title: ES-Y641F_H3K27me3_rep2

value: H3K27me3 (Cell signaling, 9733S, lot unknown)


title: ES-WT_Ezh2_rep1

status: Public on Sep 01 2016

type: SRA

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

country: USA

institute: NIH

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 genome assembly using Bowtie2 version 2.2.4 with the default configurations.
RNA-seq reads were mapped to the mm9 genome assembly using TopHat version 2.0.13 (Trapnell C, et.al 2009) with the default configurations.
peaks were called using SICER version 1.1 ( Zang et al, 2009) with the following setting: redundancy threshold (1), window size (200), fragment size (150), effective genome fraction (0.74), gap size (600),FDR (0.05) .
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peak values for each Sample;tab-delimited text files includes FPKM values for each Sample.

molecule: genomic DNA

organism: Mus musculus

source_name: ES cell line

growth_protocol: E14 wild type or mutant ES cells were maintained in ES medium ( high glucose-DMEM, 15% fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 2 mM glutamine, 0.1 mM nonessential amino acids, and 1000 U/ml mouse LIF), on tissue culture plates coated with 0.1% gelatin, in 6% CO2 at 37°C. Mouse skeletal muscle C2C12 cells  were  grown in high glucose- DMEM, 20% fetal bovine serum, 1x Penicillin/streptomycin.

extract_protocol:
For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen).
For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with anti-H3K27me1 (Millipore #07-448), anti-H3K27me2 (Cell signaling #9728S), anti-H3K27me3 (Cell signaling #9733S), anti-H3K4me1 (Abcam #ab8899), anti-H3K27ac (Abcam #4729). 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. For polyA RNA-Seq, Illumina protocol was followed.

treatment_protocol: For 24 hours differentiation, feeder-free ESC were plated at low density (1 x 106/10cm plate) for 24 hours in ES medium described above without LIF and serum. For EB culture, 1 x 106 feeder-free ESC were passaged onto 10 cm ultra low attachment culture dishes. Serum-cultured ESC were converted to ground state by culturing and passaging the cells in ESGRO-2i medium.

tag: developmental stage

value: Pluripotent ES cells

tag: chip antibody

value: Ezh2 (Cell signaling, 5246S, lot unknown)

tag: strain


title: 24h-diff-WT_H3K27ac_rep2

value: 24 hours differentiated ES cells

value: H3K27ac (Abcam ab4729, lot unknown)


title: EB8-WT_H3K4me1

value: Day 8 embryoid bodies

value: H3K4me1 (Abcam, ab8899, lot unknown)


title: Animal10_Female_Cortex_Sequencing batch 2

city: Indianapolis

first: Aaron

middle: Thomas

last: Smith

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly

description:
Sequencing batch 2 from sample Animal10_Female_Cortex
US-1456445_BC2BUMACXX_US-1456445_CTTGTA_L003_R1_001

library_source: transcriptomic

data_processing:
FastQ files were processed to remove adaptor sequence and discard reads < 17bp in length with cutadapt v. 1.4.1 [23] with options –a TGGAATTCTCGGGTGCCAAGG –quality-base 33 –q 20 –match-read-wildcards –m 17. All trimmed reads that contained an ‘N’ were discarded. Identical sequences from the same sample were combined into a single sequence in the form expected by miRDeep2
Quantifier.pl from the mirdeep2 package [v. 2.0.0.5 ] was used to generate miR alignment files (.mrd files) against known miRs from miRbase 20 with options –P –p <org>_hairpin.fa –m <org>_mature.fa –r trimmed_reads.fa –d. This was done separately for rat, mouse, human, and C. elegans known miRs.
The .mrd files were then parsed with a custom Perl script as follows. Each isomiR sequence in an alignment was associated with the corresponding mature miR identifier. If it aligned to a miRNA precursor, but not with an expected mature miR sequence, it was identified as <miR>-pre to indicate this. Usually these correspond with reverse strand miRs that have not yet been annotated as alternate mature forms. Sometimes these appear to be microRNA offset RNAs [25] and sometimes they appear to represent incompletely processed sequence. If a given sequence was identified as aligning with more than one precursor, it was associated with all potential names as a composite name. That is, a sequence that aligned to both let-7a-5p and let-7f-5p was assigned to the composite mature miR let-7a-5p;let-7f-5p to indicate for subsequent analyses that this identification was ambiguous. All sequences that had not yet been identified against known rat miRs were then looked for in the analysis with respect to known mouse miRs, and so on against human and finally C. elegans miRs. This process allows for identification of conserved rodent miRs that have not yet been annotated in rat, and against conserved mammalian miRs that have not yet been annotated in rat and mouse. The comparison with C. elegans was to identify spiked in C. elegans miRs (not used in this data set).
In parallel to the above identification of known miRs, we used miRDeep2’s novel miR identification process as well. We aligned all the unique trimmed fasta reads to the RN5 reference rat genome with miRDeep2’s mapper.pl script with default parameters and then used the miRDeep2.pl script to generate novel miR predictions and .mrd files. The .mrd files were parsed as above to assign miR names to each unique read. We then attempted to identify and merge novel predictions that were identical to known miRs as follows. If the same read sequence identified a miR in the novel analysis and in the known analysis and the known miR appeared in miRDeep’s .mrd file, we assumed that this was a duplicate identification and changed the miR name from that reported by miRDeep (chr# followed by a unique ID) to that of the known miR. Otherwise, we assumed that the novel prediction might be different from the known miR identification and added it to the list of potential identifications for the sequence. So, for example, a sequence which was aligned by miRDeep2 to a predicted miR on chrX and also identified as miR-450a is identified as “chrX_48156-5p;miR-450a-5p” because miRDeep2 does not show miR-450a as aligned to this predicted miR, indicating that these are two potentially distinctsources of this sequence. Finally, the counts associated with each unique sequence are summed for each named miR (including complex, multi-named miRs) for each sample and these are reported as the miR level counts.
Genome_build: Rn5 for novel miR identification, mirbase 20 for known miR identification
Supplementary_files_format_and_content: Tab delimited text files with raw count information at either the mature miR level or isomiR level. Both files also contain the source of the predictiion that the indicated counts go with the indicated miR or isomiR.

molecule: total RNA

organism: Rattus norvegicus

growth_protocol: Naïve Sprague Dawley rats ,12-13 weeks old, were used for organ isolation.

extract_protocol:
RNA was purified using the miRNAeasy protocol from Qiagen (Kit cat# 217004).
Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Cataloge # RS-200-0048) using a HiSeq2000.  Briefly, RNA was extracted from tissues using the miRNeasy protocol. Libraries were constructed using the Illumina TruSeq small RNA preparation guide which entails ligation of adapters on the 3' and 5' ends of the RNA molecules.  The libraries were quantitated using RiboGreen and were size selected through gel electrophoresis and libraries consistent with the size of miRNAs were gel purified.  Sequencing was performed with each sample receiving 4-5 million, 30bp, single-end reads. generated

value: Sprague Dawley

tag: animal id

tag: age

value: 12-13 weeks

tag: gender

value: female

tag: tissue

value: Cortex

tag: rin


title: Animal9_Female_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Cerebellum
US-1459958_AD1GBMACXX_US-1459958_CGGAAT_L003_R1_001

value: Cerebellum


title: Animal11_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Muscle_Biceps_Homogenate_re-extract
US-1466226_AD2C4RACXX_US-1466226_TACAGC_L004_R1_001

value: Muscle - Biceps


title: ES-Y641F_Ezh2_rep1


title: Animal3_Male_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Heart
US-1466208_AD1GBMACXX_US-1466208_CATTTT_L005_R1_001

value: male

value: Heart


title: ES-Y641F_H3K4me1


title: Animal4_Male_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Medulla
US-1458869_BC2BUMACXX_US-1458869_CCAACA_L002_R1_001

value: Medulla


title: E40E

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadpat to trim low quality bases and Illumina sequencing adapters from the 3'end of the reds.
Only paris where both reads were 20nt or longer were kept for further analysis.
Reads were mapped to the NCBIM38r73 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool
Gene counts were compiled using the HTSeq tool.
Normalization and differential expression was carried out using the EdgeR Bioconductor package with the R statistical programming environment
Genome_build: mm10

molecule: polyA RNA

source_name: wildtype

extract_protocol:
neocortices were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent followed by Rneasy Plug Micro Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The library was generated with Kapa stranded mRNA-seq Kit.

value: neocortex


title: E40F


title: E46G


title: E46F


title: Animal5_Male_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Ileum
US-1458884_AD2C4RACXX_US-1458884_GGCTAC_L004_R1_001

value: Ileum


title: E46C


title: E40B


title: Animal2_Male_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Muscle_Soleus
US-1456443_AD1GBMACXX_US-1456443_ACTGAT_L003_R1_001

value: Muscle - Soleus


title: Sample12

source_name: Emx1-Cre; MagohLox/+ 1


title: Sample13

source_name: Emx1-Cre; MagohLox/+ 2


title: Pooled (human+Drosophila) input control

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

country: Germany

institute: University Hospital Düsseldorf

data_processing:
Data processing was performed by Active Motif (Carlsbad, Ca, USA).
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq500) are mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is devided into 32-nt bins and the number of fragments in each bin is determined.
The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).
Tag Normalization: In the default analysis, the tag number of all samples is reduced (by random sampling) to the number of tags present in the smallest sample.
For the spike-adjusted analysis, the number of Drosophila tags was used to normalize the number of human tags. Compared to the standard normalization, where the same number of tags would be used for the samples to be compared (12.9 million), the effect of the spike-in adjustment was an up-scaling of sample 2 (HDACi) by a factor of about 2 relative to sample 1 (Solvent).
To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals). In locations where only one sample has an Interval, this Interval defines the Active Region. The use of Active Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples.
After defining the Intervals and Active Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined. In addition, average and peak (i.e. at “Summit”) fragment densities within Intervals and Active Regions are compiled.

organism: Homo sapiens

source_name: pooled input DNA of Romidepsin and solvent treated TCam-2 DNA, including Drosophila DNA spike-in control

growth_protocol: TCam-2, 2102P, NCCIT and JAR cells were cultivated as published (Nettersheim et al., 2015, PubMed ID: 26226633)

extract_protocol: For chromatin-immunoprecipitation-followed-by-sequencing (ChIP-seq) analysis, cells of interest were fixed by addition of 1/10 Formaldehyde solution (11 % Formaldehyde, 0.1 M NaCl, 1 mM EDTA (pH 8), 50 mM HEPES (pH7.9)) to the culture media followed by 15 minutes of incubation at room temperature. Fixation was stoped by addition of 1/20 volume Glycine solution (2.5 M) and incubation for 5 minutes at room temperature. Cells were scraped and washed once in PBS-Igepal (0.5%) solution and once more in PBS-Igepal-PMSF (1mM) solution. Cells were pelleted by centrifugation and snap frozen on dry ice and stored at -80°C.

