title: 42hpi_H9

description:
GGACTCCT_H9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H5

status: Public on Sep 08 2017

type: SRA

city: Cambridge

first: Daniel

middle: E.

last: Neafsey

state: MA

address: 415 Main St.

country: USA

institute: Broad Institute

description:
GGACTCCT_H5
42hpi.raw.tsv
42hpi.normalized.tsv

library_source: transcriptomic

data_processing:
Illumina NextSeq standard basecalling platform
Well barcode demultiplexing. Custom python script. Separates wells in 384-well plate
Unique molecular identifier demultiplexing. Custom python script. Counts reads from same mRNA molecule as only 1
Transcript alignment with bwa aln v0.7.10 allowing 4 mismatches in seed sequence and rest of sequence.
Discard reads with polyA tails (> 20 As in a row)
Additional filtering: Filter reads for rRNA. Remove samples with fewer than 300 reads. Remove genes that were found in <20 samples.
Generate normalized abundances with edgeR v3.14.0
Genome_build: PlasmoDB Plasmodium falciparum 3D7 transcript v29
Supplementary_files_format_and_content: 38hpi.raw.tsv - 38hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.raw.tsv - 42hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.raw.tsv - 46hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.filtered.tsv - 38hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.filtered.tsv - 42hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.filtered.tsv - 46hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.normalized.tsv - 38hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.normalized.tsv - 42hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.normalized.tsv - 46hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: all.normalized.tsv - all normalized read counts from all time points in matrix forrmat, where rows are samples and columns are genes

molecule: polyA RNA

organism: Plasmodium falciparum NF54

source_name: Single cell sorted Plasmodium infected human erythrocytes

growth_protocol: P.falciparum cell culture was performed as described previously (REF). Culture media consisted of RPMI-1640 supplemented with 25 mM HEPES, 100 μM hypoxanthine, 24 mM sodium bicarbonate, and gentamicin (all from Sigma-Aldrich). Serum media was generated by additional supplementation of 10% O+ human serum (The Interstate Companies) while serum-free medium was generated by additional supplementation of 0.39% fatty acid-free BSA, 30 μM oleic acid, and 30 μM palmitic acid (all from Sigma-Aldrich). To generate serum-free media supplemented with 20 μM LysoPC, LysoPC (Avanti Polar Lipids) was dissolved in ethanol and dried on culture dishes prior to culture addition. All cell cultures were maintained in a 5% CO2/1 % O2 and 95 % N2 gas mixture (Med-Tech Gases). All experiments used a clone of the Pf2004/164TdTomato P.falciparum line 14, which requires addition of 4 nM WR99210 (Jacobus Pharmaceuticals).

extract_protocol:
We used an optimized version of Single Cell RNA Barcoding and Sequencing 7 (SCRB-seq; Soumillon et al, 2014), further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from flow-sorted single Plasmodium infected erythrocytes were converted to cDNA, decorated with universal adapters, well barcodes, and unique molecular identifiers (UMIs), using a template-switching reverse transcriptase. Then, cDNA from multiple cells was pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3’ ends and preserving strand information.
Nextera XT

treatment_protocol: Parasite cultures were sorbitol-synchronized (Sigma-Aldrich) as described previously 21 to a 4-hour cycle window using 4 consecutive treatments across two growth cycles. At 28-32 hour post invasion, parasites were washed in RPMI/mFA media and plated with or without LysoPC. At 4, 8, and 12 hours post induction, cells were stained with Vybrant DyeCycle Violet (Life Technologies) in HBSS (Thermo Fisher Scientific). Stained cells were pelleted and resuspended in phenol red-free PBS supplemented with 0.3% RNaseOUT (Life Technologies). Collection Twin.tec PCR 384-well plates (Eppendorf) were prepared by addition of cell lysis buffer to each well; lysis buffer consisted of nuclease-free water (Thermo Fisher Scientific) supplemented with 0.2% HF buffer (New England Biolabs). Single Vybrant Dye Cycle Violet-positive cells were sorted using a Beckman Coulter MoFlo Astrios EQ. At each time point, 48 cells from the non-induced culture (+LysoPC) and 336 cells from the induced culture (-LysoPC) were sorted into the collection plate and snap frozen on dry ice. Cultures were maintained for an additional two cycles for parasitemia and gametocytemia measurement. The media of both non-induced and induced cultures was replaced with RPMI/serum 12 hours post induction and daily thereafter.

tag: time point

tag: induced

value: Induced


title: 42hpi_H6

description:
GGACTCCT_H6
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 16

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Bone marrow cells were collected from the femurs and tibiae of 7 week old mice.
Cells were stained with antibodies and single cells sorted using a FACS Influx5 (BD Biosciences)
Cells were sorted directly into individual wells of 96-well PCR plate containing lysis buffer.
Single-cell RNA-sequencing was performed as previously described (Picelli et al (2014) Nat. protocols 9:171)
Pooled libraries were run on an Illumina HiSeq 4000 sequencer.
RNA libraries were prepared for sequencing using Illumina XT DNA preparation kit

tag: cell type

value: All-lymphoid progenitor (ALP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D- B220-)

tag: strain

tag: age

value: 7 weeks

tag: genotype


title: 42hpi_H4

description:
GGACTCCT_H4
42hpi.raw.tsv
42hpi.normalized.tsv


title: E3.5_19

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: accessioned in GEO previously as GSM2371566

data_processing:
Quality control: Reads characterized by at least one of the following criteria were discarded from the analysis i) >50% of low quality bases (Phred score <5) ii) >5% of N bases iii) >80% of AT rate iv) ≥30% of continuous A and/or T
Genome reconstruction: The VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf) reporting all SNP sites from 36 mouse strains based on mm10 was downloaded from the Sanger database. Using SNPsplit tool (v0.3.0), these SNPs were filtered based on their quality values (FI value) and used to reconstruct the Cast genome from mm10 genome assembly.
Mapping: Single-end reads were then aligned to the mouse mm10 and Cast/EiJ genomes using the TopHat2 software (v2.1.0). Only random best alignments with less than 2 mismatches were reported for downstream analyses. The resulting mapping files for both parental genomes were then merged for each sample.
Allelic Ratio: The SAMtools mpileup utility (v1.1) was then used to extract base-pair information at each genomic position from the merged alignment file. At each SNP position, the number of paternal and maternal allele was counted. The allele-specific origin of the transcripts (or allelic ratio) has been measured by the total number of reads mapped on the paternal genome divided by the total number of reads for each gene: allelic ratio = paternal reads / (paternal+maternal) reads.
Estimation of gene expression levels: To estimate the transcript abundance, count tables of gene expression were generated using HTSeq v0.6.1 software. Read counts are then normalized based on the amplification size of each transcript (RPRT for Reads Per Retro-Transcribed length per million mapped reads)
Genome_build: mm10

source_name: single cell from E3.5 stage embryo

growth_protocol: natural matings, no embryo culture

extract_protocol:
PolyA+ mRNA extracted from each single cell was reverse transcribed from the 3’UTR and amplified following the Tang et al protocol. Care was taken to process only embryos and single blastomeres of the highest quality based on morphology, number of cells and on amplification yield. A total of 40 BC single blastomeres have been processed and passed quality controls.
Illumina manufacturer protocol

treatment_protocol: single cell cDNA amplification (Tang et al, 2010)

tag: developmental stage

tag: Sex

value: Female

tag: tissue

value: pre-implantation embryo


title: 42hpi_I14

description:
GGACTCCT_I14
42hpi.raw.tsv
42hpi.normalized.tsv


title: KO-Flt3-3

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

data_processing:
Transcript annotations for mm10 (build 75) were downloaded from Ensembl. Splice junction sequences from each gene's transcripts were generated using USeq's MakeTranscriptome application using a radius of 46.  The splice junction sequences were combined with the mm10 chromosomal sequences and run through novoindex (2.8) to create the transcriptome index file.
Reads were aligned to the transcriptome index described above using Novoalign (v2.08.01), allowing up to 50 alignments for each read.  USeq (v8.8.8) SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
USeq (v8.7.8) DefinedRegionDifferentialSeq was used to generate per gene read counts.  These counts were used in DESeq2  (v1.10.1), which normalizes the signal and identifies differently expressed genes.  Maximum likelihood estimates of the log2 fold changes were reported instead of the default 'shrunken' log2 fold changes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing raw counts, FPKM, DESeq2 log2 Fold Change and DESeq2 FDR

source_name: FLT3-ITD miR-155-/- mouse LKS cells

extract_protocol:
Total RNA was isolated from Lin-, Sca1+, cKit+ cells from FLT3-ITD and FLT3-ITD miR-155-/- mouse bone marrow using the Qiagen miRNeasy spin column kit. Each sample represents combined RNA from 3 mice in that group.
RNA libraries were prepared for sequencing using NEB Illumina library prep protocol.

