title: FL-E115-Neur1-Mm-cHiC-2

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

institute: University of Geneva

data_processing:
Library strategy: HiC
Preprocessing and mapping of paired-end sequencing data, as well as filtering of mapped di-tags was performed with the HiCUP pipeline v.0.5.8 (Wingett et al. 2015) (Nofill: 1, no size selection, Format: Sanger). The pipeline used Bowtie2 v.2.2.6 (Langmead and Salzberg 2012) for mapping short reads to reference genome (NCBI37/mm9). Replicates were combined after mapping and filtering. Filtered di-tags were further processed with Juicebox command line tools to bin di-tags (5 and 10 kb bins) and to normalize the map by Knight-Ruiz (KR) matrix balancing (Lieberman-Aiden et al. 2009; Knight and Ruiz 2013; Durand et al. 2016)+ (Durand et al, Cell Systems 3(1), 2016.). For this, only reads with a MAPQ ≥30 were considered. The DNA-capturing step enriches genomic region chr13:53,400,001-57,300,000 on mm9 leading to three different regimes in the cHi-C map: (i) enriched versus enriched, (ii) enriched versus non-enriched, and (iii) non-enriched versus non- enriched. For binning and normalization only di-tags in regime (i) were considered. Therefore di-tags were filtered for the enriched region and mm9 coordinates were shifted by 53,400,000 bp. For Juicebox, a custom chromosome sizes file containing only the enriched region on chr13 (length 3900000 bp) was used. After binning and normalization, coordinates were shifted back to their original values. All maps were processed on the WT reference genome to work with the same genomic coordinates across all samples. To account for differences between maps in their distance dependent signal decay, maps were scaled pairwise by the sum of their sub-diagonals. Therefore, each sub-diagonal vector in one matrix is divided by its sum and multiplied by the average of the sums of both matrices. To normalize for sequencing depth, each map was additionally converted to reads per million (RPM). To avoid copy number biases, a region spanning all tested deletions (chr13:55,730,001-56,500,000) was not considered for the computation of scaling factors, for the diagonal normalization as well as for the RPM normalization. cHi-C maps of count values and subtraction maps were visualized as heat maps truncating all values above the 99-th percentile for visualization purposes. The percentile was determined from absolute values within the same region used for normalisation.
Differential interactions were determined from the pairwise subtraction of normalized maps. For diagonal and RPM normalization, as well as for the computation of P-values, individual regions spanning the corresponding deletions were excluded. To avoid artefacts from KR normalization due to low coverage, maps were analysed on 10 kb resolution and a single row with very low coverage (chr1:54,450,001-54,460,000) was excluded. To account for the distance dependence of the magnitude of differences, each difference value was subtracted by the mean and divided by the standard deviation of the corresponding sub-diagonal. For the computation of mean and variance per sub-diagonal, values above the 99.5-th percentile were not included. P-values for the z-transformed difference values were computed using a standard normal distribution and further corrected for multiple testing with false discovery rate (Benjamini and Hochberg 1995). In histograms the distributions of z-scores do not fit the normal distribution perfectly, but show as well a bell-like shape.
To obtain more fine-grained interaction profiles, we generated virtual Capture-C-like profiles based on the same filtered BAM files also used for the cHi-C maps and defined several virtual viewpoints of 10 kb size. A read pair was considered in the profile, when one mate mapped to the defined viewpoint region and the other one outside of it. Reads were counted per restriction fragment and binned further to a regular 1kb grid. In case a fragment spanned more than one bin, the count value was distributed proportionally to the overlaps. Afterwards, the profiles were smoothed by averaging over a sliding window of 5 bins. For coverage normalization the profiles were divided by sum of counts on chr13 and multiplied with 103. The region ± 5kb around the viewpoint as well as the regions in Tab. XX_DEL were mutually excluded from the computation of the scaling factor in pairwise comparisons. The profiles were generated with custom Java code using htsjdk v1.139 (https://samtools.github.io/htsjdk/).

source_name: Embryonic Limb Bud

growth_protocol: Forelimb and hindlilb buds were micro-dissected from E11.5 mouse embryos

extract_protocol:
3C-libraries were prepared from homozygous E11.5 forelimb and hindlimb buds as described previously (Hagege et al. 2007). cHi-C experiments were performed as quadruplets (WT) or duplicates (mutants). Per biological replicate, 5-6 pairs of limb buds (ca. 3 ×106 cells) were micro dissected in PBS at room temperature (RT). A single cell suspension was obtained by incubating the tissue in 500 µl Trypsin-EDTA 0.05 % (Gibco) at 37°C for 10 minutes shaking at 900 RPM. The cells were resuspended and homogenised using a 0.40 µm cell strainer (Falcon) and diluted in 10% FCS/PBS. Cells were fixed by adding 650 µl 37% formaldehyde (Sigma-Aldrich) with a final concentration of 2% and mixed for 10 minutes at room temperature. Fixation was quenched using 1.425 M glycine (Merck) on ice and immediately centrifuged at 260 g for 8 minutes. Supernatant was removed, the pellet resuspended in lysis buffer (final concentration of 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 M EGTA, and 1x Complete protease inhibitors (Roche)) and incubated on ice for 10 minutes. Removal of lysis buffer was done by centrifugation at 400 g for 5 minutes at 4°C, followed by removal of supernatant, snap-freezing and storage at -80°C. On the next day, the pellet was resuspended in 520 µl 1x DpnII buffer (Thermo Fisher Scientific), and incubated with 7.4 µl 20% SDS shaking at 900 RPM at 37°C for 1 hour. Next, 75 µl 20% x-100 Triton was added and left shaking at 900 RPM at 37°C for 1 hour. A 15 µl aliquot was taken as a control for undigested chromatin (stored at -20°C). The chromatin was digested using 40 µl 10 U/µl DpnII (Thermo Fisher Scientific) shaking at 900 RPM at 37°C for 6 hours. 40 µl of DpnII was added and samples were incubated overnight shaking at 900 RPM at 37°C. On the third day, 20 µl DpnII was added to the samples shaking 5 more hours at 900 RPM at 37°C. DpnII restriction enzyme was inactivated at 65°C for 25 minutes. A 50 µl aliquot was taken to test digestion efficiency (stored at -20°C). Next, the digested chromatin was diluted and re-ligated in 5.1 ml H2O, 700 µl 10x ligation buffer (Fermentas), 5 µl 30 U/µl T4-ligase (Fermentas), incubated at 16°C for 4 hours and shake manually 3 times. The ligated samples were incubated further 30 minutes at RT. The chimeric chromatin products and test aliquots were de-crosslinked o.n. by adding 30 µl and 5 µl Proteinase K, respectively, and incubated at 65°C overnight. On the fourth day, 30 µl or 5 µl of 10 mg/ml RNase was added to the samples and aliquots, respectively, and incubated for 45 minutes at 37°C. Next, chromatin was precipitated by adding 1 volume phenol-chloroform to the samples and aliquots, vigorously shaking them, followed by centrifugation at 4000 RPM at RT for 15 minutes. The upper phase containing the chromatin was transferred to a new tube. To the aliquots, 100% ethanol was added and the samples were frozen for 30 minutes, centrifuged at 5000 RPM for 45 minutes at 4°C, washed with 70% ethanol and resuspended in 20 µl 10 mM Tris-HCl pH 7.5. To the samples, 7 ml H2O, 1 ml 3M NaAc pH 5.6 and 35 ml 100% ethanol was added. The samples were frozen at -20°C for 3 hours. The precipitated chromatin was isolated by centrifugation at 5000 RPM for 45 minutes at 4°C. The chromatin pellet was washed with 70% ethanol, and further centrifuged at 5000 RPM for 15 minutes at 4°C. Finally, the 3C-library chromatin pellet was dried at RT and resuspended in 10 mM Tris-HCl pH 7.5. To check the 3C-library, 600ng was loaded on a 1% gel together with the undigested and digested aliquots.
The 3C-library was then sheared using a Covaris sonicator (duty cycle: 10%, intensity: 5, cycles per burst: 200, time: 6 cycles of 60 s each, set mode: frequency sweeping, temperature: 4 to 7 °C). Adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed sure-select beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions.

value: Forelimb


title: FL-E115-DelL-Mm-cHiC-2

status: Public on Oct 01 2018

type: SRA

country: Switzerland

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

tag: developmental stage

tag: genotype

value: DelL


title: FL-E115-DelL-Mm-cHiC-1


title: L2_3

status: Public on Oct 02 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl DM6.gtf none -d [TAG DIR] -count 3utr -condenseGenes -strand +
Genome_build: DM6
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Second instar larvae

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places while adult refers to 3-5 days post eclosion.

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 DsRed+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Library constracted using MARS-seq technique (Jaitin et al, Science 2014). Briefly mRNA was barcoded, converted into cDNA and linearly amplified by T7 in vitro transcription.
single end protocol ( samples used read2 to read molecule barcodes and UMI)

tag: organ

value: Brain

tag: selection marker

value: DsRed +

value: Isolated γ neurons

value: Second instar larvae

value: y,w/+; UAS-RedStinger/+;71G10/+


title: FL-E115-Neur1-Mm-cHiC-1


title: FL-E115-Inv1-Mm-cHiC-2


title: MRE_HFKn_p20_KSFM_rep2

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

country: USA

institute: Washington University School of Medicine

description: Cultured in EpiX media and switched to KSFM, collected at passage 20

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The Illumina adapter sequences were trimmed from the raw sequencing reads using cutadapt v.1.9 paired-end mode with the parameters -q 10 -m 20
Trimmed reads were aligned to the hg19 genome assembly using BWA-MEM v.0.7.10 with the default parameters
The aligned reads were further processed using methylQA v.0.1.6 mre mode with the following parameters: -c 4
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

organism: Homo sapiens

source_name: human foreskin keratinocytes, neonatal

extract_protocol:
The genomic DNA was extracted by incubating the cells in genomic DNA extraction buffer (50 mM Tris, 1 mM EDTA, 0.5% SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
Five parallel digests (HpaII, Hin6I, SsiI, BstUI and HpyCH4IV; New England Biolabs) were performed, each with 20 ng of genomic DNA. Digested DNA was size-selected, end-processed, and ligated to adapters. After the second size-selection, DNA was amplified by 18 cycles of PCR and size-selected (150-500 bp) by Agencourt AMPure XP beads.

value: foreskin

tag: cell type

value: keratinocytes

tag: passages


title: MRE_HFKn_p20_KSFM_rep1


title: MRE_HFKn_p04_KSFM_rep2

description: Cultured in EpiX media and switched to KSFM, collected at passage 4


title: ER_KO4

city: Lausanne

first: George

middle: A

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

institute: EPFL

data_processing:
RNA-seq reads were aligned to the mm10 mouse genome using the RNA-Seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTS station http://htsstation.epfl.ch (David, FPA et al. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS ONE 9, e85879 (2014). We applied the ready-to-use pipeline ASAP (the Automated Single-cell Analysis Pipeline) https://asap.epfl.ch/ (https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx337) to the RNA-seq analysis.
Genome_build: mm10

molecule: total RNA

source_name: mammary gland

extract_protocol:
RNA was extracted from FACS sorted cells derived from intraductally engrafted WT.GFP+ or ERα-/-.GFP+ cells from contralateral glands of the pregnant NSG hosts using miRNeasy Mini Kit (Qiagen, cat.# 217004)
Libraries were prepared in 2 steps. The first step was performed according to Clontech's instructions accompanying the SMART-Seq v4 Ultra Low Input RNA Kit (Part# 634889). Briefly, 10 ng of RNA was reverse transcribed uning a oligo dT primer flanked with a proprietary adapter. Template switching mechanism was then used to append another proprietary adapter on the 3' end of the cDNA (corresponding to the beginning of the mRNA molecule). A PCR specific for the aforementionned adapters was used to create and amplify double-stranded cDNA molecules. The second step was performed according to Illumina's instructions accompanying the Nextera XT kit (Part# FC-131-1096). Briefly, tagmentation of the double-stranded cDNA with hyperactive Tn5 created fragments of a few hundred bp, flanked with Illumina proprietary adapters. DNA was then PCR amplified with Illumina primers for 8 cycles, generating final libraries of ~400 bp (insert plus adaptors). Libraries were sequenced on a NextSeq 500 instrument with single-end reads of 85 nt, following the manufacturer's protocols. Basecalls and Illumina adapters trimming performed using bcl2fastq v2.18. Clontech adapters trimming performed with CLC 9.

