEP_3

value: H3K4me3 (#04-745, Millipore, Billerica, MA)


title: Ctrl_3

data_processing:
Library strategy: CRISPR drop-out screen
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Analysis was performed using MAGeCK (version 0.5.6)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (TSV) file containing counts of each sgRNA (row) present in a sample (column)

extract_protocol:
Cells were selected with blasticidin and puromycin for 7 days and genomic DNA were extracted.
Genomic DNA were amplified. Amplicons were then purified and barcoded using Illumina Nextera index primers and sequenced on an Illumina HiSeq 2500.

treatment_protocol: 770 genes were selected from the RNA-seq gene list upregulated in Prdm16s expressing cells. 4-10 sgRNA per gene against these 770 genes (total 3918 sgRNA) were designed and synthesized. L-MEPs were transduced with the 770 gene gRNA lentiviral library, sorted for BFP+ cells that were infected, and then transduced with a lentiviral Cas9 vector.


title: Ctrl_4


title: H3K4me3_Ctrl-MEP_2


title: Ctrl_2


title: Ctrl_1


title: Input_Ctrl-MEP_1


title: L-MEP_3


title: Selection_2

source_name: Prdm16s Leukemic-MEP cells after selection


title: Input_Ctrl-MEP_2


title: Selection_1


title: Normal lung tissue from mouse 100104

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description:
Normal mouse lung tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Lung.100104

data_processing:
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
TPM Calculations: TPM values were calculated using a custom in-house script from the raw read counts and transcript lengths provided by Salmon.  TPM values are raw and have not been log2 transformed or further processed in any way.
Genome_build: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

source_name: Lung

growth_protocol: PDX cells were grown in various organs in NSG mice

extract_protocol:
RNA was harvested from tissue/cell samples using the Qiagen Rneasy Mini Kit.
KAPA Stranded mRNA-Seq Kit was used for library preparation.

treatment_protocol: All samples are untreated and all tissues flash frozen during extraction

tag: histologic subtype

value: Normal mouse lung

tag: intrinsic subtype

tag: model type

value: mus musculus

tag: pdx model

value: normal


title: Normal lung tissue from mouse 100105

description:
Normal mouse lung tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Lung.100105


title: Dex_Pair9_Cell2

city: Cambridge

first: Hojun

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
pair name:
6G & 6H
processed data file:
daughter_Dex.txt
dex_6H_TAGGCATG-GCGTAAGA-s_8

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 39
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

molecule: polyA RNA

source_name: burst forming unit-erythroid

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
daughter cell isolation protocol : Single BFU-E cells were FACS-deposited into individual wells of a 96-well plate containing PCM either with or without 100 nM dexamethasone.  Plates were briefly spun down and visualized by light microscopy using a Zeiss Primovert microscope to confirm the wells with only a single cell. Those wells were further assessed 16 hours later to identify the cells that completed a single cell division. Cells from wells that contained a single pair of daughter cells were removed from the 96-well plate by mouth pipetting, using hand-drawn glass capillary pipettes (Drummond Scientific) and a Nikon SMZ 1500 microscope. Both daughter cells were deposited in a 30 uL drop of 2% FBS (Gibco) in PBS and the two cells were manually separated by mouth pipetting.  Each individual daughter was then mouth pipetted into SmartSeq2 lysis buffer to perform single cell transcriptome profiling with single cell RNA sequencing.
Single cell transcriptome library preparation.  Each individual daughter was then mouth pipetted into SmartSeq2 lysis buffer to perform single cell transcriptome profiling with single cell RNA sequencing.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

value: burst forming unit-erythroid

tag: time in culture

value: 16 hours in culture giving rise to one single pair of daughter cells

tag: treatment

value: 100 nM Dexamethasone


title: Dex_Pair13_Cell1

description:
pair name:
7G & 7H
processed data file:
daughter_Dex.txt
dex_7G_CTCTCTAC-CTAAGCCT-s_8


title: Dex_Pair10_Cell1

description:
pair name:
7A & 7B
processed data file:
daughter_Dex.txt
dex_7A_CTCTCTAC-CTCTCTAT-s_8


title: Dex_Pair12_Cell2

description:
pair name:
7E & 7F
processed data file:
daughter_Dex.txt
dex_7F_CTCTCTAC-AAGGAGTA-s_8


title: Dex_Pair11_Cell2

description:
pair name:
7C & 7D
processed data file:
daughter_Dex.txt
dex_7D_CTCTCTAC-GTAAGGAG-s_8


title: Dex_Pair12_Cell1

description:
pair name:
7E & 7F
processed data file:
daughter_Dex.txt
dex_7E_CTCTCTAC-ACTGCATA-s_8


title: Dex_Pair10_Cell2

description:
pair name:
7A & 7B
processed data file:
daughter_Dex.txt
dex_7B_CTCTCTAC-TATCCTCT-s_8


title: Dex_Pair9_Cell1

description:
pair name:
6G & 6H
processed data file:
daughter_Dex.txt
dex_6G_TAGGCATG-CTAAGCCT-s_8


title: Dex_Pair13_Cell2

description:
pair name:
7G & 7H
processed data file:
daughter_Dex.txt
dex_7H_CTCTCTAC-GCGTAAGA-s_8


title: Normal lung tissue from mouse 100103

description:
Normal mouse lung tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Lung.100103


title: Dex_Pair8_Cell2

description:
pair name:
4G & 4H
processed data file:
daughter_Dex.txt
dex_4H_TCCTGAGC-GCGTAAGA-s_8


title: Normal brain tissue from mouse 100105

description:
Normal mouse brain tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Brain.100105

source_name: Brain

value: Normal mouse brain


title: Dex_Pair7_Cell2

description:
pair name:
4E & 4F
processed data file:
daughter_Dex.txt
dex_4F_TCCTGAGC-AAGGAGTA-s_8


title: Normal liver tissue from mouse 100103

description:
Normal mouse liver tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Liver.100103

source_name: Liver

value: Normal mouse liver


title: Dex_Pair6_Cell2

description:
pair name:
4C & 4D
processed data file:
daughter_Dex.txt
dex_4D_TCCTGAGC-GTAAGGAG-s_8


title: Dex_Pair6_Cell1

description:
pair name:
4C & 4D
processed data file:
daughter_Dex.txt
dex_4C_TCCTGAGC-AGAGTAGA-s_8


title: Normal brain tissue from mouse 100104

description:
Normal mouse brain tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Brain.100104


title: Dex_Pair5_Cell2

description:
pair name:
4A & 4B
processed data file:
daughter_Dex.txt
dex_4B_TCCTGAGC-TATCCTCT-s_8


title: Normal liver tissue from mouse 100105

description:
Normal mouse liver tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Liver.100105


title: Dex_Pair11_Cell1

description:
pair name:
7C & 7D
processed data file:
daughter_Dex.txt
dex_7C_CTCTCTAC-AGAGTAGA-s_8


title: Dex_Pair7_Cell1

description:
pair name:
4E & 4F
processed data file:
daughter_Dex.txt
dex_4E_TCCTGAGC-ACTGCATA-s_8


title: Dex_Pair8_Cell1

description:
pair name:
4G & 4H
processed data file:
daughter_Dex.txt
dex_4G_TCCTGAGC-CTAAGCCT-s_8


title: Normal brain tissue from mouse 100103

description:
Normal mouse brain tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Brain.100103


title: Normal liver tissue from mouse 100104

description:
Normal mouse liver tissue.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
Normal.Mouse.Liver.100104


title: Dex_Pair5_Cell1

description:
pair name:
4A & 4B
processed data file:
daughter_Dex.txt
dex_4A_TCCTGAGC-CTCTCTAT-s_8


title: Dex_Pair4_Cell2

description:
pair name:
3G & 3H
processed data file:
daughter_Dex.txt
dex_3H_AGGCAGAA-GCGTAAGA-s_8


title: Dex_Pair4_Cell1

description:
pair name:
3G & 3H
processed data file:
daughter_Dex.txt
dex_3G_AGGCAGAA-CTAAGCCT-s_8


title: Dex_Pair3_Cell2

description:
pair name:
3E & 3F
processed data file:
daughter_Dex.txt
dex_3F_AGGCAGAA-AAGGAGTA-s_8


title: Dex_Pair2_Cell2

description:
pair name:
3C & 3D
processed data file:
daughter_Dex.txt
dex_3D_AGGCAGAA-GTAAGGAG-s_8


title: Dex_Pair3_Cell1

description:
pair name:
3E & 3F
processed data file:
daughter_Dex.txt
dex_3E_AGGCAGAA-ACTGCATA-s_8


title: NoDex_Pair13_Cell2

description:
pair name:
6A & 6B
processed data file:
daughter_No_Dex.txt
noDex_6B_TAGGCATG-TATCCTCT-s_8

value: No


title: NoDex_Pair7_Cell2

description:
pair name:
2E & 2F
processed data file:
daughter_No_Dex.txt
noDex_2F_CGTACTAG-AAGGAGTA-s_8


title: NoDex_Pair10_Cell2

description:
pair name:
5C & 5D
processed data file:
daughter_No_Dex.txt
noDex_5D_GGACTCCT-GTAAGGAG-s_8


title: NoDex_Pair8_Cell1

description:
pair name:
2G & 2H
processed data file:
daughter_No_Dex.txt
noDex_2G_CGTACTAG-CTAAGCCT-s_8


title: Dex_Pair1_Cell2

description:
pair name:
3A & 3B
processed data file:
daughter_Dex.txt
dex_3B_AGGCAGAA-TATCCTCT-s_8


title: NoDex_Pair11_Cell1

description:
pair name:
5E & 5F
processed data file:
daughter_No_Dex.txt
noDex_5E_GGACTCCT-ACTGCATA-s_8


title: NoDex_Pair12_Cell1

description:
pair name:
5G & 5H
processed data file:
daughter_No_Dex.txt
noDex_5G_GGACTCCT-CTAAGCCT-s_8


title: NoDex_Pair9_Cell2

description:
pair name:
5A & 5B
processed data file:
daughter_No_Dex.txt
noDex_5B_GGACTCCT-TATCCTCT-s_8


