title: MPH5_Kit+K5+

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit+;K5-venus+)


title: MPH8_Kit-K5-

status: Public on Jan 01 2017

type: SRA

city: Bethesda

first: Matthew

middle: P

last: Hoffman

state: MD

address: 30 Convent Dr MSC4370

country: USA

institute: NIDCR

library_source: transcriptomic

data_processing:
Read QC analysis: FastQC
read mapping, STAR v2.4.2a with the following options:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None  --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 –alignIntronMax 0 --alignMatesGapMax 0
bam grooming: Sorting, Readgroup addition and duplicate marking using Picard Tools v1.129
Gene quantification. Per gene raw read counts were generated using Subread's featureCounts software v1.4.6-p3. Settings: -p -t exon -g gene_name
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: gene quantifications (raw read counts) in tab-delimited .txt format

molecule: total RNA

organism: Mus musculus

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit-;K5-venus-)

extract_protocol:
RNA was isloated using Ambions RNAqueous-4PCR kit and were treated with DNase (DNA-free Kit, Ambion).
Total RNA was extracted from epithelial cells sorted by FACS analysis and RNAseq performed by Cofactor Genomics (www.cofactorgenomics.com). Single-ended reads (50 nt in length) were produced using Illumina sequencer (Illumina). Reads were mapped to the GRCm38/mm10 using the STAR 2.4.2a aligner and gene counts generated with Subread's featureCounts tool.

treatment_protocol: Fluorescence-activated cell sorting: SMGs were prepared for FACS analysis as previously described (Knox SM, et al,. Parasympathetic innervation maintains epithelial progenitor cells during salivary organogenesis. Science 329, 1645-1647 (2010). Anti-E-cadherin APC (FAB7481A, R&D Systems) and anti-Kit PE (BD Biosciences) were also used. Fluorescence levels were analyzed using FlowJo (Tree Star).

tag: strain

tag: developmental stage

value: embryonic day 15

tag: tissue

value: submandibular salivary glands

tag: cell type

value: FACs sorted epithelial cells

tag: cell subtype


title: MPH3_Kit-K5+

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit-;K5-venus+)


title: MPH2_Kit+K5-

source_name: Submandibular gland epithelal cells E15 (Ecad+;Kit+;K5-venus-)


title: input_DNA

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

country: China

institute: South China Agricultural University

library_source: genomic

data_processing:
Initial quality-control analysis of raw data was performed using FASTX-Toolkit version 0.7
Once processed, the sequence reads were aligned to the chicken genome (Gallus Gallus 4.0) by Bowtie2 (version 2.1.0), allowing one mismatch it the seed (22bp).
HOMER software v4.7 was employed for peak calling with mapped input reads as control
Genome_build: Gallus Gallus 4.0

molecule: genomic DNA

organism: Gallus gallus

source_name: primary chicken myoblast

growth_protocol: Primary embryonic myoblast cells were isolated from thigh muscles of 11-day-old chicken embryos.The primary cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) growth medium with 20% fetal bovine serum (Gibco), 100 IU/ml penicillin, and 100ug/ml streptomycin. To purify myoblasts, the cells were serially plated into 60mm cell culture dishes (Greiner) for three times with 40-minute intervals.

extract_protocol:
Chromatin was fragmented to 300 to 500bp by sonication in the SDS-lysis buffer (50 mM Tris–HCl (pH8.1), 10 mM EDTA, 1% SDS) with 15 cycles. Fragmented soluble chromatin was immunoprecipitated with ChIP grade antibodies from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA fragments were blunted using the TruSeq Chip Library Prep Kit (Illumina), ligated to the sequencing adapter and performed on PCR amplification to construct the sequencing library. After purification by agarose gel, two DNA libraries (ChIP and input) were used for sequencing analysis by Illumina HiSeq2000 system

treatment_protocol: Chicken embryo myoblast cell differentiation was induced by culturing the cells in differentiation medium that consisted of DMEM (Gibco), supplemented with 2% horse serum (Hyclone), 100 IU/ml penicillin and 100ug/ml streptomycin.

value: Differentiated myoblast cell

value: 11-day embyo

tag: chip antibody


title: MPH1_Kit+K5+


title: FOXO1_ChIP

value: FOXO1 (sc-374427X, Santa Cruz)


title: s_261982

city: Rochester

first: Nathan

last: LeBrasseur

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
data was processed using the MAP-Rseq protocol : Kalari et al. BMC Bioinformatics 2014, 15:224
Paired-end reads are aligned by TopHat 2.0.6 against the hg19 genome build using the bowtie1 aligner option
Options we used for TopHat software are --keep-fasta-order, --keep-tmp, --no-coverage-search, --bowtie1, --library-type fr-unstranded, --max-multihits 20, --solexa1.3-quals, --fusion-search, --fusion-ignore-chromosomes chrM, --fusion-min-dist 50000
Gene counts are generated using HTseq software (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and gene annotation files are obtained from Illumina (http://cufflinks.cbcb.umd.edu/igenomes.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing a matrix of gene counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: lung tissue

extract_protocol:
RNA extract protocol not provided
RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) from 200 ng of total RNA using standard Illumina protocols

value: lung

tag: disease state

value: Control


title: s_265639


title: s_205028


title: s_280560


title: s_104702


title: 105

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) rat gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

organism: Bos taurus

source_name: Rumen

extract_protocol:
rumen tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: residual feed intake

value: High RFI

value: rumen epithelial tissue


title: s_020096


title: s_298223


title: MPH9_Kit+K5+


title: s_098820


title: s_202617


title: s_221031


title: s_072042


title: s_058471


title: s_116004

value: Idiopathic Pulmonary Fibrosis


title: s_138327


title: s_046027


title: s_074978


title: s_191307


title: s_149517


title: s_164046


title: s_280263


title: s_137431


title: s_059846


title: s_089451


title: s_022562


title: s_284489


title: s_263234


title: s_102021


title: s_186024


title: s_133378


title: s_258760


title: s_111533


title: s_131648


title: s_282634


title: s_269070


title: METSIM_4219

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description:
DNA treated with sodium bisulfite
AT9_23

data_processing:
Multiplexed Illumina sequencing runs were demultiplexed to fastq files using a custom perl script, allowing for 1 mismatch between observed and expected barcodes.
Individual fastq files were trimmed for potential RRBS adapters using the “Trim Galore!” wrapper (http://www.bioinfooption.rmatics.babraham.ac.uk/projects/trim_galore/) using the RRBS
Trimmed fastq files were mapped to the unmasked hg19 genome (whole chromosomes only) using the BSMap program (https://code.google.com/archive/p/bsmap/) with the following command line options “-p 8 -w 1 -r 0 -v 4 -D C-CGG”.
Processed ratio files were generated using a modified version of the methratio.py script included with the BSMap program.
Genome_build: hg19
Supplementary_files_format_and_content: The processed methylation ratio (*.ratio) files follow the same format document in the BSMap program for the methratio.py script for the first 10 columns. Briefly the columns should appear as “chromosome\tcoordinate\tstrand\tsequence context\tmethylation ratio\teffective total C+T counts\ttotal C counts\ttotal C+T counts\ttotal G counts\ttotal G+A counts” where “\t” represents a tab character. The final two columns of the lower and upper bounds of a 95% confidence interval are not included. In addition, the methylation ratio was reported as -1 at sites where C+T counts were equal to 0 and can be excluded from downstream analyses.

source_name: adipose tissue

extract_protocol:
DNA from adipose tissue biopsies with the DNeasy extraction kit (Qiagen)
RRBS libraries were prepared as previously described (Orozco et al., 2015. Cell Metabolism 21, 905-917) with minor modifications described in the manuscript associated with this study.