tag: cell line

tag: cell type

value: Seminoma-like cell line / Drosophila DNA (spike-in)


title: TCam-2 Romidepsin 16h

source_name: TCam-2 treated with Romidepsin for 16h

value: Seminoma-like cell line


title: E46E


title: E40D


title: Animal9_Female_Muscle_Biceps_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Muscle_Biceps
US-1463122_AD1GBMACXX_US-1463122_GACGAC_L004_R1_001


title: Sample14

source_name: Emx1-Cre; MagohLox/+ 3


title: ES-Y641F_Ezh2_rep2

value: Pluripotent ES cells

value: Ezh2 (Cell signaling, 5246S, lot unknown)


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_SEA062401C:142:C2BUMACXX:4

value: Duodenum


title: Sample11

source_name: Emx1-Cre; Rbm8aLox/+ 3


title: Sample9

source_name: Emx1-Cre; Rbm8aLox/+ 1


title: Animal10_Female_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Ileum
US-1458911_AD1GBMACXX_US-1458911_CTCAGA_L002_R1_001

value: Sprague Dawley


title: Animal7_Female_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Cerebellum
US-1456432_BC2BUMACXX_US-1456432_CAACTA_L007_R1_001

value: 12-13 weeks


title: Animal11_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Muscle_Biceps_Homogenate_re-extract
US-1466226_AD1GBMACXX_US-1466226_TACAGC_L004_R1_001

value: female


title: TCam-2 Solvent 16h

source_name: TCam-2 treated with DMSO for 16h


title: Sample8

source_name: Emx1-Cre; Eif4a3Lox/+ 3


title: Sample5

source_name: Emx1-Cre 3


title: ag-11 ap2-43 rep2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

country: China

institute: Fudan University

data_processing:
Sequenced reads were trimmed for low quality sequences and then mapped to Ler-0 genome using Tophat v2.0.13 with the parameters "-g 1 -N 0"
Mapped reads were assigned to each gene using GFOLD v1.1.2 with the default parameters
Genome_build: Ler-0
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and RPKM values for each gene

organism: Arabidopsis thaliana

source_name: Inflorescences

growth_protocol: 23°C under long-day conditions (16 hours light, 8 hours dark)

extract_protocol:
Total RNA was extracted from inflorescence tissue containing stage 7 and younger flowers using TRI reagent (MRC). total RNA was used to isolate mRNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB).
RNA libraries were constructed using the NEBNext® mRNA Library Prep Reagent Set for Illumina (NEB) following the manufacturer’s protocols.

value: Inflorescences

value: stage 7 and younger flowers

tag: genotype/variation


title: Sample10

source_name: Emx1-Cre; Rbm8aLox/+ 2


title: ag-11 ap2-43 rep3


title: Animal5_Male_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Hippocampus
US-1458648_BC2BUMACXX_US-1458648_TACAGC_L005_R1_001

value: Hippocampus


title: Sample6

source_name: Emx1-Cre; Eif4a3Lox/+ 1


title: Animal6_Male_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Brainstem
US-1466232_BC2BUMACXX_US-1466232_CGGAAT_L008_R1_001

value: male

value: Brainstem


title: Sample4

source_name: Emx1-Cre 2


title: Sample7

source_name: Emx1-Cre; Eif4a3Lox/+ 2


title: Placenta-Male-WT5

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

country: Canada

institute: McGill University

data_processing:
Convert BAM files to FASTQ files using picard-toolds-1.108, SamToFastq.jar
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containting chromosome.base handle, chromosome location, base-pair location, strand information, coverage, frequency of observed cytosine (freqC - methylation) and frequency of observed thymine

source_name: Placenta-Male-WT

extract_protocol:
Genomic DNA was extracted from embryos and placentas using DNeasy Blood & Tissue Kit (Qiagen) as per manufacturer protocols
Reduced represenation bisulfite sequencing (RRBS) libraries were prepared according to previously published prototols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplificaton.

tag: strain background

tag: Sex

value: Wildtype

value: Placenta

tag: conceived using

value: Assisted Reproductive Technologies (ART)

tag: replicate

value: Biological replicate 5


title: ag-11 ap2-35 rep2


title: Placenta-Male-WT4

value: Biological replicate 4


title: Animal5_Male_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Muscle_Biceps_Homogenate_re-extract
US-1459909_BC2BUMACXX_US-1459909_GTGAAA_L007_R1_001

value: Muscle - Biceps


title: Placenta-Male-WT3

value: Biological replicate 3


title: Animal10_Female_Liver_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Liver_Homogenate_re-extract
US-1462936_AD1GBMACXX_US-1462936_ATTCCT_L005_R1_001

value: Liver


title: Placenta-Male-WT1

value: Biological replicate 1


title: ES-WT_H3K27me3_rep1

source_name: ES cell line

value: Pluripotent ES cells

value: H3K27me3 (Cell signaling, 9733S, lot unknown)


title: Placenta-Male-WT2

value: Biological replicate 2


title: Placenta-Male-Het5

source_name: Placenta-Male-Het

value: Heterozygote


title: Animal5_Male_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Jejunum
US-1458661_BC2BUMACXX_US-1458661_CACTCA_L004_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: Jejunum


title: ag-11 rep3

value: Inflorescences

value: stage 7 and younger flowers


title: Placenta-Male-Het3

value: male

value: Placenta


title: ag-11 ap2-35 rep1


title: Animal3_Male_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_WholeBlood
US-1466241_AD1GBMACXX_US-1466241_GATCAG_L004_R1_001

value: WholeBlood


title: Placenta-Male-Het2

value: Assisted Reproductive Technologies (ART)


title: Placenta-Male-Het1


title: ag-11 ap2-43 rep1


title: Placenta-Female-WT5

source_name: Placenta-Female-WT

value: female

value: Wildtype

value: Biological replicate 5


title: ag-11 ap2-35 rep3


title: Sample3

source_name: Emx1-Cre 1

value: neocortex


title: Animal8_Female_Kidney_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Kidney
US-1455448_AD2C4RACXX_US-1455448_CCGTCC_L008_R1_001

value: Kidney


title: ag-11 rep1


title: Placenta-Female-WT4

value: Biological replicate 4


title: Placenta-Female-WT3

value: Biological replicate 3


title: Ler rep3

value: Ler


title: Animal8_Female_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Adrenal
US-1454065_BC2BUMACXX_US-1454065_CTAGCT_L005_R1_001

value: Sprague Dawley

value: Adrenal


title: 1002_Sequencing batch 1

description:
Sequencing batch 1 from sample 1002
US-1466214_AD1GBMACXX_US-1466214_CTATAC_L005_R1_001

value: 12-13 weeks

value: DRG


title: Ler rep2

value: Inflorescences

value: stage 7 and younger flowers


title: Placenta-Female-WT2

value: Placenta

value: Biological replicate 2


title: Placenta-Female-WT1

value: Assisted Reproductive Technologies (ART)

value: Biological replicate 1


title: Placenta-Female-Het5

source_name: Placenta-Female-Het

value: female

value: Heterozygote


title: Placenta-Male-Het4

value: male


title: Placenta-Female-Het4


title: Placenta-Female-Het3


title: Animal5_Male_Testicle_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Testicle
US-1456484_BC2BUMACXX_US-1456484_CACGAT_L008_R1_001

value: Testicle


title: Ler rep1


title: Animal8_Female_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Duodenum
US-1456490_AD1GBMACXX_US-1456490_CTAGCT_L002_R1_001

value: Duodenum


title: NAT-Placenta-Male-WT5

source_name: NAT-Placenta-Male-WT

value: Wildtype

value: Natural mating

value: Biological replicate 5


title: ag-11 rep2


title: Placenta-Female-Het2


title: Placenta-Female-Het1


title: NAT-Placenta-Male-WT3

value: Biological replicate 3


title: Animal3_Male_Cerebellum_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal3_Male_Cerebellum
US-1456436_AD1GBMACXX_US-1456436_TAGCTT_L005_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: Cerebellum


title: NAT-Placenta-Male-WT2


title: NAT-Placenta-Male-WT4

value: Biological replicate 4


title: Animal3_Male_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Cortex
US-1456488_AD2C4RACXX_US-1456488_TAGCTT_L001_R1_001

value: Cortex


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_AD1GBMACXX_US-1466190_CAACTA_L004_R1_001

value: Muscle - Soleus


title: NAT-Placenta-Male-WT1

value: Placenta


title: Animal2_Male_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Hippocampus
US-1454082_AD2C4RACXX_US-1454082_ATGTCA_L005_R1_001

value: Hippocampus


title: NAT-Placenta-Male-Het5

source_name: NAT-Placenta-Male-Het


title: 1501_Sequencing batch 2

description:
Sequencing batch 2 from sample 1501
US-1466192_BC2BUMACXX_US-1466192_ATGAGC_L007_R1_001

value: female

value: DRG


title: NAT-Placenta-Male-Het2

value: male

value: Heterozygote

value: Biological replicate 2


title: Animal9_Female_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Stomach_Non-Glandular
US-1466233_AD1GBMACXX_US-1466233_CACTCA_L006_R1_001


title: Animal8_Female_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Brainstem
US-1459880_AD1GBMACXX_US-1459880_ACAGTG_L003_R1_001

value: Brainstem


title: NAT-Placenta-Female-WT5

source_name: NAT-Placenta-Female-WT

value: Wildtype

value: Natural mating


title: Animal6_Male_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Heart
US-1466243_AD1GBMACXX_US-1466243_GTAGAG_L005_R1_001

value: Heart


title: NAT-Placenta-Female-WT3

value: Biological replicate 3


title: NAT-Placenta-Female-WT2


title: NAT-Placenta-Male-Het4


title: Animal6_Male_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Muscle_Soleus
US-1459871_AD1GBMACXX_US-1459871_GTTTCG_L003_R1_001

value: Sprague Dawley

value: 12-13 weeks


title: NAT-Placenta-Female-Het5

source_name: NAT-Placenta-Female-Het

value: Biological replicate 5


title: NAT-Placenta-Female-Het4

value: Biological replicate 4


title: Animal4_Male_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Stomach_Non-Glandular
US-1466223_AD2C4RACXX_US-1466223_CACGAT_L006_R1_001


title: NAT-Placenta-Female-Het3


title: NAT-Placenta-Female-Het2


title: NAT-Placenta-Female-WT1

value: Biological replicate 1


title: Ath_circRNA

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

description: Circular RNA

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low-quality sequence and the percentage of unknown bases (N) is greater than 5%. At last, the obtained “clean bases” for further analysis.
The circular RNAs were predicted using the tophat2 (Langmead, et al., 2010) and find_circ (Memczak et al., 2013) softwares.
The expression quantity were caculated by SRPBM software (Jeck et al., 2013)
The transcripts of circular RNA were annotated using bedtools software (Quinlan at al., 2010)
The targeted microRNAs of circular RNAs were predicted using miRanda software (Zhu et al. 2009)
Genome_build: TAIR10
Supplementary_files_format_and_content: BED file.  Columns: #chrom, circStart, circEnd, strand, running_number, Ath findcirc circName, Ath findcirc number, Ath findcirc srpbm, best gene, best transcript, position contain type, Entrez_id, UniProtKB-AC, Symbol, description, circRNA start site position type, circRNA end site position type, miRNA num, miRNA, more than 2 same miRNA num, more than 2 same miRNA.