title: NoDex_Pair12_Cell2

description:
pair name:
5G & 5H
processed data file:
daughter_No_Dex.txt
noDex_5H_GGACTCCT-GCGTAAGA-s_8


title: NoDex_Pair8_Cell2

description:
pair name:
2G & 2H
processed data file:
daughter_No_Dex.txt
noDex_2H_CGTACTAG-GCGTAAGA-s_8


title: NoDex_Pair9_Cell1

description:
pair name:
5A & 5B
processed data file:
daughter_No_Dex.txt
noDex_5A_GGACTCCT-CTCTCTAT-s_8


title: NoDex_Pair10_Cell1

description:
pair name:
5C & 5D
processed data file:
daughter_No_Dex.txt
noDex_5C_GGACTCCT-AGAGTAGA-s_8


title: NoDex_Pair4_Cell1

description:
pair name:
1G & 1H
processed data file:
daughter_No_Dex.txt
noDex_1G_TAAGGCGA-CTAAGCCT-s_8


title: NoDex_Pair4_Cell2

description:
pair name:
1G & 1H
processed data file:
daughter_No_Dex.txt
noDex_1H_TAAGGCGA-GCGTAAGA-s_8


title: NoDex_Pair5_Cell2

description:
pair name:
2A & 2B
processed data file:
daughter_No_Dex.txt
noDex_2B_CGTACTAG-TATCCTCT-s_8


title: NoDex_Pair11_Cell2

description:
pair name:
5E & 5F
processed data file:
daughter_No_Dex.txt
noDex_5F_GGACTCCT-AAGGAGTA-s_8


title: NoDex_Pair13_Cell1

description:
pair name:
6A & 6B
processed data file:
daughter_No_Dex.txt
noDex_6A_TAGGCATG-CTCTCTAT-s_8


title: NoDex_Pair3_Cell1

description:
pair name:
1E & 1F
processed data file:
daughter_No_Dex.txt
noDex_1E_TAAGGCGA-ACTGCATA-s_8


title: NoDex_Pair6_Cell2

description:
pair name:
2C & 2D
processed data file:
daughter_No_Dex.txt
noDex_2D_CGTACTAG-GTAAGGAG-s_8


title: NoDex_Pair2_Cell1

description:
pair name:
1C & 1D
processed data file:
daughter_No_Dex.txt
noDex_1C_TAAGGCGA-AGAGTAGA-s_8


title: NoDex_Pair6_Cell1

description:
pair name:
2C & 2D
processed data file:
daughter_No_Dex.txt
noDex_2C_CGTACTAG-AGAGTAGA-s_8


title: NoDex_Pair2_Cell2

description:
pair name:
1C & 1D
processed data file:
daughter_No_Dex.txt
noDex_1D_TAAGGCGA-GTAAGGAG-s_8


title: NoDex_Pair7_Cell1

description:
pair name:
2E & 2F
processed data file:
daughter_No_Dex.txt
noDex_2E_CGTACTAG-ACTGCATA-s_8


title: NoDex_Pair3_Cell2

description:
pair name:
1E & 1F
processed data file:
daughter_No_Dex.txt
noDex_1F_TAAGGCGA-AAGGAGTA-s_8


title: NoDex_Pair5_Cell1

description:
pair name:
2A & 2B
processed data file:
daughter_No_Dex.txt
noDex_2A_CGTACTAG-CTCTCTAT-s_8


title: Dex_Pair2_Cell1

description:
pair name:
3C & 3D
processed data file:
daughter_Dex.txt
dex_3C_AGGCAGAA-AGAGTAGA-s_8


title: NoDex_Pair1_Cell2

description:
pair name:
1A & 1B
processed data file:
daughter_No_Dex.txt
noDex_1B_TAAGGCGA-TATCCTCT-s_8


title: Dex_Pair1_Cell1

description:
pair name:
3A & 3B
processed data file:
daughter_Dex.txt
dex_3A_AGGCAGAA-CTCTCTAT-s_8


title: NoDex_Pair1_Cell1

description:
pair name:
1A & 1B
processed data file:
daughter_No_Dex.txt
noDex_1A_TAAGGCGA-CTCTCTAT-s_8


title: BFUEs_Day3_plusDex_96

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
cell culture protocol: BFU-E cell culture. FACS-isolated BFU-E enriched cells were cultured for the denoted number of days in progenitor culture media (PCM) consisting of serum free expansion media (SFEM2, Stem Cell Technologies) supplemented with 100 ng/mL murine SCF (Peprotech), 40 ng/mL murine insulin-like growth factor 1 (Peprotech), 2 U/mL human erythropoietin (Amgen), 1% penicillin/streptomycin (Gibco), and for indicated cultures 100 nM Dexamethasone (Sigma).
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