tag: flt3 status

value: Homozygous for FLT3-ITD mutation

tag: mir-155 status

value: Homozygous deletion of miR-155

value: bone marrow

tag: cell markers

value: Lin-, cKit+, Sca1+


title: E3.5_63


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 15


title: 42hpi_H3

description:
GGACTCCT_H3
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H23

description:
GGACTCCT_H23
42hpi.raw.tsv
42hpi.normalized.tsv


title: KO-Flt3-2


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 14


title: 42hpi_H22

description:
GGACTCCT_H22
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H24

description:
GGACTCCT_H24
42hpi.raw.tsv
42hpi.normalized.tsv


title: KO-Flt3-1


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 13


title: 42hpi_H21

description:
GGACTCCT_H21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H20

description:
GGACTCCT_H20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H2

description:
GGACTCCT_H2
42hpi.raw.tsv
42hpi.normalized.tsv


title: WT-Flt3-3

source_name: FLT3-ITD mouse LKS cells

value: Wild type miR-155


title: WT-Flt3-2


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 12


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 23


title: WT-Flt3-1


title: 42hpi_H18

description:
GGACTCCT_H18
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H16

description:
GGACTCCT_H16
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H19

description:
GGACTCCT_H19
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 11


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 09


title: 42hpi_H17

description:
GGACTCCT_H17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H14

description:
GGACTCCT_H14
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H15

description:
GGACTCCT_H15
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_H12

description:
GGACTCCT_H12
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 08


title: 42hpi_H13

description:
GGACTCCT_H13
42hpi.raw.tsv
42hpi.normalized.tsv


title: small antral folllicle from wild type rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

description:
SAF-WT#2
F-WT.txt

data_processing:
Reads filtering under criteria removing reads with 14% of the base quality lower than 13.
Clean Reads mapped to Mouse GRCm38 genome using hisat2 v2.0.1 with  parameters --sensitive -k 5 --dta --min-intronlen 20 --max-intronlen 500000 -p 8 -x chrAll.
Fragments counting.
Genome_build: GRCm38
Supplementary_files_format_and_content: [.txt] file contains fragments (abundance measurements) for each sample

source_name: small antral folllicle from wild type

extract_protocol:
Single follicles were separated by hypodermic needle,and stored at -80℃ before library construction. RNAs were extracted using SPRI Ampure Beads.
The cDNA library was prepared according to the protocol of SMARTer® Ultra™Low Input RNA for Sequencing (Clonetech Laboratories).

value: small antral follicle

tag: follicle source

value: WT mice

value: ovary


title: 42hpi_H11

description:
GGACTCCT_H11
42hpi.raw.tsv
42hpi.normalized.tsv


title: preantral follicle from wild type rep1

description:
PF-WT#1
F-WT.txt

source_name: preantral follicle from wild type

value: preantral follicle


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 06


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 07


title: small antral folllicle from wild type rep1

description:
SAF-WT#1
F-WT.txt


title: preantral follicle from wild type rep2

description:
PF-WT#2
F-WT.txt


title: 42hpi_G8

description:
GGACTCCT_G8
42hpi.raw.tsv
42hpi.normalized.tsv


title: preantral follicle from transplanted FGSCs rep1

description:
PF-TF#1
F-TF.txt

value: transplanted FGSCs


title: 42hpi_H1

description:
GGACTCCT_H1
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G7

description:
GGACTCCT_G7
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G5

description:
GGACTCCT_G5
42hpi.raw.tsv
42hpi.normalized.tsv


title: small antral folllicle from transplanted FGSCs rep2

description:
SAF-TF#2
F-TF.txt


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 04


title: 42hpi_G9

description:
GGACTCCT_G9
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 05


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 03


title: preantral follicle from transplanted FGSCs rep2

description:
PF-TF#2
F-TF.txt


title: small antral folllicle from transplanted FGSCs rep1

description:
SAF-TF#1
F-TF.txt


title: 42hpi_G4

description:
GGACTCCT_G4
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G21

description:
GGACTCCT_G21
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 10


title: 42hpi_G20

description:
GGACTCCT_G20
42hpi.raw.tsv
42hpi.normalized.tsv


title: PTENhom_locusHom_9560

city: New York

first: Haley

last: Hieronymus

state: New York

address: 1275 York Ave.

institute: Memorial Sloan Kettering Cancer Center

description: prostate tumor from 12 month old FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mouse, HH9560

data_processing:
FASTQ output was mapped to the genome (UCSC MM10, Mus_musculus.GRCm38.80) using the rnaStar aligner23 that maps reads genomically and resolves reads across splice junctions. The 2 pass mapping method outlined in Engström, et al.  in which the reads are mapped twice was then used.
The output SAM files were  post processed using PICARD and converted it to compressed BAM format.
Expression counts were derived from the mapped reads using HTSeq.
DESeq2 was then used to normalize the dataset and analyze differential expression.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited DESeq2 normalized counts
Supplementary_files_format_and_content: tab-delimited HTSeq raw counts

source_name: prostate

extract_protocol:
Murine prostates were removed, half was frozen at -80C, and RNA was harvested from the frozen tissue using bead-based lysis in Trizol, followed by choroform extraction, isopropanol precipitation, and RNeasy cleanup.
Illumina TruSeq RNA Sample Prep Kit  v2 with 6 cycles of PCR was used for library construction. Samples were barcoded and run on a Hiseq 2500 in a single read 50 bp run, using the TruSeq SBS Kit v3 (Illumina).

value: prostate tumor

value: 12 months


title: 42hpi_G3

description:
GGACTCCT_G3
42hpi.raw.tsv
42hpi.normalized.tsv

value: Induced


title: 42hpi_G2

description:
GGACTCCT_G2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G24

description:
GGACTCCT_G24
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G23

description:
GGACTCCT_G23
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G22

description:
GGACTCCT_G22
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G6

description:
GGACTCCT_G6
42hpi.raw.tsv
42hpi.normalized.tsv


title: PTENhom_locusHom_9628

description: prostate tumor from 12 month old FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mouse, HH9628


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 01

value: All-lymphoid progenitor (ALP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D- B220-)


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 84

value: 7 weeks


title: 42hpi_G19

description:
GGACTCCT_G19
42hpi.raw.tsv
42hpi.normalized.tsv


title: PTENhom_locusHom_9558

description: prostate tumor from 12 month old FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mouse, HH9558


title: 42hpi_G17

description:
GGACTCCT_G17
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3del/del mouse 18217 cell 02


title: 42hpi_G18

description:
GGACTCCT_G18
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 83


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 82


title: 42hpi_G15

description:
GGACTCCT_G15
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G16

description:
GGACTCCT_G16
42hpi.raw.tsv
42hpi.normalized.tsv


title: PTENhom_B457

description: prostate tumor from 12 month old PTEN-flox/flox Pb-Cre4 mouse, HHb457

value: PTEN-flox/flox Pb-Cre4


title: PTENhom_41

description: prostate tumor from 12 month old PTEN-flox/flox Pb-Cre4 mouse, HH41


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 81


title: 42hpi_G10

description:
GGACTCCT_G10
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G14

description:
GGACTCCT_G14
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G12

description:
GGACTCCT_G12
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 80


title: 42hpi_G11

description:
GGACTCCT_G11
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 78


title: 42hpi_G13

description:
GGACTCCT_G13
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_G1

description:
GGACTCCT_G1
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F8

description:
GGACTCCT_F8
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 79


title: 42hpi_F9

description:
GGACTCCT_F9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F7

description:
GGACTCCT_F7
42hpi.raw.tsv
42hpi.normalized.tsv


title: PTENhom_9228

description: prostate tumor from 12 month old PTEN-flox/flox Pb-Cre4 mouse, HH9228


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 77


title: 42hpi_F6

description:
GGACTCCT_F6
42hpi.raw.tsv
42hpi.normalized.tsv


title: E16_Input_2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: A pool of 4 dissected mouse neocortices per sample were used for this experiment.  At E13 or E16 gender is not apparent. RNA was prepared from input (unfractionated) RNA or from sucrose density gradient pooled fractions.

data_processing:
Illumina software used for base calling
Fastq files of reads were aligned with genome using TopHat (default settings) with the UCSC genes.gtf mm10 transcript map from the Illumina iGenomes archive
Bam files were compared and fragments per kilobase per million reads (FPKM) was determined by CuffDiff
Results were loaded into the R/BioConductor package cummeRbund for analysis.  repFpkmMatrix was used to output the processed data file.
Genome_build: mm10
Supplementary_files_format_and_content: The FPKM value is shown for each transcript ID (RefSeq) and each Sample.

source_name: E16, Input

extract_protocol:
Pooled sucrose density gradient fractions were extracted with Trizol to recover RNA.  Input RNA was from Trizol homogenated tissue.
Illumina TruSeq

tag: fraction

value: input (unfractionated)

value: Embryonic neocortex


title: E16_Polysomes_1

source_name: E16, Polysomes

value: Polysome


title: E16_Polysomes_2


title: 42hpi_F5

description:
GGACTCCT_F5
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F4

description:
GGACTCCT_F4
42hpi.raw.tsv
42hpi.normalized.tsv


title: E16_Polysomes_0


title: E16_Input_1


title: E16_Input_0


title: 42hpi_F24

description:
GGACTCCT_F24
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F23

description:
GGACTCCT_F23
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F22

description:
GGACTCCT_F22
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F21

description:
GGACTCCT_F21
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 73


title: E16_406080_2


title: 42hpi_F20

description:
GGACTCCT_F20
42hpi.raw.tsv
42hpi.normalized.tsv


title: E16_406080_1


title: 42hpi_F2

description:
GGACTCCT_F2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F19

description:
GGACTCCT_F19
42hpi.raw.tsv
42hpi.normalized.tsv


title: E16_406080_0


title: 42hpi_F18

description:
GGACTCCT_F18
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 71


title: E13_Polysomes_2

source_name: E13, Polysomes


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 76


title: 42hpi_F16

description:
GGACTCCT_F16
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 75


title: 42hpi_F3

description:
GGACTCCT_F3
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 70