source_name: whole plants across lifespan

growth_protocol: A. thaliana plants (Columbia-0) were cultivated at 23/18℃ under 16/8 light/dark cycle.

extract_protocol:
The whole plants from different developmental stages (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence) were collected and then were frozen in liquid nitrogen immediately after harvest and stored at -80°C until use. The total RNAs were extracted from whole plants of each developmental stage using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liao-ning, China), according to the manufacturer’s protocol, respectively, and then were mixed equally into an RNA sample. The total RNA sample was treated with Ribo-Zero™ Magnetic Kict and RNase R (Epicentre) to remove the rRNA and digest linear RNA successively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: 7 stages (cotyledons emergence, rosette leaves 1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence)

value: whole plant


title: NAT-Placenta-Female-Het1

value: female

value: Placenta


title: NAT-Placenta-Male-Het3

value: male


title: Animal9_Female_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Stomach_Glandular
US-1456516_BC2BUMACXX_US-1456516_ATTCCT_L001_R1_001


title: Embryo-Male-WT5

source_name: Embryo-Male-WT

value: Embryo

value: Assisted Reproductive Technologies (ART)


title: Animal5_Male_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Cortex
US-1456457_AD2C4RACXX_US-1456457_TTAGGC_L004_R1_001

value: Cortex


title: Embryo-Male-WT3

value: Wildtype


title: Embryo-Male-WT2

value: Biological replicate 2


title: Embryo-Male-WT4


title: Animal7_Female_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal7_Female_Muscle_Soleus_Homogenate_re-extract
US-1466190_SEA055491C:302:H0HMMADXX:2

value: Muscle - Soleus


title: NAT-Placenta-Female-WT4

value: Natural mating


title: Embryo-Male-WT1


title: NAT-Placenta-Male-Het1

value: Heterozygote


title: Animal4_Male_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Jejunum
US-1458698_AD1GBMACXX_US-1458698_CATTTT_L002_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: Jejunum


title: Embryo-Male-Het3

source_name: Embryo-Male-Het

value: Biological replicate 3


title: Animal2_Male_Jejunum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Jejunum
US-1458623_BC2BUMACXX_US-1458623_CACTCA_L001_R1_001


title: Animal2_Male_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Muscle_Biceps
US-1466197_AD2C4RACXX_US-1466197_CGATGT_L007_R1_001

value: Muscle - Biceps


title: Animal9_Female_Duodenum_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Duodenum_Homogenate_re-extract
US-1462996_AD1GBMACXX_US-1462996_TAATCG_L002_R1_001

value: Duodenum


title: Embryo-Male-Het2


title: Embryo-Male-Het1

value: Biological replicate 1


title: Embryo-Male-Het4

value: Biological replicate 4


title: Embryo-Female-WT5

source_name: Embryo-Female-WT

value: female

value: Biological replicate 5


title: Animal11_Female_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Brainstem
US-1459942_AD2C4RACXX_US-1459942_TGACCA_L004_R1_001

value: Brainstem


title: Embryo-Female-WT4

value: Embryo

value: Assisted Reproductive Technologies (ART)


title: Animal3_Male_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Stomach_Glandular
US-1456482_BC2BUMACXX_US-1456482_CGTACG_L004_R1_001

value: male


title: Embryo-Female-WT1

value: Wildtype


title: Embryo-Female-WT3


title: Embryo-Female-Het4

source_name: Embryo-Female-Het


title: Embryo-Female-Het5


title: Animal10_Female_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Stomach_Glandular
US-1456512_BC2BUMACXX_US-1456512_ATGTCA_L006_R1_001


title: Embryo-Female-Het3


title: Animal3_Male_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Pancreas_Reextract
US-1459546_AD2C4RACXX_US-1459546_GTAGAG_L008_R1_001

value: Pancreas


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal4_Male_Pancreas_Reextract
US-1462447_AD1GBMACXX_US-1462447_TGACCA_L005_R1_001


title: Animal3_Male_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Cerebellum
US-1456436_SEASDW062403C:145:D1GBMACXX:5

value: Cerebellum


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP 1843_3-2

city: Chapel Hill

first: Timothy

last: Gershon

state: NC

address: 6109 Neuroscience Research Building

department: Pediatric Hematology Oncology

institute: University of North Carolina at Chapel Hill

description:
poly-A selected
1843_3-2

data_processing:
For read pseudo-alignment and quantification, I used Kallisto v0.42.4 (mm9 genomic assembly, GRCm38 transcriptome definition).
Downstream analysis was with edgeR
Genome_build: mm9

source_name: P3 cerebellum

extract_protocol:
Cerebella were harvested, meninges were removed from cerebella, and RNA was extracted immediately using the RNeasy Mini Kit (Qiagen #74104). Sequencing and library prep were performed with 2.4ug of total RNA
Library prep was by Illumina RNA TruSeq (RS-122-2101) with final library type being stranded mRNA

value: cerebellum

value: Postnatal day 3

tag: genotype


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP 1843_9

description:
poly-A selected
1843_9


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP 1843_4

description:
poly-A selected
1843_4


title: Animal6_Male_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Ileum
US-1458861_AD1GBMACXX_US-1458861_TGACCA_L006_R1_001

value: Sprague Dawley

value: 12-13 weeks

value: Ileum


title: Embryo-Male-Het5

value: Heterozygote


title: P3 Math1-Cre;p53-loxP/loxP 1845_11

description:
poly-A selected
1845_11


title: Embryo-Female-Het1

value: Biological replicate 1


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP 1843_3

description:
poly-A selected
1843_3


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_AD1GBMACXX_US-1462955_CATTTT_L004_R1_001

value: Liver


title: P3 Math1-Cre;p53-loxP/loxP 1843_7

description:
poly-A selected
1843_7


title: 1005_Sequencing batch 1

description:
Sequencing batch 1 from sample 1005
US-1466230_AD2C4RACXX_US-1466230_GGCTAC_L008_R1_001

value: DRG


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- 1836_9

description:
poly-A selected
1836_9


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- 1836_8

description:
poly-A selected
1836_8


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- 1836_4

description:
poly-A selected
1836_4


title: Animal9_Female_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_WholeBlood
US-1466198_AD1GBMACXX_US-1466198_CGGAAT_L006_R1_001

value: female

value: WholeBlood


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- 1836_3

description:
poly-A selected
1836_3


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- 1842_4

description:
poly-A selected
1842_4


title: Animal5_Male_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Heart
US-1466191_BC2BUMACXX_US-1466191_CTTGTA_L006_R1_001

value: Heart


title: Animal6_Male_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Brainstem
US-1466232_AD1GBMACXX_US-1466232_CGGAAT_L004_R1_001

value: Brainstem


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- 1842_11

description:
poly-A selected
1842_11


title: Animal7_Female_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Cerebellum
US-1456432_AD1GBMACXX_US-1456432_CAACTA_L003_R1_001


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- 100019_9

description:
poly-A selected
100019_9


title: Embryo-Female-WT2

value: Embryo

value: Assisted Reproductive Technologies (ART)

value: Biological replicate 2


title: Embryo-Female-Het2


title: P3 Math1-Cre;Bax-loxP/loxP;Bak--/- 100019_7

description:
poly-A selected
100019_7


title: purified pachytene spermatocytes RNA_n1

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description:
processed data file: mRNA_genes_merged_counts.tx
Pachn1WT

data_processing:
RNA SEQ: Aligned each raw file to genome using BWA v0.7.8
RNA SEQ: Used HTSeq v0.6.1 to count reads aligning to .gtf file (annotation file)
RNA SEQ: Used edgeR v3.6.8 to assess fold change and differential expression
RNA SEQ annotation file: UCSC mm9 .gtf transcriptome file from: https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
Small RNA SEQ: Trimmed off adapters and filtered out low-quality reads (ones with too many N's, or which failed Illumina's Y/N overall quality metric) - custom python script.
Small RNA SEQ: Aligned reads to genome using Bowtie 0.12.7. Exact match.
Small RNA SEQ: Aligned reads to miRNA hairpin sequences from miRBase v21 using a custom script.
Small RNA SEQ: Collapsed all hairpin aligning reads by their seed sequence using a custom script; this results in raw counts per miRNA family
Small RNA SEQ: Used edgeR v3.6.8 to assess fold change and differential expression
Genome_build: RNA SEQ: UCSC mm9, used pre-built BWA indexes from https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
Genome_build: Small RNA SEQ: mm9 Bowtie Indices
Supplementary_files_format_and_content: RNA SEQ: HTSeq raw counts file for each sample for each gene in annotation file
Supplementary_files_format_and_content: Small RNA SEQ: Raw counts file for each sample for each miRNA seed family

source_name: purified pachytene spermatocytes RNA

growth_protocol: All mice were fed ad libitum with standard laboratory rodent chow, and were maintained under controlled conditions of light and temperature, according to the strict regulations outlined and approved by the Cornell Institutional Care and Use Committee (IACUC).   Whole testis were isolated from mice at day 1 postpartum (pp), day 3 pp, and day 7 pp. Spermatocytes were isolated from adult mice about 70-80 days after birth.

extract_protocol:
Illumina TruSeq RNA Seq
Testes from day 1 postpartum (pp), day 3 pp, day 7 pp, and adult (day 70-80 pp) were removed and decapsulated prior to RNA isolation using TRIzol (Life Technologies) from either whole tesits or enriched cells. Enrichment of specific spermatogenic cell types (leptotene/zygotene and pachytene) was achieved using the STA-PUT method based on separation by cell diameter/density at unit gravity (Bellvé, 1993). Purity of resulting fractions was determined by microscopy based on cell diameter and morphology. Pachytene cells were approximately 90% pure, with residual possible contamination from spermatocytes of slightly earlier or later developmental stages. Leptotene and zygotene cells were isolated in combination, and were >90% pure. Neither pachytene nor leptotene/zygotene fractions exhibited evidence of any contaminating somatic cells. RNA was used as the source material for mRNA sequencing and small RNA sequencing.
We sequenced both small RNA and RNA from wildtype whole testis or purified meiotic cells at different stages of spermatogenesis. Sequencing libraries were genereated as replicates, from two biological replicates per sample type.