value: BFUE

value: erythroid progenitor media

value: 72 hrs


title: BFUEs_Day3_plusDex_95


title: BFUEs_Day3_plusDex_86


title: BFUEs_Day3_plusDex_93


title: BFUEs_Day3_plusDex_79


title: BFUEs_Day3_plusDex_80


title: BFUEs_Day3_plusDex_88


title: BFUEs_Day3_plusDex_82


title: BFUEs_Day3_plusDex_91


title: BFUEs_Day3_plusDex_85


title: BFUEs_Day3_plusDex_77


title: BFUEs_Day3_plusDex_84


title: BFUEs_Day3_plusDex_92


title: BFUEs_Day3_plusDex_87


title: BFUEs_Day3_plusDex_90


title: BFUEs_Day3_plusDex_78


title: BFUEs_Day3_plusDex_83


title: BFUEs_Day3_plusDex_72


title: BFUEs_Day3_plusDex_81


title: BFUEs_Day3_plusDex_73


title: BFUEs_Day3_plusDex_71


title: BFUEs_Day3_plusDex_89


title: BFUEs_Day3_plusDex_74


title: BFUEs_Day3_plusDex_70


title: BFUEs_Day3_plusDex_69


title: BFUEs_Day3_plusDex_94


title: BFUEs_Day3_plusDex_68


title: BFUEs_Day3_plusDex_67


title: BFUEs_Day3_plusDex_66


title: BFUEs_Day3_plusDex_65


title: BFUEs_Day3_plusDex_75


title: BFUEs_Day3_plusDex_76


title: BFUEs_Day3_plusDex_64


title: BFUEs_Day3_plusDex_63


title: BFUEs_Day3_plusDex_60


title: BFUEs_Day3_plusDex_62


title: BFUEs_Day3_plusDex_61


title: BFUEs_Day3_plusDex_56


title: BFUEs_Day3_plusDex_55


title: BFUEs_Day3_plusDex_52


title: BFUEs_Day3_plusDex_45


title: BFUEs_Day3_plusDex_48


title: BFUEs_Day3_plusDex_44


title: BFUEs_Day3_plusDex_50


title: BFUEs_Day3_plusDex_49


title: BFUEs_Day3_plusDex_46


title: BFUEs_Day3_plusDex_42


title: BFUEs_Day3_plusDex_43


title: BFUEs_Day3_plusDex_53


title: BFUEs_Day3_plusDex_40


title: BFUEs_Day3_plusDex_41


title: BFUEs_Day3_plusDex_39


title: BFUEs_Day3_plusDex_38


title: BFUEs_Day3_plusDex_35


title: BFUEs_Day3_plusDex_37


title: BFUEs_Day3_plusDex_59


title: BFUEs_Day3_plusDex_36


title: BFUEs_Day3_plusDex_57


title: BFUEs_Day3_plusDex_54


title: BFUEs_Day3_plusDex_51


title: BFUEs_Day3_plusDex_47


title: BFUEs_Day3_plusDex_30


title: BFUEs_Day3_plusDex_58


title: BFUEs_Day3_plusDex_33


title: BFUEs_Day3_plusDex_32


title: BFUEs_Day3_plusDex_34


title: BFUEs_Day3_plusDex_29


title: BFUEs_Day3_plusDex_28


title: BFUEs_Day3_plusDex_27


title: BFUEs_Day3_plusDex_24


title: BFUEs_Day3_plusDex_25


title: BFUEs_Day3_plusDex_23


title: BFUEs_Day3_plusDex_19


title: BFUEs_Day3_plusDex_21


title: BFUEs_Day3_plusDex_12


title: BFUEs_Day3_plusDex_20


title: BFUEs_Day3_plusDex_16


title: BFUEs_Day3_plusDex_15


title: BFUEs_Day3_plusDex_11


title: BFUEs_Day3_plusDex_31


title: BFUEs_Day3_plusDex_17


title: BFUEs_Day3_plusDex_22


title: BFUEs_Day3_plusDex_14


title: BFUEs_Day3_plusDex_10


title: BFUEs_Day3_plusDex_13


title: BFUEs_Day3_plusDex_4


title: BFUEs_Day3_plusDex_6


title: BFUEs_Day3_plusDex_3


title: BFUEs_Day3_plusDex_8


title: BFUEs_Day3_plusDex_9


title: BFUEs_Day3_plusDex_26


title: BFUEs_Day2_plusDex_96

value: 48 hrs


title: BFUEs_Day3_plusDex_5


title: BFUEs_Day3_plusDex_2


title: BFUEs_Day3_plusDex_1


title: BFUEs_Day3_plusDex_18


title: BFUEs_Day2_plusDex_95


title: BFUEs_Day2_plusDex_94


title: BFUEs_Day2_plusDex_92


title: BFUEs_Day2_plusDex_93


title: BFUEs_Day2_plusDex_91


title: BFUEs_Day2_plusDex_89


title: BFUEs_Day2_plusDex_90


title: BFUEs_Day2_plusDex_83


title: BFUEs_Day2_plusDex_80


title: BFUEs_Day2_plusDex_87


title: BFUEs_Day2_plusDex_81


title: BFUEs_Day2_plusDex_84


title: BFUEs_Day2_plusDex_79


title: BFUEs_Day2_plusDex_82


title: BFUEs_Day2_plusDex_88


title: BFUEs_Day2_plusDex_85


title: BFUEs_Day2_plusDex_76


title: BFUEs_Day2_plusDex_86


title: BFUEs_Day2_plusDex_77


title: BFUEs_Day2_plusDex_74


title: BFUEs_Day2_plusDex_75


title: BFUEs_Day2_plusDex_78


title: BFUEs_Day2_plusDex_68


title: BFUEs_Day3_plusDex_7


title: BFUEs_Day2_plusDex_69


title: BFUEs_Day2_plusDex_73


title: BFUEs_Day2_plusDex_72


title: BFUEs_Day2_plusDex_65


title: BFUEs_Day2_plusDex_66


title: BFUEs_Day2_plusDex_70


title: BFUEs_Day2_plusDex_67


title: BFUEs_Day2_plusDex_64


title: BFUEs_Day2_plusDex_71


title: BFUEs_Day2_plusDex_63


title: BFUEs_Day2_plusDex_62


title: BFUEs_Day2_plusDex_61


title: BFUEs_Day2_plusDex_60


title: BFUEs_Day2_plusDex_57


title: BFUEs_Day2_plusDex_55


title: BFUEs_Day2_plusDex_56


title: BFUEs_Day2_plusDex_52


title: BFUEs_Day2_plusDex_54


title: BFUEs_Day2_plusDex_51


title: BFUEs_Day2_plusDex_59


title: BFUEs_Day2_plusDex_53


title: BFUEs_Day2_plusDex_50


title: BFUEs_Day2_plusDex_48


title: BFUEs_Day2_plusDex_42


title: BFUEs_Day2_plusDex_36


title: BFUEs_Day2_plusDex_46


title: BFUEs_Day2_plusDex_43


title: BFUEs_Day2_plusDex_38


title: BFUEs_Day2_plusDex_45


title: BFUEs_Day2_plusDex_35


title: BFUEs_Day2_plusDex_44


title: BFUEs_Day2_plusDex_49


title: BFUEs_Day2_plusDex_47


title: BFUEs_Day2_plusDex_41


title: BFUEs_Day2_plusDex_32


title: BFUEs_Day2_plusDex_40


title: BFUEs_Day2_plusDex_34


title: BFUEs_Day2_plusDex_33


title: BFUEs_Day2_plusDex_31


title: BFUEs_Day2_plusDex_30


title: BFUEs_Day2_plusDex_58


title: BFUEs_Day2_plusDex_28


title: BFUEs_Day2_plusDex_39


title: BFUEs_Day2_plusDex_22


title: BFUEs_Day2_plusDex_29


title: BFUEs_Day2_plusDex_25


title: BFUEs_Day2_plusDex_26


title: BFUEs_Day2_plusDex_20


title: BFUEs_Day2_plusDex_23


title: BFUEs_Day2_plusDex_21


title: BFUEs_Day2_plusDex_15


title: BFUEs_Day2_plusDex_18


title: BFUEs_Day2_plusDex_16


title: BFUEs_Day2_plusDex_14


title: BFUEs_Day2_plusDex_12


title: BFUEs_Day2_plusDex_7


title: BFUEs_Day2_plusDex_10


title: BFUEs_Day2_plusDex_8


title: BFUEs_Day2_plusDex_11


title: BFUEs_Day2_plusDex_19


title: BFUEs_Day2_plusDex_17


title: BFUEs_Day2_plusDex_13


title: BFUEs_Day2_plusDex_6


title: BFUEs_Day2_plusDex_27


title: BFUEs_Day2_plusDex_37


title: feather follicles_head_red morph_GF38

type: RNA

city: Sheffield

first: Kang-Wook

last: Kim

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: The University of Sheffield

description: Gene expression data from feather follicles of a red morph Gouldian finch

hyb_protocol: Following fragmentation, cRNA were hybridized on Zebra finch Gene 1.0 ST arrays according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan.

data_processing: The data were analyzed with Affymetrix Expression Console ver 1.3 using default analysis settings and RMA (robust multi-array average) as normalization method.

label: biotin

organism: Chloebia gouldiae

source_name: regenerating feathers from head of red morph

label_protocol: Biotinylated cRNA were prepared following GeneChip WT protocols.

extract_protocol: Trizol & RNeasy Mini kits (Qiagen) were used for extraction  of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: regenerating feathers were sampled from head of birds, treated with RNAlater and stored at -80C until RNA extraction

tag: tissue

value: feathers from head

tag: gender

value: male


title: BFUEs_Day2_plusDex_24


title: feather follicles_head_black morph_GF10

description: Gene expression data from feather follicles of a black morph Gouldian finch

source_name: regenerating feathers from head of black morph

value: female


title: feather follicles_head_red morph_GF17


title: BFUEs_Day2_plusDex_9


title: BFUEs_Day2_plusDex_5


title: BFUEs_Day2_plusDex_3


title: BFUEs_Day2_plusDex_2


title: Tcell noM rep1

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequenced reads were aligned to the mm9 mouse (for RAW 264-7) or hg19 human genome (for T-cell) assembly using STAR
Uniquely aligned reads were quantified at exons of annotated genes and normalized to sequence depth and gene length using HOMER. The number of reads per kilobase per million mapped (RPKM) for all RefSeq annotated genes were calculated
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all annotated genes for each sample

organism: Homo sapiens

source_name: Primary T-cell

growth_protocol: Cells were resuspended in a mix of rat tail collagen type I (Corning), 0.02N acetic acid, 10x DMEM with Phenol Red (Sigma Aldrich) and 10x reconstitution buffer (0.2M Hepes (Gibco) and 0.262M NaHCO3). To neutralize the pH, 2N NaOH was added to the reconstitution buffer before use. For all cell lines, low density (LD) and high density (HD) gels contained 1 mg/ml and 4 mg/ml collagen type I respectively. First, 300 to 400 μl of the collagen solution was plated per well of a non-tissue culture treated 24-wells plate (Corning) and allowed to polymerize at 37ºC for at least 30 min. Afterwards a second layer of collagen solution containing the cells was seeded on top of the first gel and allowed to polymerize for 1-2 h at 37ºC, after which 600 μl of culture media was added. For culturing cells in 2D conditions (no matrix), the same number of cells were seeded in the wells of a tissue culture treated 24-well plate.

extract_protocol:
Cells were treated with 3 mg/ml collagenase solution for 45-60 min to extract them from the gels and subsequently RNA was isolated using RNeasy Mini purification kit (Qiagen)
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (1000 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a HiSeq1500 platform (Illumina) with a read length of 50 bp.

treatment_protocol: Cells were cultured in high or low density type I collagen matrix. Control cells (no matrix) were cultured on rgular tissue culture treated plastic without type I collagen matrix.

value: plastic

value: CD3 positive T-cells

tag: culture

value: no matrix


title: Tcell noM rep2


title: BFUEs_Day2_plusDex_1


title: BFUEs_Day1_plusDex_96

value: 24 hrs


title: BFUEs_Day1_plusDex_94


title: Tcell LDM rep1

value: 1mg/ml Type I collagen

value: low density matrix


title: BFUEs_Day1_plusDex_95

value: 100 nM Dexamethasone


title: Tcell LDM rep3


title: Tcell LDM rep2


title: BFUEs_Day1_plusDex_90


title: BFUEs_Day1_plusDex_93


title: Tcell HDM rep1

value: 4mg/ml Type I collagen

value: high density matrix


title: BFUEs_Day1_plusDex_88


title: feather follicles_head_black morph_GF09


title: feather follicles_head_red morph_GF16


title: BFUEs_Day1_plusDex_87


title: C4-2B SG3-179

city: St. Louis

first: Kiran

last: Mahajan

state: Missouri

address: CB 8242 600 South Euclid Ave

department: Surgery

institute: Washington University

data_processing:
1.  Reference genome and transcript annotations:  hg38 from UCSC
2.  Mapping:  TopHat splice-aware aligner (Kim et al Genome Biol. 2013)
3.  Feature summarization:  Expectation-Maximization(EM) approach used to estimate transcript abundance (Jiang and Wong, Bioinformatics, 2009)
4.  Normalization:
Within sample:  RPKM (reads per kilobase of transcript per million, Mortazavi et al, Nat. Meth. 2008)
Between sample:  TMM (Trimmed mean of M values ,Robinson and Oshlack Genome Biol. 2010)
5.  Differential test:  non-replicates analysis with DESeq software (Anders and Huber Genome Biol 2010)
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: prostate cell line

growth_protocol: grown in C4-2B specialized media

extract_protocol:
Total RNA was prepared from C4-2B using the Qiagen RNeasy kit protocol followed by Dnase I treatment.  1-2ug of total RNA was used for the construction of the libraries.
The Illumina Hi-seq platform with 50 bp single end sequencing

treatment_protocol:
C4-2B treated with DMSO and or various inhibitors.
HOXB13 pKO genetic deletion were generated by CRISPR/Cas9  strategy

value: Bone-metastatic CRPC cell line-C4-2B

tag: type

value: Androgen-independent

value: BET-kinase inhibitor treated


title: C4-2B ENZ

value: Bone-metastatic CRPC cell line C4-2B

value: BET-inhibitor


title: C4-2B MA4-022-2

source_name: prostate cel line


title: BFUEs_Day2_plusDex_4

value: BFUE

value: erythroid progenitor media

value: 48 hrs


title: BFUEs_Day1_plusDex_86


title: Tcell noM rep3

value: plastic


title: BFUEs_Day1_plusDex_91


title: BFUEs_Day1_plusDex_92


title: Tcell HDM rep2

value: CD3 positive T-cells


title: C4-2B MA4-022-1 (dataset 2)


title: BFUEs_Day1_plusDex_89


title: C4-2B HOXB13 KO2


title: BFUEs_Day1_plusDex_84


title: C4-2B DMSO (rep1)

value: DMSO (Vehicle)


title: C4-2B HOXB13 KO1


title: C4-2B MA4-022-1

data_processing:
Illumina HiSeq 50bp single-end reads from RNA-Seq libraries were first adaptor trimmed
then analyzed using the TopHat and Cufflinks software.
TopHat (v2.0.13) was utilized for alignment of short reads to the reference genome.
To analyze gene expression, Cufflinks (v2.2.1) was utilized for transcript assembly and differential expression, and cummeRbund (v2.0.0) for
visualization of differential analysis. Default parameters were used
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was prepared from C4-2B using the Qiagen RNeasy kit protocol followed by DNAseI treatment.  1-2ug of total RNA was used for the construction of the libraries.
The Illumina Hi-seq platform with 50 bp single end sequencing. Total RNA-Seq libraries were constructed from 1-3 μg total RNA. Total RNA was treated with the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) from Illumina (cat. #MRZG126), and libraries were prepared from rRNA depleted samples using ScriptSeq™ v2 RNA-Seq Library Preparation Kit from Illumina (Cat. #SSV21106). Briefly, rRNA depleted samples were fragmented, reverse transcribed, fitted with appropriate adapters and amplified. RNA-Seq libraries were sequenced on an Illumina HiSeq to a sequencing depth of 40-50 million reads (50 bp single read).