value: adipose

tag: gender

value: male


title: METSIM_2513

description:
DNA treated with sodium bisulfite
AT7_23


title: METSIM_2743

description:
DNA treated with sodium bisulfite
AT8_22


title: METSIM_4008

description:
DNA treated with sodium bisulfite
AT9_22


title: METSIM_2748

description:
DNA treated with sodium bisulfite
AT8_23


title: s_254200


title: METSIM_2902

description:
DNA treated with sodium bisulfite
AT9_21


title: METSIM_2726

description:
DNA treated with sodium bisulfite
AT8_20


title: s_228552


title: METSIM_2741

description:
DNA treated with sodium bisulfite
AT8_21


title: METSIM_5166

description:
DNA treated with sodium bisulfite
AT7_21


title: s_152649


title: 23


title: s_133583


title: METSIM_6041

description:
DNA treated with sodium bisulfite
AT52_21


title: METSIM_4518

description:
DNA treated with sodium bisulfite
AT6_21


title: METSIM_4509

description:
DNA treated with sodium bisulfite
AT6_20


title: METSIM_6028

description:
DNA treated with sodium bisulfite
AT52_20


title: s_039545


title: METSIM_6010

description:
DNA treated with sodium bisulfite
AT51_23


title: METSIM_5954

description:
DNA treated with sodium bisulfite
AT51_21


title: METSIM_4856

description:
DNA treated with sodium bisulfite
AT6_23


title: METSIM_4544

description:
DNA treated with sodium bisulfite
AT6_22


title: METSIM_2808

description:
DNA treated with sodium bisulfite
AT9_20


title: METSIM_5951

description:
DNA treated with sodium bisulfite
AT50_23


title: METSIM_5953

description:
DNA treated with sodium bisulfite
AT51_20


title: METSIM_5935

description:
DNA treated with sodium bisulfite
AT50_22


title: METSIM_5923

description:
DNA treated with sodium bisulfite
AT50_21


title: METSIM_5084

description:
DNA treated with sodium bisulfite
AT7_20


title: METSIM_6277

description:
DNA treated with sodium bisulfite
AT49_22


title: METSIM_6283

description:
DNA treated with sodium bisulfite
AT49_23


title: METSIM_6203

description:
DNA treated with sodium bisulfite
AT49_21


title: METSIM_6183

description:
DNA treated with sodium bisulfite
AT48_23


title: METSIM_6501

description:
DNA treated with sodium bisulfite
AT5_21


title: METSIM_4479

description:
DNA treated with sodium bisulfite
AT5_22


title: METSIM_6425

description:
DNA treated with sodium bisulfite
AT50_20


title: METSIM_6106

description:
DNA treated with sodium bisulfite
AT5_20


title: METSIM_6083

description:
DNA treated with sodium bisulfite
AT48_21


title: METSIM_6200

description:
DNA treated with sodium bisulfite
AT49_20


title: METSIM_6761

description:
DNA treated with sodium bisulfite
AT47_23


title: METSIM_5922

description:
DNA treated with sodium bisulfite
AT48_20


title: METSIM_6101

description:
DNA treated with sodium bisulfite
AT48_22


title: METSIM_6005

description:
DNA treated with sodium bisulfite
AT51_22


title: METSIM_6684

description:
DNA treated with sodium bisulfite
AT47_22


title: METSIM_6648

description:
DNA treated with sodium bisulfite
AT47_20


title: METSIM_6666

description:
DNA treated with sodium bisulfite
AT47_21


title: METSIM_6537

description:
DNA treated with sodium bisulfite
AT46_23


title: METSIM_5210

description:
DNA treated with sodium bisulfite
AT7_22


title: METSIM_6515

description:
DNA treated with sodium bisulfite
AT46_22


title: METSIM_6194

description:
DNA treated with sodium bisulfite
AT46_20


title: METSIM_5470

description:
DNA treated with sodium bisulfite
AT45_23


title: METSIM_2321

description:
DNA treated with sodium bisulfite
AT45_22


title: METSIM_2048

description:
DNA treated with sodium bisulfite
AT45_21


title: METSIM_1892

description:
DNA treated with sodium bisulfite
AT45_20


title: METSIM_1764

description:
DNA treated with sodium bisulfite
AT44_23


title: METSIM_4481

description:
DNA treated with sodium bisulfite
AT5_23


title: METSIM_1666

description:
DNA treated with sodium bisulfite
AT44_22


title: METSIM_1524

description:
DNA treated with sodium bisulfite
AT44_21


title: METSIM_1449

description:
DNA treated with sodium bisulfite
AT44_20


title: METSIM_5919

description:
DNA treated with sodium bisulfite
AT43_23


title: METSIM_2290

description:
DNA treated with sodium bisulfite
AT43_20


title: METSIM_2044

description:
DNA treated with sodium bisulfite
AT43_21


title: METSIM_5462

description:
DNA treated with sodium bisulfite
AT43_22


title: METSIM_1757

description:
DNA treated with sodium bisulfite
AT42_22


title: METSIM_1653

description:
DNA treated with sodium bisulfite
AT42_21


title: METSIM_5859

description:
DNA treated with sodium bisulfite
AT41_22


title: METSIM_1999

description:
DNA treated with sodium bisulfite
AT40_23


title: METSIM_2267

description:
DNA treated with sodium bisulfite
AT41_20


title: METSIM_6514

description:
DNA treated with sodium bisulfite
AT46_21


title: METSIM_1885

description:
DNA treated with sodium bisulfite
AT40_22


title: METSIM_5273

description:
DNA treated with sodium bisulfite
AT41_21


title: METSIM_5949

description:
DNA treated with sodium bisulfite
AT4_23


title: METSIM_1518

description:
DNA treated with sodium bisulfite
AT42_20


title: METSIM_1747

description:
DNA treated with sodium bisulfite
AT40_21


title: METSIM_1619

description:
DNA treated with sodium bisulfite
AT40_20


title: METSIM_5668

description:
DNA treated with sodium bisulfite
AT4_22


title: METSIM_5392

description:
DNA treated with sodium bisulfite
AT4_20


title: METSIM_2760

description:
DNA treated with sodium bisulfite
AT39_20


title: METSIM_1502

description:
DNA treated with sodium bisulfite
AT39_23


title: METSIM_5481

description:
DNA treated with sodium bisulfite
AT4_21


title: METSIM_2261

description:
DNA treated with sodium bisulfite
AT38_23


title: METSIM_5849

description:
DNA treated with sodium bisulfite
AT39_21


title: METSIM_1841

description:
DNA treated with sodium bisulfite
AT38_21


title: METSIM_1445

description:
DNA treated with sodium bisulfite
AT39_22


title: METSIM_1987

description:
DNA treated with sodium bisulfite
AT38_22


title: METSIM_1736

description:
DNA treated with sodium bisulfite
AT38_20


title: METSIM_1891

description:
DNA treated with sodium bisulfite
AT42_23


title: METSIM_1599

description:
DNA treated with sodium bisulfite
AT37_23


title: METSIM_5833

description:
DNA treated with sodium bisulfite
AT37_20


title: METSIM_1438

description:
DNA treated with sodium bisulfite
AT37_21


title: METSIM_1446

description:
DNA treated with sodium bisulfite
AT41_23


title: METSIM_1490

description:
DNA treated with sodium bisulfite
AT37_22


title: METSIM_1984

description:
DNA treated with sodium bisulfite
AT36_21


title: METSIM_2242

description:
DNA treated with sodium bisulfite
AT36_22


title: METSIM_2656

description:
DNA treated with sodium bisulfite
AT36_23


title: METSIM_1590

description:
DNA treated with sodium bisulfite
AT35_22


title: METSIM_1483

description:
DNA treated with sodium bisulfite
AT35_21


title: METSIM_1409

description:
DNA treated with sodium bisulfite
AT35_20


title: METSIM_5812

description:
DNA treated with sodium bisulfite
AT34_23


title: METSIM_2176

description:
DNA treated with sodium bisulfite
AT34_21


title: METSIM_1725

description:
DNA treated with sodium bisulfite
AT35_23


title: METSIM_2655

description:
DNA treated with sodium bisulfite
AT34_22


title: METSIM_1822

description:
DNA treated with sodium bisulfite
AT33_23


title: METSIM_1462

description:
DNA treated with sodium bisulfite
AT33_20


title: METSIM_1583

description:
DNA treated with sodium bisulfite
AT33_21


title: METSIM_5571

description:
DNA treated with sodium bisulfite
AT32_22


title: METSIM_2529

description:
DNA treated with sodium bisulfite
AT32_21


title: METSIM_1722

description:
DNA treated with sodium bisulfite
AT33_22


title: METSIM_2103

description:
DNA treated with sodium bisulfite
AT32_20


title: METSIM_1942

description:
DNA treated with sodium bisulfite
AT31_23


title: METSIM_1779

description:
DNA treated with sodium bisulfite
AT31_22


title: METSIM_1580

description:
DNA treated with sodium bisulfite
AT31_20


title: METSIM_1457

description:
DNA treated with sodium bisulfite
AT30_23


title: METSIM_1303

description:
DNA treated with sodium bisulfite
AT32_23


title: METSIM_5365

description:
DNA treated with sodium bisulfite
AT3_23


title: METSIM_2430

description:
DNA treated with sodium bisulfite
AT30_20


title: METSIM_5530

description:
DNA treated with sodium bisulfite
AT30_21


title: METSIM_1974

description:
DNA treated with sodium bisulfite
AT34_20


title: METSIM_5242

description:
DNA treated with sodium bisulfite
AT3_21


title: METSIM_1702

description:
DNA treated with sodium bisulfite
AT31_21


title: METSIM_7295

description:
DNA treated with sodium bisulfite
AT3_20


title: METSIM_5283

description:
DNA treated with sodium bisulfite
AT3_22


title: METSIM_1777

description:
DNA treated with sodium bisulfite
AT29_21


title: METSIM_1840

description:
DNA treated with sodium bisulfite
AT36_20


title: METSIM_2100

description:
DNA treated with sodium bisulfite
AT29_22


title: METSIM_1455

description:
DNA treated with sodium bisulfite
AT28_23


title: METSIM_1932

description:
DNA treated with sodium bisulfite
AT29_23


title: METSIM_1165

description:
DNA treated with sodium bisulfite
AT28_21


title: METSIM_1678

description:
DNA treated with sodium bisulfite
AT28_22


title: METSIM_1559

description:
DNA treated with sodium bisulfite
AT28_20


title: METSIM_5521

description:
DNA treated with sodium bisulfite
AT29_20


title: METSIM_1896

description:
DNA treated with sodium bisulfite
AT27_21


title: METSIM_2057

description:
DNA treated with sodium bisulfite
AT27_22


title: METSIM_1768

description:
DNA treated with sodium bisulfite
AT27_20


title: METSIM_1674

description:
DNA treated with sodium bisulfite
AT26_23


title: METSIM_1545

description:
DNA treated with sodium bisulfite
AT26_22


title: METSIM_1452

description:
DNA treated with sodium bisulfite
AT26_21


title: METSIM_2348

description:
DNA treated with sodium bisulfite
AT27_23


title: METSIM_1264

description:
DNA treated with sodium bisulfite
AT30_22


title: METSIM_10071

description:
DNA treated with sodium bisulfite
AT25_23


title: METSIM_1148

description:
DNA treated with sodium bisulfite
AT26_20


title: METSIM_10070

description:
DNA treated with sodium bisulfite
AT25_22


title: METSIM_10039

description:
DNA treated with sodium bisulfite
AT25_21


title: METSIM_10016

description:
DNA treated with sodium bisulfite
AT25_20


title: seedling

city: Yangling

first: Han

last: Ran

state: Shaanxi

address: No.3 Taicheng Road

department: College of Life Sciences

institute: Northwest A&F University

description: Sample 1

data_processing:
Using CLC Geno-mic Workbe nch 4.9 (CLC b io, Aa rh us, Denmark )
Remove 3'adaptor
Removing low quality reads
Remove  sequences larger than 30-nt and smaller than 18-nt
Supplementary_files_format_and_content: fa.gz files include the serial # of the sequces (e.g. t0000001), sequences and abundance measurement of the sequence.

organism: Triticum aestivum

source_name: seedlings

growth_protocol: Wheat plants were grown under natural conditions in the experimental field of Northwest A & F University, Yangling, China (longitude 108°E , latitude 34°15’N ) in 2009-2010.

extract_protocol:
For seedlings, total RNA was extracted separately from leaves, stems and roots of the seedlings, and then mixed with equal amount of individual parts. Total RNAof the other tissue was isolated separately from each of these samples using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions
10-30 nt small RNAs were gel-purified from 15% PAGE  gel, 5’ and 3’ adaptors were added

tag: wheat cultivars

tag: sampling period

value: Five-leaf-stage seedlings

tag: localities

value: longitude 108°E , latitude 34°15’N

tag: molecule subtype

value: small RNA


title: 20-d seed

description: Sample 5

source_name: seed

value: immature seeds at 20 day


title: 10-d seed

description: Sample 4

value: immature seeds at 10 day


title: METSIM_7626

description:
DNA treated with sodium bisulfite
AT24_22


title: METSIM_10012

description:
DNA treated with sodium bisulfite
AT24_23


title: Flag leaf

description: Sample 2

source_name: flag leaf

value: flag leaves of heading plants


title: 5-d seed

description: Sample 3

value: immature seeds at 5 day


title: METSIM_7432

description:
DNA treated with sodium bisulfite
AT24_20


title: METSIM_7604

description:
DNA treated with sodium bisulfite
AT24_21


title: 621

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: human foreskin fibroblasts, replicate 3

data_processing:
HiSeq 1500 (Illumina), >Q30
casava v1.8.4, default
TopHat2 v2.0.13, default
DESeq
PGS v6.6 floored: min value=1, filtered: ignore values <10 in all cell types
Genome_build: hg19
Supplementary_files_format_and_content: csv; flored and filtered DESeq expression values

source_name: foreskin fibroblasts HNF

extract_protocol:
Trizol
TruSeq RNA Sample Preparation Kit v2

value: fibroblast

tag: replicate


title: 622

description: fetal brain-derived neural stem cells, replicate 1

source_name: fetal brain NSCs

value: WT-NSC


title: METSIM_10879

description:
DNA treated with sodium bisulfite
AT23_22


title: 623

description: fetal brain-derived neural stem cells, replicate 2


title: 624

description: fetal brain-derived neural stem cells, replicate 3


title: METSIM_7366

description:
DNA treated with sodium bisulfite
AT23_23


title: METSIM_10664

description:
DNA treated with sodium bisulfite
AT23_21


title: 619

description: human foreskin fibroblasts, replicate 1


title: 620

description: human foreskin fibroblasts, replicate 2


title: METSIM_10567

description:
DNA treated with sodium bisulfite
AT23_20


title: METSIM_10406

description:
DNA treated with sodium bisulfite
AT22_22


title: 618

description: induced human neural stem cells, replicate 3

source_name: Zfp521-induced iNSC from human fibroblasts

value: iNSC


title: 617

description: induced human neural stem cells, replicate 2


title: 616

description: induced human neural stem cells, replicate 1


title: METSIM_10548

description:
DNA treated with sodium bisulfite
AT22_23


title: METSIM_10437

description:
DNA treated with sodium bisulfite
AT22_21


title: METSIM_10390

description:
DNA treated with sodium bisulfite
AT22_20


title: METSIM_10280

description:
DNA treated with sodium bisulfite
AT21_22


title: METSIM_635

description:
DNA treated with sodium bisulfite
AT20_23


title: METSIM_634

description:
DNA treated with sodium bisulfite
AT20_22


title: N2 L4440 feeding RNAi

city: College Park

first: Antony

middle: Merlin

last: Jose

address: Rm 2136, Bioscience Research Building

department: Cell Biology and Molecular Genetics

institute: University of Maryland College Park

data_processing:
Fastq files were mapped to the ce6 genome using TopHat2 with default options.
The coverage at each gene of interest was determined using samtools and awk commands.
The normalized coveraage was determined using coverage of act-1.
Genome_build: ce6
Supplementary_files_format_and_content: excel sheets summarizing the coverage and normalized coverage for genes of interest

organism: Caenorhabditis elegans

source_name: C. elegans and bacteria

growth_protocol: The strain was grown at 20C in liquid culture with E. coli strain HT115 with plasmids as food.