treatment_protocol: Mice were wild type (C57BI/6J)

value: wild type

tag: tissue/cell type

value: purified pachytene spermatocytes

tag: molecule subtype

value: RNA


title: P3 Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP 1843_10

description:
poly-A selected
1843_10

tag: strain

value: cerebellum

value: Postnatal day 3


title: day 3 pp whole testis RNA_n1

description:
processed data file: mRNA_genes_merged_counts.tx
Day3n1WT

source_name: day 3 pp whole testis RNA

value: day 3 pp

value: whole testis


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_BC2BUMACXX_US-1462955_CATTTT_L002_R1_001

value: Sprague Dawley

tag: animal id

value: 12-13 weeks


title: purified pachytene spermatocytes SMALL RNA_n1

description:
processed data file: miRNAfamily_merged_counts.txt
Pachn1

extract_protocol:
Illumina TruSeq Small RNA Seq
Testes from day 1 postpartum (pp), day 3 pp, day 7 pp, and adult (day 70-80 pp) were removed and decapsulated prior to RNA isolation using TRIzol (Life Technologies) from either whole tesits or enriched cells. Enrichment of specific spermatogenic cell types (leptotene/zygotene and pachytene) was achieved using the STA-PUT method based on separation by cell diameter/density at unit gravity (Bellvé, 1993). Purity of resulting fractions was determined by microscopy based on cell diameter and morphology. Pachytene cells were approximately 90% pure, with residual possible contamination from spermatocytes of slightly earlier or later developmental stages. Leptotene and zygotene cells were isolated in combination, and were >90% pure. Neither pachytene nor leptotene/zygotene fractions exhibited evidence of any contaminating somatic cells. RNA was used as the source material for mRNA sequencing and small RNA sequencing.
We sequenced both small RNA and RNA from wildtype whole testis or purified meiotic cells at different stages of spermatogenesis. Sequencing libraries were genereated as replicates, from two biological replicates per sample type.

value: small RNA


title: Animal9_Female_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Adrenal
US-1458870_AD1GBMACXX_US-1458870_GTGGCC_L005_R1_001

tag: age

value: female

value: Adrenal


title: purified leptotene/zygotene spermatocytes RNA_n1

description:
processed data file: mRNA_genes_merged_counts.tx
LZn1WT


title: P3 Math1-Cre;p53-loxP/loxP 1845_4

description:
poly-A selected
1845_4


title: purified leptotene/zygotene spermatocytes SMALL RNA_n1

description:
processed data file: miRNAfamily_merged_counts.txt
LZn1


title: day 3 pp whole testis SMALL RNA_n1

description:
processed data file: miRNAfamily_merged_counts.txt
D3n1

source_name: day 3 pp whole testis SMALL RNA


title: Animal9_Female_Muscle_Soleus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Muscle_Soleus
US-1458621_AD2C4RACXX_US-1458621_CGATGT_L004_R1_001

tag: gender

value: Muscle - Soleus


title: Animal10_Female_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Medulla
US-1458841_AD1GBMACXX_US-1458841_GAGTGG_L002_R1_001

tag: tissue

value: Medulla


title: P3 Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- 1836_7

description:
poly-A selected
1836_7


title: Animal5_Male_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Pancreas_Reextract
US-1462435_AD1GBMACXX_US-1462435_CTATAC_L006_R1_001

value: male

value: Pancreas

tag: rin


title: mESC_1000cell_input_nano-hmC-Seal

city: Chicago

first: Dali

last: Han

state: IL

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

data_processing:
For nano-hmC-Seal, Illumina reads were post-processed and aligned to the mouse mm9 assembly using the bowtie program with default parameters.
To visualize sequencing signals in the genome browser, we generated bedGraph files with HOMER
Genome_build: mm9
Supplementary_files_format_and_content: For nano-hmC-Seal sample, bedGraph files for each dataset was generated by HOMER software.

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured in feeder-free gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen Cat. No. 11995) supplemented with 15% FBS (GIBCO), 2 mM L-glutamine (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), 1 × nonessential amino acids (GIBCO), 1,000 units/ml LIF (Millipore Cat. No. ESG1107), 1 × pen/strep (GIBCO), 3 mM CHIR99021 (Stemgent), and 1 mM PD0325901 (Stemgent). Half of the medium was changed every day for 5 days before harvesting mEBs by sedimentation. Hematopoietic stem and progenitor cells were harvested from sacrificed animals treated as described in the methods section of the associated manuscript. Cell surface phenotypes were LSK (lin- Sca+ cKit+xxx markers), MPP (lin- Sca+ cKit+ CD48+ CD150-), CMP (lin- Sca- cKit+ CD34+ CD16/32-), MEP (lin- Sca- cKit+ CD34- CD16/32-), GMP (lin- Sca- cKit+ CD34+ CD16/32+).

extract_protocol:
DNA was isolated using the AllPrep DNA Mini Kit from Qiagen.
The tagmentation reactions were performed in a 50μl solution with 1X tagmentation buffer from Nextera DNA sample preparation kit (FC-121-1031). The input DNA is ranged from 0.5 ng to 50 ng. The reactions were performed according to the manufacturer’s instruction. The glucosylation reactions were performed in a 20 μl solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 μM N3-UDP-Glc, and 1 μM βGT, at 37°C for 1 hr. After that, DBCO-PEG4-DBCO (Click Chemistry Tools, 20 mM stock in DMSO) was added to the reaction mixture. The reactions were incubated at 37°C for 2 hr. Next, the DNA was purified by Micro Bio-Spin 30 Column (Bio–Rad). The purified DNA incubated with 5 µL C1 Streptavidin beads (Life Technologies) in 2X buffer (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl) for 15 min. The beads were subsequently undergone six 5-min washes each with 1X buffer. All binding and washing were done at room temperature with gentle rotation. The captured DNA fragments were amplified with 12-18 cycles of PCR amplification using the enzyme mix supplied by the Nextera kit. The PCR products were purified using AMPure XP beads. Separate input libraries were made by direct PCR from fragmented DNA without labeling and capture.

tag: technology

value: nano-hmC-Seal

value: mESC

value: wild-type


title: mESC_50ng_2_nano-hmC-Seal

tag: cell type


title: mESC_5ng_2_nano-hmC-Seal


title: mESC_50ng_input_nano-hmC-Seal


title: mESC_1000cell_2_nano-hmC-Seal


title: mESC_1000cell_1_nano-hmC-Seal


title: Animal2_Male_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Cerebrum
US-1458915_BC2BUMACXX_US-1458915_CTAGCT_L002_R1_001

value: Cerebrum


title: mESC_5ng_input_nano-hmC-Seal


title: Animal2_Male_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Stomach_Non-Glandular
US-1466221_AD2C4RACXX_US-1466221_CAGATC_L004_R1_001


title: Animal11_Female_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Heart
US-1458660_AD1GBMACXX_US-1458660_CCAACA_L005_R1_001

value: Heart


title: leukemia_WT_4_gmp_RNASeq

data_processing:
For nano-hmC-Seal, Illumina reads were post-processed and aligned to the mouse mm9 assembly using the bowtie program with default parameters.
To visualize sequencing signals in the genome browser, we generated bedGraph files with HOMER
For RNA-Seq,sequencing reads were aligned to mm9 genome by STAR. Count matrices were generated by summarizeOverlaps functionality from R package GenomicAlignments. The rlog transformation were then performed by the R package "DESeq2"
Genome_build: mm9
Supplementary_files_format_and_content: For nano-hmC-Seal sample, bedGraph files for each dataset was generated by HOMER software.
Supplementary_files_format_and_content: For RNA-Seq samples, "RNASeq_rld_expr.txt" contain rlog transfomed counts per Gene.

source_name: bone marrow

extract_protocol:
DNA and RNA were isolated using the AllPrep DNA/RNA Mini Kit from Qiagen.
The tagmentation reactions were performed in a 50μl solution with 1X tagmentation buffer from Nextera DNA sample preparation kit (FC-121-1031). The input DNA is ranged from 0.5 ng to 50 ng. The reactions were performed according to the manufacturer’s instruction. The glucosylation reactions were performed in a 20 μl solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, purified DNA, 100 μM N3-UDP-Glc, and 1 μM βGT, at 37°C for 1 hr. After that, DBCO-PEG4-DBCO (Click Chemistry Tools, 20 mM stock in DMSO) was added to the reaction mixture. The reactions were incubated at 37°C for 2 hr. Next, the DNA was purified by Micro Bio-Spin 30 Column (Bio–Rad). The purified DNA incubated with 5 µL C1 Streptavidin beads (Life Technologies) in 2X buffer (5 mM Tris pH 7.5, 0.5 mM EDTA, 1 M NaCl) for 15 min. The beads were subsequently undergone six 5-min washes each with 1X buffer. All binding and washing were done at room temperature with gentle rotation. The captured DNA fragments were amplified with 12-18 cycles of PCR amplification using the enzyme mix supplied by the Nextera kit. The PCR products were purified using AMPure XP beads. Separate input libraries were made by direct PCR from fragmented DNA without labeling and capture.RNA-seq libraries are constructed by True-seq stranded mRNA sample preparation kit (Illumina). The reaction is performed according to the manufacture’s instruction. Sequencing was performed on the Hi-Seq instrument.