treatment_protocol: C4-2B treated with DMSO and or MA4-022-1 2.5uM


title: BFUEs_Day1_plusDex_82

value: 24 hrs


title: C4-2B DMSO (rep2)

value: Vehicle


title: Tcell HDM rep3


title: BFUEs_Day1_plusDex_80


title: BFUEs_Day1_plusDex_81


title: C4-2B JQ1

value: Anti-androgen


title: C4-2B DMSO


title: MouseB1

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

description: Amplicon of a portion of the targeted sequence from gDNA of PBMCs of mouse 21 weeks after transplant of CB-CD34+ cells edited with IL2RG high specificity RNP and AAV6 in presence of GSE56 mRNA

data_processing:
Library strategy: Amplicon-seq
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR
frequency count performed with in house developed script
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file, count per base of all the possible nucleotide

source_name: PBMC from xenotransplanted NSG mouse

extract_protocol:
Total DNA was isolated using QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Amplicon-seq with unique amplification step (25 cycles). Forward and reverse primers endowed with tails containing (from 5' to 3') P5/P7 sequence, i5/i7 Illumina tag to allow multiplexed sequencing and R1/R2 primer complementary sequence, respectively

value: Cord blood derived CD34+ cells

tag: time point

value: 21 weeks after HSPC transplant

tag: modification

value: HS RNP+AAV6+GSE56


title: MouseB2


title: MouseB3


title: MouseB0


title: BFUEs_Day1_plusDex_76

value: 100 nM Dexamethasone


title: BFUEs_Day1_plusDex_75


title: MouseA4

description: Amplicon of a portion of the targeted sequence from gDNA of PBMCs of mouse 21 weeks after transplant of CB-CD34+ cells edited with IL2RG high specificity RNP and AAV6 in absence of GSE56 mRNA

value: HS RNP+AAV6


title: BFUEs_Day1_plusDex_78


title: BFUEs_Day1_plusDex_85


title: feather follicles_head_black morph_GF03

value: feathers from head

value: male


title: MouseA3


title: BFUEs_Day1_plusDex_73


title: BFUEs_Day1_plusDex_83


title: BFUEs_Day1_plusDex_74


title: MouseA2


title: BFUEs_Day1_plusDex_72


title: MouseA0


title: InVitroB

description: Amplicon of a portion of the targeted sequence from gDNA of CB-CD34+ cells 72hrs after editing with IL2RG high specificity RNP and AAV6 in presence of GSE56 mRNA

source_name: Cultured HSPC

value: 72h upon gene editing procedure


title: InVitroA

description: Amplicon of a portion of the targeted sequence from gDNA of CB-CD34+ cells 72hrs after editing with IL2RG high specificity RNP and AAV6 in absence of GSE56 mRNA


title: BFUEs_Day1_plusDex_79

value: BFUE


title: MouseB4


title: BFUEs_Day1_plusDex_71

value: erythroid progenitor media


title: CREB1_A297V_5mCG_replicate2

type: protein

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

description:
SAMPLE 10
CREB1(A297V) PBM experiment, methylated DNA

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all 32,896 8-bp long DNA sequences (8-mers), a transformed median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.

molecule: protein

source_name: CREB1(A297V), HK design

label_protocol: 180 ng of plasmid containing DNA binding domains of CEBPB, CREB1, CEBPB(V285A) or CREB1(A297V) mutants were used to express proteins using PureExpress in-vitro transcription translation kit (NEB) in 25 µL reaction volume as per manufacturer’s instructions.

extract_protocol: The bZIP DNA binding domains (DBD) of wild type CREB1 and CEBPB obtained from Dr. Timothy Hughes, University of Toronto, Canada as a GST construct cloned into a modified pDEST15 MAGIC vector (N-terminal GST) vector.  Mutant constructs of CREB1 and CEBPB (CREB1(A297V) and CEBPB(V285A)) were generated via site-directed mutagenesis of the wild-type construct.

treatment_protocol: The double stranded arrays were either methylated (5mCG) or unmethylated (C). The methylation of the double stranded microarray were performed using 10 μl of M.SssI (New England Biolabs)in a total volume of 150μl at 37 °C for 3 hrs. The arrays were washed three times with PBS/0.5% Tween-20 and once with PBS.

tag: dbd

value: bZIP

tag: protein

tag: probe state

value: methylated


title: BFUEs_Day1_plusDex_70

tag: strain

tag: cell type


title: CREB1_A297V_5mCG_replicate1

description:
SAMPLE 9
CREB1(A297V) PBM experiment, methylated DNA


title: CEBPB_V285A_5mCG_replicate1

description:
SAMPLE 7
CEBPB(V285A) PBM experiment, methylated DNA

source_name: CEBPB(V285A), HK design


title: BFUEs_Day1_plusDex_77


title: BFUEs_Day1_plusDex_69


title: BFUEs_Day1_plusDex_65


title: BFUEs_Day1_plusDex_66


title: CREB1_A297V_C_replicate2

description:
SAMPLE 6
CREB1(A297V) PBM experiment, unmethylated DNA

value: unmethylated


title: BFUEs_Day1_plusDex_64


title: BFUEs_Day1_plusDex_68


title: BFUEs_Day1_plusDex_63


title: BFUEs_Day1_plusDex_61


title: BFUEs_Day1_plusDex_62


title: BFUEs_Day1_plusDex_60


title: CEBPB_V285A_C_replicate1

description:
SAMPLE 3
CEBPB(V285A) PBM experiment, unmethylated DNA


title: CEBPB_V285A_C_replicate2

description:
SAMPLE 4
CEBPB(V285A) PBM experiment, unmethylated DNA


title: CREB1_A297V_C_replicate1

description:
SAMPLE 5
CREB1(A297V) PBM experiment, unmethylated DNA


title: CREB1_C_replicate1

description:
SAMPLE 1
CREB1 PBM experiment, unmethylated DNA

source_name: CREB1, HK design


title: BFUEs_Day1_plusDex_58


title: BFUEs_Day1_plusDex_59


title: CREB1_C_replicate2

description:
SAMPLE 2
CREB1 PBM experiment, unmethylated DNA


title: CREB1_A297V_5hmC_replicate4

description:
SAMPLE 21
CREB1(A297V) PBM experiment, 5hmC

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: double-stranding treatment