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 69


title: 42hpi_F15

description:
GGACTCCT_F15
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_Polysomes_1


title: 42hpi_F12

description:
GGACTCCT_F12
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_Polysomes_0


title: 42hpi_F13

description:
GGACTCCT_F13
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F11

description:
GGACTCCT_F11
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 74


title: 42hpi_F17

description:
GGACTCCT_F17
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_Input_2

description: A pool of 4 dissected mouse neocortices per sample were used for this experiment.  At E13 or E16 gender is not apparent. RNA was prepared from input (unfractionated) RNA or from sucrose density gradient pooled fractions.

source_name: E13, Input


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 67


title: 42hpi_F10

description:
GGACTCCT_F10
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 72


title: 42hpi_F14

description:
GGACTCCT_F14
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_Input_1


title: 42hpi_E9

description:
GGACTCCT_E9
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 68


title: 42hpi_E7

description:
GGACTCCT_E7
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 65


title: E13_Input_0


title: 42hpi_E6

description:
GGACTCCT_E6
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_406080_2


title: 42hpi_E5

description:
GGACTCCT_E5
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 64


title: 42hpi_E24

description:
GGACTCCT_E24
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 63


title: 42hpi_E3

description:
GGACTCCT_E3
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_406080_1


title: 42hpi_H10

description:
GGACTCCT_H10
42hpi.raw.tsv
42hpi.normalized.tsv


title: E13_406080_0


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 62


title: 42hpi_E23

description:
GGACTCCT_E23
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 61


title: 42hpi_E4

description:
GGACTCCT_E4
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E21

description:
GGACTCCT_E21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E20

description:
GGACTCCT_E20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E2

description:
GGACTCCT_E2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E8

description:
GGACTCCT_E8
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E22

description:
GGACTCCT_E22
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 60


title: 42hpi_E19

description:
GGACTCCT_E19
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E18

description:
GGACTCCT_E18
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E17

description:
GGACTCCT_E17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_F1

description:
GGACTCCT_F1
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 59


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 58


title: 42hpi_E14

description:
GGACTCCT_E14
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E15

description:
GGACTCCT_E15
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 57


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 56


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 66


title: 42hpi_E10

description:
GGACTCCT_E10
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E12

description:
GGACTCCT_E12
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E13

description:
GGACTCCT_E13
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E1

description:
GGACTCCT_E1
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 55


title: 42hpi_D8

description:
GGACTCCT_D8
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 53


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 52


title: 42hpi_D6

description:
GGACTCCT_D6
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 51


title: 42hpi_D3

description:
GGACTCCT_D3
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D4

description:
GGACTCCT_D4
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D24

description:
GGACTCCT_D24
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D23

description:
GGACTCCT_D23
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 50


title: 42hpi_D21

description:
GGACTCCT_D21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D5

description:
GGACTCCT_D5
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D22

description:
GGACTCCT_D22
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 49


title: 42hpi_D20

description:
GGACTCCT_D20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D2

description:
GGACTCCT_D2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E16

description:
GGACTCCT_E16
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D19

description:
GGACTCCT_D19
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 47


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 54


title: 42hpi_D7

description:
GGACTCCT_D7
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D9

description:
GGACTCCT_D9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D17

description:
GGACTCCT_D17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D15

description:
GGACTCCT_D15
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D14

description:
GGACTCCT_D14
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D18

description:
GGACTCCT_D18
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D16

description:
GGACTCCT_D16
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D13

description:
GGACTCCT_D13
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D12

description:
GGACTCCT_D12
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_E11

description:
GGACTCCT_E11
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 44


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 43


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 46


title: 42hpi_C9

description:
GGACTCCT_C9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D10

description:
GGACTCCT_D10
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_D11

description:
GGACTCCT_D11
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 42


title: 42hpi_C8

description:
GGACTCCT_C8
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 48


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 41


title: 42hpi_C6

description:
GGACTCCT_C6
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C7

description:
GGACTCCT_C7
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 40


title: 42hpi_C3

description:
GGACTCCT_C3
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C4

description:
GGACTCCT_C4
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 39


title: 42hpi_C5

description:
GGACTCCT_C5
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 45


title: 42hpi_C23

description:
GGACTCCT_C23
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 38


title: 42hpi_C21

description:
GGACTCCT_C21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C20

description:
GGACTCCT_C20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C2

description:
GGACTCCT_C2
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 37


title: 42hpi_D1

description:
GGACTCCT_D1
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 36


title: 42hpi_C17

description:
GGACTCCT_C17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C24

description:
GGACTCCT_C24
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 34


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 35


title: 42hpi_C15

description:
GGACTCCT_C15
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C14

description:
GGACTCCT_C14
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C16

description:
GGACTCCT_C16
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C18

description:
GGACTCCT_C18
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C12

description:
GGACTCCT_C12
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C10

description:
GGACTCCT_C10
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 32


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 33


title: 42hpi_C11

description:
GGACTCCT_C11
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B9

description:
GGACTCCT_B9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C22

description:
GGACTCCT_C22
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B6

description:
GGACTCCT_B6
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C13

description:
GGACTCCT_C13
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 30


title: 42hpi_B5

description:
GGACTCCT_B5
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C19

description:
GGACTCCT_C19
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 29


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 28


title: 42hpi_B7

description:
GGACTCCT_B7
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B4

description:
GGACTCCT_B4
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B24

description:
GGACTCCT_B24
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 26


title: 42hpi_B23

description:
GGACTCCT_B23
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 25


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 27


title: 42hpi_B20

description:
GGACTCCT_B20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B21

description:
GGACTCCT_B21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B22

description:
GGACTCCT_B22
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B19

description:
GGACTCCT_B19
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 24


title: 42hpi_B18

description:
GGACTCCT_B18
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 23


title: 42hpi_B2

description:
GGACTCCT_B2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B16

description:
GGACTCCT_B16
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_C1

description:
GGACTCCT_C1
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 31


title: 42hpi_B15

description:
GGACTCCT_B15
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B14

description:
GGACTCCT_B14
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 22


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 21


title: 42hpi_B3

description:
GGACTCCT_B3
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B12

description:
GGACTCCT_B12
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B10

description:
GGACTCCT_B10
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 19


title: 42hpi_B11

description:
GGACTCCT_B11
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B8

description:
GGACTCCT_B8
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 18


title: 42hpi_A7

description:
GGACTCCT_A7
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 16


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 20


title: 42hpi_B17

description:
GGACTCCT_B17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A4

description:
GGACTCCT_A4
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A3

description:
GGACTCCT_A3
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 15


title: 42hpi_A23

description:
GGACTCCT_A23
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 14


title: 42hpi_A5

description:
GGACTCCT_A5
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B13

description:
GGACTCCT_B13
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 12


title: 42hpi_A20

description:
GGACTCCT_A20
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A2

description:
GGACTCCT_A2
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A21

description:
GGACTCCT_A21
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_B1

description:
GGACTCCT_B1
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A22

description:
GGACTCCT_A22
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 11


title: 42hpi_A17

description:
GGACTCCT_A17
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A6

description:
GGACTCCT_A6
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A19

description:
GGACTCCT_A19
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 10


title: 42hpi_A18

description:
GGACTCCT_A18
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A9

description:
GGACTCCT_A9
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A15

description:
GGACTCCT_A15
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 09


title: 42hpi_A14

description:
GGACTCCT_A14
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 17


title: 42hpi_A12

description:
GGACTCCT_A12
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A13

description:
GGACTCCT_A13
42hpi.raw.tsv
42hpi.normalized.tsv


title: 42hpi_A16

description:
GGACTCCT_A16
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 07


title: 42hpi_A11

description:
GGACTCCT_A11
42hpi.raw.tsv
42hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 08


title: 42hpi_A1

description:
GGACTCCT_A1
42hpi.raw.tsv
42hpi.normalized.tsv


title: 38hpi_unknown

description:
AGGCAGAA_unknown
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 05


title: 42hpi_A10

description:
GGACTCCT_A10
42hpi.raw.tsv
42hpi.normalized.tsv


title: 38hpi_P9

description:
AGGCAGAA_P9
38hpi.raw.tsv
38hpi.normalized.tsv

value: Uninduced


title: 38hpi_P8

description:
AGGCAGAA_P8
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 06


title: 38hpi_P6

description:
AGGCAGAA_P6
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 03


title: 38hpi_P5

description:
AGGCAGAA_P5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P4

description:
AGGCAGAA_P4
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 04


title: 38hpi_P24

description:
AGGCAGAA_P24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P7

description:
AGGCAGAA_P7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P23

description:
AGGCAGAA_P23
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 01


title: 38hpi_P3

description:
AGGCAGAA_P3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P20

description:
AGGCAGAA_P20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P21

description:
AGGCAGAA_P21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P2

description:
AGGCAGAA_P2
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 84


title: 38hpi_P19

description:
AGGCAGAA_P19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 42hpi_A24

description:
GGACTCCT_A24
42hpi.raw.tsv
42hpi.normalized.tsv


title: 38hpi_P18

description:
AGGCAGAA_P18
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 83


title: 38hpi_P16

description:
AGGCAGAA_P16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P15

description:
AGGCAGAA_P15
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 81


title: 38hpi_P14

description:
AGGCAGAA_P14
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 02