tag: genotype/variation

value: ER-alpha -/-. GFP+


title: FL-E115-Inv1-Mm-cHiC-1


title: VEGF Trap_Treated_1

city: Irvine

first: Hosung

last: Bae

state: CA

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

description: To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: RPE-choroidal complex

growth_protocol: 8-week-old male mice were used for generation of CNV. After dilation of the pupils with 5 mg/ml phenylephrine and 5 mg/ml tropicamide eye drops (Santen Pharmaceutical) and instillation of 0.5% proparacaine hydrochloride eye drops (Alcon) for topical anesthesia, laser photocoagulator (Lumenis Inc.) with a slit lamp delivery system was used with a glass coverslip as a contact lens to visualize the retina. Sufficient laser energy (532 nm wavelength, 250 mW power, 100 ms duration, 50 μm spot size) was delivered in 4 locations for each eye (the 3, 6, 9 and 12 o’clock positions of the posterior pole). Only burns that produced a bubble at the time of laser photocoagulation, indicating the rupture of the Bruch membrane, were included in this study. Spots containing hemorrhage at the laser site were excluded from the analysis.

extract_protocol:
collected using laser capture microdissection (PALM MicroBeam, Carl Zeiss)
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: Sex

value: male

tag: age


title: HL-E115-DelHoxc-Mm-cHiC-2

value: Hindlimb

value: DelHoxc


title: ABTAA_Treated_3

treatment_protocol: To administer indicated reagents intravitreally, 5 µg of reagent (5 mg/ml) was injected into the vitreal cavity using the micro-injector fitted with a glass capillary pipette.


title: HL-E115-DelHoxc-Mm-cHiC-1


title: MRE_HFKn_p04_KSFM_rep1


title: VEGF Trap_Treated_3


title: HL-E115-Pitx1-fs-Mm-cHiC-2


title: HL-E115-Wt-Mm-cHiC-4

value: wild type


title: HL-E115-Pitx1-fs-Mm-cHiC-1


title: MRE_HFKn_p19_EpiX_rep2

description: Cultured in EpiX media, collected at passage 19


title: MRE_HFKn_p19_EpiX_rep1


title: HL-E115-Wt-Mm-cHiC-2


title: MRE_HFKn_p03_EpiX_rep2

description: Cultured in EpiX media, collected at passage 3


title: MRE_HFKn_p12_EpiX_rep1

description: Cultured in EpiX media, collected at passage 12


title: MRE_HFKn_p12_EpiX_rep2


title: HL-E115-Wt-Mm-cHiC-1


title: MRE_HFKn_p03_EpiX_rep1


title: HL-E115-Wt-Mm-cHiC-3


title: MRE_HFKn_p05_KSFM_rep1

description: Cultured in KSFM, collected at passage 5


title: FL-E115-Wt-Mm-cHiC-2


title: FL-E115-Wt-Mm-cHiC-4


title: FL-E115-Wt-Mm-cHiC-3


title: MRE_HFKn_p02_KSFM_rep2

description: Cultured in KSFM, collected at passage 2


title: FL-E115-Wt-Mm-cHiC-1


title: MRE_HFKn_p02_KSFM_rep1


title: MeDIP_HFKn_p20_KSFM_rep2

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The Illumina adapter sequences were trimmed from the raw sequencing reads using cutadapt v.1.9 paired-end mode with the parameters -q 10 -m 20
Trimmed reads were aligned to the hg19 genome assembly using BWA-MEM v.0.7.10 with the default parameters
The aligned reads were further processed using methylQA v.0.1.6 medip mode with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

extract_protocol:
The genomic DNA was extracted by incubating the cells in genomic DNA extraction buffer (50 mM Tris, 1 mM EDTA, 0.5% SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
100 ng of DNA isolated was sonicated to a fragment size of 100-500 bp, end-processed, and ligated to paired-end adapters. The DNA was then immunoprecipitated using a mouse monoclonal anti-methylcytidine antibody. Immunoprecipitated DNA was then washed, amplified by 17 cycles of PCR, and size-selected (150-500 bp) by Agencourt AMPure XP beads.


title: MRE_HFKn_p05_KSFM_rep2


title: MeDIP_HFKn_p04_KSFM_rep2


title: MeDIP_HFKn_p04_KSFM_rep1


title: MeDIP_HFKn_p19_EpiX_rep1


title: MeDIP_HFKn_p12_EpiX_rep2


title: MeDIP_HFKn_p19_EpiX_rep2


title: MeDIP_HFKn_p20_KSFM_rep1


title: MeDIP_HFKn_p03_EpiX_rep2


title: Input_2

city: Pittsburgh

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

institute: McGowan Institute for Regenerative Medicine

data_processing:
The purity and concentration of DNA samples were determined with Qubit fluoumeter
DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA sample prep kit (Illumina). 200-1500 bp fragments were selected at the gel size fractionation step. The final size of the library was confirmed by gel electrophoresis.
The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the Illumina cBot using TruSeq Rapid SR cluster kit (Illumina).
Sequencing was performed on Illumina HiSeq 2000 using TreSeq Rapid SBS Kits (Illumina).
Images analysis and base calling→Solexa CHASTITY quality filter→Mouse genome (UCSC mm10 )alignment →peak detection and annotation
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using MACS;contains chrom# chromStart chromEnd and dataValue

source_name: CD4+ T helper 9 cell

growth_protocol: Naïve CD4+ T cell were isolated from spleen of C57BL6/J wild type mice and cutured under Th9 cell conditioned media ( IL-4 20ng/ml, hTGFb 2ng/ml, a-CD28 2.5ug/ml,a-CD3 2ug/ml, a-IFNg 10ug/ml ,a-IL-10R 20ug/ml, hIL-2 20U/ml) for 5 days.

extract_protocol: Nuclear lysates were isolated throughcell lysis and nuclear lysis buffer. Lysates were fragmented by sonication and diluted with Chip dilution buffer following pre clear step. Then P300 antibody was added and incubated for overnight at 4 degree. Next day, after washing step, eltuion step, DNA was enriched using phenol chloroform method for ChIP assay.

treatment_protocol: On Day5, cells were re-stimulated with a-CD3 for 5hours and collected, fixed with 10% formaldehyde for 15 mins at RT.

value: CD4+ T helper 9 cell

tag: cultured day

value: 5 days

tag: chip antibody


title: MeDIP_HFKn_p03_EpiX_rep1


title: DCA_HDAC3_ChIPseq  rep2

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
Transcripts were aligned to the mm10 reference genome using Bowtie2-2.2.3, sorting reads in Samtools-0.1.19.
Genomic bins of 1000bp upstream and downstream of each transcription start site for each gene were created. Read counts per genomic bin were obtained from the mapped reads using HTSeq-0.6.1
Differential binding testing was conducted in EdgeR-3.8.6.
Quality examination on aligned reads was performed using ChIPQC-1.2.2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig file plotting the p-value of enrichment over input for each replicate

extract_protocol:
Chromatin IP was performed according to a previously published protocol (Schmidt et al., 2009) with a few adjustments. Briefly, DRG pellets (20 mice/sample) were crushed using an automatic pestle and chemically cross-linked with a 1% formaldehyde solution containing 50mM Hepes-KOH pH7.5, 100mM NaCl, 1mM EDTA and 0.5mM EDTA, for 15 minutes at room temperature. Nuclear extracts were then sonicated for 30 min using a Bioruptor (Diagenode) and successful chromatin shearing (200-800 bp) was confirmed by agarose gel analysis. Immunoprecipitation was performed overnight with Protein G Dynabeads (Invitrogen) bound to 20 μg of HDAC3 antibody (Millipore 17-10238). After washing, elution and reverse crosslinking, DNA was treated with RNAse A and Proteinase K and purified using Qiagen PCR purification columns. The concentration of the recovered DNA was quantified with Picogreen assay and the enrichment of the immunoprecipitate calculated with respect to the input and IgG.
Library preparation was performed using the NEBNext Ultra DNA Library Prep Kit from Illumina (NEW ENGLAND BioLabs) following the manufacturer’s protocol. Briefly, 2 ng of Input and IP DNA were end repaired and adaptor ligated, using a dilution of 1:20 of adaptors. Samples were cleaned to remove unligated adaptors and size selection was performed to select and enrich fragments of 200bp in size. Libraries were amplified by PCR using multiplex oligo following manufacturer’s protocol. Prior to sequencing, libraries were run on an Agilent Bioanalyser for size and quality control checking. Sequencing was performed in an Illumina HiSeq2000, generating 50bp single ended reads.

treatment_protocol: Mice (6-8 weeks old) underwent the following procedures: a) spinal cord dorsal column injury b) laminectomy c) sciatic nerve injury   d) sham

value: 6-8 weeks old

tag: treatment

value: spinal cord dorsal column injury

tag: tisue

value: Dorsal Root Ganglia (DRG)

value: HDAC3 Millipore 17-10238

tag: index sequence

value: GTGAAA


title: DCA_HDAC3_ChIPseq  rep1

value: GATCAG


title: MeDIP_HFKn_p05_KSFM_rep1


title: SNA_HDAC3_ChIPseq  rep2

value: sciatic nerve injury

value: GTCCGC


title: MeDIP_HFKn_p02_KSFM_rep2

value: foreskin


title: MeDIP_HFKn_p05_KSFM_rep2

value: keratinocytes


title: Sham_HDAC3_ChIPseq rep2

value: sham

value: CCGTCC


title: SNA_HDAC3_ChIPseq  rep1

value: CAGATC


title: DCA_Input  rep1

value: TTAGGC


title: LAM_Input  rep2

value: laminectomy

value: ATCACG


title: Sham_HDAC3_ChIPseq rep1

value: GCCAAT


title: RNA_HFKn_p20_KSFM_rep2

data_processing:
Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq
The raw sequence reads were aligned to the reference genome and transcriptome (gencode v19) using STAR v.2.5.0 with the following parameters: --sjdbScore 1 --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with gencode v19 gtf file and the following parameters: -O -s 1 --primary -p
Genome_build: hg19
Supplementary_files_format_and_content: TXT

extract_protocol:
The mRNA was extracted directly from the cells by using Dynabeads mRNA DIRECT Purification Kit according to the manufacturer’s instructions.
RNA-seq libraries were constructed using ScriptSeq RNA-Seq Library Preparation Kit (Illumina) from all the extracted mRNA according to the manufacturer’s instructions.