title: BFUEs_Day1_plusDex_67


title: CEBPB_V285A_5mCG_replicate2

description:
SAMPLE 8
CEBPB(V285A) PBM experiment, methylated DNA


title: BFUEs_Day1_plusDex_55


title: BFUEs_Day1_plusDex_56


title: CREB1_A297V_5hmC_replicate2

description:
SAMPLE 19
CREB1(A297V) PBM experiment, 5hmC


title: BFUEs_Day1_plusDex_57


title: BFUEs_Day1_plusDex_54


title: CREB1_A297V_5hmC_replicate3

description:
SAMPLE 20
CREB1(A297V) PBM experiment, 5hmC


title: CREB1_A297V_5hmC_replicate1

description:
SAMPLE 18
CREB1(A297V) PBM experiment, 5hmC


title: CEBPB_V285A_5hmC_replicate2

description:
SAMPLE 17
CEBPB(V285A) PBM experiment, 5hmC


title: CREB1_5hmC_replicate2

description:
SAMPLE 15
CREB1 PBM experiment, 5hmC


title: BFUEs_Day1_plusDex_53


title: CEBPB_V285A_5hmC_replicate1

description:
SAMPLE 16
CEBPB(V285A) PBM experiment, 5hmC


title: CREB1_5hmC_replicate1

description:
SAMPLE 14
CREB1 PBM experiment, 5hmC


title: BFUEs_Day1_plusDex_52


title: BFUEs_Day1_plusDex_50


title: CEBPB_5hmC_replicate2

description:
SAMPLE 13
CEBPB PBM experiment, 5hmC

source_name: CEBPB, HK design

value: CEBPB


title: CEBPB_V285A_5mC_replicate2

description:
SAMPLE 9
CEBPB(V285A) PBM experiment, 5mC


title: CREB1_5mC_replicate1

description:
SAMPLE 7
CREB1 PBM experiment, 5mC


title: CREB1_A297V_5mC_replicate2

description:
SAMPLE 11
CREB1(A297V) PBM experiment, 5mC


title: CREB1_A297V_C_replicate2

description:
SAMPLE 6
CREB1(A297V) PBM experiment, cytosine

value: cytosine


title: BFUEs_Day1_plusDex_47

value: 24 hrs


title: BFUEs_Day1_plusDex_48


title: BFUEs_Day1_plusDex_46


title: CREB1_A297V_C_replicate1

description:
SAMPLE 5
CREB1(A297V) PBM experiment, cytosine


title: CEBPB_V285A_C_replicate2

description:
SAMPLE 4
CEBPB(V285A) PBM experiment, cytosine


title: BFUEs_Day1_plusDex_43


title: BFUEs_Day1_plusDex_44


title: BFUEs_Day1_plusDex_40


title: BFUEs_Day1_plusDex_45


title: BFUEs_Day1_plusDex_42


title: BFUEs_Day1_plusDex_51


title: BFUEs_Day1_plusDex_39


title: CEBPB_V285A_C_replicate1

description:
SAMPLE 3
CEBPB(V285A) PBM experiment, cytosine


title: CREB1_C_replicate2

description:
SAMPLE 2
CREB1 PBM experiment, cytosine


title: CEBPB_5hmC_replicate1

description:
SAMPLE 12
CEBPB PBM experiment, 5hmC


title: BFUEs_Day1_plusDex_37


title: BFUEs_Day1_plusDex_36


title: CREB1_C_replicate1

description:
SAMPLE 1
CREB1 PBM experiment, cytosine


title: BFUEs_Day1_plusDex_38


title: CREB1_A297V_5mC_replicate1

description:
SAMPLE 10
CREB1(A297V) PBM experiment, 5mC


title: BFUEs_Day1_plusDex_49


title: BFUEs_Day1_plusDex_35


title: BFUEs_Day1_plusDex_41


title: BFUEs_Day1_plusDex_33


title: BFUEs_Day1_plusDex_34


title: BFUEs_Day1_plusDex_32


title: BFUEs_Day1_plusDex_30


title: BFUEs_Day1_plusDex_31


title: BFUEs_Day1_plusDex_29


title: BFUEs_Day1_plusDex_28


title: BFUEs_Day1_plusDex_27


title: BFUEs_Day1_plusDex_26


title: BFUEs_Day1_plusDex_25


title: BFUEs_Day1_plusDex_24


title: BFUEs_Day1_plusDex_23


title: CEBPB_V285A_5mC_replicate1

description:
SAMPLE 8
CEBPB(V285A) PBM experiment, 5mC


title: BFUEs_Day1_plusDex_22


title: BFUEs_Day1_plusDex_21


title: BFUEs_Day1_plusDex_20


title: 113010-HA

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Standard Illumina hybridization protocol:  A total of 750ng of cRNA per sample was loaded into the Illumina Human HT-12 v4 Gene Expression BeadChip for hybridization at 58 degrees C for 17 hours.

scan_protocol: Standard Illumina scan protocol: Used Illumina iScan system

data_processing: GenomeStudio V2011.1 with GeneExpression Module V1.9.0 was used with HumanHT-12_v4_0_R2_15002873_B.bgx manifest to create a GenomeStudio project.  Matrix reports at the probe level were created with/without Average Normalization and with/without background subtraction. Non-normalized and normalized data provided for this series are with background-subtraction.

source_name: Human_Hemangioma_Treated with Propanol_beta blockers

label_protocol: Illumina TotalPrep RNA amplification kit (Illumina, San Diego, CA) was used to prepare biotinylated antisense cRNA from 500ng of high-quality total RNA

extract_protocol: Total RNA was isolated and purified from frozen tissues using the RNeasy Plus Mini Kit (Qiagen,Valencia, CA).

treatment_protocol: Fresh tissue was harvested by surgical removal from 28 children.  Upon harvesting, tissues were stored at -80 ◦C until the RNA extraction was performed.

value: Hemangioma

value: Treated with Propanol_beta blockers


title: 101910-NOR

value: skin


title: BFUEs_Day1_plusDex_19


title: 93-H


title: 030411-NOR


title: 111910-NOR


title: 78-H


title: 262630-NOR


title: 100110-HA


title: BFUEs_Day1_plusDex_17


title: 070910-HA

tag: age

value: 24 months

value: No Propanol


title: BFUEs_Day1_plusDex_15

value: 100 nM Dexamethasone


title: 40-H


title: 52100-NOR


title: 39-H


title: 050410-HA


title: 081010H


title: BFUEs_Day1_plusDex_18


title: BFUEs_Day1_plusDex_14


title: 082410-HA

value: 12 months


title: 43-H


title: 119-H


title: BFUEs_Day1_plusDex_16


title: 432513-H


title: 031610_HA


title: 232961H


title: 071210-H


title: 35-H


title: BFUEs_Day1_plusDex_12


title: BFUEs_Day1_plusDex_13


title: BFUEs_Day1_plusDex_10


title: BFUEs_Day1_plusDex_9


title: BFUEs_Day1_plusDex_7


title: BFUEs_Day1_plusDex_6


title: BFUEs_Day1_plusDex_5


title: BFUEs_Day1_plusDex_11


title: BFUEs_Day1_plusDex_3


title: BFUEs_Day1_plusDex_2


title: BFUEs_Day1_plusDex_4


title: BFUEs_Day3_95

value: 72 hrs

value: No


title: BFUEs_Day1_plusDex_1

value: BFUE


title: BFUEs_Day1_plusDex_8

value: erythroid progenitor media


title: BFUEs_Day3_94


title: sample13: veh+acute+veh

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description: HPC treated with veh at veh+acute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Microarray expression analysis was performed in R. All probes (n~47,000 probes) were first filtered by an Illumina detection p-value of 0.05 in at least 50% of the samples, leaving 12,574 expressed probes for further analysis. Subsequently, each transcript was transformed and normalized through variance stabilization and normalization (VSN). Raw data are available on the series record. Processed data contains the VSN normalized and transformed signal.

source_name: HPC

label_protocol: Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.

extract_protocol: RNA was isolated using the Allprep RNA mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions.

tag: cell line

value: immortalized, multipotent human fetal HPC line HPC03A/07

value: veh

value: veh+acute

tag: cell vial


title: sample14: veh+acute+dex

description: HPC treated with dex at veh+acute

value: dex


title: 052810 HA

value: 6 months


title: 111910-HB


title: 37-H


title: 081910-HA


title: BFUEs_Day3_93

tag: time in culture


title: sample12: Pro-diff+WO+acute+dex

description: HPC treated with dex at Pro-diff+WO+acute

tag: treatment

value: Pro-diff+WO+acute


title: BFUEs_Day3_92


title: sample11: veh+acute+dex

description: HPC treated with dex at veh+acute


title: sample15: veh+acute+veh

description: HPC treated with veh at veh+acute


title: BFUEs_Day3_96


title: sample9: veh+acute+veh

description: HPC treated with veh at veh+acute


title: BFUEs_Day3_91


title: 211602-H

tag: tissue

value: Hemangioma


title: BFUEs_Day3_90


title: BFUEs_Day3_89


title: 45922-H


title: BFUEs_Day3_88


title: BFUEs_Day3_86


title: BFUEs_Day3_87


title: sample5: Pro-diff+WO+acute+dex


title: sample6: veh+acute+veh

description: HPC treated with veh at veh+acute


title: sample7: Pro-diff+WO+acute+dex


title: BFUEs_Day3_84


title: BFUEs_Day3_85


title: BFUEs_Day3_83


title: BFUEs_Day3_82


title: BFUEs_Day3_81


title: BFUEs_Day3_80


title: sample10: Pro-diff+WO+acute+dex


title: sample2: veh+acute+dex

description: HPC treated with dex at veh+acute


title: sample3: Pro-diff+WO+acute+dex


title: sample8: veh+acute+dex

description: HPC treated with dex at veh+acute


title: sample46: pro-diff+WO+dex

description:
8381670069_K
HPC treated with dex at pro-diff+WO

data_processing: Microarray expression analysis was performed in R. All probes (n~47,000 probes) were first filtered by an Illumina detection p-value of 0.05 in at least 50% of the samples, leaving 17,377  expressed probes for further analysis. Subsequently, each transcript was transformed and normalized through variance stabilization and normalization (VSN). Raw data are available on the series record. Processed data contains the VSN normalized and transformed signal.