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 79


title: 38hpi_P12

description:
AGGCAGAA_P12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P22

description:
AGGCAGAA_P22
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 80


title: 38hpi_P13

description:
AGGCAGAA_P13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P11

description:
AGGCAGAA_P11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P1

description:
AGGCAGAA_P1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P10

description:
AGGCAGAA_P10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_P17

description:
AGGCAGAA_P17
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 78


title: 38hpi_O8

description:
AGGCAGAA_O8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O9

description:
AGGCAGAA_O9
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 77


title: 38hpi_O5

description:
AGGCAGAA_O5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O6

description:
AGGCAGAA_O6
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 82


title: 38hpi_O7

description:
AGGCAGAA_O7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O3

description:
AGGCAGAA_O3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O4

description:
AGGCAGAA_O4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O23

description:
AGGCAGAA_O23
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 74


title: 38hpi_O24

description:
AGGCAGAA_O24
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 75


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 73


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 71


title: 38hpi_O21

description:
AGGCAGAA_O21
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 72


title: 38hpi_O17

description:
AGGCAGAA_O17
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 69


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 76


title: 38hpi_O2

description:
AGGCAGAA_O2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O18

description:
AGGCAGAA_O18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O19

description:
AGGCAGAA_O19
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 70


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 66


title: 38hpi_O12

description:
AGGCAGAA_O12
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 67


title: 38hpi_O14

description:
AGGCAGAA_O14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O16

description:
AGGCAGAA_O16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O10

description:
AGGCAGAA_O10
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 68


title: 38hpi_O13

description:
AGGCAGAA_O13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O11

description:
AGGCAGAA_O11
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 65


title: 38hpi_O1

description:
AGGCAGAA_O1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N7

description:
AGGCAGAA_N7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N5

description:
AGGCAGAA_N5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N8

description:
AGGCAGAA_N8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N9

description:
AGGCAGAA_N9
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N6

description:
AGGCAGAA_N6
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 63


title: 38hpi_N3

description:
AGGCAGAA_N3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_O20

description:
AGGCAGAA_O20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N24

description:
AGGCAGAA_N24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N23

description:
AGGCAGAA_N23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N22

description:
AGGCAGAA_N22
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 62


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 60


title: 38hpi_N21

description:
AGGCAGAA_N21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N20

description:
AGGCAGAA_N20
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 61


title: 38hpi_O22

description:
AGGCAGAA_O22
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 59


title: 38hpi_N19

description:
AGGCAGAA_N19
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 64


title: 38hpi_O15

description:
AGGCAGAA_O15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N4

description:
AGGCAGAA_N4
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 57


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 58


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 55


title: 38hpi_N17

description:
AGGCAGAA_N17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N16

description:
AGGCAGAA_N16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N15

description:
AGGCAGAA_N15
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 54


title: 38hpi_N10

description:
AGGCAGAA_N10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N14

description:
AGGCAGAA_N14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N1

description:
AGGCAGAA_N1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N11

description:
AGGCAGAA_N11
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 53


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 52


title: 38hpi_M8

description:
AGGCAGAA_M8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M7

description:
AGGCAGAA_M7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M9

description:
AGGCAGAA_M9
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N2

description:
AGGCAGAA_N2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M5

description:
AGGCAGAA_M5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M6

description:
AGGCAGAA_M6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M4

description:
AGGCAGAA_M4
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 51


title: 38hpi_M3

description:
AGGCAGAA_M3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M24

description:
AGGCAGAA_M24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_N13

description:
AGGCAGAA_N13
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 56


title: 38hpi_N18

description:
AGGCAGAA_N18
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 50


title: 38hpi_M23

description:
AGGCAGAA_M23
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 49


title: 38hpi_M20

description:
AGGCAGAA_M20
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 48


title: 38hpi_M22

description:
AGGCAGAA_M22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M21

description:
AGGCAGAA_M21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M19

description:
AGGCAGAA_M19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M2

description:
AGGCAGAA_M2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M18

description:
AGGCAGAA_M18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M17

description:
AGGCAGAA_M17
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 46


title: 38hpi_M16

description:
AGGCAGAA_M16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M15

description:
AGGCAGAA_M15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M12

description:
AGGCAGAA_M12
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 44


title: 38hpi_M13

description:
AGGCAGAA_M13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M11

description:
AGGCAGAA_M11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M14

description:
AGGCAGAA_M14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M10

description:
AGGCAGAA_M10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_M1

description:
AGGCAGAA_M1
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 43


title: 38hpi_L9

description:
AGGCAGAA_L9
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 42


title: 38hpi_N12

description:
AGGCAGAA_N12
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 41


title: 38hpi_L6

description:
AGGCAGAA_L6
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 47


title: 38hpi_L7

description:
AGGCAGAA_L7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L5

description:
AGGCAGAA_L5
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 40


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18220 cell 13


title: 38hpi_L4

description:
AGGCAGAA_L4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L23

description:
AGGCAGAA_L23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L8

description:
AGGCAGAA_L8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 42hpi_A8

description:
GGACTCCT_A8
42hpi.raw.tsv
42hpi.normalized.tsv


title: 38hpi_L22

description:
AGGCAGAA_L22
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 38


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 37


title: 38hpi_L3

description:
AGGCAGAA_L3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L21

description:
AGGCAGAA_L21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L2

description:
AGGCAGAA_L2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L20

description:
AGGCAGAA_L20
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 36


title: 38hpi_L19

description:
AGGCAGAA_L19
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 35


title: Suva_KO_ATRX_ChIPSeq

city: Headington

first: Richard

last: Gibbons

address: John Radcliffe Hospital

department: MHU, WIMM

institute: University of Oxford

library_source: genomic

data_processing:
Paired-end reads from ChIP-Seq and input samples were aligned to the mouse genome build using Bowtie (version 0.12.3) using standard parameters other than -M option set to 5
Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments
ATRX binding sites were identified in Seqmonk using the contig probe generator.
ATRX binding at repeat DNA in WT and Suv39h 1/2 double knockout was determined using Repeats Enrichment Estimator (Day DS et al. Genome Biol. 2010;11(6):R69.)
Genome_build: mm9
Supplementary_files_format_and_content: 3-column bed files containing coordinates of peaks for the mapped raw data of ATRX ChIP-seq in C57BL/6 MEFs and FL erythroid cells

molecule: genomic DNA

source_name: Mouse embryonic fibroblast

growth_protocol: MEFs were grown in DMEM supplemented with 10% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM. A single cell suspension was made by gently dissociating the E14.5 fetal livers and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences)). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using a magnetic column, MACS (miltenyi biotec).