title: RNA_HFKn_p20_KSFM_rep1


title: p300_1

value: CD4+ T helper 9 cell

value: 5 days

value: SC-584X and SC-585X (santa cruz)


title: MeDIP_HFKn_p12_EpiX_rep1


title: Input_1


title: SNA_Input  rep2

value: 6-8 weeks old

value: Dorsal Root Ganglia (DRG)

value: AGTTCC


title: RNA_HFKn_p04_KSFM_rep2


title: LAM_Input  rep1

value: ACAGTG


title: SNA_Input  rep1

value: sciatic nerve injury

value: TGACCA


title: Sham_Input  rep2

value: AGTCAA


title: Sham_Input rep1

value: sham

value: CGATGT


title: p300_2


title: RNA_HFKn_p04_KSFM_rep1

value: foreskin

value: keratinocytes


title: LAM_HDAC3_ChIPseq  rep2

value: laminectomy

value: HDAC3 Millipore 17-10238

value: ACTTGA


title: RNA_HFKn_p19_EpiX_rep2


title: KO-4s [RNA-seq]

city: Memphis

first: Lance

middle: E

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
RNA-Seq reads were aligned to the NCBIM37 mouse genome using the St. Jude Children’s Research Hopsital’s Strongarm pipeline
Htseq-count (HTSeq framework, version 0.6.1p1) was used to associate  aligned reads to annotations from Mus_musculus.NCBIM37.67 to get per-gene counts.  Hemoglobin and small nucleolar RNAs were removed from further analysis.
For intron counts, exon coordinates were extracted from mm10 mouse annotations defined by gencode.vM7.annotation.gtf. All overlapping exon coordinates from all isoforms from a gene were combined, and then any intron-only sequences that did not map to any other exons from other genes on the same strand were retained.
RNA-Seq read sequences were aligned to the mm10 genome using STAR  with the gencode.vM7.annotation.gtf annotation set.
Any reads that were spliced or mapped to more than one location were removed.  Bedmap from BEDOPS was used to map reads to the intron list that had been created.  For each sample, per gene intron counts were tabulated. Intron and exon counts (from the RNA-SEQ section  above) for each gene combined in a table and loaded into the R statistical environment.  Genes with less than 10 exon hits or 10 intron hits were removed from analysis.
Genome_build: NCBIM37, mm10
Supplementary_files_format_and_content: Tab-delimited plain text file containing number of reads per gene at exon an intron levels (Exon only=RNASeqCountsMinusHBMT.NCBIM37.txt   Exon and intron counts =ExonIntronCounts.txt)  For the ExonIntronCounts.txt file, only genes with at least one read matching an intron was retained.

source_name: Fetal liver

extract_protocol:
RNA was extracted from 5 million FL cells from 3 replicates each of miR-144/451 WT and KO embryos using the RNeasy Mini kit (Qiagen).
PolyA+ RNA was prepared using the mRNA seq Sample Prep kit and used to create libraries for HiSeq2000 sequencing (Illumina).


title: WT-3s [RNA-seq]

value: WT


title: KO-6s [RNA-seq]


title: WT-2s [RNA-seq]


title: DCA_Input  rep2

value: spinal cord dorsal column injury

value: ATGTCA


title: KO-5s [RNA-seq]


title: RNA_HFKn_p12_EpiX_rep2


title: MeDIP_HFKn_p02_KSFM_rep1


title: WT-1s [RNA-seq]


title: RNA_HFKn_p12_EpiX_rep1


title: WT-3s

description: miRNA-Seq

data_processing:
Cutadapt was used to trim adapter sequence.
A blast database was created from unique trimmed reads using formatdb.
All annotated mature miRNNAs from miRBase (version r21) were used as queires inna  a BLAST search agains the database (parameters –W 7 –F F –e 1000).
The BLAST output were parsed with an ad hoc perl script by keeping the exact matches with e-value less than 0.0001.
Supplementary_files_format_and_content: miR451KO_miRNAseq_abundance.txt contains both raw counts and percentages for each miRNA in each sample.

extract_protocol:
5 million FL cells from 3 replicates each of miR-144/451 WT and KO embryos using the Qiagen miRNeasy Mini kit.
The NEXTflex Small RNA Sequencing Kit (BIOO Scientific) was used to created libraries for HiSeq2000 sequencing (Illumina)


title: KO-5s

description: miRNA-Seq


title: WT-2s

description: miRNA-Seq


title: RNA_HFKn_p05_KSFM_rep2


title: RNA_HFKn_p03_EpiX_rep2


title: KO-6s

description: miRNA-Seq


title: RNA_HFKn_p03_EpiX_rep1


title: 11WT-IgG

description: HITS-CLIP sequence

data_processing:
Adapters were trimmed from FASTQ sequences using CUTADAPT (Martin, M. 2011) (https://cutadapt.readthedocs.org/en/stable/) using the following parameters a=GTGTCAGTCACTTCCAGCGG, g=AGGGAGGACGATGCGG, n=3, m=15.  Untrimmed sequences were placed in a separate output file.
FASTQ file were filtered for quality.  The first and last ten bases of each read were required to have a Q score >=20.
Sequences from each sample were collapsed by distinct sequences using fastx_collapser from the FASTX-Toolkit with the –Q33 parameter
All collapsed sequences from all samples were collapsed together.
The set of collapsed sequences from all samples were aligned with STAR using the following parameters “--outSAMunmapped Within”, “ --outSAMtype BAM SortedByCoordinate”,  “--quantMode TranscriptomeSAM”,  “--chimSegmentMin 10”, “--chimJunctionOverhangMin 10”.    GENCODE annotations (gencode.vM7.annotation.gtf http://www.gencodegenes.org/mouse_releases/7.html ) were used for alignment.
Reads were classified based on GENCODE features to which they were aligned.   Sequences aligning to the following categories were excluded from further analysis: Mt_rRNA, Mt_tRNA, miRNA, misc_RNA, rRNA, snRNA, snoRNA, ribozyme, sRNA, scaRNA, tRNA_pseudogene, snoRNA_pseudogene, snRNA_pseudogene, scRNA_pseudogene, rRNA_pseudogene, misc_RNA_pseudogene, miRNA_pseudogene.  Sequence with a Mapping quality <3 were excluded from analysis.  Sequences mapping chr11:32,269,363-32,309,558  (Hba) , chr7:103,794,687-103,866,211 (Hbb) , chr11:109,011,611-109,012,166 (unannotated rRNA) , chr17:39,842,424-39,849,380 (unannotated  Rn45s) were also excluded.
Start and end coordinates of mapped reads were extended based on soft clipping distance.   Sequences with the same start and end coordinates, after the soft clipping adjustment were collapsed together.  In each set of these fully collapsed sequences, the individual read sequences were stored  along with an alignment score and total number of reads with that sequence.
Bed graph coverage files and bigwig files were generated from BAM files using genomeCoverageBed (bedtools) and bedGraphToBigWig. Files for individual samples as well as combined samples are created.
Bed files were generated from the BAM files using bamToBed (bedtools) with the -split option and sorted using the linux sort command (LC_COLLATE=C sort  -k1,1 -k2,2n)  Bed files were clustered using the bedtools cluster command with the –s option so that clusters would be stranded.
YODEL (Palmer 2017) was used for peak calling
Gene features were mapped to peaks by finding overlaps between  feature and peak coordinates.   miR-451/144 seed matches and control (miR-16-5p, miR-122-5p, miR-486a-5p) seed matches were mapped to peaks.
For each of the WT, KO, WT-IgG, and KO-IgG samples, a sum of read counts was determined.  4 ratios were calculated a) (WT-IgG+.1)/(WT+.1),  b) (KO-IgG+.1)/(WT+.1) , c) (WT-IgG+.1)/(KO+.1), d) (KO-IgG+.1)/(KO+.1).  If WT were <= KO counts *.75 then a&b were excluded.  If KO counts were <= WT counts*.75 then c&d were excluded.  The highest ratio from remaining values was retained as the IgG ratio.  Peak  with an IgG ratio >= .2 were discarded.
For each gene, the total amount of bases covered by both WT and KO Argonaute  samples was calculated for both CDS and 3’ UTR or CDS+3’UTR.  An average background value was calculated by dividing the total number of bases covered by the length of the feature being analyzed.    For each peak, the largest background value from the associated gene was used as a background value.  If the background ratio was <= 5, then the peak was discarded.
Peaks counts were analyzed by VOOM normalization and LIMMA  differential expression analysis ) within the R statistical environment.  The library size value of the DGEList object was altered manually as a large number of KO depleted peaks skewed the average value of controls as having more reads in KO samples.  The read counts from peaks containing 7mer-A1, 7mer-m8 and 8mer seed matches were used to adjust the library size.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are plain text files that contain information on each called peak within each row.  Column descriptions can be found in miR451_144.HITSCLIP.tableDescription.txt

extract_protocol:
HITS-CLIP was performed on 100 million FL cells from 3 replicates each of miR-144/451 WT and KO embryos
Methods previously described in Chi et al., 2009. (https://doi.org/10.1038/nature08170)

tag: antibody

value: Control IgG


title: 8KO-IgG

description: HITS-CLIP sequence

tag: strain


title: WT-1s

description: miRNA-Seq


title: RNA_HFKn_p05_KSFM_rep1

tag: tissue


title: 14KO-IgG

description: HITS-CLIP sequence


title: LAM_HDAC3_ChIPseq rep1

value: 6-8 weeks old

value: Dorsal Root Ganglia (DRG)

value: CTTGTA


title: 6WT-IgG

description: HITS-CLIP sequence


title: 4KO-IgG

description: HITS-CLIP sequence


title: RNA_HFKn_p02_KSFM_rep2


title: RNA_HFKn_p19_EpiX_rep1


title: 13KO

description: HITS-CLIP sequence

value: Ago


title: 2WT-IgG

description: HITS-CLIP sequence


title: 3KO

description: HITS-CLIP sequence


title: 12KO

description: HITS-CLIP sequence


title: KO-4s

description: miRNA-Seq


title: 10WT

description: HITS-CLIP sequence


title: HSC [KY046]

city: New York City

first: Kang

last: Liu

state: New York

department: Dept of Microbiology & Immunology

institute: Columbia University

data_processing:
RNA-Seq reads were aligned to the Ensembl GRCh 37 genome assembly using STAR with default parameters
featureCounts was used to obtain gene read counts.
DESeq2 was used to normalize the read counts for library size difference correction.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: hematopoietic stem cell

extract_protocol:
2,000-30,000 progenitor cells of each population were purified using flowcytometry sorting. After cell lysis, mRNA was purified using LNA-Oligo-(dT) coated streptavidin-coated C1 DynabeadsRNA was extracted
RNA was amplified with clonetech SMARTer Ultra Low RNA Kit (634935 and 639207, Clontech)

value: cord blood


title: BNK [KY043]

source_name: B/natural killer cell progenitor


title: RNA_HFKn_p02_KSFM_rep1


title: 9WT

description: HITS-CLIP sequence


title: HSC [KY042]


title: 1WT

description: HITS-CLIP sequence


title: BNK [KY041]


title: CD4 sorted RHOA G17V replicate 2

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming
We map the reads to a reference genome using STAR (version 2.4.2a) with option --outFilterIntronMotifs RemoveNoncanonical
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required)
We prepared libraries were using Illumina TruSeq RNA prep kit
We multiplex samples in each lane, which yields targeted number paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane

value: Lymphoma

value: Tet2-/-, RHOA G17V

tag: tumor type

value: CD4 sorted PTCL tumor cells RHOA G17V


title: CD4 sorted RHOA G17V replicate 1

tag: genotype


title: RHOA G17V replicate 4

value: PTCL tumor RHOA G17V


title: CD4 sorted RHOA G17V replicate 3


title: LMPP [KY039]

source_name: lymphoid-primed multipotent progenitors


title: RHOA G17V replicate 2


title: Rhoa G17V replicate 1


title: Rhoa WT replicate 3

value: Leukemia

value: HD-delta-Pest NOTCH1, Rhoa WT

value: ALL tumor Rhoa wild type


title: Rhoa WT replicate 2


title: BNK [KY040]


title: MPP [KY036]

source_name: multipotent progenitor


title: Rhoa WT replicate 1


title: CMP [KY033]

source_name: common myeloid progenitor


title: CDP [KY034]

source_name: common dendritic cell progenitor


title: MLP [KY032]

source_name: multilymphoid progenitor


title: LMPP [KY031]


title: MPP [KY035]