extract_protocol:
Total RNA were exracted from worm pellets using standard protocols.
RNA libraries were prepared as per standard Illumina protocols.

treatment_protocol: Worms were harvested using centrifugation and separated from E.coli using sucrose floatation.

value: Mixed-stage liquid culture


title: N2 bli-1 feeding RNAi


title: METSIM_539

description:
DNA treated with sodium bisulfite
AT20_21


title: METSIM_535

description:
DNA treated with sodium bisulfite
AT20_20


title: Spermine NONOate

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

data_processing:
Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings
Differentially expressed genes were idenified using DESeq program
Genome_build: Galgal4 - Ensembl Release 75 database

source_name: whole embryo

growth_protocol: The embryos were allowed to develop through stages in hatching incubator. At 6th day embryo was collected and processed for RNA extraction

extract_protocol:
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos of stage HH8 were pretreated with thalidomide (40µg /ml) and spermine NONOate (10µM) separately and in combiantion. The embryos were collected on 6th day for isolation of total RNA

value: whole embryo

tag: treatment

value: Spermine NONOate (10 µM)


title: Thalidomide

value: Thalidomide (40µg /ml)


title: METSIM_6854

description:
DNA treated with sodium bisulfite
AT2_20


title: METSIM_6875

description:
DNA treated with sodium bisulfite
AT2_21


title: METSIM_7096

description:
DNA treated with sodium bisulfite
AT2_22


title: Control

value: DMSO


title: METSIM_7136

description:
DNA treated with sodium bisulfite
AT2_23

value: adipose


title: METSIM_441

description:
DNA treated with sodium bisulfite
AT19_22

value: male


title: METSIM_495

description:
DNA treated with sodium bisulfite
AT19_23


title: METSIM_379

description:
DNA treated with sodium bisulfite
AT19_21


title: METSIM_1147

description:
DNA treated with sodium bisulfite
AT18_23


title: METSIM_1058

description:
DNA treated with sodium bisulfite
AT18_21


title: METSIM_10377

description:
DNA treated with sodium bisulfite
AT21_23


title: METSIM_377

description:
DNA treated with sodium bisulfite
AT19_20


title: METSIM_1049

description:
DNA treated with sodium bisulfite
AT18_20


title: METSIM_816

description:
DNA treated with sodium bisulfite
AT17_22


title: METSIM_1004

description:
DNA treated with sodium bisulfite
AT17_23


title: METSIM_10886

description:
DNA treated with sodium bisulfite
AT21_21


title: METSIM_758

description:
DNA treated with sodium bisulfite
AT17_20


title: METSIM_697

description:
DNA treated with sodium bisulfite
AT21_20


title: METSIM_1082

description:
DNA treated with sodium bisulfite
AT18_22


title: METSIM_718

description:
DNA treated with sodium bisulfite
AT16_23


title: Thalidomide + Spermine NONOate

value: Thalidomide (40µg /ml) +  Spermine NONOate (10 µM)


title: METSIM_1738

description:
DNA treated with sodium bisulfite
AT16_21


title: METSIM_787

description:
DNA treated with sodium bisulfite
AT17_21


title: METSIM_1517

description:
DNA treated with sodium bisulfite
AT15_23


title: METSIM_1530

description:
DNA treated with sodium bisulfite
AT16_20


title: METSIM_1744

description:
DNA treated with sodium bisulfite
AT16_22


title: METSIM_1436

description:
DNA treated with sodium bisulfite
AT15_22


title: METSIM_1301

description:
DNA treated with sodium bisulfite
AT15_21


title: METSIM_1208

description:
DNA treated with sodium bisulfite
AT14_22


title: METSIM_1234

description:
DNA treated with sodium bisulfite
AT14_23


title: METSIM_1280

description:
DNA treated with sodium bisulfite
AT15_20


title: METSIM_2264

description:
DNA treated with sodium bisulfite
AT14_21


title: METSIM_2262

description:
DNA treated with sodium bisulfite
AT14_20


title: METSIM_2230

description:
DNA treated with sodium bisulfite
AT13_23


title: METSIM_2129

description:
DNA treated with sodium bisulfite
AT13_20


title: METSIM_2226

description:
DNA treated with sodium bisulfite
AT13_22


title: METSIM_2480

description:
DNA treated with sodium bisulfite
AT11_23


title: METSIM_1813

description:
DNA treated with sodium bisulfite
AT12_22


title: METSIM_2469

description:
DNA treated with sodium bisulfite
AT11_22


title: METSIM_1796

description:
DNA treated with sodium bisulfite
AT12_21


title: METSIM_1944

description:
DNA treated with sodium bisulfite
AT12_23


title: METSIM_2481

description:
DNA treated with sodium bisulfite
AT12_20


title: METSIM_2421

description:
DNA treated with sodium bisulfite
AT11_20


title: METSIM_2403

description:
DNA treated with sodium bisulfite
AT10_23


title: METSIM_2368

description:
DNA treated with sodium bisulfite
AT10_22


title: METSIM_2436

description:
DNA treated with sodium bisulfite
AT11_21


title: METSIM_2320

description:
DNA treated with sodium bisulfite
AT10_21


title: METSIM_6639

description:
DNA treated with sodium bisulfite
AT1_22


title: METSIM_2273

description:
DNA treated with sodium bisulfite
AT10_20


title: METSIM_6632

description:
DNA treated with sodium bisulfite
AT1_21


title: Batch 11 (DA-low)

city: Lund

first: Malin

last: Parmar

address: BMC A11

country: Sweden

institute: Wallenberg Neuroscience Center, and Lund Stem Cell Centre, Department of Experimental Medical Science, Lund University

data_processing:
All reads were aligned to the human (hg19) genome sequence using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl  (May 2014) and ERCC-spike in annotations.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

source_name: H9_VM diff d16_DA-low group

growth_protocol: Differentiation towards VM progenitors was done according Kirkeby et al 2012 with minor modifications.

extract_protocol:
cDNA was generated from isolated RNA from differentiated H9 hESC line using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

tag: differentiated hesc line

value: H9, VM progenitors d16

tag: sample group

value: DA-low group


title: Batch 6 (DA-high)

source_name: H9_VM diff d16_DA-high group

value: DA-high group


title: Batch 7B (DA-low)


title: Batch 27 (DA-high)


title: Batch 24 (DA-low)


title: Batch 25 (DA-low)


title: Batch 7A (DA-low)


title: Batch 14 (DA-low)


title: Batch 13 (DA-low)


title: Batch 23A (DA-high)


title: SC261_D143

first: Robert

middle: D

last: Morrison

address: 307 Westlake Ave N

institute: Center for Infectious Disease Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to human genome GRC38.p2 using bowtie2 v2.2.2 with parameters  " -q --phred33-quals  --trim5 4  --trim3 6  --very-sensitive   -k 10  "
RPKM values for each gene (Reads Per Kilobase of exon per Million mapped reads) were calculated using R package DuffyNGS v1.5.0, using only reads landing within exon boundaries.
Genome_build: GRC 38 p2

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene tubes from vaccinees and controls and stored at -80C. Total RNA was extracted using the PAXgene miRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: timepoint

value: Post Vaccination

tag: group

value: Vaccine

tag: day

tag: outcome

value: Infected


title: Batch 3 (DA-high)


title: SC261_Dneg7

value: Pre Vaccination


title: METSIM_6807

description:
DNA treated with sodium bisulfite
AT1_23

tag: tissue


title: SC253_D143

value: Placebo


title: SC251_Dneg7


title: SC247_Dneg7

value: Uninfected


title: Batch 4 (DA-high)


title: METSIM_6564

description:
DNA treated with sodium bisulfite
AT1_20


title: Batch 1 (DA-high)


title: SC271_D143


title: SC241_Dneg7


title: SC251_D143


title: SC253_Dneg7


title: SC241_D143


title: Batch 23B (DA-high)


title: SC231_Dneg7


title: SC230_D143


title: SC230_Dneg7


title: SC222_D143


title: SC216_D143


title: SC216_Dneg7


title: SC237_D143


title: SC176_Dneg7


title: SC141_Dneg7


title: SC141_D143


title: SC237_Dneg7


title: SC176_D143


title: Batch 2 (DA-high)


title: SC207_Dneg7


title: SC231_D143


title: SC271_Dneg7


title: SC130_D143


title: SC130_Dneg7


title: SC120_D143


title: SC021_Dneg7


title: SC222_Dneg7


title: SC207_D143


title: SC019_D143


title: SC247_D143


title: SC120_Dneg7


title: SC018_Dneg7


title: SC084_D143


title: Melphalan-treated non-silencing shRNA-transduced JJN3-2

city: Houston

first: Li

last: Zhang

state: TX

address: 1400 Pressler, unit 1410

institute: The University of Texas MD Anderson Cancer Center

description:
Sample_SC8
Cell line was transduced by lentivirus carrying a non-silencing shRNA and treated with melphalan.

data_processing:
tophat2 -p 12 -o tophat --prefilter-multihits --mate-inner-dist 48 --library-type fr-unstranded
RNASeq-MATS.py -len 76 -a 8
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: List_of_aberrantly_spliced_genes_in_ILF2_shRNA-transduced_as_compared_to_non-silencing_shRNA-transduced_JJN3_cells.xlsx. File format: Excel table output from MATS algorithm.
Supplementary_files_format_and_content: List_of_aberrantly_spliced_genes_in_untreated_as_compared_to_melphalan-treated_JJN3_cells.xlsx. File format: Excel table output from MATS algorithm.
Supplementary_files_format_and_content: List_of_aberrantly_spliced_genes_in_melphalan-treated_ILF2_shRNA-transduced_as_compared_to_melphalan-treated_non-silencing_shRNA-transduced_JJN3_cells.xlsx. File format: Excel table output from MATS algorithm.

source_name: JJN3 cells, non-silencing shRNA, melphalan

growth_protocol: RPMI+10% PBS.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using the Trustseq total RNA kit (Illumina).
Transcriptomic RNA-Seq was performed on the Illumina HiSeq 2000 platform using the standard paired-end protocol. In total, 60-160 million 76-bp reads were generated per sample.

treatment_protocol: 25μM melphalan for 10 hours.

tag: cell line

tag: cell type

value: multiple myeloma cell line

tag: shRNA

value: non-silencing

value: melphalan


title: Melphalan-treated ILF2 shRNA-transduced JJN3-1

description:
Sample_SC11
Cell line was transduced by lentivirus carrying ILF2-targeting shRNA and treated with melphalan.

source_name: JJN3 cells, ILF2-targeting shRNA, melphalan

value: ILF2 targeting


title: ILF2 shRNA-transduced JJN3-2

description:
Samepl_SC6b
Cell line was transduced by lentivirus carrying ILF2-targeting shRNA.

source_name: JJN3 cells, ILF2-targeting shRNA, untreated


title: ILF2 shRNA-transduced JJN3-1

description:
Sample_SC6a
Cell line was transduced by lentivirus carrying ILF2-targeting shRNA.


title: SC026_D143


title: SC021_D143


title: Non-silencing shRNA-transduced JJN3-1

description:
Sample_SC1
Cell line was transduced by lentivirus carrying a non-silencing shRNA.

source_name: JJN3 cells, non-silencing shRNA, untreated


title: SC026_Dneg7


title: A2780 INPUT

city: Singapore

first: Vinay

last: Tergaonkar

address: 61, Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

data_processing:
Reads from cell lines were mapped to the hg19 genome using bowtie (version. 2.2.3) keeping uniquely aligned reads
Replicate bam files were merged using Samtools
PCR duplicates were removed from merged file and sorted indexed files were used for peak calling using MACS (version 2.1.10) with default parameters using q value of 0.05 to identified significantly enriched region/ peaks compared to input control sample
Coverage file for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig (.bw) for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries.

source_name: Ovarian cancer cells

growth_protocol: P493 cells were grown in RPMI medium. A2780, BLM, LOXIMVI, HCT116 cells were grown in DMEM medium. hESC cells were cultured onto matrigel coated plates using media and additional supplements as suggested by STEM Cell Technologies. All cells were cultured at 37 degree celcius with 5% Carbon dioxide.