extract_protocol:
I. Dynabead Preparation -Make PBS/BSA -For each ChIP reaction. Wash 100ul of beads 3-4 times with PBS BSA (5mg/ml) -Transfer beads to a 500ul PCR tube. -For ATRX antibody binding, Add 200ul ATRX H300, 22ul 50mg/ml BSA, 4ul ssDNA (Invitrogen 10mg/ml) -For NoAb Rxn. Add 222ul PBS BSA 4ul ssDNA -Incubate 3-4 hrs on roller at 4 oC -Wash 4 times in PBS BSA -Resuspend in 100ul PBSBSA and add 4ul (40ug) ssDNA For each preclear reaction -Take 100ul of Dynabeads -Wash 3-4 times with 1ml PBS BSA (5mg/ml freshly prepared) -Add 100ul of PBS BSA(5ug/ul) -Add 4ul ssDNA (10ug/ul) -Incubate at 4oC on roller with antibody binding reactions -Use 100ul for each preclearing reaction II. Cell cross-linking: Need 4oC PBS, Formaldehyde, EGS 1M glycine, Trypan blue, gilsons, timer 1.5ml tubes, calculator, A. Suspension Cells: 1. Make up EGS (Pierce 21565) stock fresh: 0.046g EGS in 200ul DMSO for 500mM stock 2. Chill PBS 3. Wash twice in PBS and resuspend in 20mls PBS (Important as FCS inhibits EGS) 4. Count cells 5. Use 3x107 – 5x107 cells for each ChIP reaction 6. Add EGS (it will form a white PPT which disperses afer a second) to 2mM and incubate at room temperature of 45 mins with occasional mixing. (80ul per 20mls of PBS). 7. Add formaldehyde solution to 1% for 20mins (526ul /20mls. 4 x 131.5ul) 8. Add 1/8 volume of 1M glycine to tubes to quench formaldehyde.(2.5ml glycine / 20ml PBS). 9. Spin cells at 1k for 5 min at 4oC. Make up protease inhibitors and add to lysis buffers. 10.Wash twice with 20ml 4oC PBS III. Cell sonication (keep all steps on ice): Note: Add protease inhibitors to all lysis buffers before use. If using a protease inhibitor cocktail tablet from Complete, dissolve one tablet in 2 ml water for 25X solution. Store aliquots at -20oC. 1. Resuspend each tube of cells in 10 ml of lysis buffer I. Rock at 4oC for 10 min, and then spin at 2k in a table-top centrifuge for 2 min at 4oC. 2. Resuspend each tube of cells in 5-10 ml of lysis buffer 2. Pellet nuclei in table-top centrifuge by spinning at 2.5k for 2 min at 4oC. 3. Resuspend the pellet in each tube in 3 ml lysis buffer 3. (Retain the buffer for step 6) 4. Sonicate the suspension in 15ml corning blue top tubes. 2mls per tube. Use the Bioruptor at high power for 20mins (4x5mins). After each 5 minute pulse, replenish the ice. 5. Add 1/10 volume of 10% Triton X-100. Transfer to 1.5 ml centrifuge tubes. Spin out debris at 14k for 10 min at 4oC. The lysate contains the fragmented DNA. 6. Save pellet for western analysis and take 50ul lysate for western analysis 7. Transfer lysate to 15 ml conical tube, adjusting the volume to 3 ml using lysis buffer 3. 8. Save 50µl of cell lysate from each sample as input. Save 50ul to assess sonication efficiency. IV. Chromatin immunoprecipitation: -Add 100ul of the preclearing beads from step I to the 3mls of chromatin lysate -Preclear on roller at 4 oC for 1 hour -Precipitate beads from chromatin using magnet and remove chromatin to new 3ml tubes -Add the washed antibody bound beads from step 1 -Incubate overnight on roller at 4 oC V. Washing, eluting, and reverse cross-linking: Note: Carry steps 1-3 in the cold room and all wash solution must be ice cold. 1. Transfer lysates from the 3 ml tubes to a 1.5ml tube. 2. Wash the IPs 5 times with 1 ml wash buffer (be sure to add protease inhibitors to the wash buffer). Use the magnetic stand to precipitate the beads. 3. Wash once with 1 ml cold PBS. Aspirate residual PBS. 4. Add 250µl of elution buffer. Elute on a roller at room temperature for 15 minutes. 5. Add 250ul more of elution buffer to beads, vortex, precipitate and combine with previous round of elution. 6. Take 50ul of eluate for western blot analysis 7. PPT beads and remove eluate to a new tube. Add 20ul 5M NaCl and incubate at 65oC for 4 hours. Thaw input, make up to 500ul with elution buffer, add 20ul 5M NaCl and incubate for 4hrs at 65oC. VI. RNase, Proteinase K, Phenol/Chloroform, EtOH PPT: Remove beads. Then add 20ul of 1M Tris pH6.5, 10ul 0.5M EDTA, 2ul 10mg/mg Proteinase K. Incubate for 1hrs at 45°C. Phenol chloroform and EtOH PPT with 20ug of carrier glycogen. Resuspend in 21ul sigma water.
Samples were quantified using the High Sensitivity Qubit system (Invitrogen) and distribution of fragments was determined using Agilent High Sensitivity DNA Kit and a 2100 Bioanalyzer Instrument system (Agilent). Libraries were constructed using the NEBNext DNA Sample Prep Kit (NEB) with the following modifications: End Repair was performed with 1µl of Enzyme mix and adapters were ligated using 4µl of Ligase. We used 10µl of a 1 in 100 dilution of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit) for 10ng of DNA and amplified with 25 µM each of the following custom primers: PCR primer 1.0 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ Index primer 5’-CAAGCAGAAGACGGCATACGAGAT[INDEX]CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’ *Indexes were according to the six bases tags developed by Illumina. The amplified libraries were purified using Ampure beads and size selected using 2% E-Gel® EX (Invitrogen), the distribution of fragments in the purified fraction was determined using a High Sensitivity Bioanalyzer kit and a 2100 Bioanalyzer Instrument system (Agilent). For equimolar pooling of the libraries, the relative concentration of the libraries was determined by realtime using Agilent QPCR Library Quantification Kit and a MX3005P instrument (Agilent). Finally, in order to determine the volume to use for sequencing, a second realtime was performed to measure the relative concentration of the pool compared to a previously sequenced ChIP library. Sequencing was performed as 50bp paired end on a GAIIx according to Illumina specifications using Cluster Generation Kit v4 and Sequencing Kit v4 in combination with illumina SCS 2.6/ RTA 1.6 software.

value: MEF

tag: chip antibody

value: ATRX H300 (Santa Cruz Biotechnology)

tag: genotype/variation

value: Suv39h1/2 knockouts


title: W8_MEF_input_ChIPSeq


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 34


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 33


title: 38hpi_L16

description:
AGGCAGAA_L16
38hpi.raw.tsv
38hpi.normalized.tsv


title: W8_MEF_ATRX_ChIPSeq


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 32


title: 38hpi_L17

description:
AGGCAGAA_L17
38hpi.raw.tsv
38hpi.normalized.tsv


title: C57_FL_ATRX_ChIPSeq

source_name: Mouse foetal liver

value: Foetal liver

value: Erythroid


title: 38hpi_L14

description:
AGGCAGAA_L14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L13

description:
AGGCAGAA_L13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L24

description:
AGGCAGAA_L24
38hpi.raw.tsv
38hpi.normalized.tsv


title: C57_MEF_input_ChIPSeq


title: C57_MEF_ATRX_ChIPSeq


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 30


title: 38hpi_L12

description:
AGGCAGAA_L12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L18

description:
AGGCAGAA_L18
38hpi.raw.tsv
38hpi.normalized.tsv


title: in vivo_KO 3_SL142927

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

data_processing:
Basecalls performed using CASAVA
Data were aligned to the mm9 genome using STAR version 3.0
Aligned reads were counted against genes from the UCSC mm9 annotation using the featureCounts from the SubRead package
Data were normalized for library size using the DESeq2 median ration normalization procedure described in Ander and Huber (2010).
Differential gene expression was assessed using the DESeq2 package in R
Genome_build: mm9
Supplementary_files_format_and_content: Counts of reads aligning to genes from the mm9 annotation as output from featureCounts

source_name: Col15a1 -/-_Atherosclerosis lesion

extract_protocol:
BCA were removed and flash frozen and RNA was harvested using standar Trizol reagent/protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were maintened in a Western Diet for 18 weeks

tag: strain background

tag: fed on

value: Western diet for 18 weeks

value: Atherosclerosis lesion

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 29


title: in vivo_KO 2_SL142926


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 28


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 27


title: 38hpi_L11

description:
AGGCAGAA_L11
38hpi.raw.tsv
38hpi.normalized.tsv

tag: time point

tag: induced


title: in vivo_KO 1_SL142925

tag: cell type


title: in vivo_WT 3_SL142924

source_name: WT_Atherosclerosis lesion

value: wild type


title: 38hpi_L1

description:
AGGCAGAA_L1
38hpi.raw.tsv
38hpi.normalized.tsv

value: Induced


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 31

value: All-lymphoid progenitor (ALP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D- B220-)

tag: strain

tag: age


title: 38hpi_L15

description:
AGGCAGAA_L15
38hpi.raw.tsv
38hpi.normalized.tsv


title: in vivo_WT 2_SL142923


title: 38hpi_K9

description:
AGGCAGAA_K9
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 24

value: 7 weeks

tag: genotype


title: 38hpi_K8

description:
AGGCAGAA_K8
38hpi.raw.tsv
38hpi.normalized.tsv


title: in vivo_WT 1_SL142922


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 23


title: 38hpi_K7

description:
AGGCAGAA_K7
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 22


title: C10_C/EBPa.24h_Ebf1

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure

data_processing:
reads were mapped using STAR (parameters: -outFilterMultimapNmax 1 -outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 -alignIntronMax 1 -alignEndsType EndToEnd).
Duplicates reads were removed using picard
bigwig tracks were made using DeepTools BamCoverage (parameters: -normalizeUsingRPKM -fragmentLength 200 -binSize 1)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, track of fragment signal (elongated to 200b)

growth_protocol: C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 μM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2

extract_protocol:
ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564).
Libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer

treatment_protocol: C10 cells were induced by the addition 100 nM of β-estradiol (Calbiochem) and grown with 10 nM of IL-3 and CSF-1 (Peprotech). Control cells were treated with 0.1% ethanol (solvent)

tag: cell line

value: C10 (HFATL-1 + ER-C/EBPa)

tag: target

value: ChIP Ebf1

tag: antibody vendor/catalog#

value: abnova 1879-mol clone 1c12


title: 38hpi_K6

description:
AGGCAGAA_K6
38hpi.raw.tsv
38hpi.normalized.tsv


title: C10_C/EBPa.12h_Ebf1


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 21


title: 38hpi_K5

description:
AGGCAGAA_K5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_L10

description:
AGGCAGAA_L10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K4

description:
AGGCAGAA_K4
38hpi.raw.tsv
38hpi.normalized.tsv


title: C10_C/EBPa.03h_Ebf1


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 20


title: C10_Ebf1


title: C10_Foxo1

value: ChIP Foxo1

value: abcam Anti-FOXO1A ab39670


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 26


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 19


title: 38hpi_K24

description:
AGGCAGAA_K24
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 18