title: LMPP [KY028]


title: MLP [KY026]


title: MPP [KY027]


title: GMDP [KY018]

source_name: Gmonocyte/dendritic cell progenitor


title: CDP [KY030]


title: CMP [KY019]


title: MLP [KY025]


title: GMDP [KY014]


title: HSC [KY013]


title: RHOA G17V replicate 3


title: GMDP [KY006]


title: MDP [KY003]

source_name: monocyte/dendritic cell progenitor


title: CMP [KY005]


title: L23

city: Beijing

first: Yurong

last: Wang

address: 28 Fu-Xing Road

country: China

institute: Chinese PLA General Hospital

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression. In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value). Hierarchical clustering was performed. miRNA target prediction was performed by targetscan and other popular method, then the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNAs.
Genome_build: Reads aligned to known Human pre-miRNA in miRBase21
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: LC_serum exosomes

extract_protocol:
exosomes were extracted by polyethylene glycol precipitation, and RNA was harvested using miRNeasy mini Kit. Illumina TruSeq Rapid SBS Kits (#FC-402-4002) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject group

value: Liver cirrhosis (LC) patients

tag: age (yrs)

value: male

value: serum exosomes


title: L22


title: L21


title: L20


title: H59

source_name: HCC_serum exosomes

value: Hepatocellular carcinoma (HCC) patients with liver cirrhosis


title: L18


title: PV_WT2

city: Boston

first: Bo

last: Zhu

state: MA

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

description:
Processed data file: PG_vs_PV_rawCounts.csv
Processed data file: PG_vs_PV_normCounts.tab

data_processing:
Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2
Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads.
Reads were aligned to Danio rerio genome version GRCz10 from Ensembl using Tophat2. Parameters: -p 6
StringTie and prepDE.py Python script provided with StringTie tool was used to assemble the alignments into transcripts and extract the raw read counts for reference genomic features respectively. The read count matrix was processed by DeSeq2 package for differential gene expression analysis.
Genome_build: GRCz10 (Ensembl build 84)
Supplementary_files_format_and_content: PG_vs_PV_rawCounts.csv: Raw read counts for each sample.
Supplementary_files_format_and_content: PG_vs_PV_normCounts.tab: Normalized read counts for each sample.

organism: Danio rerio

source_name: PV WT2

extract_protocol:
Both PG and PV follicles were isolated and  followed by RNA extraction using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB

value: follicle

tag: developmental stage

value: pre-vitellogenin

value: WT


title: PV_WT3

source_name: PV WT3

value: follice


title: PV_WT1

source_name: PV WT1


title: CDP [KY020]

tag: cell type

value: cord blood


title: H57


title: PG_WT3

source_name: PG WT3

value: primary growth


title: MDP [KY017]


title: H48


title: H53


title: PG_WT2

source_name: PG WT2


title: LV78

city: Guangzhou

first: Shilong

last: Zhong

state: Guangdong Province

address: 106 Zhongshan Road, Weilun Bldg

institute: Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention

data_processing:
Illumina’s Casava1.7 software used for base-calling
TopHat used for alignment
Filter_fq used for filtering
edgeR used for filtering and  calculating Fragments Per Kilobase of exon per Megabase of library size (RPKM) using standard of log2|Fold Change| > 1 && FDR < 0.05
Genome_build: hg38
Supplementary_files_format_and_content: a tab-delimited text file include FPKM values for each Sample

source_name: liver-cancer patient

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: case

value: liver-cancer patient

tag: gender

value: unknown

value: liver


title: LV95


title: LV96


title: H46

tag: Sex


title: LV85

value: female


title: LV75


title: LV64


title: LV61


title: LV57


title: LV58


title: LV84


title: LV55


title: LV47


title: PG_WT1

source_name: PG WT1


title: LV49


title: LV48


title: LV67


title: LV40


title: LV81


title: LV44


title: LV45


title: LV35


title: LV27


title: LV32


title: LV94

source_name: non-liver-cancer patient

value: non-liver-cancer patient


title: LV29


title: LV51


title: LV89


title: LV93


title: LV28


title: LV91


title: LV86


title: LV82


title: LV39


title: LV76


title: LV83


title: LV71


title: LV77


title: LV72


title: LV73


title: LV68


title: LV53


title: LV66


title: LV60


title: LV59


title: LV46


title: LV37


title: LV56


title: LV25


title: LV65


title: LV26


title: LV36


title: 92.1 cells FR900359 day3 exp2

city: Saint Louis

first: Michael

middle: D

last: Onken

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

data_processing:
FastQ files aligned with STAR
Biologic replicates analyzed by edgeR and Sailfish for gene-level features
normalized abundance measurements generated from edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of edgeR normalized abundance measurements

source_name: 92.1 uveal melanoma cell line

growth_protocol: 5% CO2, 37˚C, RPMI 1640 with 10% FBS

extract_protocol:
Qiagen RNeasy mini kit
RNA-polyA

treatment_protocol: 100 nM FR900359 in DMSO added to medium at start

tag: time

value: 3 days


title: LV34


title: 92.1 cells FR900359 day1 exp1

value: 1 day


title: 92.1 cells FR900359 day1 exp2


title: 92.1 cells FR900359 day3 exp1


title: 92.1 cells DMSO day3 exp2

value: DMSO


title: 92.1 cells DMSO day1 exp1


title: 92.1 cells DMSO day1 exp2


title: Sample_1675

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

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

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against themm10 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: mm10
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference genome

extract_protocol:
Spleen DCs were FACS-sorted in FCS, the purity was determined and RNA was isolated by resuspending the cells in TRIZOL (Invitrogen) following the manufacturers’ protocol
1µg of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

treatment_protocol: Mice were not treated

value: Spleen Dendritic Cells (DCs)

value: Ppef2+/+ CD8+ DCs

tag: sort


title: Sample_1679


title: Sample_1681

value: Ppef2-/- CD8+ DCs


title: LV74

value: male


title: Sample_1673


title: Sample_1669


title: Sample_1667


title: Sample_1663


title: LHG3-2

first: Tai-Jie

last: Zhang

state: Guangdong

address: No. 55 West Zhongshan Avenue, Tianhe District

department: School of Life Science

institute: South China Normal University

description:
HG
HG_all_gene_FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Trinity (version: v2.0.6; parameters: --min_contig_length 150 --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stderr') was used to perform de novo assembly with clean reads with  PCR duplication removed (in order to improve the efficiency), then use Tgicl to cluster transcripts to unigenes.
Blast (version: v2.2.23; parameters: default) was used align Unigenes to NT, NR, COG, KEGG and SwissProt to get the annotation, Blast2GO (version: v2.5.0, parameters: default) with NR annotation was used to get the GO annotation, and InterProScan5 (version: v5.11-51.0, parameters: default) was used to get the InterPro annotation.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to unigenes.
Normalized gene expression levels were calculated using RSEM (version: 1.2.12) with default parameters (Li et al.2011) and are reported as fragments per transcript kilobase per million fragments mapped (FPKM)
Genome_build: de novo assembly. FASTA files with transcript sequences are available on series record.
Supplementary_files_format_and_content: text file with FPKM

organism: Cryptocarya concinna

source_name: young leaf or mature leaf

extract_protocol:
Leaves were removed, flash frozen in liquid nitrogen, and RNA was harvested from leaves of S. superba and C concinna using Spin Column Plant total RNA Purification Kit (Sangon, Shanghai, China) and HiPure Total RNA Mini Kit (Magen, Shanghai, China),respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The seedlings of S. superba and C. concinna were collected from the subtropical evergreen forest of Dinghu mountain,separately divided into two groups and grown  under 100% full sunlight (FL) and two layer of black nylon shading net with 30% of full sunlight (low light, LL) conditions, respectively.

value: leaf

value: mature

tag: environmental light level

value: low light


title: LHG1-3

description:
HG
HG_all_gene_FPKM.txt

value: young


title: LHG1-1

description:
HG
HG_all_gene_FPKM.txt


title: 92.1 cells DMSO day3 exp1

tag: treatment


title: LHG3-1

description:
HG
HG_all_gene_FPKM.txt


title: FHG3-1

description:
HG
HG_all_gene_FPKM.txt

value: full light


title: FHG1-3

description:
HG
HG_all_gene_FPKM.txt


title: LMH3-3

description:
MH
MH_all_gene_FPKM.txt

organism: Schima superba


title: FHG3-2

description:
HG
HG_all_gene_FPKM.txt


title: Sample_1665


title: LHG1-2

description:
HG
HG_all_gene_FPKM.txt


title: LMH3-2

description:
MH
MH_all_gene_FPKM.txt


title: LHG3-3

description:
HG
HG_all_gene_FPKM.txt


title: FHG1-1

description:
HG
HG_all_gene_FPKM.txt


title: LMH1-3

description:
MH
MH_all_gene_FPKM.txt


title: Sample_1677


title: FHG3-3

description:
HG
HG_all_gene_FPKM.txt


title: Sample_1671


title: LMH3-1

description:
MH
MH_all_gene_FPKM.txt


title: LMH1-1

description:
MH
MH_all_gene_FPKM.txt


title: FMH3-3

description:
MH
MH_all_gene_FPKM.txt


title: NZ9000 Delta ArgX stat A

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
NZ9000 Delta ArgX stat A
CC29

data_processing:
For the analysis, all reads were mapped on MG1363.  Mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Lactococcus lactis subsp. cremoris MG1363 (firmicutes) | 2007/02/06 | RefSeq assembly accession: GCF_000009425.1 | plus addition of ncRNAs
Supplementary_files_format_and_content: [00.normalized.rpkm.txt] final data of all samples and is used and described in the manuscript
[.rpkm] supplementary files containing the raw counts, raw RPKM and normalized RPKM per sample

organism: Lactococcus cremoris

source_name: Cell culture

growth_protocol: Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: delta ArgX strain were compared to that of the wildtype L. lactis NZ9000 strain

tag: accession

value: NZ9000 ArgX mutant

tag: growth stage

value: Stationary


title: NZ9000 Delta ArgX exp B

description:
NZ9000 Delta ArgX exp B
BB28

tag: strain

value: Exponential


title: NZ9000 Delta ArgX exp A

description:
NZ9000 Delta ArgX exp A
AA27


title: FMH3-2

description:
MH
MH_all_gene_FPKM.txt

tag: tissue


title: FHG1-2

description:
HG
HG_all_gene_FPKM.txt


title: NZ9000 stat B

description:
NZ9000 stat B
Z26

value: NZ9000 wild type


title: FMH1-2

description:
MH
MH_all_gene_FPKM.txt


title: FMH1-3

description:
MH
MH_all_gene_FPKM.txt


title: MG1363 Delta ArgR C

description:
MG1363 Delta ArgR C
H8

value: argR mutant


title: MG1363 Delta CodY A

description:
MG1363 Delta CodY A
E5

value: codY mutant


title: FMH1-1

description:
MH
MH_all_gene_FPKM.txt


title: NZ9000 exp A

description:
NZ9000 exp A
W33


title: MG1363 Delta CcpA A

description:
MG1363 Delta CcpA A
C3

value: ccpA mutant


title: MG1363 B

description:
MG1363 B
B2

value: Wild type


title: FMH3-1

description:
MH
MH_all_gene_FPKM.txt


title: NZ9000 stat A

description:
NZ9000 stat A
Y25


title: MG1363 Delta CcpA C

description:
MG1363 Delta CcpA C
D4


title: MG1363 A

description:
MG1363 A
A1


title: NZ9000 exp B

description:
NZ9000 exp B
X24


title: MG1363 Delta ArgR A

description:
MG1363 Delta ArgR A
G7


title: MG1363 Delta CodY C

description:
MG1363 Delta CodY C
F6


title: NZ9000 Delta ArgX stat B

description:
NZ9000 Delta ArgX stat B
DD30


title: wt xyl3

city: Utrecht

first: Wieke

middle: R

last: Teertstra

address: Padualaan 8

department: Science, Biology

institute: Utrecht University

data_processing:
Illumina Casava pipeline version 1.8.3 was used for base calling
The RNA-Seq pipeline used the TRIMMOMATIC read trimmer version 0.32 (Bolger et al., 2014) to remove low quality regions and the Illumina adapters from the reads
Tophat version 2.1.13 (Trapnell et al., 2009) was used to align sequence reads to the A. niger ATCC 1015 genome assembly
The program Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al., 2010), was used to identify reads mapping to predicted genes and to identify differentially expressed genes.
Genome_build: http://genome.jgi.doe.gov/Aspni7/Aspni7.home.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium

growth_protocol: Conidia of Aspergillus niger strains MA234.1 and ΔmsnB were grown as liquid shaken cultures at 200 rpm and 30 °C in 300 ml Transformation Medium + 1% glucose for 16 hours. Subsequently, the mycelium was transferred to 150 ml Minimal Medium + 25 mM xylose and grown for another 4 hours at 250 rpm and 30 °C.