extract_protocol:
Lysates were clarified from sonicated nuclei and TERT-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying theNEB NEXT ULTRA ILLUMINA Library preparation kit (E7370L).

treatment_protocol: All the cells were fixed in medium except hESC cells which were trypsinized first. Cells were fixed directly in growth medium with 1% formaldehyde for 10 minutes at room temprature with shaking.


title: Anti-TERT_A2780

description: antibody: TERT (Epitomics, 1531-1, lot Y1012704C)


title: Anti-TERT_LOXIMVI_Replicate 2

source_name: Melanoma cells

value: LOXIMVI


title: Non-silencing shRNA-transduced JJN3-2

description:
Sample_SC2
Cell line was transduced by lentivirus carrying a non-silencing shRNA.


title: SC019_Dneg7


title: Anti-TERT_BLM_Replicate 1

value: BLM


title: SC018_D143


title: SC017_D143


title: Melphalan-treated non-silencing shRNA-transduced JJN3-1

description:
Sample_SC7
Cell line was transduced by lentivirus carrying a non-silencing shRNA and treated with melphalan.


title: SC017_Dneg7


title: Melphalan-treated ILF2 shRNA-transduced JJN3-2

description:
Sample_SC12
Cell line was transduced by lentivirus carrying ILF2-targeting shRNA and treated with melphalan.


title: SC084_Dneg7


title: LOXIMVI INPUT


title: Anti-TERT_HCT116

source_name: Colon cancer cells


title: Anti-TERT_hESC-1_Replicate 1

source_name: Embryonic stem cells


title: Anti-TERT_P493_Replicate 2

source_name: Lymphoma derived


title: Anti-TERT_LOXIMVI_Replicate 1


title: BLM INPUT


title: HCT-116 ODD pool #2

city: Copenhagen

first: Anders

middle: H

last: Lund

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Center

country: Denmark

institute: University of Copenhagen

description:
Replicate 2
processed data file: ODD.optimal.xls

data_processing:
Library strategy: RNA pulldown
Base-calling done by Vendor (BGI)
Sequences were aligned to hg19 using STAR aligner with: --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16
Peak-calling was done using MACS v2 run repeatedly with different parameters as suggested for IDR. See: https://sites.google.com/site/anshulkundaje/projects/idr
Performed IDR as outlined in http://genome.cshlp.org/content/22/9/1813.full
Genome_build: hg19
Supplementary_files_format_and_content: Peaklists as generated by MACS

source_name: CRC cell line HCT-116

growth_protocol: HCT-116 were kept in culture with McCoy's Medium 10% FBS in square PS petri dish (120 mmx 120mm)

extract_protocol:
Cells were lysed, and the total lysate incubated with biotinylated DNA oligos complementary to the SNHG5 transcript. Pull down was carried out using streptavidin-beads and the RNA extracted with miRNeasy kit (invitrogen)
TruSeq protocol for low RNA input samples (illumina's protocol) performed at BGI

treatment_protocol: Cells were cross-linked in 1% Gluteraldehyde

tag: oligo pool

value: ODD


title: HCT-116 INPUT #2

description: Replicate 2

value: INPUT


title: hESC-3 INPUT


title: Anti-TERT_BLM_Replicate 2


title: human ERK1, overexpressed in HMEC cells_3

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

data_processing:
Quality checking with FASTQC
Alignment and quantification with R package Rsubread
FPKM normalization with edgeR and limma
TPM normalization from the FPKM values
log2 values of the TPM normalized gene counts
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TPM-log2 normalized gene count processed file is a tab-delimited .txt file

source_name: Breast

growth_protocol: Human mammary epithelial cells, grown in Stemgent WIT-P culture medium at 3% CO2 and 37°C

extract_protocol:
Cells were scraped into RNA-Later and stored on ice until processing.  Then RNA was isolated from pelleted cells using a Qiagen Rneasy mini kit (with Rnase-free DNase set) and QIAshredders.
Illumina TruSeq stranded mRNA kit

treatment_protocol: Genes were introduced for over-expression by way of adenovirus.  Cells were infected with MOI 500 Adenovius for 18 hours.

value: mammary epithelial cells

tag: overexpression of


title: human ERK1, overexpressed in HMEC cells_4


title: human ERK1, overexpressed in HMEC cells_2


title: Anti-TERT_hESC-3_Replicate 2


title: Anti-TERT_hESC-3_Replicate 1


title: hESC-1 INPUT


title: HCT116 INPUT


title: Anti-TERT_hESC-1_Replicate 2


title: P493 INPUT


title: Anti-TERT_P493_Replicate 1


title: HCT-116 EVEN pool #2

description:
Replicate 2
processed data file: SNHG5_5_peaks.sorted.xls

value: EVEN


title: human AKT1, overexpressed in HMEC cells_1


title: human ERK1, overexpressed in HMEC cells_5


title: HCT-116 ODD pool #1

description:
Replicate 1
processed data file: ODD.optimal.xls


title: human BAD, overexpressed in HMEC cells_6

value: BAD


title: HCT-116 INPUT #1

description: Replicate 1


title: human ERK1, overexpressed in HMEC cells_6


title: human BAD, overexpressed in HMEC cells_1


title: human AKT1, overexpressed in HMEC cells_6


title: human ERK1, overexpressed in HMEC cells_1


title: human RAF1, overexpressed in HMEC cells_4


title: human RAF1, overexpressed in HMEC cells_3


title: human AKT1, overexpressed in HMEC cells_3


title: human BAD, overexpressed in HMEC cells_5


title: human BAD, overexpressed in HMEC cells_3


title: human AKT1, overexpressed in HMEC cells_5


title: human BAD, overexpressed in HMEC cells_2


title: human AKT1, overexpressed in HMEC cells_2


title: human RAF1, overexpressed in HMEC cells_6


title: human HER2/ERBB2, overexpressed in HMEC cells_2


title: human RAF1, overexpressed in HMEC cells_5


title: human BAD, overexpressed in HMEC cells_4


title: human HER2/ERBB2, overexpressed in HMEC cells_1


title: human RAF1, overexpressed in HMEC cells_1


title: humanIGF1R, overexpressed in HMEC cells_5


title: human AKT1, overexpressed in HMEC cells_4


title: humanIGF1R, overexpressed in HMEC cells_6


title: human RAF1, overexpressed in HMEC cells_2


title: human HER2/ERBB2, overexpressed in HMEC cells_5


title: human HER2/ERBB2, overexpressed in HMEC cells_6


title: human HER2/ERBB2, overexpressed in HMEC cells_3


title: pre-mRNA-seq_met-2set-25_OP50

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7].
rpkm value for each 1kb is calculated by the number of reads that perfectly aligned to both strands of 1kb-non-overlaping regions, normalized by the sequencing depth of the library in million.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: .xlsx file containing rpkm values of all 1kb regions for 5 pre-mRNA-seq libraries. GRH and GRTS regions are previously defined germline nuclear RNAi-dependent heterochromatin (GRH) and transcriptional silencing (GRTS) targets.H3K9me3 ChIP-seq results of OP50 feeding experiments were used as replica 1 to identify different HMT-dependent K9 targets replica 1. H3K9me3 ChIP-seq results from RNAi control experiment (GFP RNAi) were used as replica 2 to identify HMT-dependent K9 targets replica 2. All replica HMT-dependent K9 target lists are reported in the table. In addition, miss-annotated regions are also reported in the table. Whole genome classification of H3K9me3 level is also labeled in the table as K9 tire: 1-3 correspond to the top 5% H3K9me3 regions, 4 correspond to the next 5-25%, tire 5 is 25-50%, tire 6 is 50-75%, tire 7 is 75-100% (bottom H3K9me3 quartile, correspond to the background level) excluding tire 8 - extreme low values (=0 or ~0).

source_name: Young adult whole animal

growth_protocol: C. elegans strains N2, hrde-1 (tm1200), set-32(ok1457), met-2(n4256);set-25(ok5021), and met-2(n4256);set-25(ok5021);set-32(ok1457) were cultured on NGM plates with E. coli OP50  as the food source in a temperature controlled incubator at 19°C.  Synchronized worms were raised at 19°C and young adult worm samples were collected.

extract_protocol:
100-200 μl frozen synchronized young adult worm pellets were used for each pre-mRNA-seq experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). For each immumoprecipiation experiment, 2 μg of anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 1.5-2 hours with agitation every 30 minutes and then subject to organic extraction and precipitation of total DNA and RNA. DNA/RNA mix was treated with DNase I (NEB) and resulted RNA was used for the pre-mRNA-seq library preparation.
pre-mRNA library was prepaed using the following protocol: RNA was fragmented by hydrolysis using Fragmentation Reagent Kit (Ambion). RNA was treated with T4 PNK (NEB). Then RNA 3’ end was ligated to IDT linker-1 (5’-rAppCTGTAGGCACCATCAATC-3’) using T4 RNA ligase 2, truncated (NEB, M0242S). RNA library of about 35-60 nt was size selected using 8 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea (size selection also eliminated excess IDT linker-1). RNA 5’end was ligated to DNA-RNA hybrid oligo (5’-ACGCTCTTCCGATCTrNrNrNrN-3’, where rNrNrNrN is a 4-nt barcode) using T4 RNA ligase 1 (NEB) with ATP. First strand cDNA was synthesized using SuperScript III RT kit (Life Technologies) and primer SG-460 (5’-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’). cDNA library was PCR amplified at early cycle (tested by different cycle number to capture linear amplification phase and avoid over amplification). PCR was done using a common primer SG-465 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and primer with 6-nt index for multiplexing (5’-CAAGCAGAAGACGGCATACGAGAT[ index]GTGACTGGAGTTCAGACGTGTGCTCTTCC-3’). Amplified library was size selected by 2% agarose gel and gel purified using QIAquick Gel Extraction Kit (QIAGEN).

tag: genotype/variation

tag: temperature

tag: feeding

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2)

value: RNA extracted from anty-Pol II (S2) IP fragmented chromatin


title: pre-mRNA-seq_hrde-1_OP50

tag: molecule subtype


title: pre-mRNA-seq_met-2set-25set-32_OP50


title: humanIGF1R, overexpressed in HMEC cells_1


title: mRNA-seq_met-2set-25_OP50

data_processing:
The raw reads were processed by trimming 4-nt inline barcode at the 5' end and linker sequence from the 3' end
The processed reads were aligned to the C. elegans annoated gene database (spliced) using bowtie[0.12.7]
The mRNA expression level for each gene was calculated by counting the number of reads that were aligned to the sense strand of  the gene. One pseudo-count was added to each gene to avoid zero counts. The counts were normalized by the sequencing depth (in millions) for each sample.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: .xlsx file containing the mRNA expression levels (rpkm) in all 5 samples for all annotated C. elegans genes. Number correspond to the total 100%-matching reads aligned in sense orientation to the mRNA and normalized by mRNA length and total sequencing depth in million. Additional columns define germline expression (oocyte only, sperm only or germline (both) = intrinsic) and germline nuclear RNAi target type: heterochromatin (GHR) or transcriptional silencing (GRTS).