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 25


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 17


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 16


title: 38hpi_K23

description:
AGGCAGAA_K23
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 15


title: 38hpi_K21

description:
AGGCAGAA_K21
38hpi.raw.tsv
38hpi.normalized.tsv


title: E18_5

city: Madrid

first: Patricia

last: Boya

state: Comunidad de Madrid

address: Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biológicas

description: Strand-specific RNA-seq (dUTP)

data_processing:
RNA-seq processing:
RNA-seq data was analyzed with the nextpresso pipeline as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cuffnorm (Cufflinks package)

source_name: Retina from E18.5 mouse embryo

extract_protocol:
At least 6 retinas were dissected  pooled and RNA was extracted with TRIZOL
1 µg of total RNA, with RIN (RNA integrity number) numbers in the range 8.6 to 9.9 (Agilent 2100 Bioanalyzer), was used. PolyA+ fractions were processed using the TruSeq Stranded mRNA Sample Preparation kit (Agilent). The resulting directional cDNA libraries were sequenced for 50 bases in a single-read format (Illumina HiSeq 2000)
Strand-specific RNA-Seq (dUTP)

tag: tissue

value: retina


title: E15_5

description: Strand-specific RNA-seq (dUTP)

source_name: Retina from E15.5 mouse embryo


title: E14_5

description: Strand-specific RNA-seq (dUTP)

source_name: Retina from E14.5 mouse embryo


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 14

source_name: Bone marrow


title: 38hpi_K20

description:
AGGCAGAA_K20
38hpi.raw.tsv
38hpi.normalized.tsv

source_name: Single cell sorted Plasmodium infected human erythrocytes


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 13


title: 38hpi_K3

description:
AGGCAGAA_K3
38hpi.raw.tsv
38hpi.normalized.tsv


title: E12_5

description: Strand-specific RNA-seq (dUTP)

source_name: Retina from E12.5 mouse embryo


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 12


title: 38hpi_K2

description:
AGGCAGAA_K2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K18

description:
AGGCAGAA_K18
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 10


title: P0

description: Strand-specific RNA-seq (dUTP)

source_name: Retina from postnatal day 1 mouse


title: 38hpi_K19

description:
AGGCAGAA_K19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K17

description:
AGGCAGAA_K17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K16

description:
AGGCAGAA_K16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K22

description:
AGGCAGAA_K22
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 08


title: 38hpi_K15

description:
AGGCAGAA_K15
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ppargc1a 3 paired-end

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_MCK201_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_MCK201_1_1.fastq__NCBIM37_minus_1e7.bedGraph

data_processing:
Libraries were sequenced for 50 cycles (1x single-end and 1x paired-end) on an Illumina HiSeq 2000, according to the manufacturer’s instructions.
RNA-seq reads were quality filtered with the FASTX software (-q 10 -p 97). Reads mapping to rRNA were removed with Bowtie.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.9 (-N 2 -g 20 --no-mixed)
Bedgraphs were generated using the HOMER software from combined tagDirectories (per sample type, i.e. single end and paired end reads were pooled in the tagDirectory creation step). Data analysis was performed using HOMER http://biowhat.ucsd.edu/homer/ and the R/Bioconductor packages edgeR and limma.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph RNA-seq signal files, separately for plus and minus strand

source_name: heart

growth_protocol: The animals were kept in standard housing conditions in The National Laboratory Animal Center of the University of Eastern Finland. Animals were fed ad libitum.

extract_protocol:
Total RNA was isolated from left ventricular tissue with Trizol reagent using TissueLyserII (Qiagen) to lyse the tissue.
Strand-specific dUTP protocol with rRNA depletion. The final libraries were sequenced using an Illumina HiSeq 2000 once in single-end mode and once in paired-end mode.
dUTP method, RNA-seq

treatment_protocol: Male mice (C57BL/6) expressing transgenic PGC-1α1 under MCK promoter (or WT control mic) were sacrificed at the age of 16 weeks and left ventricular tissue was snap freezed in liquid nitrogen.

tag: treatment

value: Ppargc1a overexpression

tag: replicate

value: heart


title: Ppargc1a 1 paired-end

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_MCK136_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_MCK136_1_1.fastq__NCBIM37_minus_1e7.bedGraph


title: Ppargc1a 2

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_MCK169_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_MCK169_1_1.fastq__NCBIM37_minus_1e7.bedGraph


title: Ppargc1a 3


title: Ppargc1a 2 paired-end


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 07


title: 38hpi_K14

description:
AGGCAGAA_K14
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ppargc1a 1


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 06


title: E13_5

description: Strand-specific RNA-seq (dUTP)

source_name: Retina from E13.5 mouse embryo


title: 38hpi_K13

description:
AGGCAGAA_K13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K12

description:
AGGCAGAA_K12
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 11


title: control 3 paired-end

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_K7_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_K7_1_1.fastq__NCBIM37_minus_1e7.bedGraph

value: control


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 05


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 09


title: control 3


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 04


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 03


title: control 2

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_K2_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_K2_1_1.fastq__NCBIM37_minus_1e7.bedGraph


title: 38hpi_K10

description:
AGGCAGAA_K10
38hpi.raw.tsv
38hpi.normalized.tsv


title: control 2 paired-end


title: 38hpi_K1

description:
AGGCAGAA_K1
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 02


title: control 1 paired-end

description:
rRNA depleted total RNA
RNA expression profiles were generated using RNA-seq from control and Ppargc1a overexpressing mice
tavi_comb_filt_K1_1_1.fastq__NCBIM37_plus_1e7.bedGraph
tavi_comb_filt_K1_1_1.fastq__NCBIM37_minus_1e7.bedGraph


title: 38hpi_J8

description:
AGGCAGAA_J8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J9

description:
AGGCAGAA_J9
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 01


title: control 1


title: 38hpi_J7

description:
AGGCAGAA_J7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J5

description:
AGGCAGAA_J5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J23

description:
AGGCAGAA_J23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J3

description:
AGGCAGAA_J3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J4

description:
AGGCAGAA_J4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J24

description:
AGGCAGAA_J24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_K11

description:
AGGCAGAA_K11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J20

description:
AGGCAGAA_J20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J21

description:
AGGCAGAA_J21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J19

description:
AGGCAGAA_J19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J22

description:
AGGCAGAA_J22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J2

description:
AGGCAGAA_J2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J16

description:
AGGCAGAA_J16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J15

description:
AGGCAGAA_J15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J17

description:
AGGCAGAA_J17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J14

description:
AGGCAGAA_J14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J13

description:
AGGCAGAA_J13
38hpi.raw.tsv
38hpi.normalized.tsv


title: CC_25h_repl2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8)
Sequences were aligned to the genome reference sequence of X. laevis  (genome build 9.1, available at Xenbase, http://www.xenbase.org/) using the STAR alignment software (version 2.5) allowing for 5 mismatches within 190 bases.
Counting of uniquely mapping hits was conducted with featureCounts.
Data was preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DEseq2 package (version 1.8).
Genome_build: Xla.v91
Supplementary_files_format_and_content: tab-delimited text file including raw read counts for each gene

organism: Xenopus laevis

source_name: animal caps

growth_protocol: Injected Xenopus laevis embryos were cultivated in 0.1X MBS culture buffer. After excision of the ectodermal explants at blastula stage, the explants were cultivated in 0.8X MBS culture buffer.

extract_protocol:
Total RNA was extracted using Trizol reagent (peqGOLD TriFast reagent, peQlab) according to instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectodermal explants were cultivated for 6 hours or 25 hours in 0.8 MBS culture buffer supplemented with 0.4 μm/ml dexamethasone (DEX) .

value: ectodermal explants

tag: treatment period

value: dexamethasone (DEX)

value: 25 hours


title: CC_25h_repl1


title: 38hpi_J18

description:
AGGCAGAA_J18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J12

description:
AGGCAGAA_J12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J11

description:
AGGCAGAA_J11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_J6

description:
AGGCAGAA_J6
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1aW224A/W242A-GR_25h_ repl2

tag: injected mrna


title: Ptf1aW224A/W242A-GR_25h_ repl1


title: 38hpi_J10

description:
AGGCAGAA_J10
38hpi.raw.tsv
38hpi.normalized.tsv


title: Neurog_25h_ repl2


title: Neurog2_25h_ repl1


title: 38hpi_J1

description:
AGGCAGAA_J1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I9

description:
AGGCAGAA_I9
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I8

description:
AGGCAGAA_I8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I7

description:
AGGCAGAA_I7
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1a_25h_ repl2


title: CC_6h_repl2

value: 6 hours


title: 38hpi_I6

description:
AGGCAGAA_I6
38hpi.raw.tsv
38hpi.normalized.tsv


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 45


title: 38hpi_I4

description:
AGGCAGAA_I4
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1aW224A/W242A_6h_ repl2


title: All-lymphoid progenitor (ALP) Mbd3flox/flox mouse 18218 cell 39


title: CC_6h_repl1


title: 38hpi_I5

description:
AGGCAGAA_I5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I3

description:
AGGCAGAA_I3
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1aW224A/W242AR_6h_ repl1