extract_protocol:
Mycelium was flash-frozen in liquid nitrogen and ground using the TissueLyzer II (Qiagen, Venlo, The Netherlands). RNA was isolated using a standard TRIzol isolation procedure, followed by purification using the Nucleospin® RNA kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: d06900 xyl1

value: {delta}msnB


title: LMH1-2

description:
MH
MH_all_gene_FPKM.txt


title: wt xyl2


title: wt xyl1


title: d06900 xyl2


title: d06900 xyl3


title: E14.5 WT MALE GUT REP2

status: Public on Sep 30 2018

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
Broad Institute’s Picard Pipeline was used for de-multiplexing and data aggregation
The resultant BAM files were sorted and conveted to fastq files for each paierd end using bam2fastq-1.1.0
The files were thenmapped to the mouse genome mm10 index file uisng Tophat2 with the following attributes --library-type fr-unstranded -G (unstranded and pair end)
Successfully mapped reads were used to assemble transcripts and estimate their abundances ((FPKM) using Cufflinks
assembled transcripts  for replicates for each genotype were merged using cuffmerge and differential expression test was done using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Cufflink output file  showing FPKM values for each gene at both genotypes and all replicates

source_name: Gut

extract_protocol:
Guts were dissected out in cold leibovitz medium and RNA was extracted and cleaned using a Trizol Rneasy column hybrid method
cDNA  was prepared  by oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template as part of the Illumina Tru Seq™ RNA Sample Preparation protocol. The resultant cDNA then was used for library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using standard Illumina protocols.

tag: development stage

tag: genotype/variation

value: Wildtype


title: E14.5 WT FEMALE GUT REP3


title: E14.5 WT FEMALE GUT REP1


title: E14.5 WT FEMALE GUT REP2


title: E14.5 WT MALE GUT REP1


title: E14.5 NULL MALE GUT REP3

value: Ret Null


title: E14.5 NULL MALE GUT REP1


title: E14.5 NULL FEMALE GUT REP1


title: E12.5 WT FEMALE GUT REP3


title: E14.5 NULL MALE GUT REP2


title: E14.5 NULL FEMALE GUT REP3


title: E12.5 WT MALE GUT REP2


title: E12.5 NULL MALE GUT REP3


title: E12.5 WT MALE GUT REP3


title: E12.5 NULL MALE GUT REP1


title: E12.5 NULL MALE GUT REP2


title: E12.5 WT MALE GUT REP1


title: E12.5 NULL FEMALE GUT REP3


title: E12.5 WT FEMALE GUT REP1


title: E12.5 WT FEMALE GUT REP2


title: E14.5 WT MALE GUT REP3


title: E10.5 WT MALE GUT REP5


title: E12.5 NULL FEMALE GUT REP2


title: E10.5 WT MALE GUT REP4


title: E10.5 WT FEMALE GUT REP3


title: E10.5 WT FEMALE GUT REP2


title: E10.5 WT MALE GUT REP3


title: E10.5 NULL MALE GUT REP3


title: E10.5 WT FEMALE GUT REP1


title: E10.5 NULL MALE GUT REP1


title: E10.5 NULL FEMALE GUT REP3


title: E14.5 NULL FEMALE GUT REP2


title: E10.5 NULL FEMALE GUT REP1


title: HIP_wt1

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description:
Rett syndrome mouse model
countsHIP_KO1_KO2_wt1_wt2.bed

data_processing:
Illumina Casava1.7 software used for basecalling
Reads were mapped to the mouse reference genome mm9 (NCBI Build 37) using Tophat v1.4.1 with default parameters.
Counts per transcript were obtained using multicov option in bedtools suite, reporting the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a  mm9 BED file
Genome_build: mm9
Supplementary_files_format_and_content: Raw counts per transcript

source_name: Wild-type

growth_protocol: Brain tissues were snap-frozen upon dissection and kept frozen until RNA extraction

extract_protocol:
RNA was extracted using Trizol (Life Technologies) reagent followed by an additional purification step through RNeasy kit (Qiagen)
2ug RNA was prepared for sequencing using the TruSeq RNA Sample Preparation v2 Guide with all kit reagents purchased from Illumina.

tag: zone

value: Hippocampus

value: Brain

value: Wild-type


title: FC_KO1

description:
Rett syndrome mouse model
countsFC_KO1_KO2_wt1_wt2.bed

source_name: MeCP2 knock-out

value: Frontal Cortex

value: MeCP2 knock-out


title: FC_wt1


title: FC_KO2


title: HIP_wt2


title: HIP_KO1


title: HIP_KO2


title: FC_wt2


title: NTM_16

city: Denver

first: Jennifer

last: Honda

state: CO

address: 1400 Jackson St. Neustadt D504

institute: National Jewish Health

description: NTM(+) clinical sample 1

data_processing:
Base calling and adapter trimming was performed with the Torrent Suite (version 5.0.4).
Sequence reads of 80 or more nucleotides were mapped with the STAR aligner (version 2.5.1b) against the human amplicon sequences and additionally against the RefSeq transcript from which the amplicons were designed, as well as similar sequences (to avoid false positive alignments of homologous sequences).
Amplicons with at least 95% sequence identity over a length of 80 nucleotides or more were combined for the analysis, and all reads mapping unambiguously to an amplicon or combination were counted.
Transcripts per million (TPM), a measure for normalizing RNASeq data, were calculated by dividing the counts for each amplicon by the sum of all counts for that sample and multiplying by 1 million.
Genome_build: custom, based on the vendor-supplied hg19_AmpliSeq_Transcriptome_ERCC_v2_04042016.fasta, which contains select RefSeq transcripts
Supplementary_files_format_and_content: tab-delimited text file of raw read counts and transcripts per million (TPM) for each amplicon annotated with RefSeq transcript ID, Entrez gene ID, and gene symbol

source_name: cells from bronchoalveolar lavage

extract_protocol:
Total RNA was extracted from 1-5x106 BAL cells using standard kits from Qiagen (Valencia, CA, USA).
An Ion AmpliSeq Transcriptome Human Gene Expression Kit (Carlsbad, CA, USA) was used on the Ion Chef to target more than 20,000 human RefSeq genes. Library construction started from total RNA, followed by reverse transcription using random priming, target amplification, adaptor ligation, amplification, and bead templating. Once validated, the libraries were sequenced as barcoded-pooled samples on a 540 S5XL chip.

value: cells from bronchoalveolar lavage

tag: infection

value: Mycobacterium intracellulare

value: female

tag: age

tag: race/ethnicity

value: white, non-Hispanic

tag: state

value: Florida


title: Ctrl_22

description: NTM(-) clinical sample 1

value: West Virginia


title: Ctrl_24

description: NTM(-) clinical sample 2

value: Minnesota


title: NTM_20

description: NTM(+) clinical sample 3

value: Michigan


title: Palau 10_1A

city: Pago Pago

first: Ndeme

last: Atibalentja

state: AS

address: 5319 College Road

department: Division of Agriculture, Community, and Natural Resources

institute: American Samoa Community College

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 161 cycles from each end of the fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3.
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina).
Each sample's pair of fastq files were processed by Trimmomatic v0.33 to remove Illumina PE v3 adapters, then to remove bases from both ends with quality below 5, and finally to remove individual reads shorter than 25 bp and their paired read, regardless of length  (parameters "ILLUMINACLIP:TruSeq3‐PE‐2.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:25").
Trimmed paired reads for each sample were aligned to our de novo Niue genome assembly, with genome annotation derived from running MAKER, using STAR v3.5.0a was used in two pass mode.
Fragment counts for each gene were obtained using featureCounts (part of Subread v1.4.6‐p4) "-p -g gene_id -t exon"
Supplementary_files_format_and_content: tab-delimited text files of raw fragment counts per gene per sample

organism: Colocasia esculenta

source_name: Leaf

growth_protocol: Tissue culture plantlets were transferred into potting mix and grown for 8 months in a growth chamber at 27 C, 85% humidity, and 12 h photoperiod

extract_protocol:
Total RNA was extracted, using the CTAB method, from 4 grams of leaf tissues obtained from the youngest two leaves. After extraction, the RNA was applied to GenTegra-RNA tubes and dried in a vacuum desiccator for 40 h before shipping.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit'.

treatment_protocol: In the absence of liquid nitrogen or dry ice, samples were processed immediately after collection.

tag: cultivar

value: Ngerruuch

tag: developmental stage

value: Vegetative

value: 8 months

value: Leaf

tag: location

value: American Samoa

tag: collector

value: Ndeme Atibalentja


title: Sam-07_2A

value: Samasama


title: Sam-07_3A


title: Sam-07_1A


title: Palau 10_2A


title: E10.5 NULL MALE GUT REP2

value: Ret Null


title: Niue_3A

value: Niue


title: Niue_4A


title: E12.5 NULL FEMALE GUT REP1


title: Niue_2A


title: PARE Library from leaves of mock - inoculated plants

status: Public on Sep 28 2018

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

data_processing:
FastX tool kit (http://hannonlab.cshl.edu/fastx_toolkit/) was used for elaboration of row data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.Then converted to FASTA
Fasta files form sRNA datasets mock-inoculated and virus-infected were filtered for 16-26nt long sequences
Fasta files from PARE datasets mock-inoculated and virus-infected were filtered for 20-21nt long sequences
sRNAs and PARE libraries from same plant tissues either from virus-infected or mock-inoculated plants were used as input in the PAREsnp software (http://srna-workbench.cmp.uea.ac.uk) in order to identify miRNA-mediated cleaved transcripts. The output is contained in two different files denoted as outputPARETomatoMock#2.xltx and outputPARETomatoTYLCS#2.xltx
Supplementary_files_format_and_content: tab-delimited text files  for each sample containing the filtered 16-26nt long sRNAs or 20-21nt long 5'-remnants of RNAs.The outputs of PARE analysis is in the XlS format and contain the 5'RNA remnants from sample PARE1 or PARE2 explained by each sRNA from sample sRNA1 or sRNA2, respectively.

organism: Solanum lycopersicum

source_name: mock-inoculated

growth_protocol: Samples were collected from plants grown in greenhouse under controlled conditions of light (16 h light- 8 h dark) and temperature (20-22 °C)

extract_protocol:
Tri-Reagent (Sigma-Aldrich)
TrueSeq sRNA Illumina kit's instructions for sRNAseq and German et al., 2008 (Nature protocol) for PARE libraries

treatment_protocol: Geminiviruses were infected by agroinfiltration following the procedure previously described by Miozzi et al., 2013-Virus research.