value: RNA-Seq

value: GMP


title: Animal4_Male_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_WholeBlood
US-1459904_AD1GBMACXX_US-1459904_AGTTCC_L002_R1_001

value: WholeBlood


title: leukemia_T2F3_3_gmp_RNASeq


title: Animal11_Female_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Hippocampus
US-1458692_BC2BUMACXX_US-1458692_GGCTAC_L006_R1_001

value: Sprague Dawley

value: Hippocampus


title: leukemia_WT_5_gmp_RNASeq


title: leukemia_WT_4_mpp_RNASeq

value: MPP


title: leukemia_WT_1_gmp_RNASeq


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 6

description:
Sequencing batch 6 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_SEASDW062403C:145:D1GBMACXX:6

value: 12-13 weeks

value: female

value: Cortex


title: leukemia_T2F3_2_gmp_RNASeq


title: mESC_50ng_1_nano-hmC-Seal


title: leukemia_T2F3_1_gmp_RNASeq


title: mESC_5ng_1_nano-hmC-Seal


title: leukemia_WT_5_mpp_RNASeq


title: leukemia_WT_3_mpp_RNASeq


title: Animal11_Female_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Kidney_Homogenate_re-extract
US-1462979_AD1GBMACXX_US-1462979_CATGGC_L003_R1_001

value: Kidney


title: leukemia_WT_1_mpp_RNASeq


title: Animal4_Male_Kidney_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Kidney
US-1458682_AD2C4RACXX_US-1458682_CTATAC_L003_R1_001

value: male


title: leukemia_WT_2_gmp_RNASeq


title: leukemia_T2F3_mpp_input_NanoSeal


title: leukemia_T2F3_1_mpp_RNASeq


title: leukemia_T2F3_gmp_input_NanoSeal


title: Animal2_Male_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Heart
US-1458627_AD1GBMACXX_US-1458627_GATCAG_L006_R1_001


title: leukemia_WT_3_gmp_RNASeq


title: Animal7_Female_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Medulla
US-1458876_BC2BUMACXX_US-1458876_CACCGG_L008_R1_001

value: Medulla


title: leukemia_T2F3_3_mpp_RNASeq


title: Animal7_Female_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Ileum
US-1458863_BC2BUMACXX_US-1458863_GACGAC_L005_R1_001

value: Ileum


title: Animal9_Female_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_WholeBlood
US-1466198_BC2BUMACXX_US-1466198_CGGAAT_L002_R1_001


title: leukemia_WT_mpp_input_NanoSeal

value: nano-hmC-Seal


title: leukemia_T2F3_2_mpp_RNASeq


title: leukemia_WT_5_gmp_NanoSeal

value: wild-type


title: leukemia_WT_3_gmp_NanoSeal


title: leukemia_WT_2_gmp_NanoSeal


title: leukemia_T2F3_3_gmp_NanoSeal


title: Animal9_Female_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Cortex
US-1456509_AD1GBMACXX_US-1456509_CATGGC_L006_R1_001


title: leukemia_T2F3_2_gmp_NanoSeal


title: leukemia_T2F3_1_gmp_NanoSeal


title: Animal9_Female_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Jejunum
US-1458713_AD2C4RACXX_US-1458713_CGTACG_L002_R1_001

value: Jejunum


title: Animal3_Male_Liver_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Liver
US-1454029_AD1GBMACXX_US-1454029_GACGAC_L006_R1_001

value: Liver


title: Animal11_Female_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Cerebellum
US-1466172_AD2C4RACXX_US-1466172_TAGCTT_L004_R1_001

value: Cerebellum


title: leukemia_WT_5_mpp_NanoSeal


title: leukemia_WT_3_mpp_NanoSeal


title: Animal6_Male_Jejunum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Jejunum
US-1458707_AD1GBMACXX_US-1458707_CGGAAT_L002_R1_001


title: leukemia_WT_2_mpp_NanoSeal


title: leukemia_T2F3_3_mpp_NanoSeal


title: Animal5_Male_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Stomach_Glandular
US-1456434_AD1GBMACXX_US-1456434_GAGTGG_L004_R1_001


title: Animal3_Male_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Heart
US-1466208_BC2BUMACXX_US-1466208_CATTTT_L008_R1_001

value: Heart


title: leukemia_WT_1_gmp_NanoSeal

value: GMP


title: Animal10_Female_Uterus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Uterus
US-1456455_AD1GBMACXX_US-1456455_CCAACA_L003_R1_001

value: Sprague Dawley

value: Uterus


title: Animal8_Female_Kidney_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Kidney
US-1455448_AD1GBMACXX_US-1455448_CCGTCC_L004_R1_001


title: hematopoiesis_input

value: mix


title: leukemia_WT_1_mpp_NanoSeal

value: MPP


title: hematopoiesis_mep_1

value: MEP


title: Animal6_Male_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Muscle_Soleus
US-1459871_BC2BUMACXX_US-1459871_GTTTCG_L007_R1_001

value: 12-13 weeks

value: Muscle - Soleus


title: hematopoiesis_cmp_3

value: CMP


title: leukemia_T2F3_1_mpp_NanoSeal


title: leukemia_T2F3_2_mpp_NanoSeal


title: leukemia_WT_4_gmp_NanoSeal


title: hematopoiesis_mep_3


title: hematopoiesis_cmp_2


title: hematopoiesis_mep_2


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_SEA062401C:142:C2BUMACXX:6

value: female

value: Cortex


title: hematopoiesis_gmp_3

value: nano-hmC-Seal


title: Animal3_Male_Testicle_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Testicle
US-1456496_BC2BUMACXX_US-1456496_GTCCGC_L003_R1_001

value: male

value: Testicle


title: DN1 gl/glTR rep1(from 3 biological rep)

first: Jean

last: Vacher

state: QC

address: 110 pine avenue west

department: Development and cellular interactions

institute: IRCM

description: Sorted DN1 (LIN-CD44+CD25-) from 3 mice

data_processing:
Reads were aligned to the mm10 genome using tophat 2.0.10 with options: b2-sensitive, library-type fr-firststrand (stranded sequencing)
FPKM values calculated using CuffDiff 2.2.1
Note that read files were provided by the sequencing platform as .bam files aligned to the mm10 genome, not as .fastq files
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx file of FPKM values of transcripts for the 3 samples (wt, gl/gl, gl/gltr)

source_name: Thymus

extract_protocol:
DN1 cells were enriched from total thymus extract using Moflo sorter, RNA was harvested using MagMax total RNA isolation kit (Life technologies). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thymus

value: post natal day 19

value: Transgenic CD2-Ostm1 gl/gl


title: DN1 wt rep1 ( from 2 biological rep)

description: Sorted DN1 (LIN-CD44+CD25-) from 2 mice

value: Wild-type


title: hematopoiesis_lsk_1

value: LSK

value: wild-type


title: Animal11_Female_Cerebellum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Cerebellum
US-1466172_AD1GBMACXX_US-1466172_TAGCTT_L003_R1_001

value: Sprague Dawley

value: Cerebellum


title: hematopoiesis_gmp_2

value: GMP


title: hematopoiesis_gmp_1


title: hematopoiesis_cmp_1


title: leukemia_WT_4_mpp_NanoSeal

value: MPP


title: Animal9_Female_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Muscle_Soleus
US-1458621_AD1GBMACXX_US-1458621_CGATGT_L003_R1_001

value: 12-13 weeks

value: Muscle - Soleus


title: Animal2_Male_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Cerebrum
US-1458915_AD1GBMACXX_US-1458915_CTAGCT_L003_R1_001

value: Cerebrum


title: hematopoiesis_lsk_2


title: Lgr5_epcam+_2_paired-end

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

description:
Genomic DNA of region that accessible to Tn5 transposase
ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013

data_processing:
Library strategy: ATAC-seq
Libraries are sequenced by Illumina HiSeq 2000
Raw reads are alligned to mouse genome version mm10 though bowtie2
Peak calling were performed using HOMER on individual sequence data and pooled by mergeBed in Bedtools
Genome_build: mm10
Supplementary_files_format_and_content: The bed file with called peaks contains the union of all peaks called on individual files; text files contain read counts for genomic features. The *.count.gz file is the HTseq-count output using ATAC_peaks.bed.gz and individual bam file from sequencing alignment. The coordinates of the genomic features are contained within the file "ATAC_peaks.bed.gz".

source_name: hair follicle

extract_protocol:
Tumours were dissected, minced, digested and filtered to get single cell suspension. Specific cell populations were isolated by FACS using PE-conjugated anti-CD45, PE-conjugated anti CD31, PE-conjugated anti-CD140a and APC-Cy7-conjugated anti-Epcam. Sorted cells were collected into lysis buffer for RNA extraction and ATAC-Seq.
Illumina Nextera DNA Library Prep Kit

value: hair follicle

value: female

value: mixed


title: IFE_normal_single-end

source_name: interfollicular epidermis

value: WT

value: interfollicular epidermis


title: Animal4_Male_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Duodenum
US-1459883_AD1GBMACXX_US-1459883_AGTCAA_L002_R1_001

value: male

value: Duodenum


title: Lgr5_epcam+_2_single-end


title: Lgr5_Epcam+_single-end


title: Animal4_Male_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Hippocampus
US-1459916_AD2C4RACXX_US-1459916_CACGAT_L003_R1_001

value: Hippocampus


title: DN1 gl/gl rep1 (from 3 biological rep)

description: Sorted DN1 (LIN-CD44+CD25-) from 3 mice

value: Thymus

value: post natal day 19

value: gl/gl (Ostm1-/-);grey-lethal


title: Lgr5_Epcam+_paired-end


title: K14_Epcam+_single-end


title: Animal6_Male_Cerebellum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Cerebellum
US-1456495_BC2BUMACXX_US-1456495_GGTAGC_L004_R1_001

value: Sprague Dawley

value: Cerebellum


title: Lgr5_epcam-_single-end


title: Lgr5_epcam-_paired-end


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_SEA055491C:302:H0HMMADXX:1

value: Liver


title: Animal2_Male_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Pancreas_Reextract
US-1459548_BC2BUMACXX_US-1459548_CATTTT_L005_R1_001

value: 12-13 weeks

value: Pancreas


title: Animal6_Male_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Cerebrum
US-1459963_AD2C4RACXX_US-1459963_ATCACG_L004_R1_001

value: Cerebrum


title: 1504_Sequencing batch 2

description:
Sequencing batch 2 from sample 1504
US-1466203_AD2C4RACXX_US-1466203_CATGGC_L003_R1_001

value: DRG


title: Animal3_Male_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Ileum
US-1458880_BC2BUMACXX_US-1458880_CAGGCG_L008_R1_001

value: Ileum


title: Animal11_Female_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Brainstem
US-1459942_AD1GBMACXX_US-1459942_TGACCA_L002_R1_001

value: female

value: Brainstem


title: K14_Epcam+_paired-end

value: interfollicular epidermis

value: mixed


title: Animal9_Female_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Heart
US-1466231_AD2C4RACXX_US-1466231_CAAAAG_L006_R1_001

value: Heart


title: Animal7_Female_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Stomach_Glandular
US-1456517_AD2C4RACXX_US-1456517_CCAACA_L003_R1_001


title: IFE_normal_paired-end

value: WT


title: hematopoiesis_lsk_3

value: nano-hmC-Seal

value: LSK

value: wild-type


title: Animal11_Female_Stomach_Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_Stomach_Glandular
US-1458903_AD2C4RACXX_US-1458903_CCGTCC_L005_R1_001

value: Sprague Dawley


title: Animal4_Male_Muscle_Biceps_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Muscle_Biceps
US-1459894_AD1GBMACXX_US-1459894_CCGTCC_L003_R1_001

value: male

value: Muscle - Biceps


title: Animal7_Female_Brainstem_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Brainstem
US-1466205_AD1GBMACXX_US-1466205_AGTCAA_L004_R1_001