title: 38hpi_I24

description:
AGGCAGAA_I24
38hpi.raw.tsv
38hpi.normalized.tsv


title: Neuorg2_6h_ repl2


title: Ptf1a_6h_ repl2


title: Neurog2_6h_ repl1


title: 38hpi_I22

description:
AGGCAGAA_I22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I21

description:
AGGCAGAA_I21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I20

description:
AGGCAGAA_I20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I2

description:
AGGCAGAA_I2
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1a_6h_ repl1


title: 38hpi_I17

description:
AGGCAGAA_I17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I12

description:
AGGCAGAA_I12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I13

description:
AGGCAGAA_I13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I15

description:
AGGCAGAA_I15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I16

description:
AGGCAGAA_I16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I19

description:
AGGCAGAA_I19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H9

description:
AGGCAGAA_H9
38hpi.raw.tsv
38hpi.normalized.tsv


title: Ptf1a_25h_ repl1


title: 38hpi_I11

description:
AGGCAGAA_I11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I23

description:
AGGCAGAA_I23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H7

description:
AGGCAGAA_H7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I18

description:
AGGCAGAA_I18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H6

description:
AGGCAGAA_H6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H5

description:
AGGCAGAA_H5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I1

description:
AGGCAGAA_I1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H4

description:
AGGCAGAA_H4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H21

description:
AGGCAGAA_H21
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I10

description:
AGGCAGAA_I10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H23

description:
AGGCAGAA_H23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H20

description:
AGGCAGAA_H20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H3

description:
AGGCAGAA_H3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H22

description:
AGGCAGAA_H22
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H2

description:
AGGCAGAA_H2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H18

description:
AGGCAGAA_H18
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H19

description:
AGGCAGAA_H19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H16

description:
AGGCAGAA_H16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H15

description:
AGGCAGAA_H15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H13

description:
AGGCAGAA_H13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H12

description:
AGGCAGAA_H12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H14

description:
AGGCAGAA_H14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H10

description:
AGGCAGAA_H10
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H11

description:
AGGCAGAA_H11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H1

description:
AGGCAGAA_H1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H24

description:
AGGCAGAA_H24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G7

description:
AGGCAGAA_G7
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G9

description:
AGGCAGAA_G9
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G8

description:
AGGCAGAA_G8
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G6

description:
AGGCAGAA_G6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G4

description:
AGGCAGAA_G4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G5

description:
AGGCAGAA_G5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G3

description:
AGGCAGAA_G3
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G24

description:
AGGCAGAA_G24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G23

description:
AGGCAGAA_G23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H17

description:
AGGCAGAA_H17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G22

description:
AGGCAGAA_G22
38hpi.raw.tsv
38hpi.normalized.tsv


title: H33 MNase-seq input

city: Bronx

first: Kami

last: Kim

address: 1300 Morris Park Avenue

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Alignment: Bowtie, 2 mismatches and single hit
Genome_build: Toxoplasma gondii strain ME49 version 12
Supplementary_files_format_and_content: wig files of read coverage

organism: Toxoplasma gondii

source_name: Toxoplasma gondii RH∆hxgprt∆ku80

growth_protocol: Confluent human foreskin fibroblast cells were infected with tachyzoite forms of Toxoplasma gondii (RHΔhxgprt) at a ratio of 3-5 parasites per cell.  After around 40hs of infection, cells were harvested and lysed sequentially with 20G/23G/25G needles.

extract_protocol:
Parasites were lysed in lysis buffer to release nuclei. Nuclei were digested with micrococcal nuclease and centrifuged to remove cell debris and harvest digested DNA.
Libraries were prepared according to Illumina's instructions.

tag: developmental stage

value: tachyzoite

value: intracellular tachyzoites from human skin


title: 38hpi_G20

description:
AGGCAGAA_G20
38hpi.raw.tsv
38hpi.normalized.tsv

value: Induced


title: H2Ax MNase-seq input


title: 38hpi_G19

description:
AGGCAGAA_G19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G21

description:
AGGCAGAA_G21
38hpi.raw.tsv
38hpi.normalized.tsv


title: H2Bv MNase-seq input


title: 38hpi_G2

description:
AGGCAGAA_G2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G18

description:
AGGCAGAA_G18
38hpi.raw.tsv
38hpi.normalized.tsv


title: H4 MNase-seq input


title: 38hpi_G15

description:
AGGCAGAA_G15
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G17

description:
AGGCAGAA_G17
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G14

description:
AGGCAGAA_G14
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G13

description:
AGGCAGAA_G13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G12

description:
AGGCAGAA_G12
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G11

description:
AGGCAGAA_G11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G1

description:
AGGCAGAA_G1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_I14

description:
AGGCAGAA_I14
38hpi.raw.tsv
38hpi.normalized.tsv


title: fcs_Library_24_H3K4me3

city: College Station

first: Jennifer

last: Goldsby

state: TX

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

institute: Texas A&M University

data_processing:
Illumina CASAVA v 1.8.2 used for basecalling
ChIP-seq : mapped to the reference rat genome (rn4) with commonly used BWA for Illumina (version 1.2.3) settings and only non-identical uniquely mapped reads were retained
ChIP-seq : The peak caller programme MACS (version 1.4.1) (5) was used to identify peaks with the following parameter settings: --bw=300 --keep-dup=1.
ChIP-seq : Islands were defined (using merge function of BEDTools (6)) as the genomic areas enriched with the ChIPed protein (peaks) in at least one sequenced sample, and reads were quantified using coverageBed function of BEDTools (6)
ChIP-seq : Regions showing differences in histone modification were identified using the edgeR package (8, 9) for the R software environment.  .  Read counts per gene were normalized using the scaling factor method of Anders and Huber (10).  Differential expression testing of genes was performed using likelihood ratio tests on the negative binomial GLMs estimated by edgeR (8, 9).  Regions with FDR < 0.1 and minimal threshold of one count per million mapped reads in at least four samples were selected as differentially enriched regions (DERs).
RNA: Reads were mapped with the STAR aligner using the default parameters and rn5 genome assembly
RNA: Read counts per gene were normalized using the scaling factor method of Anders and Huber  (10).  The read counts were modeled directly using negative binomial generalized linear models accounting for the differences in diet and subsequently fit with the R programming language (5) and Bioconductor package edgeR (8, 9). Differential expression was then tested using likelihood ratio tests involving the fitted models.   Genes with false discovery rate adjusted p-value (FDR) less than 0.1 were selected as differentially expressed transcripts (DE).
Genome_build: rn4
Supplementary_files_format_and_content: xls files include counts processed with Bedtools(number of reads that mapped to the specified locations).  EdgeR was used to determine FDR, and differential expression(in the form of fold change experimental over control)

organism: Rattus norvegicus

source_name: colonocytes

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP .  For RNA colonic crypts were homogenized on ice in lysis buffer (RNAqueous Isolation kit, Ambion)
generate multiplex libraries for whole-transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Libraries from 24 individual rats per treatment were sequenced on an Illumina HiSeq 2000.   BioScientific NETflex (ChIPseq kit 5143-01, Barcodes kit 514120) multiplex libraries from ChIPed DNA (10 nM) were sequenced using a Illumina Hiseq 2000 DNA Sequencer.  Libraries from  biological replicates of pooled ChIPed samples per treatment were individully sequenced on an Illumina HiSeq 2000.
ChIP-seq with BioScientific NETflex (ChIPseq kit 5143-01, Barcodes kit 514120)and RNA-seq (Illumina’s TruSeq RNA v2 )

treatment_protocol: After 2 weeks of feeding weanling male rats with specified oil/fiber, 24 rats were injected with saline (control), and 43 rats were AOM (Sigma, St. Louis, MO) injected s.c. at 15 mg/kg body weight. Each rat subsequently received a second AOM or saline injection 1 week later and animals were terminated 10 weeks after the first AOM injection.