value: pro-diff+WO


title: BFUEs_Day3_79


title: sample1: veh+acute+dex

description: HPC treated with dex at veh+acute


title: sample43: pro-diff+WO+veh

description:
8381670069_H
HPC treated with veh at pro-diff+WO


title: BFUEs_Day3_78


title: BFUEs_Day3_77


title: sample47: pro-diff+WO+veh

description:
8381670069_L
HPC treated with veh at pro-diff+WO


title: BFUEs_Day3_76


title: BFUEs_Day3_75


title: sample42: pro-diff+WO+dex

description:
8381670069_G
HPC treated with dex at pro-diff+WO


title: sample44: post+WO+dex

description:
8381670069_I
HPC treated with dex at post+WO

value: post+WO


title: sample41: post+WO+veh

description:
8381670069_F
HPC treated with veh at post+WO


title: BFUEs_Day3_74


title: sample39: pro-diff+WO+veh

description:
8381670069_D
HPC treated with veh at pro-diff+WO


title: BFUEs_Day3_73


title: sample38: pro-diff+WO+dex

description:
8381670069_C
HPC treated with dex at pro-diff+WO


title: BFUEs_Day3_72


title: sample45: post+WO+veh

description:
8381670069_J
HPC treated with veh at post+WO


title: sample37: post+WO+veh

description:
8381670069_B
HPC treated with veh at post+WO


title: BFUEs_Day3_71


title: sample40: post+WO+dex

description:
8381670069_E
HPC treated with dex at post+WO


title: sample36: post+WO+dex

description:
8381670069_A
HPC treated with dex at post+WO


title: BFUEs_Day3_69


title: BFUEs_Day3_68


title: BFUEs_Day3_67


title: BFUEs_Day3_70


title: BFUEs_Day3_66


title: sample33: pro-diff+WO+veh

description:
8381670033_J
HPC treated with veh at pro-diff+WO


title: BFUEs_Day3_65


title: sample34: post+WO+dex

description:
8381670033_K
HPC treated with dex at post+WO


title: BFUEs_Day3_63


title: sample35: post+WO+veh

description:
8381670033_L
HPC treated with veh at post+WO


title: BFUEs_Day3_64


title: BFUEs_Day3_62


title: sample32: pro-diff+WO+dex

description:
8381670033_I
HPC treated with dex at pro-diff+WO


title: BFUEs_Day3_61


title: sample31: post+WO+veh

description:
8381670033_H
HPC treated with veh at post+WO


title: sample30: post+WO+dex

description:
8381670033_G
HPC treated with dex at post+WO


title: sample28: pro-diff+WO+dex

description:
8381670033_E
HPC treated with dex at pro-diff+WO


title: BFUEs_Day3_60


title: BFUEs_Day3_59


title: sample29: pro-diff+WO+veh

description:
8381670033_F
HPC treated with veh at pro-diff+WO


title: BFUEs_Day3_58


title: BFUEs_Day3_57


title: sample23: pro+veh

description:
8381670028_G
HPC treated with veh at pro

value: pro


title: sample26: post+WO+dex

description:
8381670033_C
HPC treated with dex at post+WO


title: BFUEs_Day3_56


title: sample25: pro-diff+WO+dex

description:
8381670033_A
HPC treated with dex at pro-diff+WO


title: sample20: pro+dex

description:
8381670025_G
HPC treated with dex at pro


title: sample24: pro+dex

description:
8381670028_H
HPC treated with dex at pro


title: BFUEs_Day3_54


title: BFUEs_Day3_53


title: BFUEs_Day3_55


title: sample22: pro-diff+dex

description:
8381670028_D
HPC treated with dex at pro-diff

value: pro-diff


title: sample19: pro+veh

description:
8381670025_F
HPC treated with veh at pro


title: sample18: pro-diff+dex

description:
8381670025_C
HPC treated with dex at pro-diff


title: BFUEs_Day3_51


title: sample27: post+WO+veh

description:
8381670033_D
HPC treated with veh at post+WO


title: BFUEs_Day3_52


title: sample17: pro-diff+veh

description:
8381670025_B
HPC treated with veh at pro-diff


title: sample16: pro+dex

description:
8381670022_F
HPC treated with dex at pro


title: BFUEs_Day3_50


title: sample21: pro-diff+veh

description:
8381670028_C
HPC treated with veh at pro-diff


title: BFUEs_Day3_48


title: BFUEs_Day3_49


title: BFUEs_Day3_47


title: sample15: pro+veh

description:
8381670022_E
HPC treated with veh at pro


title: sample14: pro-diff+dex

description:
8381670022_B
HPC treated with dex at pro-diff


title: sample13: pro-diff+veh

description:
8381670022_A
HPC treated with veh at pro-diff


title: BFUEs_Day3_44


title: BFUEs_Day3_45


title: sample12: pro-diff+veh

description:
8381670020_L
HPC treated with veh at pro-diff


title: sample11: pro-diff+dex

description:
8381670020_K
HPC treated with dex at pro-diff


title: BFUEs_Day3_43


title: sample8: pro-diff+veh

description:
8381670015_K
HPC treated with veh at pro-diff


title: sample9: pro+veh

description:
8381670020_D
HPC treated with veh at pro


title: BFUEs_Day3_41


title: sample10: pro+dex

description:
8381670020_E
HPC treated with dex at pro


title: sample5: pro+veh

description:
8381670015_C
HPC treated with veh at pro


title: sample7: pro-diff+dex

description:
8381670015_J
HPC treated with dex at pro-diff


title: sample6: pro+dex

description:
8381670015_D
HPC treated with dex at pro


title: BFUEs_Day3_40


title: sample3: pro-diff+dex

description:
8381670009_I
HPC treated with dex at pro-diff


title: sample4: pro-diff+veh

description:
8381670009_J
HPC treated with veh at pro-diff


title: BFUEs_Day3_38


title: BFUEs_Day3_39


title: BFUEs_Day3_34


title: BFUEs_Day3_35


title: BFUEs_Day3_46


title: BFUEs_Day3_33


title: BFUEs_Day3_36


title: sample2: pro+dex

description:
8381670009_C
HPC treated with dex at pro


title: BFUEs_Day3_32


title: BFUEs_Day3_30


title: BFUEs_Day3_29


title: BFUEs_Day3_28


title: BFUEs_Day3_42


title: BFUEs_Day3_26


title: BFUEs_Day3_27


title: BFUEs_Day3_15


title: BFUEs_Day3_19


title: BFUEs_Day3_18


title: BFUEs_Day3_16


title: BFUEs_Day3_13


title: BFUEs_Day3_22


title: BFUEs_Day3_14


title: BFUEs_Day3_37


title: BFUEs_Day3_12


title: BFUEs_Day3_21


title: BFUEs_Day3_17


title: BFUEs_Day3_11


title: BFUEs_Day3_23


title: sample1: pro+veh

description:
8381670009_B
HPC treated with veh at pro


title: BFUEs_Day3_20


title: BFUEs_Day3_8


title: BFUEs_Day3_7


title: BFUEs_Day3_31


title: BFUEs_Day3_10


title: BFUEs_Day3_5


title: BFUEs_Day3_6


title: BFUEs_Day3_3


title: BFUEs_Day3_25


title: BFUEs_Day3_2


title: BFUEs_Day3_24


title: BFUEs_Day3_4


title: BFUEs_Day3_1


title: BFUEs_Day2_96

value: 48 hrs


title: BFUEs_Day3_9


title: BFUEs_Day2_93


title: BFUEs_Day2_94


title: BFUEs_Day2_95


title: BFUEs_Day2_92


title: BFUEs_Day2_84


title: BFUEs_Day2_86


title: BFUEs_Day2_83


title: BFUEs_Day2_89


title: BFUEs_Day2_90


title: BFUEs_Day2_88


title: BFUEs_Day2_85


title: BFUEs_Day2_87


title: BFUEs_Day2_80


title: BFUEs_Day2_82


title: BFUEs_Day2_81


title: BFUEs_Day2_79


title: BFUEs_Day2_78


title: BFUEs_Day2_91


title: sample4: veh+acute+veh

description: HPC treated with veh at veh+acute


title: BFUEs_Day2_74


title: BFUEs_Day2_75


title: BFUEs_Day2_72


title: BFUEs_Day2_70


title: BFUEs_Day2_71


title: BFUEs_Day2_73


title: BFUEs_Day2_68


title: BFUEs_Day2_77


title: BFUEs_Day2_76


title: 13904269

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

description:
dimboa2cy3 vs dmso2dimcy5
Date:2012/08/06

hyb_protocol: Corning Pronto : 750.0 ng at 42 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Unnormalized, log (base 2) transform of the (Ch1/Ch2) ratio of the medians shown in the data table below. Normalized data [i.e., Log (base 2) transform of the (Ch1/Ch2) ratio of the medians;limma package: normalizeWithinArray(loess, background:subtract) normalizeBetweenArrays (quantile); lmFit ;eBayes] linked as supplementary files on the Series record.

organism: Spodoptera frugiperda

label_protocol: cDNA Pronto Promega

extract_protocol: Trizol

tag: label

tag: sample/extract

tag: subject

value: L6 larvae

value: midgut


title: 13904270

description:
dmso3dimcy3 vs dimboa3cy5
Date:2012/06/08


title: 13904283

description:
B73_4_Cy3 vs bx3_4_cy5
Date:2011/02/08

value: L6 larva midgut

value: stage 6

tag: fed with

value: control genotype B73

value: 10d-old bx3 maize mutant plant


title: 13904268

description:
dmso2dimcy3 vs dimboa2cy5
Date:2012/06/08


title: 13904707

description:
B73_3_Cy3 vs bx3_3_cy5
Date:2011/02/07


title: 13904284

description:
bx3_4_cy3 vs B73_4_Cy5
Date:2011/02/08


title: BFUEs_Day2_69

value: BFUE

value: erythroid progenitor media

value: No


title: 13904700

description:
H88_3_cy3 vs bx1_3_cy5
Date:2011/01/25

value: control genotype H88

value: 10d-old bx1 maize mutant plant


title: 13904708

description:
bx3_3_cy3 vs B73_3_Cy5
Date:2011/02/07


title: 13904709

description:
B73_5_Cy3 vs bx3_5_cy5
Date:2011/02/08


title: 13904699

description:
bx1_2_cy3 vs H88_2_cy5
Date:2011/01/25


title: 13904275

description:
dmsodi1cy3 vs diboa1cy5
Date:2012/06/02


title: 13904274

description:
diboa1cy3 vs dmsodi1cy5
Date:2012/06/02


title: 13904701

description:
bx1_3_cy3 vs H88_3_cy5
Date:2011/01/25


title: 13904710

description:
bx3_5_cy3 vs B73_5_Cy5
Date:2011/02/08


title: BFUEs_Day2_67


title: BFUEs_Day2_66


title: 13904276

description:
diboa2cy3 vs dmsodi2cy5
Date:2012/08/06


title: BFUEs_Day2_64


title: BFUEs_Day2_65


title: 13904695

description:
H88_1_cy3 vs bx1_1_cy5
Date:2011/08/24


title: 13904696

description:
bx1_1_cy3 vs H88_1_cy5
Date:2011/04/24


title: 13904698

description:
H88_2_cy3 vs bx1_2_cy5
Date:2011/01/25


title: BFUEs_Day2_63


title: 13619558

description:
diboa3cy3 vs dmsodi3cy5
Date:2012/06/02


title: BFUEs_Day2_62


title: BFUEs_Day2_60


title: BFUEs_Day2_61


title: BFUEs_Day2_59


title: BFUEs_Day2_57


title: 13904282

description:
dmsodi2cy3 vs diboa2cy5
Date:2012/08/06


title: 13904286

description:
dmsodi3cy3 vs diboa3cy5
Date:2012/06/02


title: BFUEs_Day2_54


title: BFUEs_Day2_53


title: BFUEs_Day2_55


title: BFUEs_Day2_51


title: BFUEs_Day2_52


title: 13904281

description:
dimboa1cy3 vs dmso1dimcy5
Date:2012/08/06


title: 13904287

description:
dmso1dimcy3 vs dimboa1cy5
Date:2012/06/08


title: 13619559

description:
dimboa3cy3 vs dmso3dimcy5
Date:2012/08/06


title: BFUEs_Day2_50


title: BFUEs_Day2_58


title: 557274A12 - Mutant-3_3 vs Ctrl-3_3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description: Mitochondrial transcriptome regulation and coordination with the nucleus

hyb_protocol: Ctrl-3_3 Cy5 / Mutant-3_3 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: whole plant - Media=MS-255 with 5% w/v sucrose and 10uM Estradiol Temperature=day 21°C / night 17°C Light=16h light / 8h darkMuy

extract_protocol: Ctrl-3_3:4ug. (Total-RNA-Isolation.doc)

treatment_protocol: Name:Estradiol - compound based treatment - compound addition,estradiol:quantity 10uM . Plants were transferred to 6 well plates with the roots dipping into MS-255 liquid medium with estradiol at a 10 micromolar final concentration.