extract_protocol:
Total RNA was extracted from frozen synchronized adult worm grinds (100-200 μl, pulverized in liquid nitrogen by grinding) using Trizol reagent (Life Technologies). mRNA was enriched using Poly(A)Purist MAG kit (Life Technologies).
0.5-1 μg of mRNA was used for each mRNA-seq library. DNA was removed from the RNA sample by DNase I treatment according to manufacture’s instruction (New England Biolabs).  RNA was fragmented by hydrolysis using Fragmentation Reagent Kit (Ambion). RNA was treated with T4 PNK (NEB). Then RNA 3’ end was ligated to IDT linker-1 (5’-rAppCTGTAGGCACCATCAATC-3’) using T4 RNA ligase 2, truncated (NEB, M0242S). RNA library of about 35-60 nt was size selected using 8 % polyacrylamide (acrylamide:bis-acrylamide = 19:1) gels containing 8 M urea (size selection also eliminated excess IDT linker-1). RNA 5’end was ligated to DNA-RNA hybrid oligo (5’-ACGCTCTTCCGATCTrNrNrNrN-3’, where rNrNrNrN is a 4-nt barcode) using T4 RNA ligase 1 (NEB) with ATP. First strand cDNA was synthesized using SuperScript III RT kit (Life Technologies) and primer SG-460 (5’-GGAGTTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3’). cDNA library was PCR amplified at early cycle (tested by different cycle number to capture linear amplification phase and avoid over amplification). PCR was done using a common primer SG-465 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and primer with 6-nt index for multiplexing (5’-CAAGCAGAAGACGGCATACGAGAT[ index]GTGACTGGAGTTCAGACGTGTGCTCTTCC-3’). Amplified library was size selected by 2% agarose gel and gel purified using QIAquick Gel Extraction Kit (QIAGEN).


title: GFP control, overexpressed in HMEC cells_12

value: GFP control


title: mRNA-seq_met-2set-25set-32_OP50


title: GFP control, overexpressed in HMEC cells_11


title: pre-mRNA-seq_set-32_OP50


title: humanIGF1R, overexpressed in HMEC cells_4


title: humanIGF1R, overexpressed in HMEC cells_3


title: H3K9me3_ChIP-seq_hrde-1_OP50

data_processing:
50 nt Illumina sequencing reads were aligned to the C. elegans genome using bowtie[0.12.7].
rpkm value for each 1kb is calculated by the number of reads that perfectly aligned to both strands of 1kb-non-overlaping regions, normalized by the sequencing depth of the library in million.
Genome_build: WS190/ce6
Supplementary_files_format_and_content: .xlsx file containing rpkm values of all 1kb regions for 15  H3K9me3 Chip-seq, 10 Pol II (S2) ChIP-seq libraries. H3K9me3 ChIP-seq results of OP50 feeding experiments were used as replica 1 to identify different HMT-dependent K9 targets replica 1. H3K9me3 ChIP-seq results from RNAi control experiment (GFP RNAi) were used as replica 2 to identify HMT-depende.xlsx file containing rpkm values of all 1kb regions for 15  H3K9me3 Chip-seq, 10 Pol II (S2) ChIP-seq libraries. GRH and GRTS regions are previously defined germline nuclear RNAi-dependent heterochromatin (GRH) and transcriptional silencing (GRTS) targets.H3K9me3 ChIP-seq results of OP50 feeding experiments were used as replica 1 to identify different HMT-dependent K9 targets replica 1. H3K9me3 ChIP-seq results from RNAi control experiment (GFP RNAi) were used as replica 2 to identify HMT-dependent K9 targets replica 2. All replica HMT-dependent K9 target lists are reported in the table. In addition, miss-annotated regions are also reported in the table. Whole genome classification of H3K9me3 level is also labeled in the table as K9 tire: 1-3 correspond to the top 5% H3K9me3 regions, 4 correspond to the next 5-25%, tire 5 is 25-50%, tire 6 is 50-75%, tire 7 is 75-100% (bottom H3K9me3 quartile, correspond to the background level) excluding tire 8 - extreme low values (=0 or ~0).   nt K9 targets replica 2. All replica HMT-dependent K9 target lists are reported in the table. In addition, miss-annotated regions are also reported in the table. Whole genome classification of H3K9me3 level is also labeled in the table as K9 tire: 1-3 correspond to the top 5% H3K9me3 regions, 4 correspond to the next 5-25%, tire 5 is 25-50%, tire 6 is 50-75%, tire 7 is 75-100% (bottom H3K9me3 quartile, correspond to the background level) excluding tire 8 - extreme low values (=0 or ~0).

growth_protocol: C. elegans strains N2, hrde-1 (tm1200), set-32(ok1457), met-2(n4256);set-25(ok5021), and met-2(n4256);set-25(ok5021);set-32(ok1457) were cultured on NGM plates with E. coli OP50 or oma-1 RNAi or GFP RNAi as the food source in a temperature controlled incubator at 19°C for all experiments. For OP50 ChIP-seq experiments synchronized worms were raised at 19°C and young adult worm samples were collected. Worms were synchronized by using the standard egg-prep protocol. For oma-1 and GFP RNAi experiments worms were raised at 19°C on NGM plates with corresponding RNAi feeding for ~3 generations and until majority of worms reached gravid adult stage. These worms were synchronized and L1 (~4500 worms per plate) worms were released on the corresponding RNAi feeding NGM plates, raised at 19°C and young adults worm samples were collected.

extract_protocol:
100-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

tag: chip antibody

value: Anti-Histone H3 (tri methyl K9)

value: DNA extracted from immunoprecipitated chromatin


title: mRNA-seq_hrde-1_OP50


title: humanIGF1R, overexpressed in HMEC cells_2


title: mRNA-seq_set-32_OP50


title: GFP control, overexpressed in HMEC cells_8


title: GFP control, overexpressed in HMEC cells_10


title: H3K9me3_ChIP-seq_WT_OP50

value: WT (N2)


title: H3K9me3_ChIP-seq_met-2set-25set-32_OP50


title: ChIP_Input_met-2set-25set-32

value: ChIP Input


title: GFP control, overexpressed in HMEC cells_9


title: ChIP_Input_set-32


title: H3K9me3_ChIP-seq_met-2set-25_OP50


title: GFP control, overexpressed in HMEC cells_3


title: GFP control, overexpressed in HMEC cells_2


title: H3K9me3_ChIP-seq_set-32_OP50


title: Pol II_ChIP-seq_met-2set-25set-32_GFP_RNAi

value: GFP RNAi


title: pre-mRNA-seq_WT_OP50


title: GFP control, overexpressed in HMEC cells_6


title: GFP control, overexpressed in HMEC cells_7


title: GFP control, overexpressed in HMEC cells_5


title: H3K9me3_ChIP-seq_met-2set-25_GFP_RNAi


title: H3K9me3_ChIP-seq_met-2set-25set-32_GFP_RNAi


title: ChIP_Input_met-2set-25


title: Pol II_ChIP-seq_met-2set-25_oma-1_RNAi

value: oma-1 RNAi

value: DNA extracted from fragmented chromatin


title: Pol II_ChIP-seq_met-2set-25set-32_oma-1_RNAi


title: GFP control, overexpressed in HMEC cells_1


title: Pol II_ChIP-seq_WT_oma-1_RNAi


title: Pol II_ChIP-seq_set-32_oma-1_RNAi


title: Pol II_ChIP-seq_met-2set-25_GFP_RNAi


title: Pol II_ChIP-seq_set-32_GFP_RNAi


title: H3K9me3_ChIP-seq_hrde-1_GFP_RNAi


title: H3K9me3_ChIP-seq_met-2set-25set-32_oma-1_RNAi


title: Pol II_ChIP-seq_hrde-1_GFP_RNAi


title: H3K9me3_ChIP-seq_hrde-1_oma-1_RNAi


title: H3K9me3_ChIP-seq_set-32_GFP_RNAi


title: H3K9me3_ChIP-seq_set-32_oma-1_RNAi


title: H3K9me3_ChIP-seq_WT_GFP_RNAi


title: mRNA-seq_WT_OP50


title: Pol II_ChIP-seq_WT_GFP_RNAi


title: Pol II_ChIP-seq_hrde-1_oma-1_RNAi


title: ChIP_Input_hrde-1


title: IF biological rep3

city: New York

first: Alana

last: Mendelsohn

state: NY

address: 3227 Broadway

institute: Columbia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.9 with parameters -X 20000 -k 2 -m 2 -q -p. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008.
Differenetial gene expression was calculated using the R statistical package DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and differenetial gene expression for the samples

source_name: motor neurons supplying IF muscle

extract_protocol:
RNA was extracted with the Absolutely RNA Nanoprep Kit (Agilent). cDNA was synthesized using the Ovation RNA-Seq System V2 kit (Nugen). cDNA libraries were constructed using the Nextera DNA Sample Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2000 to a depth of 25-30 million single-end reads per sample.
cDNA libraries were constructed using the Nextera DNA Sample Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2000 to a depth of 25-30 million single-end reads per sample.

treatment_protocol: Individual motor pools were labeled by injecting 0.1% CTB-Alexa 555 into individual muscles of p4 mice. At p6, the animals were anaesthetized on ice, then decapitated and eviscerated. In all instances possible, bench spaces and tools were subsequently cleaned with RNAzap (Life Technologies). Ventral laminectomies were quickly performed in cold PBS and the unfixed spinal cords were embedded longitudinally, ventral side down, in OCT and frozen at -80°. The muscles were then examined under epifluorescence for specificity, and spinal cords from non-specific injections were discarded.     Prior to cryosectioning, RNAse free 1.0 PEN MembraneSlides (Zeiss) were UV crosslinked for 30 minutes at optimal power. The cryostat was cleaned with 95% EtOH. Frozen blocks were cryosectioned at 12 µm, with the angle of the block adjusted to section the spinal cord at a perpendicular cutting surface. The MembraneSlides were then placed in a slide box and frozen at -80° for laser capture microdissection. Laser capture microdissection was performed on the PALM Microbeam System (Zeiss). A solution of 300 µl lysis buffer with 2.1 µl BME was prepared for cell lysis. Cells from a set of slides corresponding to a single animal were preserved in 40 µl of the lysis buffer/BME mixture. The surface area captured in um2 was recorded for each set of slides.     Each biological replicate required approximately 1 ng of RNA, corresponding to approximately 170000 um2 of laser captured surface area. For RNA purification, samples from individual animals were pooled to provide at least 250000 um2 of laser captured surface area per biological replicate.

tag: age

value: motor neuron


title: GFP control, overexpressed in HMEC cells_4


title: GS biological rep2

source_name: motor neurons supplying GS muscle


title: GS biological rep1


title: ChIP_Input_WT


title: PL biological rep3

source_name: motor neurons supplying PL muscle


title: H3K9me3_ChIP-seq_WT_oma-1_RNAi


title: H3K9me3_ChIP-seq_met-2set-25_oma-1_RNAi


title: PL biological rep1


title: PL biological rep2


title: EDL biological rep3

source_name: motor neurons supplying EDL muscle


title: EDL biological rep1


title: GS biological rep3


title: TA biological rep3

source_name: motor neurons supplying TA muscle


title: EDL biological rep2


title: TA biological rep2


title: TA biological rep1


title: KO-R2_RNA

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

description:
processed data file
KO_R2_htseq_strict_a3_s_counts.txt
DEGs_Chd7.xls