value: 12-13 weeks


title: HF_normal_single-end

value: hair follicle


title: Animal3_Male_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Medulla
US-1458847_AD1GBMACXX_US-1458847_GTAGAG_L004_R1_001

value: Medulla


title: Animal6_Male_Testicle_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Testicle
US-1456506_AD1GBMACXX_US-1456506_GCCAAT_L004_R1_001

value: Testicle


title: Animal5_Male_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Stomach_Glandular
US-1456434_BC2BUMACXX_US-1456434_GAGTGG_L007_R1_001


title: HF_normal_paired-end

description:
Genomic DNA of region that accessible to Tn5 transposase
ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013


title: Animal6_Male_Hippocampus_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Hippocampus
US-1454031_AD1GBMACXX_US-1454031_TTAGGC_L002_R1_001

value: Hippocampus


title: Animal4_Male_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Muscle_Soleus
US-1466220_AD2C4RACXX_US-1466220_ACTGAT_L002_R1_001

value: Muscle - Soleus


title: Animal10_Female_Kidney_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal10_Female_Kidney_Homogenate_re-extract
US-1462930_AD1GBMACXX_US-1462930_GTCCGC_L002_R1_001

value: female

value: Kidney


title: 1501_Sequencing batch 1

description:
Sequencing batch 1 from sample 1501
US-1466192_AD1GBMACXX_US-1466192_ATGAGC_L004_R1_001

value: DRG


title: Animal8_Female_Muscle_Biceps_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Muscle_Biceps_Homogenate_re-extract
US-1459950_AD2C4RACXX_US-1459950_CTTGTA_L008_R1_001


title: Animal2_Male_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Medulla
US-1458843_AD2C4RACXX_US-1458843_ATTCCT_L006_R1_001


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_SEASDW062403C:145:D1GBMACXX:4

value: Liver


title: Animal5_Male_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Adrenal
US-1458862_BC2BUMACXX_US-1458862_ACTGAT_L007_R1_001

value: Adrenal


title: Animal3_Male_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Ileum
US-1458880_AD1GBMACXX_US-1458880_CAGGCG_L002_R1_001

value: Ileum


title: Animal4_Male_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Duodenum
US-1459883_AD2C4RACXX_US-1459883_AGTCAA_L008_R1_001

value: Duodenum


title: Animal2_Male_Liver_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal2_Male_Liver
US-1454084_BC2BUMACXX_US-1454084_AGTTCC_L003_R1_001


title: Animal8_Female_Adrenal_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Adrenal
US-1454065_AD1GBMACXX_US-1454065_CTAGCT_L006_R1_001


title: Animal7_Female_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Medulla
US-1458876_AD1GBMACXX_US-1458876_CACCGG_L002_R1_001


title: Animal4_Male_Liver_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Liver
US-1454077_BC2BUMACXX_US-1454077_CACCGG_L004_R1_001


title: Animal9_Female_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Stomach_Non-Glandular
US-1466233_AD2C4RACXX_US-1466233_CACTCA_L003_R1_001


title: Animal11_Female_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Hippocampus
US-1458692_AD1GBMACXX_US-1458692_GGCTAC_L005_R1_001


title: Animal7_Female_Duodenum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Duodenum
US-1459905_BC2BUMACXX_US-1459905_CTATAC_L002_R1_001


title: Animal6_Male_Medulla_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Medulla
US-1458871_AD2C4RACXX_US-1458871_AGTTCC_L001_R1_001


title: Animal2_Male_Cortex_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Cortex
US-1456489_AD1GBMACXX_US-1456489_ATCACG_L004_R1_001

value: Cortex


title: Animal11_Female_Cerebrum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Cerebrum
US-1459923_AD1GBMACXX_US-1459923_CAGATC_L003_R1_001

value: Sprague Dawley

value: Cerebrum


title: Animal3_Male_Hippocampus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Hippocampus
US-1466189_AD1GBMACXX_US-1466189_ACTTGA_L004_R1_001

value: male


title: Animal8_Female_Duodenum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Duodenum
US-1456490_BC2BUMACXX_US-1456490_CTAGCT_L008_R1_001

value: 12-13 weeks


title: Animal11_Female_Liver_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Liver_Homogenate_re-extract
US-1462928_AD2C4RACXX_US-1462928_GTCCGC_L008_R1_001


title: 1001_Sequencing batch 1

description:
Sequencing batch 1 from sample 1001
US-1466212_AD1GBMACXX_US-1466212_GACGAC_L005_R1_001


title: Animal9_Female_Medulla_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal9_Female_Medulla
US-1458872_AD1GBMACXX_US-1458872_CTAGCT_L005_R1_001


title: 1001_Sequencing batch 2

description:
Sequencing batch 2 from sample 1001
US-1466212_BC2BUMACXX_US-1466212_GACGAC_L008_R1_001


title: Animal8_Female_Heart_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal8_Female_Heart
US-1458639_AD2C4RACXX_US-1458639_ATCACG_L001_R1_001

value: Heart


title: Animal7_Female_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal7_Female_Stomach_Glandular
US-1456517_AD1GBMACXX_US-1456517_CCAACA_L006_R1_001


title: Animal5_Male_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Heart
US-1466191_AD1GBMACXX_US-1466191_CTTGTA_L005_R1_001


title: Animal4_Male_Cerebrum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Cerebrum
US-1459937_AD1GBMACXX_US-1459937_GTGAAA_L002_R1_001


title: Animal2_Male_Brainstem_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_Brainstem
US-1466193_AD2C4RACXX_US-1466193_CAGGCG_L006_R1_001

value: Brainstem


title: 1502_Sequencing batch 2

description:
Sequencing batch 2 from sample 1502
US-1463116_AD1GBMACXX_US-1463116_ACTGAT_L005_R1_001


title: Animal11_Female_Muscle_Soleus_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal11_Female_Muscle_Soleus
US-1463120_AD1GBMACXX_US-1463120_CAGGCG_L005_R1_001


title: Animal6_Male_Ileum_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Ileum
US-1458861_AD2C4RACXX_US-1458861_TGACCA_L001_R1_001


title: Animal3_Male_Testicle_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Testicle
US-1456496_AD1GBMACXX_US-1456496_GTCCGC_L003_R1_001

value: Testicle


title: Animal8_Female_Pancreas_Reextract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Pancreas_Reextract
US-1459539_AD2C4RACXX_US-1459539_CACCGG_L006_R1_001

value: Pancreas


title: Animal8_Female_Heart_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal8_Female_Heart
US-1458639_AD1GBMACXX_US-1458639_ATCACG_L006_R1_001


title: Animal9_Female_Duodenum_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal9_Female_Duodenum_Homogenate_re-extract
US-1462996_BC2BUMACXX_US-1462996_TAATCG_L005_R1_001


title: 1505_Sequencing batch 1

description:
Sequencing batch 1 from sample 1505
US-1466236_AD1GBMACXX_US-1466236_CACTCA_L005_R1_001


title: Animal2_Male_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal2_Male_WholeBlood
US-1459961_AD1GBMACXX_US-1459961_CTATAC_L003_R1_001

value: WholeBlood


title: Animal6_Male_Stomach_Non-Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal6_Male_Stomach_Non-Glandular
US-1466200_AD1GBMACXX_US-1466200_GTTTCG_L006_R1_001


title: Animal7_Female_Liver_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Liver_Homogenate_re-extract
US-1462955_SEA055491C:302:H0HMMADXX:2

value: female


title: Animal5_Male_WholeBlood_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_WholeBlood
US-1459924_AD2C4RACXX_US-1459924_CATTTT_L003_R1_001


title: Animal4_Male_Ileum_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Ileum
US-1458916_BC2BUMACXX_US-1458916_ATGAGC_L004_R1_001


title: Animal5_Male_Stomach_Non-Glandular_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal5_Male_Stomach_Non-Glandular
US-1466229_AD1GBMACXX_US-1466229_GAGTGG_L006_R1_001


title: Animal3_Male_Cortex_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal3_Male_Cortex
US-1456488_AD1GBMACXX_US-1456488_TAGCTT_L006_R1_001


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 3

description:
Sequencing batch 3 from sample Animal4_Male_Pancreas_Reextract
US-1462447_SEA055491C:302:H0HMMADXX:1


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_SEA055491C:302:H0HMMADXX:1


title: Animal7_Female_Adrenal_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Adrenal
US-1458839_BC2BUMACXX_US-1458839_CAGATC_L006_R1_001


title: Animal11_Female_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal11_Female_WholeBlood
US-1459951_BC2BUMACXX_US-1459951_CTCAGA_L005_R1_001


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_BC2BUMACXX_US-1462958_TTAGGC_L006_R1_001


title: Animal4_Male_Stomach_Glandular_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Stomach_Glandular
US-1460652_BC2BUMACXX_US-1460652_TACAGC_L008_R1_001


title: Animal6_Male_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_WholeBlood
US-1459946_BC2BUMACXX_US-1459946_CAAAAG_L007_R1_001


title: Animal4_Male_Cortex_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal4_Male_Cortex_Homogenate_re-extract
US-1462932_AD1GBMACXX_US-1462932_ATCACG_L005_R1_001


title: Animal3_Male_WholeBlood_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_WholeBlood
US-1466241_AD2C4RACXX_US-1466241_GATCAG_L008_R1_001


title: Animal3_Male_Muscle_Soleus_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal3_Male_Muscle_Soleus_Homogenate_re-extract
US-1462968_AD1GBMACXX_US-1462968_TAATCG_L004_R1_001

value: Muscle - Soleus


title: Animal5_Male_Duodenum_Homogenate_re-extract_Sequencing batch 5

description:
Sequencing batch 5 from sample Animal5_Male_Duodenum_Homogenate_re-extract
US-1462953_SEA055491C:302:H0HMMADXX:1


title: Animal5_Male_Brainstem_Homogenate_re-extract_Sequencing batch 1

description:
Sequencing batch 1 from sample Animal5_Male_Brainstem_Homogenate_re-extract
US-1466237_BC2BUMACXX_US-1466237_ACAGTG_L002_R1_001


title: Animal7_Female_Cortex_Homogenate_re-extract_Sequencing batch 4

description:
Sequencing batch 4 from sample Animal7_Female_Cortex_Homogenate_re-extract
US-1462958_SEA055491C:302:H0HMMADXX:2


title: Animal6_Male_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal6_Male_Pancreas_Reextract
US-1462455_AD1GBMACXX_US-1462455_ACTTGA_L006_R1_001


title: Animal4_Male_Pancreas_Reextract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal4_Male_Pancreas_Reextract
US-1462447_BC2BUMACXX_US-1462447_TGACCA_L006_R1_001


title: mRNA-seq Toll rm9/rm10 replicate 3

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

data_processing:
RNA-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to FlyBase r5.57 genome and gene annotations using Tophat v2.0.14.
Differential gene expression was determined using cuffdiff (Cufflinks v2.2.1) between the three mutant genotypes (Toll10b, Toll rm9/rm10, gd7)
----------------------------------------------
ATAC-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 25 bp each and aligned to the UCSC Drosophila melanogaster dm3 genome with Bowtie 1.1.2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
Genome_build: UCSC dm3
BigWig files contain per-base coverage of all aligned read pairs
----------------------------------------------
ChIP-Seq
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

organism: Drosophila melanogaster

source_name: Toll rm9/rm10 embryos

growth_protocol: Adult flies were used in population cages for embryo collections and embryos were collected on apple juice plates for 2 h at 25°C in cages and then matured at 25°C for another 2 h (2-4 h after egg deposition (AED)).