value: cv. Money maker

tag: infected with

value: mock-inoculated

value: leaves

tag: molecule subtype

value: 3'-poly-adenylated, RNA 5'-uncapped


title: E10.5 NULL FEMALE GUT REP2


title: PARE Library from leaves of plants infected with Tomato Leaf Curl Sardinia Virus

source_name: Virus-infected

value: Tomato Leaf Curl Sardinia Virus


title: short RNA extracted from leaves of mock - inoculated plants

value: short RNAs


title: Ctrl_26

description: NTM(-) clinical sample 3

value: cells from bronchoalveolar lavage

tag: Sex

value: female

value: white, non-Hispanic

value: Florida


title: NTM_18

description: NTM(+) clinical sample 2

value: Mycobacterium intracellulare


title: Palau 10_3A

value: Ngerruuch

value: Vegetative

value: 8 months

value: Leaf


title: PMA_F1_41

city: Shanghai

first: Gang

middle: Biao

state: Shanghai

address: 2005 Songhu Rd

department: School of life science

institute: Fudan univeristy

data_processing:
The libraries were sequenced as paired-end 100 bases using the HiSeq2000,Illumina Casava1.7 software used for basecalling.
FastQC (v0.10.1) was used to assess the quality of reads.then the raw reads were processed by using the FastX Toolkit v0.0.13.
All processed reads were aligned to reference genome using TopHat v2.0.10 (Kim et al. 2013) and bowtie2 v2.1.0 (Langmead and Salzberg 2012)
The unique mapped reads were assembled and the expression level of a gene were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) using cufflinks v2.1.1 (Trapnell et al. 2010)
Genome_build: KH
Genome_build: Pmarinus7.0
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Petromyzon marinus

source_name: Heart

extract_protocol:
All dissected heart tissues were stored in RNAlater (Ambion) before processing. Total RNA was extracted using the Trizol (Invitrogen). following the manufacturer’s protocol. RNA quality was monitored using Narodrop 2000.
The cDNA libraries were constructed according to the standard Illumina protocols.

value: Heart


title: RB1CC1KO/FIP200KO 3

first: Janneke

last: Peeters

address: Heidelberglaan 100

institute: UMC Utrecht

data_processing:
Reads were aligned to the human reference genome GRCh37 using STAR version 2.4.2a.
Picard’s AddOrReplaceReadGroups (v1.98) was used to add read groups to the BAM files, which were sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1 using the union mode.
Reads per kilobase million reads sequenced (RPKMs) were calculated with edgeR’s RPKM function.
Differentially expressed genes were identified using the DESeq2 package with standard settings. Genes with absolute padj<0.05 were considered as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: txt, containing raw counts of sequencing reads

growth_protocol: Cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% heat-inactivated fetal calf serum (all obtained from Life Technologies) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted from three independent biological replicates using the RNAeasy kit. mRNA was isolated using Poly(A) Beads (NEXTflex)
Libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex) and samples were sequenced 75 bp single-end on Illumina NextSeq500 (Utrecht DNA Sequencing Facility).

treatment_protocol: For amino acid and serum starvation, cells were cultured for 6h in Earle's Balanced Salt Solution (EBSS; Life Technologies).

tag: cell line

tag: genotype

tag: treatment


title: RB1CC1KO/FIP200KO 1 starved

value: 6h EBSS


title: short RNA extracted from leaves of plants infected with Tomato Leaf Curl Sardinia Virus

value: cv. Money maker

tag: tissue


title: CIN_mix_03

organism: Ciona intestinalis


title: RB1CC1KO/FIP200KO 3 starved


title: RB1CC1KO/FIP200KO 2


title: LV87

tag: case

value: non-liver-cancer patient

tag: gender

tag: age (yrs)

value: liver


title: RB1CC1KO/FIP200KO 2 starved


title: ATG7KO 3 starved


title: ATG7KO 2 starved


title: WT 3 starved

value: WT/Parental


title: ATG7KO 1 starved


title: WT 2 starved


title: ATG7KO 1


title: ATG7KO 2


title: WT 1 starved


title: RB1CC1KO/FIP200KO 1


title: Input.

data_processing:
Peaks were called using Cisgenome 2.0 (–e 150 -maxgap 200 –minlen 200).
Peak coordinates were stretched to at least 2000 base pairs and collapsed into a single list. Overlapping peaks were merged based on their outmost coordinates.
Only peaks identified by at least 2 independent datasets were further analyzed.
Peaks with differential H3K27ac, H3K56ac or H3K4me3 occupancy were identified using DESeq (padj<0.05) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Cod file, containing peak coordinates

extract_protocol:
Cells from two independent biological replicates were crosslinked in 1% formaldehyde, 5 mM Hepes-KOH (pH 7.5), 10 mM NaCl, 0.1 mM EDTA, and 50 µM EGTA and after 10 min crosslinking was stopped by adding 0.1 M glycine. Nuclei were isolated in 50 mM Tris (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, and 1% Triton X-100 and lysed in 20 mM Tris (pH 7.5), 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.3% SDS. Lysates were reduspended in 20 mM Tris (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% X-100 and sonicated using Covaris (8 min, maximum output). Sheared DNA was incubated overnight with the indicated antibodies pre-coupled to protein A/G magnetic beads. Cells were washed and crosslinking was reversed by adding 1% SDS, 100 mM NaHCO3, 200 mM NaCl, and 300 mg/ml proteinase K. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research).
Endrepair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified and barcoded libraries were sequenced 75 bp single-end on Illumina NextSeq500 sequencer.

treatment_protocol: For amino acid and serum starvation, cells were cultured for 3h in Earle's Balanced Salt Solution (EBSS; Life Technologies).

tag: chip-antibody


title: WT 3


title: WT 1


title: WT 2


title: POLII starved 1

value: 3h EBSS

value: Mouse anti-RBP1 (PB-7C2; Euromedex)


title: POLII starved 2


title: POLlI 1


title: POLII 2


title: H3K56ac starved 2

value: Rabbit anti-histone H3 acetyl K56 (39281; Active Motif)


title: H3K56ac starved 1


title: H3K56ac 2


title: ATG7KO 3


title: H3K27ac starved 1

value: Rabbit anti-histone H3 acetyl K27 (ab4729; Abcam)


title: H3K56ac 1


title: H3K4me3 1

value: Rabbit anti-histone H3 trimethyl K4 (39159; Active Motif)


title: H3K4me3 starved 1


title: H3K27ac 1


title: DRE_mix_02


title: NT2D1_PRMT6_CT_+RA_rep2

status: Public on Sep 27 2018

city: Marburg

first: Uta

middle: Maria

last: Bauer

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research

institute: Philipps University Marburg

description:
CRISPR/Cas9 control NT2/D1 cells.
Processed data file: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using Tophat2.
Exon counts were aggregated for each gene to build a read count table using SubRead function featureCount.
Counts for each gene were normalized by DESeq2 according to instructions by authors.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt: Tab-delimited text file includes raw counts for each Sample.

source_name: embryonal carcinoma cell line

growth_protocol: NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS.

extract_protocol:
RNA was prepared using RNA-Mini-Kit (Seqlab, Göttingen, Germany).
Library preparation was done with Illumina TruSeq stranded mRNA Kit.

treatment_protocol: 1 µM all-trans retinoic acid (ATRA) for 3 days.

tag: cell type

value: pluripotent embryonal carcinoma cell line

tag: genotype/variation

value: CRISPR/Cas9 control

tag: atra


title: NT2D1_PRMT6_KO-2_+RA_rep2

description:
CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells.
Processed data file: PRMT6_CT_KO+-ATRA_raw_tagcounts.txt

value: CRISPR/Cas9-mediated deletion of PRMT6


title: NT2D1_PRMT6_KO-2_+RA_rep1


title: NT2D1_PRMT6_KO-2_-RA_rep3


title: NT2D1_PRMT6_CT_+RA_rep3


title: NT2D1_PRMT6_KO-2_-RA_rep2


title: NT2D1_PRMT6_CT_-RA_rep2


title: NT2D1_PRMT6_CT_+RA_rep1


title: NT2D1_PRMT6_CT_-RA_rep1


title: NT2D1_PRMT6_KO-2_-RA_rep1


title: NT2D1_PRMT6_CT_-RA_rep3


title: IgG_KO-2_+RA

description: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells.

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2.
Aligned files (bam) were filtered for duplicated aligned reads.
MACS 1.4 was used to perform the peak calling.
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function.
Supplementary_files_format_and_content: *peaks.txt.: Tab-delimited text; Peak files incorporate the number of peaks after filtering for given sample.

extract_protocol:
Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonicated and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies.
Libraries were prepared according to the manufacturer’s protocol (Diagenode, MicroPlex Library Preparation Kit).

tag: chip antibody

value: IgG rabbit (I5006, Sigma)


title: IgG_CT_-RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3R2me2a_KO-2_-RA

value: rat monoclonal generated in the laboratory


title: IgG_CT_+RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3R2me2a_KO-2_+RA


title: H3K4me3 2


title: H3K4me3 starved 2


title: H3K27ac starved 2


title: H3R2me2a_CT_-RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: NT2D1_PRMT6_KO-2_+RA_rep3


title: H3K4me3_KO-2_-RA

value: H3K4me3 (07-473, Merck Millipore)


title: H3R2me2a_CT_+RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3K4me3_CT_+RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3K4me1_KO-2_-RA

value: H3K4me1 (39297, Active Motif)


title: H3K4me3_KO-2_+RA


title: H3K4me1_CT_-RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3K27ac_KO-2_-RA

value: H3K27ac (39133, Active Motif)


title: H3K27ac_KO-2_+RA


title: H3K4me1_KO-2_+RA


title: H3R2me2a_KO-1_-RA


title: H3K27ac_CT_-RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: ESCC 4

city: Shenzhen

first: Rihong

last: Zhai

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

description:
lncRNA, mRNA
SD_C4

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: ESCC, Exosomes

extract_protocol:
Exosomes were isolated from plasma using the Ribo-Exosome-Isolation-Reagent-Kit C10110. Total RNA was isolated from exosome using the Trizol (invitrogen) reagents.
cDNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (ENB, USA). The products were then purified with Agencourt Ampure XP beads (Beckman Coulter, USA) and library quality was assessed using the Agilent 2200 TapeStation system (Agilent Technologies, USA) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair-end flow cell. The clustering of the index-coded samples was performed using the HiSeq Rapid PE Cluster Kit V2 (Illumina). After cluster generation, the libraries were sequenced (2×150 bp) on HiSeq 3000 platform.

tag: disease state

value: ESCC

value: Plasma-derived exosomes


title: ESCC 6

description:
lncRNA, mRNA
SD_C6


title: IgG_KO-1_-RA


title: H3K4me1_CT_+RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: H3K27ac_CT_+RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: ESCC 5

description:
lncRNA, mRNA
SD_C5


title: IgG_KO-2_-RA


title: ESCC 3

description:
lncRNA, mRNA
SD_C3


title: ESCC 2

description:
lncRNA, mRNA
SD_C2


title: ESCC 1

description:
lncRNA, mRNA
SD_C1


title: Esophagitis 6

description:
lncRNA, mRNA
SD_B6

source_name: Esophagitis, Exosomes

value: Esophagitis


title: Esophagitis 5

description:
lncRNA, mRNA
SD_B5


title: Esophagitis 4

description:
lncRNA, mRNA
SD_B4


title: Esophagitis 3

description:
lncRNA, mRNA
SD_B3


title: Esophagitis 2

description:
lncRNA, mRNA
SD_B2


title: Control 6

description:
lncRNA, mRNA
SD_A6

source_name: Control, Exosomes

value: Control


title: Control 5

description:
lncRNA, mRNA
SD_A5


title: H3K4me3_CT_-RA

description: CRISPR/Cas9 control NT2/D1 cells.