data_processing:
ATAC-seq:
15bp was trimmed from the raw sequencing reads using trim_galore [version 0.4.1] with parameters as follows: trim_galore --nextera --paired --quality 20 --stringency 5 --gzip --clip_R1 15 --clip_R2 15 --length 25 -o [output_filename]
Reads were uniquely aligned to the mouse reference genome (mm10) using Bowtie [version 1.1.1]  with a maximum insert size for valid paired-end alignments of 2000 and a maximum number of attempts of 200 to match an alignment for one mate with an alignment for the opposite mate.
bam files were sorted and indexed using samtools [version 0.1.19-96b5f2294a]
Peaks were called in three WT replicates by comparing them to three KO samples and vice versa using MultiGPS [version 0.5] with the minimum q-value for reported peaks set at 0.05 and the mitochondrial genome excluded.
The bedtools window function from BEDTools [version 2.17.0] was used to identify ATAC-seq peaks within 1000bp of DEGs, and Dnase-seq peaks within 100bp of ATAC-seq peaks.
RNA-seq:
RNAseq reads were aligned to the mouse reference genome (mm10) using TopHat [version 2.0.14] with an expected inner distance between mate pairs of 150bp and standard deviation for the distribution on inner distances between mate pairs of 50bp.  The transcriptome index was created using ENSEMBL build 75
HTseq [version 0.6.1p1] was used to estimate the number of RNA sequencing reads supporting the expression of protein coding genes. For this, an intersection-strict mode was used and all reads with alignment quality lower than 3 skipped.
Differential expression was analyzed with DESeq2 1.8.1. Genes with an FDR<0.05 were considered differentially expressed.
ChIP-seq:
Reads were aligned to the mouse reference genome (mm10) using Bowtie [version 1.1.0] , only allowing uniquely mapping reads, with an insert size of 1000 bases. Default values were used for all other parameters
Following mapping, PCR duplicates were removed using the samtools 'rmdup' command
Identification of enriched regions was performed by comparing the ChIP to the input reads using macs2 [2.1.0.20140616], with a p-value cutoff of 0.0001 and 3,90 as the model building parameters. The bedGraph output generated by macs2 was used to visualise the ChIP and input signals.
Genome_build: mm10
Supplementary_files_format_and_content: master_sheet_atac_all_datav2.xlsx: Excel document with sheets containing coordinates of all identified peaks,i.e.   CTRL Vs. KO peaks  KO Vs. CTRL peaks  All ATAC peaks  All DNase Peaks  CTRL Vs. KO peaks within 1kb of a downregulated gene (incl. names of all unique genes)  CTRL Vs. KO peaks within 1kb of a upregulated gene (incl. names of all unique genes)  KO Vs. CTRL  peaks within 1kb of a downregulated gene (incl. names of all unique genes)  KO Vs. CTRL  peaks within 1kb of a upregulated gene (incl. names of all unique genes)
Supplementary_files_format_and_content: DEGs_Chd7.xls Excel file containing all differentially expressed genes as identified by DESeq2, including log2 fold change values and FDR.
Supplementary_files_format_and_content: WT_R1_htseq_strict_a3_s_counts.txt  WT_R2_htseq_strict_a3_s_counts.txt   KO_R1_htseq_strict_a3_s_counts.txt   KO_R2_htseq_strict_a3_s_counts.txt   → All text files containing raw  read counts for the corresponding fastq file
Supplementary_files_format_and_content: H3K4me1_WT.bw; Signal profile file showing the extent of H3K4me1-DNA binding genome wide

extract_protocol:
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the excpetion that the Nuclei EZ Prep Nuclei Isolation Kit (Sigma, NUC-101) was used for nuclei isolation.
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.
RNA-seq: The cerebella of post natal day 7 Chd7f/f (cn) and Math1cre;Chd7f/f (cko) pups were dissected in DPBS (Gibco) and lobules IX and X were removed. The cerebella of the individuals from each genotype were pooled. Cells were dissociated using Papain I (100U, Worthington) followed by trituration. Granule cell precursors were isolated by Percoll fractionation with a 35% and 65% Percoll gradient (Sigma) as described (Yu T, Meiners LC, Danielsen K, Wong MT, Bowler T, Reinberg D, Scambler PJ, van Ravenswaaij-Arts CM, and Basson MA. Deregulated FGF and homeotic gene expression underlies cerebellar vermis hypoplasia in CHARGE syndrome. eLife. 2013;2(e01305.). Total RNA was extracted from freshly isolated cells (5x106/cerebellum) with an Agilent Absolutely RNA miniprep kit (Agilent Technologies, Stockport, UK)
RNA-seq: RNA quality and integrity was assessed on a 2100 Bioanalyzer and 2200 Tapestation using an R6K screenTape (Agilent Technologies, Stockport, UK). After quantification on Qubit using Quant-iT RNA assay kit (Life Technologies, Paisley, UK), 2g total RNA was used from each sample for library preparation using an Illumina TruSeq kit (Illumina, Cambridge, UK). Libraries were resolved by agarose gel electrophoresis, 250-550bp DNA fragments isolated and gel purified with a Qiagen DNA gel extraction kit (Qiagen, Manchester, UK). Two libraries with unique barcodes were combined and sequenced per lane on a HiSeq2000 (Illumina, Cambridge, UK) at the Biomedical Research Centre, King’s Health Partners.
ChIP-seq: The cerebella of post natal day 7 Chd7f/f (cn) and Math1cre;Chd7f/f (cko) pups were dissected in DPBS (Gibco) and lobules IX and X were removed. The cerebella of the individuals from each genotype were pooled. Cells were dissociated using Papain I (100U, Worthington) followed by trituration. Granule cell precursors were isolated by Percoll fractionation with a 35% and 65% Percoll gradient (Sigma) as described (Yu T, Meiners LC, Danielsen K, Wong MT, Bowler T, Reinberg D, Scambler PJ, van Ravenswaaij-Arts CM, and Basson MA. Deregulated FGF and homeotic gene expression underlies cerebellar vermis hypoplasia in CHARGE syndrome. eLife. 2013;2(e01305.).
ChIP-seq: Freshly isolated cells (2-3x107) of each genotype were fixed, chromatin isolated, precipitated with an antibody to H3K4me1 (Abcam, Cambridge UK) and ChIP-seq libraries produced and sequenced as previously described (Tee WW, Shen SS, Oksuz O, Narendra V, and Reinberg D. Erk1/2 activity promotes chromatin features and RNAPII phosphorylation at developmental promoters in mouse ESCs. Cell. 2014;156(4):678-90.).

tag: strain background

value: cerebellar granule cell precursors (GCps)


title: HEXIM1+A771726 iCLIP Biological Replicate 1

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: Protein enriched RNA

data_processing:
Library strategy: iCLIPseq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique RT stops from the high confidence intersection of biological replicates of HEXIM1 iCLIP

source_name: A375 melanoma cell line

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
To isolate HEXIM-bound RNAs HEXIM1 antibody (Abcam, ab25388) conjugated to Protein A Dynabeads (Life Technologies) were incubated with RNaseI-digested lysate overnight at 4°C on rotation.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)

treatment_protocol: A375 cells  were treated with DMSO or 25 μM A771726.  Drugs used were DMSO (Sigma) and A771726 (Enzo Life Sciences). After a 48 hr treatment, cells were UV-C crosslinked to a total of 0.3J/cm2. Each iCLIP experiment was normalized for total protein amount, typically 2.5mg, and partially digested with RNaseI (Life Technologies) for 10 minutes at 37°C and quenched on ice.

tag: treatment


title: HEXIM1+A771726 iCLIP Biological Replicate 2

description: Protein enriched RNA


title: IF biological rep1


title: Q3hy5-2

city: Norman

first: Ben

middle: F

last: Holt

state: OK

address: 770 Van Vleet Oval

department: Microbiology and Plant Biology

institute: University of Oklahoma

data_processing:
Illumina CASAVA v1.8.2 was used for sample demultiplexing and base-calling
FASTX Trimmer was used to trim the first 9 bases of each read, followed by Sickle Quality Based Trimming with a quality threshold of 20, both within the iPlant/CyVerse pipeline.
Quality controlled reads were mapped to TAIR10 through Burrows-Wheeler Alignment.
Differential gene expression was determined through the Bioconductor package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Table S1 is a DEG matrix table with differentially expressed gene comparisons between each genotype.

organism: Arabidopsis thaliana

source_name: nf-yc3 c4 c9 hy5_whole seedlings

growth_protocol: Seedlings were grown for seven days in continuous white light on Gamborg B5 media.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. Plant RNA Kit from (Omega Biotek, Cat#R6827).  To ensure low levels of contaminating ribosomal RNA, two rounds of poly-A mRNA purification were performed using the µMACS mRNA Isolation Kit (Miltenyi Biotech, Cat#130-090-276)
Indexed RNASeq libraries were prepared from 100 ng of poly-A RNA starting material using the NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific, Cat#5130).

tag: ecotype

value: nf-yc3 c4 c9 hy5

value: 7 day old seedlings

value: Whole seedlings


title: Q3hy5-1


title: IF biological rep2


title: HEXIM1+DMSO iCLIP Biological Replicate 1

description: Protein enriched RNA

value: DMSO


title: HEXIM1+DMSO iCLIP Biological Replicate 2

description: Protein enriched RNA


title: WTK4me1

value: wild type

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: hy5-2

source_name: hy5_whole seedlings

tag: tissue


title: WT-R1_RNA

description:
processed data file
WT_R1_htseq_strict_a3_s_counts.txt
DEGs_Chd7.xls

tag: cell type


title: WT-R2_RNA

description:
processed data file
WT_R2_htseq_strict_a3_s_counts.txt
DEGs_Chd7.xls


title: Q3-2

source_name: nf-yc3 c4 c9_whole seedlings

value: nf-yc3 c4 c9


title: hy5-1


title: KO-R1_RNA

description:
processed data file
KO_R1_htseq_strict_a3_s_counts.txt
DEGs_Chd7.xls


title: wt LV

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: non-infarcted left ventricle, 3 days post myocardial infarction

data_processing:
Before alignment, raw reads were filtered by removing adaptor sequences, contamination and low-quality reads
Clean reads were aligned using SOAP2 (Version 2.21)
To normalize the data from the three libraries, the global rank-invariant set normalization method was adapted.
Based on the normalized tag counts, the modification abundance of specific CCGG sites were determined as the ratio between tag counts of two libraries.
Genome_build: UCSC mouse reference genome (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each library

source_name: Left ventricle

extract_protocol:
Genomic DNA was isolated using the Dneasy Blood and Tissue Kit (Qiagen) according to manufacturer's protocol
Three independent libraries with initially different enzyme digestion were constructed for each sample, which were termed "C", "C+mC" and "C+mC+hmC", respectively. For "C+mC" library construction, an aliquot of genomic DNA from each sample was first glucosylated and then digested with MspI. For the "C" or "C+mC+hmC" libraries, the genomic DNA was directly digested with HpaII or Msp!, respectively. The digested DNA from all threee libraries were ligated with biotinylated linker, fragmented, captured, digested to generate short sequence tags and ligated with sequencing linkers.
HMST-seq

tag: strain

tag: genotype

value: heart

value: 8 weeks


title: N3 INF

description: infarcted left ventricle, 3 days post myocardial infarction


title: wt INF


title: 4817 RNA-seq

city: Bethesda

first: Jean

last: Winter

address: 50 South Driver

department: NHGRI

institute: NIH

description:
F1 offspring from TRAMP x J:DO cross
TgNegative_samples_TPM_counts.txt
TgNegative_samples_raw_counts.txt

data_processing:
Basecalling performed by CASAVA-1.8.2
The 17 5'-most bases and the 3'-most base were trimmed from all RNA-seq reads
RSEM (v 1.2.20) was used to perform RNA-seq read mapping (calling Bowtie2 v. 2.2.5) and counting. RNA-seq reads were mapped to Ensembl transcripts (release 81).
Genome_build: GRCm38
Supplementary_files_format_and_content: TgPositive_samples_TPM_counts.txt: tab-delimied text matrix of RNA-seq normalized RNA-seq read counts (TPM) for transgene positive samples.
Supplementary_files_format_and_content: TgNegative_samples_TPM_counts.txt:  tab-delimied text matrix of RNA-seq normalized RNA-seq read counts (TPM) for transgene negative samples
Supplementary_files_format_and_content: TgPositive_samples_raw_counts.txt:  tab-delimied text matrix of RNA-seq read expected counts from RSEM for transgene positive samples.
Supplementary_files_format_and_content: TgNegative_samples_raw_counts.txt:  tab-delimied text matrix of RNA-seq read expected counts from RSEM for transgene negative samples.