extract_protocol:
Total mRNA was extracted from 20-100 mg non-cross-linked 2-4 h AED in duplicates using the Maxwell Total mRNA purification kit (Promega, #AS1225) according to manufacturer’s instructions. PolyA-mRNA was isolated using DynaI oligo(dT) beads (Life Technologies, #61002).
Libraries were prepared following the instructions of the TruSeq DNA Sample Preparation Kit (Illumina, #FC-121-2001)

treatment_protocol: Embryos were dechorionated for 1 min with 100% bleach and then cross-linked for 15 min with 1.8% formaldehyde (final concentration in water phase).

tag: developmental stage

value: 2-4 hr after egg deposition

tag: barcode-kit

value: Illumina TRU-Seq

tag: library-kit


title: mRNA-seq Toll rm9/rm10 replicate 1


title: mRNA-seq Toll rm9/rm10 replicate 2


title: input DNA 2

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

description: input DNA

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.9 with parameters -m 1 -v 2 --best --strata
Peaks were called using HOMER through "findpeaks" function with -style factor and default parameters for K ChIP sample and -F 3 -P 0.01 -L 3 -fdr 0.05 -style factor for J ChIP sample
Common peaks between K ChIP and J ChIP samples were found using BedTools v2.25.0 "intersectBed" command using default settings
for Heat Map Figure 4E.  Macs2 command line macs2 callpeak -t *.bam -c input.bam --gsize=1.87e9 --broad --broad-cutoff 0.1 -B
Genome_build: mm9

source_name: pancreas

extract_protocol:
Lysates were clarified from sonicated nuclei and MIST1-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina True-seq protocols

value: pancreas


title: mRNA-seq gd7 replicate 2

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to FlyBase r5.57 genome and gene annotations using Tophat v2.0.14.
Aligned reads were compared to previously-published Toll10b RNA-seq (GSE34281) using cuffdiff (Cufflinks v2.2.1).

source_name: gd7 embryos

growth_protocol: Fly stocks gd7 were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males. Offspring of this cross was used for embryo collections. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol:
mRNA-seq: polyA mRNA was purified from total RNA with oligo(dT) selection. After RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions for the Tru-seq kit
RNA libraries were prepared for sequencing using the Illumina Tru Seq DNA Sample Prep Kit (Illumina, #15012999)

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min, washed with water and frozen in liquid nitrogen. Embryos were not fixed

tag: genotype/variation


title: mRNA-seq gd7 replicate 1


title: mRNA-seq gd7 replicate 3


title: MIST1_ChIPSeq K2

description: rabbit antibody against rat MIST1 provided by Konieczny SF. (Dev Biol. 1997 Feb 1;182(1):101-13.)


title: MIST1_ChIPSeq J1

description: rabbit antibody against human MIST1 provided by Mills JC. (Am J Pathol. 2010 Sep;177(3):1514-33.)


title: Mist1 knockout 3

data_processing:
Illumina HiSeq Control Software version 2.0.10.0 used for basecalling
Sequences were mapped to mm9 mouse genome using TopHat v2.0.8 with parameters -N 2 --segment-length 15
Sequences per gene were counted using HTSeq v0.5.3p9
Differential gene expression analysis was performed with edgeR v3.0.8 (FDR < 0.05)
Genome_build: mm9
Supplementary_files_format_and_content: .xlsx file of Htseq counts for each sample

extract_protocol:
Homogenization in Guanidine thiocyanate followed by differential precipitations as in Isolation of RNA using guanidinium salts. MacDonald RJ, Swift GH, Przybyla AE, Chirgwin JM. Methods Enzymol. 1987;152:219-27. PMID: 2443794
Standard Illumina TruSeq


title: MIST1_ChIPSeq J2


title: input DNA 1

description: input DNA


title: Mist1 het control 2


title: Mist1 knockout 1


title: Mist1 knockout 2


title: Mist1 het control 1


title: RPE1_nutlin_2

first: Chris

middle: W

last: Seidel

department: Genomics

institute: Stowers Institute

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned to hg19 using tophat2 with the option -g 1 and gene models from Ensembl 75.
RPKM values on gene models from Ensembl 75 were tallied using the GenomicRanges and edgeR packages in R.
Genome_build: hg19
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

growth_protocol: Cells were grown at 37°C in 5% CO2 in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA isolation was performed using Maxwell 16 LEV simplyRNA Tissue kit on a Maxwell 16 Research Instrument (Promega).
PolyA Stranded RNA Seq libraries were constructed using TruSeq Stranded mRNA LT kit (RS-122-2101).

treatment_protocol: Cells were treated with 2.5 uM Nutlin-3 or vechicle (DMSO) for 24 hours.

tag: cell line

tag: replicate

tag: drug


title: RPE1_nutlin_1


title: RPE1_dmso_1

value: dmso


title: RPE1_dmso_2


title: RPE1_nutlin_3


title: s3_4N_C

treatment_protocol: Asynchronously growing cells were treated with 2.5 uM ZM447439 for 72 hours and were allowed to survive for several weeks, until proliferating populations emerged.  Proliferating cells were plated in 96-well plates at one cell per well density. The ploidy content of each single cell clone was analyzed by FACS.  Isogenic diploid single cell clones (2N 1-3) were picked from the same 96-well plates as the corresponding tetraploid clones.  Single cell clones 4N-2 and 2N-2 underwent Hoechst 33342 labeling before sub-cloning.

tag: ploidy

tag: isolate

value: C


title: Animal10_Female_Kidney_Homogenate_re-extract_Sequencing batch 2

description:
Sequencing batch 2 from sample Animal10_Female_Kidney_Homogenate_re-extract
US-1462930_AD2C4RACXX_US-1462930_GTCCGC_L002_R1_001

data_processing:
FastQ files were processed to remove adaptor sequence and discard reads < 17bp in length with cutadapt v. 1.4.1 [23] with options –a TGGAATTCTCGGGTGCCAAGG –quality-base 33 –q 20 –match-read-wildcards –m 17. All trimmed reads that contained an ‘N’ were discarded. Identical sequences from the same sample were combined into a single sequence in the form expected by miRDeep2
Quantifier.pl from the mirdeep2 package [v. 2.0.0.5 ] was used to generate miR alignment files (.mrd files) against known miRs from miRbase 20 with options –P –p <org>_hairpin.fa –m <org>_mature.fa –r trimmed_reads.fa –d. This was done separately for rat, mouse, human, and C. elegans known miRs.
The .mrd files were then parsed with a custom Perl script as follows. Each isomiR sequence in an alignment was associated with the corresponding mature miR identifier. If it aligned to a miRNA precursor, but not with an expected mature miR sequence, it was identified as <miR>-pre to indicate this. Usually these correspond with reverse strand miRs that have not yet been annotated as alternate mature forms. Sometimes these appear to be microRNA offset RNAs [25] and sometimes they appear to represent incompletely processed sequence. If a given sequence was identified as aligning with more than one precursor, it was associated with all potential names as a composite name. That is, a sequence that aligned to both let-7a-5p and let-7f-5p was assigned to the composite mature miR let-7a-5p;let-7f-5p to indicate for subsequent analyses that this identification was ambiguous. All sequences that had not yet been identified against known rat miRs were then looked for in the analysis with respect to known mouse miRs, and so on against human and finally C. elegans miRs. This process allows for identification of conserved rodent miRs that have not yet been annotated in rat, and against conserved mammalian miRs that have not yet been annotated in rat and mouse. The comparison with C. elegans was to identify spiked in C. elegans miRs (not used in this data set).
In parallel to the above identification of known miRs, we used miRDeep2’s novel miR identification process as well. We aligned all the unique trimmed fasta reads to the RN5 reference rat genome with miRDeep2’s mapper.pl script with default parameters and then used the miRDeep2.pl script to generate novel miR predictions and .mrd files. The .mrd files were parsed as above to assign miR names to each unique read. We then attempted to identify and merge novel predictions that were identical to known miRs as follows. If the same read sequence identified a miR in the novel analysis and in the known analysis and the known miR appeared in miRDeep’s .mrd file, we assumed that this was a duplicate identification and changed the miR name from that reported by miRDeep (chr# followed by a unique ID) to that of the known miR. Otherwise, we assumed that the novel prediction might be different from the known miR identification and added it to the list of potential identifications for the sequence. So, for example, a sequence which was aligned by miRDeep2 to a predicted miR on chrX and also identified as miR-450a is identified as “chrX_48156-5p;miR-450a-5p” because miRDeep2 does not show miR-450a as aligned to this predicted miR, indicating that these are two potentially distinctsources of this sequence. Finally, the counts associated with each unique sequence are summed for each named miR (including complex, multi-named miRs) for each sample and these are reported as the miR level counts.
Genome_build: Rn5 for novel miR identification, mirbase 20 for known miR identification
Supplementary_files_format_and_content: Tab delimited text files with raw count information at either the mature miR level or isomiR level. Both files also contain the source of the predictiion that the indicated counts go with the indicated miR or isomiR.

extract_protocol:
RNA was purified using the miRNAeasy protocol from Qiagen (Kit cat# 217004).
Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Cataloge # RS-200-0048) using a HiSeq2000.  Briefly, RNA was extracted from tissues using the miRNeasy protocol. Libraries were constructed using the Illumina TruSeq small RNA preparation guide which entails ligation of adapters on the 3' and 5' ends of the RNA molecules.  The libraries were quantitated using RiboGreen and were size selected through gel electrophoresis and libraries consistent with the size of miRNAs were gel purified.  Sequencing was performed with each sample receiving 4-5 million, 30bp, single-end reads. generated

tag: strain

value: Kidney


title: s3_2N_B

value: B


title: s3_4N_A

value: A


title: s2_4N_C


title: MIST1_ChIPSeq K1


title: s2_4N_A


title: s2_4N_B


title: s2_2N_C


title: s1_4N_A


title: s1_4N_B


title: s1_4N_C


title: s2_2N_A


title: s2_2N_B


title: RPE1_dmso_3


title: s1_2N_B


title: s3_4N_B


title: s1_2N_A


title: anil_4n_19

extract_protocol:
RNA isolation was performed using Maxwell 16 LEV simplyRNA Tissue kit on a Maxwell 16 Research Instrument (Promega).
Ribo-depleted Stranded RNA Seq libraries were constructed using TruSeq Stranded mRNA LT kit (RS-122-2101).