tag: chip antibody

value: H3K4me3 (Active Motif 39160)

tag: carcinogen

value: saline

tag: oil

value: fish oil

tag: fiber

value: cellulose


title: cps_Library_28_H3K4me3

value: corn oil

value: pectin


title: input_Library_29_H3K4me3

value: saline/AOM

value: cellulose/pectin


title: 38hpi_F9

description:
AGGCAGAA_F9
38hpi.raw.tsv
38hpi.normalized.tsv

tag: time point

tag: induced


title: cps_Library_27_H3K4me3


title: fcs_Library_25_H3K4me3


title: fcs_Library_23_H3K4me3


title: fps_Library_21_H3K4me3


title: fps_Library_22_H3K4me3


title: 38hpi_F8

description:
AGGCAGAA_F8
38hpi.raw.tsv
38hpi.normalized.tsv


title: cps_Library_26_H3K4me3


title: ccs_Library_19_H3K4me3


title: 38hpi_F6

description:
AGGCAGAA_F6
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F5

description:
AGGCAGAA_F5
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_G16

description:
AGGCAGAA_G16
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F3

description:
AGGCAGAA_F3
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs_Library_18_H3K4me3


title: 38hpi_F4

description:
AGGCAGAA_F4
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F24

description:
AGGCAGAA_F24
38hpi.raw.tsv
38hpi.normalized.tsv


title: ccs_Library_17_H3K4me3


title: H9_hESCs

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

description:
H9E6
hESC-H9

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to hg19 whole genome using Tophat v1.2.  Alignments were then quantified using HTSeq and analyzed using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file

organism: Homo sapiens

source_name: Day 12 of differentiation from hESCs

extract_protocol:
Cells were FACS sorted for reporter signal and Trizol was added to the cells and frozen.  RNA was extracted using a combination of phase lock gels and the Rneasy Mini Elute kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: H9 hESCs


title: 38hpi_G10

description:
AGGCAGAA_G10
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_Library_16_H3K4me3

value: AOM


title: 38hpi_F7

description:
AGGCAGAA_F7
38hpi.raw.tsv
38hpi.normalized.tsv


title: fps_Library_20_H3K4me3


title: NNE_2

description:
NNE2
Non-neural Ectoderm #2

value: non-neural ectoderm


title: NNE_1

description:
NNE1
Non-neural Ectoderm #1


title: cpa_Library_15_H3K4me3


title: cpa_Library_13_H3K4me3


title: 38hpi_F2

description:
AGGCAGAA_F2
38hpi.raw.tsv
38hpi.normalized.tsv


title: CP_Six1GFP_2

description:
T2
Cranial Placode #2

value: SIX1+ cranial placodes


title: CP_Six1GFP_1

description:
T1
Crainal Placode #1


title: 38hpi_F19

description:
AGGCAGAA_F19
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F20

description:
AGGCAGAA_F20
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F17

description:
AGGCAGAA_F17
38hpi.raw.tsv
38hpi.normalized.tsv


title: NC_Sox10GFP_1

description:
S1
Neural Crest #1

value: SOX10+ neural crest


title: 38hpi_F18

description:
AGGCAGAA_F18
38hpi.raw.tsv
38hpi.normalized.tsv


title: fca_Library_11_H3K4me3


title: NNE_3

description:
NNE3
Non-neural Ectoderm #3


title: NC_Sox10GFP_2

description:
S2
Neural Crest #2


title: NC_Sox10GFP_3

description:
S3
Neural Crest #3


title: fca_Library_9_H3K4me3


title: fca_Library_10_H3K4me3


title: 38hpi_F23

description:
AGGCAGAA_F23
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F15

description:
AGGCAGAA_F15
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa_Library_7_H3K4me3


title: 38hpi_F22

description:
AGGCAGAA_F22
38hpi.raw.tsv
38hpi.normalized.tsv


title: cpa_Library_14_H3K4me3


title: 38hpi_F14

description:
AGGCAGAA_F14
38hpi.raw.tsv
38hpi.normalized.tsv


title: fca_Library_12_H3K4me3


title: fpa_Library_6_H3K4me3


title: 38hpi_F13

description:
AGGCAGAA_F13
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_H8

description:
AGGCAGAA_H8
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa_Library_5_H3K4me3


title: 38hpi_F16

description:
AGGCAGAA_F16
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa_Library_8_H3K4me3


title: 38hpi_F12

description:
AGGCAGAA_F12
38hpi.raw.tsv
38hpi.normalized.tsv


title: cca_Library_4_H3K4me3


title: 38hpi_F1

description:
AGGCAGAA_F1
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F11

description:
AGGCAGAA_F11
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_F10

description:
AGGCAGAA_F10
38hpi.raw.tsv
38hpi.normalized.tsv


title: Q25_UUS

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
The paired-end sequence reads were aligned to the human genome (hg19) with Subread (version 1.5.0) using default settings
Reads were summarized using default settings of the featureCounts program for paired-end reads, and single nucleotide polymorphisms were identified using default settings of the exactSNP program within the Subread package
Variants were annotated with wANNOVAR web interface (http://wannovar.usc.edu)
Mutations were filtered for <0.1% presence in any population included in 1000 Genomes or ExAC studies, exonic location, and nonsynonymous or stopgain effect.
Genome_build: hg19
Supplementary_files_format_and_content: subread_counts.txt files contain reads summarized using default settings of the featureCounts program for paired-end reads

source_name: UUS

extract_protocol:
Total RNA was extracted from frozen tissue specimens using the miRNeasy Mini Kit (Qiagen), including DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was verified using Bio-Rad Experion system (Bio-Rad Laboratories).
Samples were prepared with the Illumina TruSeq RNA Sample Preparation Kit (Illumina). The insert sizes of the libraries were assessed using Agilent Technologies 2100 Bioanalyzer. Validated DNA libraries were pooled, clustered on the cBot cluster generation station (Illumina), and sequenced on a HiSeq 2000 platform (Illumina). Prepared libraries were sequenced using HiSeq 2000 (Illumina) operated in paired-end 2x100 bp mode. Reads were quality-filtered using a standard Illumina pipeline.

tag: tumor type

value: Undifferentiated


title: cca_Library_1_H3K4me3


title: Q7_UUS


title: Q11_UUS


title: 38hpi_E8

first: Daniel

last: Neafsey

description:
AGGCAGAA_E8
38hpi.raw.tsv
38hpi.normalized.tsv

data_processing:
Illumina NextSeq standard basecalling platform
Well barcode demultiplexing. Custom python script. Separates wells in 384-well plate
Unique molecular identifier demultiplexing. Custom python script. Counts reads from same mRNA molecule as only 1
Transcript alignment with bwa aln v0.7.10 allowing 4 mismatches in seed sequence and rest of sequence.
Discard reads with polyA tails (> 20 As in a row)
Additional filtering: Filter reads for rRNA. Remove samples with fewer than 300 reads. Remove genes that were found in <20 samples.
Generate normalized abundances with edgeR v3.14.0
Genome_build: PlasmoDB Plasmodium falciparum 3D7 transcript v29
Supplementary_files_format_and_content: 38hpi.raw.tsv - 38hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.raw.tsv - 42hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.raw.tsv - 46hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.filtered.tsv - 38hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.filtered.tsv - 42hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.filtered.tsv - 46hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.normalized.tsv - 38hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.normalized.tsv - 42hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.normalized.tsv - 46hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: all.normalized.tsv - all normalized read counts from all time points in matrix forrmat, where rows are samples and columns are genes

extract_protocol:
We used an optimized version of Single Cell RNA Barcoding and Sequencing 7 (SCRB-seq; Soumillon et al, 2014), further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from flow-sorted single Plasmodium infected erythrocytes were converted to cDNA, decorated with universal adapters, well barcodes, and unique molecular identifiers (UMIs), using a template-switching reverse transcriptase. Then, cDNA from multiple cells was pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3’ ends and preserving strand information.
Nextera XT


title: Q5_UUS


title: cca_Library_3_H3K4me3


title: Q8_UUS


title: 38hpi_E7

description:
AGGCAGAA_E7
38hpi.raw.tsv
38hpi.normalized.tsv


title: inp29_IgG

value: IgG


title: cca_Library_2_H3K4me3


title: inp30_IgG


title: Q9_UUS


title: Q6_UUS


title: fps22_H3K9ac

value: H3K9ac (Abcam ab10812)


title: 38hpi_E6

description:
AGGCAGAA_E6
38hpi.raw.tsv
38hpi.normalized.tsv

value: Induced


title: CME297594_ESSLG

source_name: ESS low grade

value: Low grade


title: Q4_UUS


title: 38hpi_E9

description:
AGGCAGAA_E9
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E5

description:
AGGCAGAA_E5
38hpi.raw.tsv
38hpi.normalized.tsv


title: fps20_H3K9ac

value: saline


title: Q24_ESSLG


title: CME256003_ESSLG


title: 38hpi_E4

description:
AGGCAGAA_E4
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa8_H3K9ac

value: fish oil


title: Q23_ESSLG


title: fpa7_H3K9ac


title: 38hpi_E23

description:
AGGCAGAA_E23
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa6_H3K9ac


title: 38hpi_E3

description:
AGGCAGAA_E3
38hpi.raw.tsv
38hpi.normalized.tsv


title: Q3_ESSLG


title: 38hpi_E22

description:
AGGCAGAA_E22
38hpi.raw.tsv
38hpi.normalized.tsv


title: fpa5_H3K9ac


title: fcs24_H3K9ac

value: cellulose


title: Q10_ESSLG


title: 38hpi_E24

description:
AGGCAGAA_E24
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E20

description:
AGGCAGAA_E20
38hpi.raw.tsv
38hpi.normalized.tsv


title: Q20_ESSLG


title: fcs25_H3K9ac


title: 38hpi_E21

description:
AGGCAGAA_E21
38hpi.raw.tsv
38hpi.normalized.tsv


title: fps21_H3K9ac


title: fcs23_H3K9ac


title: Q17_ESSLG


title: Q19_ESSHG

source_name: ESS high grade

value: High grade


title: 38hpi_E2

description:
AGGCAGAA_E2
38hpi.raw.tsv
38hpi.normalized.tsv


title: 38hpi_E19

description:
AGGCAGAA_E19
38hpi.raw.tsv
38hpi.normalized.tsv


title: Q18_ESSHG


title: 38hpi_E18

description:
AGGCAGAA_E18
38hpi.raw.tsv
38hpi.normalized.tsv


title: fca12_H3K9ac


title: fca11_H3K9ac