source_name: prostate tissue

extract_protocol:
total RNA was extracted from snap frozen (TRAMP x J:DO) F1 bulk tumor samples using TRIzol Reagent (Life Technologies, Inc.) according to the manufacturer’s protocol, and purified using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocol.
RNA-Seq libraries were constructed from 1 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions. The cDNAs were fragmented to ~275 bp using a Covaris E210. Libraries were  pooled together for sequencing. The pooled libraries were sequenced on multiple lanes of a HiSeq 2500 using version 4 chemistry to achieve a minimum of 43 million 126 base read pairs

tag: mouse breeding

value: (TRAMP x J:DO) F1

value: Transgene negative


title: 4538 RNA-seq


title: Q3-1

tag: genotype/variation


title: WT-1

source_name: WT_whole seedlings

value: WT


title: 4834 RNA-seq


title: WT-2


title: 4876 RNA-seq


title: 4802 RNA-seq


title: 4782 RNA-seq


title: 4792 RNA-seq


title: 4819 RNA-seq


title: 4066 RNA-seq


title: 4435 RNA-seq


title: 5114 RNA-seq


title: N3 LV


title: 4988 RNA-seq


title: 4140 RNA-seq


title: 4098 RNA-seq


title: 4804 RNA-seq


title: 4811 RNA-seq


title: 4345 RNA-seq


title: 5108 RNA-seq


title: 4607 RNA-seq


title: 4398 RNA-seq


title: 5029 RNA-seq


title: CD36OE-1

city: 遵义市

first: 健

last: 黄

state: 贵州省

address: 汇川区大连路149号遵义医学院附属医院

institute: 遵义医学院附属医院

description: Processed data file: All_Counts.txt

data_processing:
Base calling using Torrent Suite Software and Torrent Server.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
Mapsplice v2.1.8 mapping to reference genome.
Reads counting using HTSeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All_Counts.txt: Tab-delimited text file contains raw counts for each sample.

source_name: HepG2.2.15-CD36 overexpression cell

growth_protocol: Modified Eagle Medium (MEM) containing 10% fetal calf serum and 500g of G418/ml.

extract_protocol:
Total RNA was extracted from cells by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
Ion Proton Sequencing Protocol.

treatment_protocol: CD36-overexpression-lentivirus and Vector-lentivirus were transfected into HepG2.2.15 cells.

tag: cell line

tag: lentivirus

value: CD36 overexpression


title: CD36OE-2

address: 汇川区大连路149号遵义医学院附属医院

description: Processed data file: All_Counts.txt


title: Vector-2

address: 汇川区大连路149号遵义医学院附属医院

description: Processed data file: All_Counts.txt

source_name: HepG2.2.15-vector cell

value: vector


title: 4410 RNA-seq


title: CD36OE-3

address: 汇川区大连路149号遵义医学院附属医院

description: Processed data file: All_Counts.txt


title: Vector-3

address: 汇川区大连路149号遵义医学院附属医院

description: Processed data file: All_Counts.txt


title: Vector-1

address: 汇川区大连路149号遵义医学院附属医院

description: Processed data file: All_Counts.txt


title: 4436 RNA-seq


title: 4789 RNA-seq


title: 4775 RNA-seq


title: 4348 RNA-seq


title: 4825 RNA-seq


title: 4541 RNA-seq


title: 4407 RNA-seq


title: 4092 RNA-seq


title: 5025 RNA-seq


title: 4527 RNA-seq


title: 4890 RNA-seq


title: 4036 RNA-seq


title: 4037 RNA-seq


title: 4836 RNA-seq


title: 4814 RNA-seq


title: 4352 RNA-seq


title: 4570 RNA-seq


title: 4373 RNA-seq


title: 4416 RNA-seq


title: 4024 RNA-seq


title: 5032 RNA-seq


title: 5007 RNA-seq


title: 4796 RNA-seq


title: 4343 RNA-seq


title: 4505 RNA-seq


title: 4521 RNA-seq


title: 4025 RNA-seq


title: 4830 RNA-seq


title: 4347 RNA-seq


title: 4077 RNA-seq


title: 4891 RNA-seq


title: 4400 RNA-seq


title: 4667 RNA-seq


title: 4813 RNA-seq


title: 4592 RNA-seq


title: 4510 RNA-seq


title: 5120 RNA-seq


title: 4346 RNA-seq


title: 4779 RNA-seq


title: 4365 RNA-seq


title: 4357 RNA-seq


title: 4888 RNA-seq


title: 4784 RNA-seq


title: 4368 RNA-seq


title: 4530 RNA-seq


title: 5035 RNA-seq


title: 4476 RNA-seq


title: 4778 RNA-seq


title: 4007 RNA-seq


title: 4084 RNA-seq


title: 4361 RNA-seq


title: 4067 RNA-seq


title: 4511 RNA-seq


title: 4574 RNA-seq


title: 4828 RNA-seq


title: 4374 RNA-seq


title: 4877 RNA-seq


title: 4872 RNA-seq


title: 4829 RNA-seq


title: 4078 RNA-seq


title: RbnullTET-MYCN4

city: Seattle

first: David

last: MacPherson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.17 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's CASAVA Software v1.8.2
Reads of low quality were filtered out prior to alignment to mm9 using TopHat v2.0.8b.  Counts were generated from TopHat alignments for gene using “intersection-strict” overlap mode in HTSeq v0.5.4p3.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.5.4p3

source_name: microdissected peripheral retina

extract_protocol:
Retinas were removed from postnatal day 12 mice and peripheral retina was microdissected and flash frozen on dry ice. Total RNA was isolated using Trizol reagent.
RNA libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

value: Postnatal Day 12

value: peripheral retina

value: Rb null, TET-MYCN


title: 4882 RNA-seq


title: RbnullTET-MYCN3


title: RbnullTET-MYCN2


title: 4471 RNA-seq

description:
F1 offspring from TRAMP x J:DO cross
TgPositive_samples_TPM_counts.txt
TgPositive_samples_raw_counts.txt

source_name: prostate tumor tissue

value: Transgene positive


title: 4870 RNA-seq


title: RbnullTET-MYCN1


title: 5016 RNA-seq


title: Rbnull_4

value: Rb null


title: 4826 RNA-seq


title: 4878 RNA-seq


title: Rbnull_3


title: Rbnull_2


title: Rbnull_1


title: Wildtype 3

city: Grand Rapids

first: Casey

middle: James

last: Droscha

state: Michigan

address: 333 Bostwick Ave.

department: Program for Skeletal Disease and Tumor Microenviroment

institute: Van Andel Institute

data_processing:
Reads were generated on a HiSeq 2500 System and Casava version 1.7 at
Sequenced reads were aligned to the mm10 genome using the subjunc aligner from the Rsubread R package using default parameters
Raw counts for gene-level features were computed using the featureCounts function in the Rsubread package using NCBI RefSeq annotation for mm10 (build 38.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including a matrix of raw counts for each sample

source_name: Neonatal mouse calavri

growth_protocol: Calvari were harvested from 5 day-old pups, washed/collagenase digested and strained prior to cell sorting based on transgenic GFP expression controlled by Osteocalcin-Cre. Cells were sorted into Trizol and stored at -80C until RNA isolation

extract_protocol:
RNA was isolated using phenol/chloroform and precipitated over night in isopropanol, pelleted, dried and resuspended in water
Library construction was performed by Hudson Alpha

treatment_protocol: Cells from wildtype and Cdc73/Hrpt2 cKO mice were isolated and sorted uniformily

value: Osteoblast

value: Wildtype


title: 4372 RNA-seq


title: Wildtype 2


title: 4536 RNA-seq


title: 4832 RNA-seq


title: 4041 RNA-seq


title: 4795 RNA-seq


title: Cdc73/Hrpt2 Flox 2

value: Cdc73/Hrpt2 KO


title: Cdc73/Hrpt2 Flox 3


title: 2996 RNA-seq


title: Wildtype 1


title: 4401 RNA-seq


title: 3230 RNA-seq


title: 4065 RNA-seq


title: Cdc73/Hrpt2 Flox 1


title: LSK_TTCTCC

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Basecalls performed using Illumina's CASAVA software, version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The first 6 bases were trimmed using Trimgalore v0.4.0 and Cutadapt v1.2.1 using the parameters --clip_R1 6 --clip_R2 6 –paired. Trimmed fastq files were aligned using Novoalign version V3.02.10 (www.novocraft.com) to the mouse assembly GRCm38 (mm10). Alignments were done in paired-end mode using the options -b4 (non-directional), -t 20,3 (optimized for SNP concordance), –a (adapter trimming), --hlimit 8 (homopolymer filter), and -H 20 (removes trailing bases with quality ≤ 20), and –u8 (penalty for unconverted CHG or CHH cytosine) as recommended by Novoalign. Aligned reads were output into the BAM format and sorted using SAMtools V0.1.17. Duplicates were marked with Picard V1.31 (http://picard.sourceforge.net).
Methylation of each cytosine was called using SAMtools mpileup (-B -C 0 -q 30 -d 500) followed by Novomethyl V1.01 (-o Consensus -%) (www.novocraft.com). Cytosine calls with Phred quality score ≤15 were discarded. Methylation percentage of each CpG di-nucleotide (found by searching the genome with a custom java script) was calculated by taking a weighted average of each cytosine using the map command from the bedtools suite (Quinlan and Hall, 2010). In most cases, only one base within a CpG dinucleotide had coverage; in these cases, the methylation information of the covered base was extrapolated to the other base.
Genome_build: mm10
Supplementary_files_format_and_content: bed file for CpG methylation. Columns are as follows: chr, start, end, fractional methylation, methylated C's, total C's, # of CpGs covered in the dinucleotide (1=just one, 2=both C and G covered)

source_name: Hematopoetic Progenitor Cell

extract_protocol:
Sorted cells were lysed in 96 well plates in 4 uL of lysis buffer (20 mM Tris-HCl, pH 8.0, 20 mM KCl, 0.3% Triton-X 100, 1 mg/mL Qiagen Protease) for 30 minutes at 50 degrees.
The lysed cells were then spiked-in with 1 uL of 60 fg/uL purified T7 phage DNA (GeneON). The DNA mixture was then bisulfite converted with the MethylEdge Bisulfite Conversion kit (Promega) using a modified bead-based protocol which enables automation (Domanico et al., 2013): 5 uL of the lysis/spike-in mixture was combined with 32.5 uL of MethylEdge Conversion reagent and incubated at 98°C for 8 minutes and 54°C for 60 minutes in a PCR machine. After incubation, the plate was briefly spun down and placed on an Agilent Bravo robot for subsequent steps. The 37.5 uL of bisulfite converted DNA was mixed with 180 uL of MethylEdge Binding Buffer and 1.8 uL of 20 mg/mL MagSi-DNA allround magnetic silica beads (MagnaMedics) and incubated at room temperature for 15 minutes. The beads were then collected on a magnet for 3 minutes and washed twice with 220 uL of 80% ethanol for 30 seconds while on the magnet. 60 uL of MethylEdge desulfonation buffer was added and incubated for 15 minutes. The desulfonation buffer was then removed and the beads were washed twice with 100 uL of 80% ethanol. The beads were then air-dried for 3 minutes, resuspended in 20 uL of Qiagen elution buffer, and incubated at 56°C in a shaking incubator at 2,000 rpm for 15 minutes. The beads were then collected on a magnet for 30 seconds and the supernatant containing the DNA was removed. The bisulfite-converted ssDNA from above was added directly into a mixture containing 1.25 uL of 10 mM dNTPs and 1 uL of 500 uM random hexamers (3’ phosphothioate). The reactions were incubated at 98°C for 1 minute and snap frozen on ice for 2 minutes. A mastermix of 0.5 uL of 50 U/uL Klenow fragment [3’→5’ exo-] (NEB M0212M), and 2.5 uL of 10X NEB Buffer 2 was added on ice and mixed well. The reactions incubated in a PCR machine as follows: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes. The entire reaction was denatured again at 98˚C for 1 minute and snap frozen on ice for 2 minutes. The reaction was transferred on a pre-chilled CoolRack by robot into a new plate containing 5 uL mixture of 20 uM random hexamers (3’ phosphothioate), 0.5 mM dNTPs, 1X NEB buffer and 25 U of Klenow fragment [3’→5’ exo-]. The wells were mixed well and the reaction was cycled once again: 4˚C for 10 minutes, ramped from 4°C to 37°C at 4°C/s, and held at 37°C for 30 minutes, and heat-inactivated at 70°C for 10 minutes. 20 uL of Qiagen Elution Buffer was added to each reaction to make it up to 50 uL, and each reaction was purified using 50 uL of Sera-Mag beads before proceeding to the standard illumina adapter ligation library construction protocol. The 25 uL of cleaned-up adapter-ligated fragments were PCR amplified in 50 uL containing 1 U of Phusion U Hot Start DNA Polymerase (Life Technologies F-555S), 1X HF buffer, 3% DMSO, 200 uM dNTPs, 0.5 uM PCR primer 1.0 (need sequence) (IDT), and corresponding 0.5 uM indexing PCR primer 2.0. The reactions were incubated in a PCR machine as follows: initial 98˚C for 1 minute; 10 cycles of 98˚C for 30 seconds, 65˚C for 15 seconds, 72˚C for 15 seconds; and a final extension of 72˚C for 5 minutes. The 50 uL reaction was cleaned up with 40 uL of Sera-Mag beads and eluted in 15 uL.