tag: ecotype

value: columbia

tag: genotype

value: wild type

value: mutant


title: BFUEs_Day2_56


title: 557274A10 - Mutant-3_2 vs Ctrl-3_2

hyb_protocol: Ctrl-3_2 Cy5 / Mutant-3_2 Cy3 : 30pmol.

extract_protocol: Ctrl-3_2:4ug. (Total-RNA-Isolation.doc)

organism: Cephalanthera damasonium

growth_protocol: whole plant - Media=MS-255 with 5% w/v sucrose and 10uM Estradiol Temperature=day 21°C / night 17°C Light=16h light / 8h dark


title: 557274A05 - Ctrl-1_3 vs Mutant-1_3

hyb_protocol: Mutant-1_3 Cy5 / Ctrl-1_3 Cy3 : 30pmol.

extract_protocol: Ctrl-1_3:4ug. (Total-RNA-Isolation.doc)


title: 557274A07 - Col-3_1 vs Mutant-3_1

hyb_protocol: Mutant-3_1 Cy5 / Col-3_1 Cy3 : 30pmol.

extract_protocol: Col-3_1:4ug. (Total-RNA-Isolation.doc)


title: 557274A06 - Mutant-1_3 vs Ctrl-1_3

hyb_protocol: Ctrl-1_3 Cy5 / Mutant-1_3 Cy3 : 30pmol.


title: 557274A08 - Mutant-3_1 vs Col-3_1

hyb_protocol: Col-3_1 Cy5 / Mutant-3_1 Cy3 : 30pmol.


title: BFUEs_Day2_48


title: 557274A04 - Mutant-1_2 vs Ctrl-1_2

hyb_protocol: Ctrl-1_2 Cy5 / Mutant-1_2 Cy3 : 30pmol.

extract_protocol: Ctrl-1_2:4ug. (Total-RNA-Isolation.doc)


title: BFUEs_Day2_49


title: BFUEs_Day2_47


title: 557274A09 - Ctrl-3_2 vs Mutant-3_2

hyb_protocol: Mutant-3_2 Cy5 / Ctrl-3_2 Cy3 : 30pmol.


title: Jak1_Mu2

city: Chicago

first: Jason

middle: B

last: Williams

state: Illinois

address: 929 E. 57th St GCIS W423H

department: Pathology

institute: University of Chicago

data_processing:
Read alignment and averaging of raw read counts from duplicate lanes was performed using the Kallisto software.
Genes with lcpm < 1 in fewer than 3 samples were removed.
Raw read counts were processed by TMM normalization
Differentially expressed genes were identified using Limma voom
Supplementary_files_format_and_content: tsv: average both lanes
Supplementary_files_format_and_content: IFNgR2KO_vs_WT_Processed_NoPvalCuttOff.txt: 3 mouse triplicate samples were averaged and the fold-change compared to wild-type was calculated
Supplementary_files_format_and_content: Jak1KO_vs_WT_Processed_NoPvalCuttOff.txt: 3 mouse triplicate samples were averaged and the fold-change compared to wild-type was calculated

source_name: Purified tumor cells on day 7 after tumor engraftment.

growth_protocol: Tumor cells were grown in DMEM containing 10% FBS, 0.01M MOPS, 100U/mL penicillin/streptomycin, 1% MEM Non-Essential Amino Acids

extract_protocol:
Wild-type, IFNgR2-, and Jak1-mutant tumor cells were inoculated into C57BL/6 mice and tumors were extracted 7 days later. Tumors were enzymatically digested for 30 min at 37oC with rotation. Tumor suspension was Ficolled and buffer layer was washed twice with PBS. Cells were stained with CD45, CD3, Thy1, CD19 antibodies and a live-dead permeability dye to gate out hematopoietic cells and dead cells. Tumor cells were cell sorted based on dsRed and BFP expression into RLT buffer and quickly frozen.  RNA was extracted using the RNEasy micro kit (QIAGEN) and submitted for single-end RNA sequencing.
RNA was extracted using the RNEasy Kit (QIAGEN) following manufacturer's proctocol.


title: IFNgR2KO_Mu3


title: BFUEs_Day2_46

source_name: burst forming unit-erythroid


title: BFUEs_Day2_45


title: Jak1_Mu1


title: Jak1_Mu3


title: IFNgR2KO_Mu2


title: BFUEs_Day2_44


title: WT_Mu3


title: IFNgR2KO_Mu1


title: WT_Mu2


title: 557274A02 - Mutant-1_1 vs Col-1_1

hyb_protocol: Col-1_1 Cy5 / Mutant-1_1 Cy3 : 30pmol.

extract_protocol: Col-1_1:4ug. (Total-RNA-Isolation.doc)


title: WT_Mu1


title: BFUEs_Day2_42

extract_protocol:
cell extraction protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).  For quantification of erythroid differentiation markers, cultured BFU-E cells were stained with PE anti-CD71 (clone R127217, E-Biosciences) and APC anti-Ter119 (E-Biosciences).  Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
cell culture protocol: BFU-E cell culture. FACS-isolated BFU-E enriched cells were cultured for the denoted number of days in progenitor culture media (PCM) consisting of serum free expansion media (SFEM2, Stem Cell Technologies) supplemented with 100 ng/mL murine SCF (Peprotech), 40 ng/mL murine insulin-like growth factor 1 (Peprotech), 2 U/mL human erythropoietin (Amgen), 1% penicillin/streptomycin (Gibco), and for indicated cultures 100 nM Dexamethasone (Sigma).
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).


title: BFUEs_Day2_41


title: 557274A01 - Col-1_1 vs Mutant-1_1

hyb_protocol: Mutant-1_1 Cy5 / Col-1_1 Cy3 : 30pmol.


title: MycERt2 60min 4-OHT Rep3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description: RNA-Seq of chromatin associated RNA from MycERt2 60min 4-OHT Rep3

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm10
Supplementary_files_format_and_content: reads counts on genes

source_name: MycERt2 60min 4-OHT

growth_protocol: Mouse pre-B cell line B3 was grown in IMDM, 10% FCS and  1% penicillin-streptomycin

extract_protocol:
Cells were fractionated according to the protocol described in Pandya-Jones and Black, RNA 2009. Briefly, cells were lysed in 0.15% NP40 buffer and spun over a sucrose cushion to obtain nuclei. Nuclei were lysed in buffer containing 1% NP40 and 1M urea. RNA from chromatin pellet was purified using Qiagen RNeasy columns according to manufacturer protocol. 10 ug of RNA from each sample was depleted of ribosomal RNA using the Invitrogen Human/Mouse Ribominus kit.
Libraries were constructed from 500 ng of rRNA-depleted RNA using the dUTP method described in Levin et al, Nat Methods 2010

treatment_protocol: Cells containing inducible Ikaros were generated by transducing mouse pre-B cell line B3 with mouse stem cell virus (MSCV) retroviral vectors encoding a fusion protein of haemagglutinin-tagged wild type Ikaros (HA-Ikaros) and the estrogen receptor hormone-binding domain (ERt2), followed by an internal ribosomal entry site (IRES) and GFP. B3 cells containing inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP) were plated at a density of 0.5 million cells/ml in IMDM medium containing 10% FCS and 1% penicillin-streptomycin. 0.5uM 4 hydroxy-tamoxifen was added to the cells 2h before collection. Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin.

tag: cell line background

value: pre-B cell line

tag: cell line reference

value: Brown et al. 1997

tag: genotype/variation

value: 4-OHT 60min


title: MycERt2 60min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from MycERt2 60min 4-OHT Rep1

tag: cell type


title: MycERt2 60min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from MycERt2 60min 4-OHT Rep4


title: 511773A02 - nad9_Induction_2 vs nad9_Mock_2

hyb_protocol: nad9_Mock_2 Cy5 / nad9_Induction_2 Cy3 : 30pmol.

growth_protocol: whole plant - Media=MS-255 with 5% w/v sucrose Temperature=day 21°C / night 17°C  Light=16h light / 8h dark

treatment_protocol: Name:Estradiol - compound based treatment - compound addition,estradiol:quantity 10uM . Plants were transferred to 6 well plates with the roots dipping into MS-255 liquid medium with or without estradiol at a 10 micromolar final concentration.

value: Columbia

value: nad9 mutant

value: mock

value: induction


title: MycERt2 60min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from MycERt2 60min 4-OHT Rep2


title: BFUEs_Day2_43

tag: strain

value: 48 hrs


title: BFUEs_Day2_39


title: MycERt2 30min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from MycERt2 30min 4-OHT Rep4

source_name: MycERt2 30min 4-OHT

value: 4-OHT 30min


title: MycERt2 30min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from MycERt2 30min 4-OHT Rep3


title: MycERt2 30min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from MycERt2 30min 4-OHT Rep1


title: 557274A11 - Ctrl-3_3 vs Mutant-3_3

hyb_protocol: Mutant-3_3 Cy5 / Ctrl-3_3 Cy3 : 30pmol.

value: columbia)

tag: age


title: BFUEs_Day2_38

value: BFUE

value: erythroid progenitor media


title: Peripheral blood PROBLEM Sample23

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Peripheral blood PROBLEM Sample23

hyb_protocol: Hybridization were performed according to manufacturers protocol (WG-DASL) (illumina)

scan_protocol: According to Illumina protocols with Illumina iScan. Protocols can be found on the illumina web page.

data_processing: Data were transformed in log2 and normalised by quantiles using Bioconductor v3.3

source_name: Peripheral blood

label_protocol: Labeling were performed according to manufacturers protocol (WG-DASL) (illumina)

extract_protocol: Blood also collected in a PAXgene Blood miRNA tube was used to obtain RNA (including miRNAs) for expression analysis and was isolated using the PAXgene blood RNA kit (PreAnalytiX, Hombrechtikon, Switzerland) following the manufacturer’s protocol. Tumor RNA was isolated using the RNeasy FFPE kit (QIAGEN, Redwood City, USA) as instructed.