treatment_protocol: Cells were transfected with siRNA using Lipofectamine RNAiMAX for 24 hours, labeled  with 2 μg/mL Hoechst 33342 for 60 minutes at 37˚C and FACS-sorted into 2N and 4N populations.

tag: RNAi

value: Anillin

tag: molecule subtype

value: ribo-depleted Total RNA


title: anil_4n_21


title: s3_2N_C


title: anil_4n_20


title: nt_4n_15

value: Random


title: anil_2n_17


title: anil_2n_16


title: nt_2n_11


title: anil_2n_18


title: nt_2n_10


title: nt_2n_12


title: s3_2N_A


title: relapsed 2

city: Cambridge

first: Fang

last: Li

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research, Inc.

description: poly(A)-selected RNA for sequencing

data_processing:
Transcriptomic alignments and gene expression quantification were performed using Array Studio 6.0 (OmicSoft, Cary, NC).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.  FPKM, Fragments Per Kilobase of transcript per Million fragments mapped.

source_name: cell line derived xenograft tumor

extract_protocol:
High-quality total RNA was extracted from each fresh frozen tumor tissue samples using RNeasy plus mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cancer type

value: neuroblastoma

tag: agent

value: ceritinib


title: nt_4n_14


title: vehicle-treated 2

description: poly(A)-selected RNA for sequencing


title: s1_2N_C


title: vehicle-treated 1

description: poly(A)-selected RNA for sequencing


title: relapsed 1

description: poly(A)-selected RNA for sequencing


title: 1731 exon 2 clone 7 rep3

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: human HG19
Supplementary_files_format_and_content: Read Count Table

source_name: 1729_exon 2 clone 7

extract_protocol:
RNA was isolated with TRI Reagent (Molecular Research Center) and purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
libraries were constructed using the Illumina TruSeq Stranded mRNA kit following the manufacturer's supplied protocol. 2960 libraries were constructed using the Illumina TruSeq Stranded Total RNA kit (Catalog No. RS-122-2201) following the manufacturer's supplied protocol.

value: human oral cavity carcinoma cell line

value: LDBI knockout


title: 1729 exon 2 clone 7 rep1


title: 1729 P rep 1

value: parental


title: 1730 exon 2 clone 7 rep2


title: 1729 P rep 3


title: 1729 P rep 2


title: nt_4n_13


title: Input_MYC_pool3

city: Kowloon

first: Jian

last: Yan

address: 83 Tat Chee Ave

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

extract_protocol:
The ChIP-seq has been carried out as previously described6,7. Briefly, 2 million cells were crosslinked with 1% formadehyde for 10 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit.
TruSeq

tag: genotype

value: C-terminal Flag tagging of MYC, pool 3


title: Input_TCF7L2_mono10

value: C-terminal Flag tagging of TCF7L2, clone 2


title: Input_MYC_mono5

value: C-terminal Flag tagging of MYC, clone 2


title: Input_SP1_pool2

value: C-terminal Flag tagging of SP1, pool 2


title: Input_MYC_pool1

value: C-terminal Flag tagging of MYC, pool 1


title: Input_SP1_pool1

value: C-terminal Flag tagging of SP1, pool 1


title: Input_SP1_mono3

value: C-terminal Flag tagging of SP1, clone 3


title: Input_MYC_mono14

value: C-terminal Flag tagging of MYC, clone 3


title: Flag_TCF7L2_mono3

value: C-terminal Flag tagging of TCF7L2, clone 3


title: Input_SP1_mono2

value: C-terminal Flag tagging of SP1, clone 2


title: Flag_TCF7L2_mono1

value: C-terminal Flag tagging of TCF7L2, clone 1


title: Flag_MYC_pool3


title: Flag_MYC_pool2

value: C-terminal Flag tagging of MYC, pool 2


title: Flag_MYC_pool1


title: Input_TCF7L2_mono24


title: Flag_TCF7L2_mono2


title: Flag_MYC_mono14


title: Input_MYC_pool2


title: Input_TCF7L2_mono1


title: Flag_MYC_mono5


title: Flag_MYC_mono4

value: C-terminal Flag tagging of MYC, clone 1


title: Flag_SP1_mono3


title: Flag_SP1_pool2


title: Flag_SP1_pool3

value: C-terminal Flag tagging of SP1, pool 3


title: Flag_SP1_mono2


title: Input_MYC_mono4


title: Flag_SP1_mono1

value: C-terminal Flag tagging of SP1, clone 1


title: Input_SP1_pool3


title: Input_SP1_mono1


title: pLV5

city: Beijing

first: Zhen

last: Xie

state: Beijing

address: Qinghua yuan street, Haidian district

department: Department of Automation

institute: Tsinghua University

description: total small RNA

data_processing:
The Bowtie2 index was created based on the miRNA precursors,  and single-end reads were aligned directly to this index using mirdeep2 with the default settings.
The scripts for analyzing data based on miRNAs_expressed_all_samples_*.csv files generated by mirdeep2 were using the Ruby language.
Genome_build: mirna.fa and mature_mirna.fa
Supplementary_files_format_and_content: Both *.csv files and * *.mrd files were comma-delimited text files,*.mrd files were generated by using mirdeep2.

source_name: human cell lines

growth_protocol: high-glucose DMEM complete media (Dulbecco’s modified Eagle’s medium (DMEM),  4.5 g/L glucose,  0.045 units/mL of penicillin and 0.045 g/mL streptomycin and 10% FBS (Invitrogen) at 37 ºC,  100% humidity and 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol (Life Technologies) 48 h post-transfection as described in the manual and the quantity of total RNA was analyzed by Agilent 2100 bioanalyzer (Agilent).
Berry Genomics performed the small RNA library preparation and sequencing.
Single end 50bp, Hiseq 2500.

treatment_protocol: The transfection experiments were done by using Lipofectamine LTX (Life technologies) and Attractene transfection reagent (Qiagen) following manufacturer’s protocol.

value: HEK293 cell lines

tag: passages

tag: treatment

tag: expression

value: Synthetic miRNA precursor miR-FF5 expressed in lentiviral vector


title: SCL3

description: total small RNA

value: Synthetic miRNA precursor miR-FF3 expressed in the cell lines integrated by lentiviral vector


title: SCL5

description: total small RNA

value: Synthetic miRNA precursor miR-FF5 expressed in the cell lines integrated by lentiviral vector


title: pLV3

description: total small RNA

value: Synthetic miRNA precursor miR-FF3 expressed in lentiviral vector


title: miR-LZ3

description: total small RNA

value: A synthetic miRNA


title: pZD5

description: total small RNA

value: Synthetic miRNA precursor miR-FF5 expressed in one transient expressing vector


title: miR-RR-19nt

description: total small RNA

value: Mixture of  synthetic miRNA precursors miR-RR9s, -RR10s, -RR11s, -RR12s, -RR13s and -RR14s


title: pZD3

description: total small RNA

value: Synthetic miRNA precursor miR-FF3 expressed in one transient expressing vector


title: miR-FF3

description: total small RNA


title: M9

description: total small RNA

value: A synthetic miRNA (miR-FF3) precursor embedded in one derivative backbone of murine pri-miR-155


title: miR_mix_18multi

description: total small RNA

value: Mixture of synthetic miRNA precursors miR-FF3, -FF4, -FF5, -FF6, -FF7, -LZ1, -RR3, -LZ4, -LZ5, -LZ6, -RR1, -RR11, -RR12, -RR2, -RR4, -RR5, -RR6, and -RR8


title: M7

description: total small RNA


title: miR-RR-21nt

description: total small RNA

value: Mixture of  synthetic miRNA precursors miR-RR9l, -RR10l, -RR11l, -RR12l, -RR13l and -RR14l.


title: M4

description: total small RNA


title: M5

description: total small RNA


title: Flag_SP1_pool1

value: C-terminal Flag tagging of SP1, pool 1


title: M3

description: total small RNA


title: M13

description: total small RNA


title: M2

description: total small RNA


title: M6

description: total small RNA


title: M11

description: total small RNA


title: M12

description: total small RNA


title: 6R

description: total small RNA

value: A synthetic miRNA cluster expressed synthetic miRNA precursors miR-FF3, -FF4, -FF5, -RR1, -RR2, and -RR6


title: 6F

description: total small RNA


title: M10

description: total small RNA


title: M1

description: total small RNA


title: 18R

description: total small RNA

value: A synthetic miRNA cluster expressed synthetic miRNA precursors miR-FF3, -FF4, -FF5, -FF6, -FF7, -LZ1, -LZ3, -LZ4, -LZ5, -LZ6, -RR1, -RR11, -RR12, -RR2, -RR4, -RR5, -RR6, and -RR8


title: M8

description: total small RNA


title: tl10b_wce_4

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were aligned to the UCSC dm3 reference genome using bowtie v1.1.1 retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

source_name: tl10b embryos

growth_protocol: Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections. For Trl, Sna, Pc ChIPs wild type embryos (Oregon-R) were used. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).

extract_protocol: ChIP-seq was performed according to He et al. (2011) with whole cell extract (WCE) derived from 100 mg embryos per ChIP

treatment_protocol: Embryos were dechorionated in 100% bleach for ~1 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

tag: developmental stage

value: 2-4 hr after egg deposition

tag: chip antibody

tag: barcode kit

value: custom

tag: library kit

value: NEB-next-DNA


title: 18F

description: total small RNA

tag: cell line

value: HEK293 cell lines


title: 12R

description: total small RNA

value: A synthetic miRNA cluster expressed synthetic miRNA precursors miR-FF3, -FF4, -FF5, -LZ1, -LZ3, -RR1, -RR12, -RR2, -RR4, -RR5, -RR6, and -RR8


title: tl10b_wce_3

tag: genotype/variation


title: 12F

description: total small RNA


title: tl10b_h3k27ac_1

value: H3K27ac (Active Motif Carlsbad, CA, catalog #39133)


title: tl10b_dl_2

value: Custom GenScript Dl (aa 39-346) 126740-44


title: tl10b_dl_1


title: tl10b_wce_2

value: Biooscientific

value: Millipore


title: orer_pc_1

source_name: orer embryos

value: wild type

value: Pc (d-220) (Santa Cruz, catalog #sc-25762)