title: Esophagitis 1

description:
lncRNA, mRNA
SD_B1


title: Control 3

description:
lncRNA, mRNA
SD_A3


title: Control 2

description:
lncRNA, mRNA
SD_A2


title: Uri_Ex_miRNA

city: Rongchang

first: Jie

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

institute: Southwest University

description: microRNA

data_processing:
Illumina bcl2fastq 2.17 software used for basecalling.All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 21.0. The reads originated from porcine known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 10 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V21.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data

organism: Sus scrofa

source_name: Urine derived exsome

extract_protocol:
Exsome was collected unsing RiboTM Exosome Isolation Reagent, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.In general, approximately 15 ug of small RNA-enriched total RNA was prepared for High-throughput sequencing. In brief, High-throughput sequencing was performed as following successive step: For each library, the small RNA ranged from 14 to 40 nt were purified by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). Then the modified small RNA was reverse transcribed and amplified by RT-PCR. Finally, the enriched cDNA were sequenced on Genome Analyzer II (GAI, Illumina, San Diego, CA, USA) according to manufacturer instructions.

tag: breed

value: Rongchang

tag: age

value: postnatal day 180

value: Urine


title: Pla_Ex_miRNA

description: microRNA

source_name: Plasma derived exsome

value: Plasma


title: KOminus (2 independent samples)

status: Public on Sep 26 2018

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

institute: Universitat Pompeu Fabra

description: Antibodies were described in Lopez-Rodriguez et al., 1999, Proc Natl Acad Sci USA, vol 96: 7214-7219

data_processing:
ChIP-seq reads were aligned to the reference genome using Bowtie aligner version 0.12.7 with the parameter --best and allowing 2 mismatches within the seed alignment
profile were calculated by using bedtools
Genome_build: NCBIM37.57
Supplementary_files_format_and_content: bedgraph profiles

source_name: Unstimulated NFAT5-deficient BMDM

growth_protocol: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days.

extract_protocol:
Formaldehyde crosslinked chromatin was sonicated to fragments DNA to about 200-300 bp, the immunoprecipitated with anti-NFAT5 antibodies. Immunoprecipitated chromatin was purified and sequenced. Chromatin aliquots from the wild-type and NFAT5-deficient BMDMs sample were separated to use as a measure of chromatin input.
Libraries were sequenced using the TrueSeq Kit V5 from Illumina

treatment_protocol: BMDM were immediately processed for ChIP-sequencing in unstimulated conditions (steady state BMDM)

value: BMDM

tag: mouse strain

value: anti-NFAT5 antibodies were a mixture of two rabbit polyclonal antibodies to the amino-terminal or DNA binding domain regions of NFAT5


title: Sem_Ex_miRNA

description: microRNA

source_name: Semen derived exsome

value: Semen


title: WTminus (2 independent samples)

source_name: Unstimulated wild-type BMDM

value: wild type


title: Ser_Ex_miRNA

description: microRNA

source_name: Serum derived exsome

value: Serum


title: BJ_MYO_R2_T72_H02_scRNA-seq

city: Seattle

first: Cole

middle: Bruce

last: Trapnell

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
 Gene expression profiles for each cell were computed using TopHat (v 2.1.1) and Cufflinks (2.2.0) software packages, which were provided with the hg19 genomic reference and GENCODE v17 transcriptome index.
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix in FPKM values (gene level)

growth_protocol: Foreskin Human Fibroblasts obtained from commercial vendor (Stemgent) were expanded in alpha-mem supplemented with glutamax, 10% FBS and 16ng/ul of FGF-b (ThermoFisher Scientific).

extract_protocol:
To perform reprogramming and differentiation experiments HSMM and hFib-MYOD cells were plated in 24-well formats at a density of 50.000 cells per well. Gelatin was sometime used as a coating agent with no significant difference with respect to uncoated dishes. Differentiation and reprogramming was induced using a differentiation media containing alpha-mem supplemented with glutamax and 2% HS (ThermoFisher Scientific), supplemented with 2ug/ml of doxycycline to enact MYOD expression. When indicated, Insulin was used at 8ug/ml (ThermoFisher Scientific), BMP inhibitor LDN-193189 was used at 0.1uM (Stemgent), LSD1 inhibitor RN-1 was used at 1uM (EMD Millipore).
At the indicated time points, cells were harvested by gentle dissociation using TrypLE (ThermoFisher Scientific) and processed for full-length transcriptome sequencing using the Fluidigm C1 Single Cell or bulk mRNA sequencing as previously described ( Trapnell et al., 2014). Cells were loaded onto the microfluidic chip at a concentration of ~250 cells/μl to maximize the number of single cells captured and minimize the occurrence of doublets.  In some instances, cells were reloaded if the majority of capture sites were not occupied on the first attempt. As in Trapnell et al, 2014, captured cells were scored by manual on-chip microscopic inspection to determine if they were singletons and free of other debris.

treatment_protocol: The fibroblasts were then infected with a mixture of lentiviruses encoding hTERT (and Puromycin resistance gene), Tetracycline Repressor (and Geneticin resistance gene) and TR-controlled hMYOD (and Blasticidin resistance gene) (ThermoFisher Scientific). All the resistance genes are constitutively expressed and therefore triple selection was performed and maintained using 1ug/ml of Puromycin, 500ug/ml of Geneticin and 2ug/ml of Blasticidin to generate the hFib-MYOD line.

value: Foreskin Human Fibroblasts

value: hFib-MYOD line

tag: debris

value: FALSE

tag: clump

tag: control

tag: media

value: DM

tag: replicate

tag: time


title: BJ_MYO_R2_T72_H07_scRNA-seq

tag: cell line


title: BJ_MYO_R2_T72_H09_scRNA-seq


title: BJ_MYO_R2_T72_H08_scRNA-seq


title: BJ_MYO_R2_T72_H03_scRNA-seq


title: BJ_MYO_R2_T72_H10_scRNA-seq


title: BJ_MYO_R2_T72_H11_scRNA-seq


title: BJ_MYO_R2_T72_H12_scRNA-seq


title: BJ_MYO_R2_T72_H06_scRNA-seq


title: BJ_MYO_R2_T72_G10_scRNA-seq


title: BJ_MYO_R2_T72_H05_scRNA-seq


title: BJ_MYO_R2_T72_H01_scRNA-seq


title: BJ_MYO_R2_T72_G11_scRNA-seq


title: BJ_MYO_R2_T72_G12_scRNA-seq


title: BJ_MYO_R2_T72_H04_scRNA-seq


title: Bil_Ex_miRNA

description: microRNA

source_name: Bile derived exsome

tag: tissue

value: Bile


title: Control 4

description:
lncRNA, mRNA
SD_A4

value: Plasma-derived exosomes


title: H3K27ac 2

tag: treatment

tag: chip-antibody

value: Rabbit anti-histone H3 acetyl K27 (ab4729; Abcam)