tag: markers

tag: type

value: Single-cell


title: 4522 RNA-seq

state: MD


title: LSK_TTATTTG


title: 4831 RNA-seq


title: 4324 RNA-seq


title: LSK_TTAGTCA


title: 2912 RNA-seq


title: LSK_TTAGGC


title: 5026 RNA-seq


title: LSK_TTAATAT

value: NTC


title: 2806 RNA-seq


title: LSK_TGGCGC


title: 4540 RNA-seq


title: LSK_TGCTGG


title: 2136 RNA-seq


title: 2797 RNA-seq


title: LSK_TGCCAT


title: 4793 RNA-seq


title: LSK_TGACCA


title: LSK_TGAATG


title: LSK_TGACTAG


title: 2943 RNA-seq


title: 3263 RNA-seq


title: LSK_TCCCAGC


title: LSK_TCATTC


title: 4518 RNA-seq


title: 3261 RNA-seq


title: LSK_TATAAT


title: LSK_TCGGCA

value: Ten-cell


title: LSK_TCTCTTC


title: LSK_TAGCTT


title: 4537 RNA-seq


title: 4816 RNA-seq


title: 4808 RNA-seq


title: 4499 RNA-seq


title: 4810 RNA-seq


title: 4402 RNA-seq


title: LSK_TACAGC


title: LSK_TAATGAA


title: 2406 RNA-seq


title: 4699 RNA-seq


title: 2666 RNA-seq


title: LSK_GTGGCC


title: 5005 RNA-seq


title: LSK_TCGAAG


title: LSK_GTCCGC


title: LSK_GTGAAA


title: LSK_GGCTAC


title: LSK_GTAGAG


title: 5045 RNA-seq


title: 4164 RNA-seq


title: 4514 RNA-seq


title: 4787 RNA-seq


title: 4783 RNA-seq


title: LSK_GGCACA


title: LSK_GCTATTG


title: LSK_GCGGGAC


title: 3843 RNA-seq


title: 4481 RNA-seq


title: LSK_TAATCG


title: 4479 RNA-seq


title: LSK_GCGCATA


title: LSK_GCCTTA


title: 3207 RNA-seq


title: 4883 RNA-seq


title: LSK_GCCGCG


title: LSK_GCCTAAA


title: LSK_GCCAAT


title: LSK_GCACTT


title: 4507 RNA-seq


title: 3617 RNA-seq


title: LSK_GATGGGT


title: LSK_GATGCT


title: 4529 RNA-seq


title: 4176 RNA-seq


title: LSK_GAGGTAA


title: 4780 RNA-seq


title: 4029 RNA-seq


title: 4097 RNA-seq


title: LSK_GAGAACC


title: 2660 RNA-seq


title: 4959 RNA-seq


title: 3451 RNA-seq


title: 4909 RNA-seq


title: LSK_CTTGTTG


title: LSK_CTCTTTT


title: 4905 RNA-seq


title: 3538 RNA-seq


title: LSK_CTATAC


title: 4618 RNA-seq


title: LSK_CTAGCT


title: 3824 RNA-seq


title: 4417 RNA-seq


title: LSK_CTATACA


title: 5119 RNA-seq


title: LSK_GATCAAA


title: 4000 RNA-seq


title: 1599 RNA-seq


title: LSK_GACTCCG


title: LSK_CTTACAC


title: LSK_CTCATAA


title: 5086 RNA-seq


title: LSK_CGTTGAT


title: LSK_CGTACG


title: LSK_CGTACCA


title: LSK_CGGACGG


title: LSK_GACGGA


title: LSK_CGATTCC


title: 1944 RNA-seq


title: 3413 RNA-seq


title: LSK_CGATGT


title: LSK_GATCAG


title: LSK_CGACAAA


title: 4801 RNA-seq


title: 1598 RNA-seq


title: LSK_CCTCAAC


title: 3482 RNA-seq


title: LSK_CGAGAA


title: LSK_CCCATG


title: 4035 RNA-seq


title: LSK_CCGTCC


title: 4500 RNA-seq


title: 4573 RNA-seq


title: LSK_CCAACA


title: 4528 RNA-seq


title: 1572 RNA-seq


title: 4815 RNA-seq


title: LSK_CATCGTC


title: LSK_CACTCA


title: LSK_CAGGCG


title: 2959 RNA-seq


title: 4805 RNA-seq


title: LSK_CACGAT


title: LSK_CAGATC


title: 4987 RNA-seq


title: 4421 RNA-seq


title: LSK_ATGTCA


title: 3509 RNA-seq


title: 4091 RNA-seq


title: LSK_ATGGGGT


title: LSK_CACCGG


title: LSK_CAAAAG


title: 3616 RNA-seq


title: 4576 RNA-seq


title: LSK_ATGAGC


title: 3492 RNA-seq


title: 4776 RNA-seq


title: LSK_CATGGC


title: LSK_ATCCTA


title: 4336 RNA-seq


title: LSK_ATCCACA


title: 4323 RNA-seq


title: 4531 RNA-seq


title: 2769 RNA-seq


title: LSK_ATCACG


title: 4610 RNA-seq


title: LSK_AGGTTTT


title: LSK_ATAATT


title: LSK_ATACGG


title: 4786 RNA-seq


title: 3867 RNA-seq


title: LSK_AGGTTT


title: 4394 RNA-seq


title: 3247 RNA-seq


title: LSK_ATGGTCG


title: 3262 RNA-seq


title: LSK_AGCGCT


title: 2765 RNA-seq


title: LSK_AGCATC


title: LSK_AGAGTCT


title: LSK_ATCTAT


title: LSK_AGATAG


title: 4961 RNA-seq


title: 4580 RNA-seq


title: 3468 RNA-seq


title: LSK_ACTTGA


title: LSK_ACTGAT


title: LSK_ACTCTC


title: 3414 RNA-seq


title: 4871 RNA-seq


title: LSK_ACGTAGC


title: LSK_ACGATA


title: 4906 RNA-seq


title: LSK_ACCCAG


title: LSK_ACCGGC


title: 4892 RNA-seq


title: 2962 RNA-seq


title: 3573 RNA-seq


title: 3220 RNA-seq


title: LSK_ACAGTG


title: 1623 RNA-seq


title: LSK_ACATCT


title: LSK_AATAGG


title: 2154 RNA-seq


title: LSK_AGAAGA


title: LSK_AATTCGA


title: LSK_ACAAAC


title: 4516 RNA-seq


title: LSK_AATACCC


title: LSK_AAGGGTG


title: 4341 RNA-seq


title: 4506 RNA-seq


title: LSK_AAGCCCA


title: 3224 RNA-seq


title: LSK_AAGCGA


title: 2764 RNA-seq


title: 5024 RNA-seq


title: LSK_AAGGAC


title: 3354 RNA-seq


title: 4492 RNA-seq


title: LSK_AAGACT


title: 5004 RNA-seq


title: LSK_AACCCC


title: 1239 RNA-seq


title: LSK_AAATGC


title: 2152 RNA-seq


title: 3402 RNA-seq


title: LSK_AAACAT


title: ESLAM_TTGACCA

source_name: Hematopoetic Stem Cell


title: 3919 RNA-seq


title: 3204 RNA-seq


title: 4145 RNA-seq


title: ESLAM_TTTAGGC


title: 5014 RNA-seq


title: ESLAM_TTCTCC


title: ESLAM_TTAGGC


title: ESLAM_TGCTCCA


title: 2404 RNA-seq


title: ESLAM_TGCCTTA


title: 4873 RNA-seq


title: 4855 RNA-seq


title: 4999 RNA-seq


title: ESLAM_TGCCGCG


title: 4434 RNA-seq


title: LSK_AACTTG


title: 4595 RNA-seq


title: 4655 RNA-seq


title: 4137 RNA-seq


title: LSK_AAAGCA


title: ESLAM_TGCACTT


title: ESLAM_TGCCAAT


title: 4509 RNA-seq


title: ESLAM_TGCAAGG


title: 3528 RNA-seq


title: ESLAM_TGAATG


title: 2942 RNA-seq


title: 4418 RNA-seq


title: 2290 RNA-seq


title: ESLAM_TCGAAG


title: ESLAM_TCATTC


title: 4396 RNA-seq


title: ESLAM_TCGATGT


title: 4403 RNA-seq


title: 4494 RNA-seq


title: 4344 RNA-seq


title: 4482 RNA-seq


title: 4524 RNA-seq


title: ESLAM_TCAGATC


title: ESLAM_TATCACG


title: ESLAM_TATACGG


title: 2752 RNA-seq


title: ESLAM_TATAATT


title: ESLAM_TAGGCCG


title: ESLAM_TAGCTT


title: ESLAM_TGACCA


title: 5003 RNA-seq


title: 1326 RNA-seq


title: 4986 RNA-seq


title: 4833 RNA-seq


title: ESLAM_TAGCGCT


title: 4399 RNA-seq


title: ESLAM_TACAGTG


title: 3532 RNA-seq


title: 2119 RNA-seq


title: ESLAM_TAATCG


title: 2772 RNA-seq


title: ESLAM_GTGAAA


title: 4038 RNA-seq


title: 4326 RNA-seq


title: ESLAM_GTCGTT


title: 4508 RNA-seq


title: ESLAM_GTCGAAG


title: ESLAM_TGCCAT


title: 4468 RNA-seq


title: 4393 RNA-seq


title: ESLAM_GTCATTC


title: 4493 RNA-seq


title: 3687 RNA-seq


title: 1616 RNA-seq


title: 2739 RNA-seq


title: 2116 RNA-seq


title: 4606 RNA-seq


title: 4550 RNA-seq


title: 3997 RNA-seq


title: 4812 RNA-seq


title: 4512 RNA-seq


title: 3530 RNA-seq


title: 3913 RNA-seq


title: 2095 RNA-seq


title: 3459 RNA-seq


title: ESLAM_GTATAAT


title: 5109 RNA-seq


title: ESLAM_GGCTAC


title: ESLAM_GTACAGC


title: 4005 RNA-seq


title: ESLAM_GTAGCTT


title: ESLAM_GCTTGTA


title: ESLAM_GCTCCA


title: 2648 RNA-seq


title: 5044 RNA-seq


title: ESLAM_GCCAAT


title: ESLAM_GGATCAG


title: 1802 RNA-seq


title: ESLAM_GGGCTAC


title: 4596 RNA-seq


title: 4317 RNA-seq


title: 3491 RNA-seq


title: 3415 RNA-seq


title: ESLAM_GCAAAAG


title: 4800 RNA-seq


title: 2794 RNA-seq


title: ESLAM_GATGCT


title: 4473 RNA-seq


title: 4320 RNA-seq


title: ESLAM_GATCAG


title: 5055 RNA-seq


title: 5028 RNA-seq


title: 3771 RNA-seq


title: 3529 RNA-seq


title: 4594 RNA-seq


title: 4788 RNA-seq


title: 4976 RNA-seq


title: ESLAM_GAATAA


title: ESLAM_GAAATGC


title: ESLAM_GAGTGG


title: 5110 RNA-seq


title: ESLAM_GAAACC


title: ESLAM_GCACGAT


title: 4360 RNA-seq


title: 4006 RNA-seq


title: ESLAM_CTTGTA


title: ESLAM_CTTCTCC