tag: group

value: NO PORTER


title: Peripheral blood PROBLEM Sample22

description: Peripheral blood PROBLEM Sample22

value: PORTER


title: 508883A10 - nad9_Mock_2 vs nad9_Induction_2

hyb_protocol: nad9_Induction_2 Cy5 / nad9_Mock_2 Cy3 : 30pmol.


title: MycERt2 30min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from MycERt2 30min 4-OHT Rep2


title: MycERt2 180min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from MycERt2 180min 4-OHT Rep2

source_name: MycERt2 180min 4-OHT

value: 4-OHT 180min


title: MycERt2 180min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from MycERt2 180min 4-OHT Rep1


title: Peripheral blood CCR Sample21

description: Peripheral blood CCR Sample21

value: CCR


title: 557274A03 - Ctrl-1_2 vs Mutant-1_2

hyb_protocol: Mutant-1_2 Cy5 / Ctrl-1_2 Cy3 : 30pmol.

value: columbia

value: mutant

value: wild type


title: BFUEs_Day2_40

value: No


title: 508883A02 - nad9_Mock_1 vs nad9_Induction_1

hyb_protocol: nad9_Induction_1 Cy5 / nad9_Mock_1 Cy3 : 30pmol.

value: Columbia


title: Peripheral blood CCR Sample20

description: Peripheral blood CCR Sample20


title: 508883A06 - nad9_Induction_1 vs nad9_Mock_1

hyb_protocol: nad9_Mock_1 Cy5 / nad9_Induction_1 Cy3 : 30pmol.

value: nad9 mutant


title: IkERt2_MycERt2 60min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 60min 4-OHT Rep3

source_name: IkERt2_MycERt2 60min 4-OHT

value: pre-B cell line

value: Brown et al. 1997

value: 4-OHT 60min


title: BFUEs_Day2_35

value: 48 hrs


title: BFUEs_Day2_37


title: IkERt2_MycERt2 60min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 60min 4-OHT Rep2


title: CTCL-TCRgd

city: New York

first: Eleni

last: Mimitou

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
TCRgd transcripts
processed data file:
CTCL-TCRgd.csv.gz
CTCL-TCRgd.csv.gz includes: raw counts for gd clonotypes
raw data submitted to dbGaP

data_processing:
Library strategy: ECCITE-seq
10x data were processed using cellranger and cellranger vdj pipeline
R1 includes cell barcode, UMI read
R2 is the  biological read
ADT data were mapped to a 12 bases or a 15 bases reference ADT list separately using CITE-seq-count
HTO data were mapped to a 12 bases reference HTO list using CITE-seq-count
GDO data were mapped to a 19 bases reference GDO list using CITE-seq-count
ADT, HTO and GDO sequence lists are available at: https://www.biorxiv.org/content/10.1101/466466v1
Genome_build: hg19 for human only samples
Genome_build: samples with both human and mouse cells were mapped to the hg19-mm10 concatenated reference as provided by cell-ranger
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT, HTO, GDO and clonotype mapping

source_name: Peripheral blood mononuclear cells

extract_protocol:
‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017). For sgRNA capture a custom RT primer was spiked in during the RT reaction.
library construction was performed with the 10x Genomics single cell 5' (VDJ) product.

treatment_protocol: K562, NIH-3T3 and peripheral blood mononuclear cells (PBMCs) were stained as described for CITE-seq (Stoeckius et al, 2017)

value: Peripheral blood mononuclear cells

tag: antibodies/tag


title: IkERt2_MycERt2 60min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 60min 4-OHT Rep1


title: IkERt2_MycERt2 30min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 30min 4-OHT Rep4

source_name: IkERt2_MycERt2 30min 4-OHT

value: 4-OHT 30min


title: BFUEs_Day2_34

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 39
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

value: BFUE

value: erythroid progenitor media

tag: time in culture


title: CTCL-TCRab

description:
TCRab transcripts
processed data file:
CTCL-TCRab.csv.gz
CTCL-TCRab.csv.gz includes: raw counts for ab clonotypes
raw data submitted to dbGaP


title: IkERt2_MycERt2 30min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 30min 4-OHT Rep2

tag: treatment


title: IkERt2_MycERt2 30min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 30min 4-OHT Rep3


title: ctrl-TCRab

description:
TCRab transcripts
processed data file:
ctrl-TCRab.csv.gz
ctrl-TCRab.csv.gz includes: raw counts for ab clonotypes
raw data submitted to dbGaP


title: IkERt2_MycERt2 180min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 180min 4-OHT Rep1

source_name: IkERt2_MycERt2 180min 4-OHT


title: IkERt2_MycERt2 30min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 30min 4-OHT Rep1


title: ctrl-TCRgd

description:
TCRgd transcripts
processed data file:
ctrl-TCRgd.csv.gz
ctrl-TCRgd.csv.gz includes: raw counts for gd clonotypes
raw data submitted to dbGaP


title: BFUEs_Day2_36


title: BFUEs_Day2_33


title: IkERt2_MycERt2 180min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 180min 4-OHT Rep2


title: IkERt2 60min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from IkERt2 60min 4-OHT Rep4

source_name: IkERt2 60min 4-OHT


title: QSG_miR-150-1

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

country: China

institute: Capital Medical University

data_processing:
The RNA-Seq reads were aligned to human reference genome (hg19) using Tophat (version 2.0.10) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Read counts were scaled to reads per kilo-base of exon model per million mapped reads (RPKM).

source_name: Human normal liver cell line

extract_protocol:
Total RNA from LX-2 or QSG cells was purified using Trizol (Sigma, USA) protocol with no modifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: normal liver cell line QSG

tag: passages

value: MiR-150-5p mimics


title: IkERt2_MycERt2 60min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from IkERt2_MycERt2 60min 4-OHT Rep4


title: Peripheral blood CCR Sample19

description: Peripheral blood CCR Sample19

value: CCR


title: IkERt2 60min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2 60min 4-OHT Rep2


title: Peripheral blood CCR Sample18

description: Peripheral blood CCR Sample18


title: Peripheral blood CONTROL Sample17

description: Peripheral blood CONTROL Sample17

value: CONTROL


title: QSG_C2

value: control


title: Peripheral blood CONTROL Sample14

description: Peripheral blood CONTROL Sample14


title: BFUEs_Day2_32


title: IkERt2 30min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2 30min 4-OHT Rep2

source_name: IkERt2 30min 4-OHT


title: Peripheral blood CONTROL Sample15

description: Peripheral blood CONTROL Sample15


title: IkERt2 60min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from IkERt2 60min 4-OHT Rep3


title: Peripheral blood CONTROL Sample16

description: Peripheral blood CONTROL Sample16


title: QSG_C1


title: IkERt2 60min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2 60min 4-OHT Rep1


title: BFUEs_Day2_30


title: IkERt2 30min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from IkERt2 30min 4-OHT Rep3


title: IkERt2 30min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from IkERt2 30min 4-OHT Rep4


title: QSG_miR-150-2


title: BFUEs_Day2_27


title: BFUEs_Day2_28


title: LX-2_miR-150-1

source_name: Human Hepatic stellate cell line

value: hepatic stellate cell line LX-2


title: IkERt2 180min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2 180min 4-OHT Rep1

source_name: IkERt2 180min 4-OHT

value: 4-OHT 180min


title: IkERt2 30min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from IkERt2 30min 4-OHT Rep1


title: IkERt2 180min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from IkERt2 180min 4-OHT Rep2


title: BFUEs_Day2_29

value: No


title: LX-2_C2


title: BFUEs_Day2_31


title: Empty vector 60min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from Empty vector 60min 4-OHT Rep2

source_name: Empty vector 60min 4-OHT

value: Empty vector


title: Empty vector 60min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from Empty vector 60min 4-OHT Rep3

value: pre-B cell line


title: BFUEs_Day2_25


title: Empty vector 30min 4-OHT Rep4

description: RNA-Seq of chromatin associated RNA from Empty vector 30min 4-OHT Rep4

source_name: Empty vector 30min 4-OHT

value: Brown et al. 1997


title: LX-2_C1


title: LX-2_miR-150-2


title: BFUEs_Day2_24


title: Empty vector 60min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from Empty vector 60min 4-OHT Rep1

value: 4-OHT 60min


title: Empty vector 30min 4-OHT Rep3

description: RNA-Seq of chromatin associated RNA from Empty vector 30min 4-OHT Rep3


title: BFUEs_Day2_26

value: 48 hrs


title: Empty vector 30min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from Empty vector 30min 4-OHT Rep2


title: BFUEs_Day2_23


title: Empty vector 30min 4-OHT Rep1

description: RNA-Seq of chromatin associated RNA from Empty vector 30min 4-OHT Rep1


title: Morula C5E2 RNA-seq

city: Boston

first: Wenhao

last: Zhang

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

data_processing:
RNA-seq reads were were mapped to human reference genome (hg19) using TopHat (version 2.1.1) paired-end alignment mode (parameters: --no-coverage-search --no-mixed --no-discordant). Mapped reads were further processed to calculate gene FPKM using Cufflinks (version 2.2.1) by default parameters. RefSeq database (hg19) from UCSC genome browser was used as annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for RNA-seq including FPKM values for each sample

source_name: human morula embryo

growth_protocol: Human morula embryos were generated by ICSI from patients who have singed consents for providing their otherwise discarded material for research. Briefly, 2PN zygotes were cultured in global® total® medium supplemented with HAS (LifeGlobal, CT, USA) under 5% O2, 6-7% CO2, and 88-89% N2. Then, embryos did not meet the freezing criteria for clinical purpose but developed to the morula like stage were collected and stored at -80 degree centigrade for ChIP-seq and RNA-seq.

extract_protocol: SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech) was used to perform reverse transcription and cDNA amplification (13 cycles) using whole-embryo lysate. cDNAs (80pg) were then fragmented, adaptor-ligated and amplified (12 cycles) using Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. Paired-end 100bp sequencing was performed on a HiSeq 2500 sequencer (Illumina).

tag: tissue

value: embryo

tag: developmental stage

value: morula

tag: chip-antibody

value: WT


title: Empty vector 180min 4-OHT Rep2

description: RNA-Seq of chromatin associated RNA from Empty vector 180min 4-OHT Rep2

source_name: Empty vector 180min 4-OHT