title: Control 1

description:
lncRNA, mRNA
SD_A1

value: Control


title: BJ_MYO_R2_T72_G07_scRNA-seq

tag: cell type


title: BJ_MYO_R2_T72_G06_scRNA-seq


title: BJ_MYO_R2_T72_G03_scRNA-seq


title: BJ_MYO_R2_T72_G02_scRNA-seq


title: BJ_MYO_R2_T72_G05_scRNA-seq


title: BJ_MYO_R2_T72_G08_scRNA-seq


title: BJ_MYO_R2_T72_G01_scRNA-seq


title: BJ_MYO_R2_T72_G04_scRNA-seq


title: BJ_MYO_R2_T72_G09_scRNA-seq


title: BJ_MYO_R2_T72_F12_scRNA-seq


title: BJ_MYO_R2_T72_F07_scRNA-seq


title: BJ_MYO_R2_T72_F08_scRNA-seq


title: BJ_MYO_R2_T72_F09_scRNA-seq


title: BJ_MYO_R2_T72_F06_scRNA-seq


title: BJ_MYO_R2_T72_F05_scRNA-seq


title: BJ_MYO_R2_T72_F10_scRNA-seq


title: BJ_MYO_R2_T72_F04_scRNA-seq


title: BJ_MYO_R2_T72_F02_scRNA-seq


title: BJ_MYO_R2_T72_F01_scRNA-seq


title: BJ_MYO_R2_T72_E12_scRNA-seq


title: BJ_MYO_R2_T72_E10_scRNA-seq


title: BJ_MYO_R2_T72_E09_scRNA-seq


title: BJ_MYO_R2_T72_E11_scRNA-seq


title: BJ_MYO_R2_T72_E07_scRNA-seq


title: BJ_MYO_R2_T72_E08_scRNA-seq


title: BJ_MYO_R2_T72_E03_scRNA-seq


title: BJ_MYO_R2_T72_F11_scRNA-seq


title: BJ_MYO_R2_T72_E02_scRNA-seq


title: BJ_MYO_R2_T72_E06_scRNA-seq


title: BJ_MYO_R2_T72_E01_scRNA-seq


title: BJ_MYO_R2_T72_F03_scRNA-seq


title: BJ_MYO_R2_T72_D12_scRNA-seq


title: BJ_MYO_R2_T72_D11_scRNA-seq


title: BJ_MYO_R2_T72_D08_scRNA-seq


title: BJ_MYO_R2_T72_D06_scRNA-seq


title: BJ_MYO_R2_T72_D09_scRNA-seq


title: BJ_MYO_R2_T72_D05_scRNA-seq


title: BJ_MYO_R2_T72_D03_scRNA-seq


title: BJ_MYO_R2_T72_D04_scRNA-seq


title: BJ_MYO_R2_T72_D10_scRNA-seq


title: BJ_MYO_R2_T72_C11_scRNA-seq


title: BJ_MYO_R2_T72_C09_scRNA-seq


title: BJ_MYO_R2_T72_C10_scRNA-seq


title: BJ_MYO_R2_T72_D02_scRNA-seq


title: BJ_MYO_R2_T72_E04_scRNA-seq


title: BJ_MYO_R2_T72_C06_scRNA-seq


title: BJ_MYO_R2_T72_C08_scRNA-seq


title: BJ_MYO_R2_T72_C03_scRNA-seq


title: BJ_MYO_R2_T72_C05_scRNA-seq


title: BJ_MYO_R2_T72_E05_scRNA-seq


title: BJ_MYO_R2_T72_C12_scRNA-seq


title: BJ_MYO_R2_T72_C07_scRNA-seq


title: BJ_MYO_R2_T72_C04_scRNA-seq


title: BJ_MYO_R2_T72_C02_scRNA-seq


title: BJ_MYO_R2_T72_C01_scRNA-seq


title: BJ_MYO_R2_T72_D07_scRNA-seq


title: BJ_MYO_R2_T72_B11_scRNA-seq


title: BJ_MYO_R2_T72_B12_scRNA-seq


title: BJ_MYO_R2_T72_B10_scRNA-seq


title: BJ_MYO_R2_T72_B09_scRNA-seq


title: BJ_MYO_R2_T72_B08_scRNA-seq


title: BJ_MYO_R2_T72_B07_scRNA-seq


title: BJ_MYO_R2_T72_B06_scRNA-seq


title: BJ_MYO_R2_T72_B04_scRNA-seq


title: BJ_MYO_R2_T72_B01_scRNA-seq


title: BJ_MYO_R2_T72_B02_scRNA-seq


title: BJ_MYO_R2_T72_B03_scRNA-seq


title: BJ_MYO_R2_T72_A12_scRNA-seq


title: BJ_MYO_R2_T72_D01_scRNA-seq


title: BJ_MYO_R2_T72_A08_scRNA-seq


title: BJ_MYO_R2_T72_A11_scRNA-seq


title: BJ_MYO_R2_T72_A09_scRNA-seq


title: BJ_MYO_R2_T72_A07_scRNA-seq


title: BJ_MYO_R2_T72_A10_scRNA-seq


title: BJ_MYO_R2_T72_A06_scRNA-seq


title: BJ_MYO_R2_T72_A03_scRNA-seq


title: BJ_MYO_R2_T72_A04_scRNA-seq


title: BJ_MYO_R2_T72_A05_scRNA-seq


title: BJ_MYO_R2_T48_H09_scRNA-seq


title: BJ_MYO_R2_T48_H07_scRNA-seq


title: BJ_MYO_R2_T72_B05_scRNA-seq


title: BJ_MYO_R2_T48_H05_scRNA-seq


title: BJ_MYO_R2_T48_H04_scRNA-seq


title: BJ_MYO_R2_T72_A01_scRNA-seq


title: BJ_MYO_R2_T48_H12_scRNA-seq


title: BJ_MYO_R2_T48_H11_scRNA-seq


title: BJ_MYO_R2_T72_A02_scRNA-seq


title: BJ_MYO_R2_T48_H03_scRNA-seq


title: BJ_MYO_R2_T48_H10_scRNA-seq


title: BJ_MYO_R2_T48_H02_scRNA-seq


title: BJ_MYO_R2_T48_H08_scRNA-seq


title: BJ_MYO_R2_T48_G12_scRNA-seq


title: BJ_MYO_R2_T48_G11_scRNA-seq


title: BJ_MYO_R2_T48_G07_scRNA-seq


title: BJ_MYO_R2_T48_G08_scRNA-seq


title: BJ_MYO_R2_T48_G10_scRNA-seq


title: BJ_MYO_R2_T48_H06_scRNA-seq


title: BJ_MYO_R2_T48_G06_scRNA-seq


title: BJ_MYO_R2_T48_G05_scRNA-seq


title: BJ_MYO_R2_T48_G03_scRNA-seq


title: BJ_MYO_R2_T48_G01_scRNA-seq


title: BJ_MYO_R2_T48_G04_scRNA-seq


title: BJ_MYO_R2_T48_F11_scRNA-seq


title: BJ_MYO_R2_T48_F12_scRNA-seq


title: BJ_MYO_R2_T48_F10_scRNA-seq


title: BJ_MYO_R2_T48_F09_scRNA-seq


title: BJ_MYO_R2_T48_H01_scRNA-seq


title: BJ_MYO_R2_T48_G09_scRNA-seq


title: BJ_MYO_R2_T48_F08_scRNA-seq


title: BJ_MYO_R2_T48_F07_scRNA-seq


title: BJ_MYO_R2_T48_F05_scRNA-seq


title: BJ_MYO_R2_T48_F02_scRNA-seq


title: BJ_MYO_R2_T48_F04_scRNA-seq


title: BJ_MYO_R2_T48_E11_scRNA-seq


title: BJ_MYO_R2_T48_E08_scRNA-seq


title: BJ_MYO_R2_T48_F01_scRNA-seq


title: BJ_MYO_R2_T48_F03_scRNA-seq


title: BJ_MYO_R2_T48_E09_scRNA-seq


title: BJ_MYO_R2_T48_E05_scRNA-seq


title: BJ_MYO_R2_T48_E07_scRNA-seq


title: BJ_MYO_R2_T48_E04_scRNA-seq


title: BJ_MYO_R2_T48_E06_scRNA-seq


title: BJ_MYO_R2_T48_E03_scRNA-seq


title: BJ_MYO_R2_T48_E02_scRNA-seq


title: BJ_MYO_R2_T48_E01_scRNA-seq


title: BJ_MYO_R2_T48_F06_scRNA-seq


title: BJ_MYO_R2_T48_E12_scRNA-seq


title: BJ_MYO_R2_T48_E10_scRNA-seq


title: BJ_MYO_R2_T48_G02_scRNA-seq


title: BJ_MYO_R2_T48_C09_scRNA-seq


title: BJ_MYO_R2_T48_C10_scRNA-seq


title: BJ_MYO_R2_T48_D06_scRNA-seq


title: BJ_MYO_R2_T48_D12_scRNA-seq


title: BJ_MYO_R2_T48_D03_scRNA-seq


title: BJ_MYO_R2_T48_D08_scRNA-seq


title: BJ_MYO_R2_T48_D09_scRNA-seq


title: BJ_MYO_R2_T48_D04_scRNA-seq


title: BJ_MYO_R2_T48_C12_scRNA-seq


title: BJ_MYO_R2_T48_D01_scRNA-seq


title: BJ_MYO_R2_T48_C11_scRNA-seq


title: BJ_MYO_R2_T48_D10_scRNA-seq


title: BJ_MYO_R2_T48_C08_scRNA-seq


title: BJ_MYO_R2_T48_D07_scRNA-seq


title: BJ_MYO_R2_T48_D02_scRNA-seq


title: BJ_MYO_R2_T48_D05_scRNA-seq


title: BJ_MYO_R2_T48_C07_scRNA-seq


title: BJ_MYO_R2_T48_D11_scRNA-seq


title: BJ_MYO_R2_T48_C05_scRNA-seq


title: BJ_MYO_R2_T48_C06_scRNA-seq


title: BJ_MYO_R2_T48_C01_scRNA-seq


title: BJ_MYO_R2_T48_C02_scRNA-seq


title: BJ_MYO_R2_T48_C03_scRNA-seq


title: BJ_MYO_R2_T48_B11_scRNA-seq


title: BJ_MYO_R2_T48_C04_scRNA-seq


title: BJ_MYO_R2_T48_B02_scRNA-seq


title: BJ_MYO_R2_T48_B08_scRNA-seq


title: BJ_MYO_R2_T48_B07_scRNA-seq


title: BJ_MYO_R2_T48_B05_scRNA-seq


title: BJ_MYO_R2_T48_B04_scRNA-seq


title: BJ_MYO_R2_T48_B01_scRNA-seq


title: BJ_MYO_R2_T48_B10_scRNA-seq


title: BJ_MYO_R2_T48_B03_scRNA-seq


title: BJ_MYO_R2_T48_B12_scRNA-seq


title: BJ_MYO_R2_T48_A08_scRNA-seq


title: BJ_MYO_R2_T48_A03_scRNA-seq


title: BJ_MYO_R2_T48_A11_scRNA-seq


title: BJ_MYO_R2_T48_A09_scRNA-seq


title: BJ_MYO_R2_T48_A07_scRNA-seq


title: BJ_MYO_R2_T48_A05_scRNA-seq


title: BJ_MYO_R2_T48_A12_scRNA-seq


title: BJ_MYO_R2_T48_A04_scRNA-seq


title: BJ_MYO_R2_T48_A06_scRNA-seq


title: BJ_MYO_R2_T48_A01_scRNA-seq


title: BJ_MYO_R2_T24_H12_scRNA-seq


title: BJ_MYO_R2_T24_H09_scRNA-seq


title: BJ_MYO_R2_T24_H07_scRNA-seq


title: BJ_MYO_R2_T24_H10_scRNA-seq


title: BJ_MYO_R2_T24_H11_scRNA-seq


title: BJ_MYO_R2_T48_A02_scRNA-seq


title: BJ_MYO_R2_T48_A10_scRNA-seq


title: BJ_MYO_R2_T24_H08_scRNA-seq


title: BJ_MYO_R2_T48_B06_scRNA-seq


title: BJ_MYO_R2_T48_B09_scRNA-seq


title: BJ_MYO_R2_T24_H05_scRNA-seq


title: BJ_MYO_R2_T24_H06_scRNA-seq


title: BJ_MYO_R2_T24_G09_scRNA-seq


title: BJ_MYO_R2_T24_G10_scRNA-seq


title: BJ_MYO_R2_T24_G12_scRNA-seq


title: BJ_MYO_R2_T24_H03_scRNA-seq


title: BJ_MYO_R2_T24_G11_scRNA-seq


title: BJ_MYO_R2_T24_H04_scRNA-seq


title: BJ_MYO_R2_T24_H02_scRNA-seq


title: BJ_MYO_R2_T24_H01_scRNA-seq


title: BJ_MYO_R2_T24_F10_scRNA-seq


title: BJ_MYO_R2_T24_G06_scRNA-seq


title: BJ_MYO_R2_T24_F11_scRNA-seq


title: BJ_MYO_R2_T24_F12_scRNA-seq


title: BJ_MYO_R2_T24_G05_scRNA-seq


title: BJ_MYO_R2_T24_F09_scRNA-seq


title: BJ_MYO_R2_T24_G07_scRNA-seq


title: BJ_MYO_R2_T24_F07_scRNA-seq


title: BJ_MYO_R2_T24_G01_scRNA-seq


title: BJ_MYO_R2_T24_F08_scRNA-seq


title: BJ_MYO_R2_T24_F05_scRNA-seq


title: BJ_MYO_R2_T24_F03_scRNA-seq


title: BJ_MYO_R2_T24_F04_scRNA-seq


title: BJ_MYO_R2_T24_F02_scRNA-seq


title: BJ_MYO_R2_T24_F01_scRNA-seq


title: BJ_MYO_R2_T24_E11_scRNA-seq


title: BJ_MYO_R2_T24_G08_scRNA-seq


title: BJ_MYO_R2_T24_E12_scRNA-seq


title: BJ_MYO_R2_T24_G04_scRNA-seq


title: BJ_MYO_R2_T24_G02_scRNA-seq


title: BJ_MYO_R2_T24_G03_scRNA-seq


title: BJ_MYO_R2_T24_E08_scRNA-seq


title: BJ_MYO_R2_T24_E09_scRNA-seq


title: BJ_MYO_R2_T24_E10_scRNA-seq


title: BJ_MYO_R2_T24_E05_scRNA-seq


title: BJ_MYO_R2_T24_E07_scRNA-seq


title: BJ_MYO_R2_T24_E03_scRNA-seq


title: BJ_MYO_R2_T24_E06_scRNA-seq


title: BJ_MYO_R2_T24_E01_scRNA-seq


title: BJ_MYO_R2_T24_D11_scRNA-seq


title: BJ_MYO_R2_T24_D12_scRNA-seq


title: BJ_MYO_R2_T24_E02_scRNA-seq


title: BJ_MYO_R2_T24_D10_scRNA-seq


title: BJ_MYO_R2_T24_D09_scRNA-seq


title: BJ_MYO_R2_T24_D05_scRNA-seq


title: BJ_MYO_R2_T24_D06_scRNA-seq


title: BJ_MYO_R2_T24_D08_scRNA-seq


title: BJ_MYO_R2_T24_D04_scRNA-seq


title: BJ_MYO_R2_T24_D01_scRNA-seq


title: BJ_MYO_R2_T24_D02_scRNA-seq


title: BJ_MYO_R2_T24_D03_scRNA-seq


title: BJ_MYO_R2_T24_D07_scRNA-seq


title: BJ_MYO_R2_T24_C12_scRNA-seq


title: BJ_MYO_R2_T24_C11_scRNA-seq


title: BJ_MYO_R2_T24_C10_scRNA-seq


title: BJ_MYO_R2_T24_C08_scRNA-seq


title: BJ_MYO_R2_T24_F06_scRNA-seq


title: BJ_MYO_R2_T24_C09_scRNA-seq


title: BJ_MYO_R2_T24_C04_scRNA-seq


title: BJ_MYO_R2_T24_C06_scRNA-seq


title: BJ_MYO_R2_T24_C02_scRNA-seq


title: BJ_MYO_R2_T24_C01_scRNA-seq


title: BJ_MYO_R2_T24_E04_scRNA-seq


title: BJ_MYO_R2_T24_B10_scRNA-seq


title: BJ_MYO_R2_T24_B12_scRNA-seq


title: BJ_MYO_R2_T24_B09_scRNA-seq


title: BJ_MYO_R2_T24_B08_scRNA-seq


title: BJ_MYO_R2_T24_C07_scRNA-seq


title: BJ_MYO_R2_T24_B06_scRNA-seq