title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D9_AD004_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D9_AD007_indexed

status: Public on Aug 20 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOs

tag: age

tag: strain


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD012_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D9_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D9_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD008_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD006_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD007_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD004_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D7_AD012_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D8_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D7_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D7_AD004_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D7_AD006_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_D7_AD002_indexed


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title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A6_AD006_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A4_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A5_AD007_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD012_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD008_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD006_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD007_indexed


title: P17_OIR_whole_retina_rep2

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description:
Drop-seq data
Sample_OIR-P17_R2
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt

library_source: transcriptomic

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Supplementary_files_format_and_content: NORM and OIR samples were merged and aligned together into a single matrix. log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt: Normalized UMI Count, Digital gene expression matrix. Compressed, flat text file with tab delimiters.

molecule: total RNA

source_name: OIR mouse retina

growth_protocol: Mouse pups were bred until postnatal day 14 or 17 with their biological (NORM) or a foster (OIR) mum.

extract_protocol:
Dissociated cells were processed by single cell RNAseq using the DROPseq technology. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.  Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Illumina NextSeq500 paired-end, at a coverage around 50 000 reads per cells.

treatment_protocol: OIR pups were submitted to Hyperoxia (75% O2) from postnatal day 7 to 12 then returned to normal air while control pups were maintained in normoxic conditions all along.

tag: cell type

value: Whole retina

tag: condition

value: OIR


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD004_indexed


title: WT-2_ATAC-seq

city: Athens

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: Physiology and Pharmacology

institute: University of Georgia

description: wildtype litter mate

data_processing:
Data filtered to leave only reads that are not duplicates, pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis
Genome mapping to the reference genome performed by BAW with default parameters
To analyze fragment density, reads are extended to 200 bp and genome is divided into 32 bp bins and the number of fragments in each bin is determined
Peak calling was performed using DEseq2 algorithm in GUAVA for two sets of parameters in GUAVA:
In standard ATAC-Seq - log2(fold change) >= 2.00, adjusted p value <= 0.001, 5000 bp upstream and 3000 bp downstream of Transcription Start Site - produced the annotated gene excel file
In Integrative Analysis - log2(fold change) >= 1.00, adjusted p value <= 0.05, 5000 bp upstream and 3000 bp downstream of Transcription Start Site - produced the annotated gene excel file
Genome_build: mm10
Supplementary_files_format_and_content: Annotated peak files

source_name: MEF WT rep2

growth_protocol: Primary mouse embryonic fibroblasts were collected from E18 control and Cbx2-/- mouse embryos and cultured for 2 passages under standard conditions before collection of cells and subsequent analysis.

extract_protocol: Assays for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) were used for mapping chromatin accessibility genome-wide by probing DNA accessibility with hyperactive Tn5 transposase and insertion of sequencing adapters into accessible regions of chromatin. Sequencing reads were used to infer regions of increased accessibility.

tag: passage

value: Passage 2

value: embryonic day 18

tag: genotype

value: wild type

tag: tissue

value: mouse embryonic fibroblasts


title: WT-1_ATAC-seq

description: wildtype litter mate

source_name: MEF WT rep1


title: Cbx2-ko-1_ATAC-seq

description: targeted deletion of Chromobox domain protein 2

source_name: MEF Cbx2-KO rep1


title: P17_NORM_whole_retina_rep1

description:
Drop-seq data
Gael_181106_WR_nor_P17_R2_1000ST
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt

source_name: Normoxic mouse retina

value: Normoxia


title: P17_OIR_Rod_depleted_rep1

description:
Drop-seq data
Gael_180830_R5_wt_2400st
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt

value: Rod-depleted retina


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A3_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD012_indexed


title: P17_NORM_Rod_depleted_rep1

description:
Drop-seq data
Gael_181106_CD73FT_nor_P17_R1_2000ST
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: Cbx2-ko-2_ATAC-seq

source_name: MEF Cbx2-KO rep2


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD008_indexed


title: P14_OIR_whole_retina_rep2

description:
Drop-seq data
Gael_170523_R1_2400STAMPS
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: P14_OIR_whole_retina_rep3

description:
Drop-seq data
Gael_170523_R2_2400STAMPS
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: P14_OIR_whole_retina_rep1

description:
Drop-seq data
Gael_20170413_R2_1800STAMPS
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD007_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD004_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD006_indexed


title: P14_OIR_Rod_depleted_rep2

description:
Drop-seq data
Gael-181212-2000_STAMPS_OIR_CD73FT_P14
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A2_AD001_indexed


title: GSC-control

type: RNA

city: Kyoto city

first: Seisuke

last: Tanigawa

state: Kyoto

address: 465 Kajii-cho,Kawaramachi-Hirokoji

department: Neurosurgery

country: Japan

institute: Kyoto prefectural university of medicine

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: murine glioblastoma stem cell line

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The glioblastoma stem cell line was established with the neurosphere method from SB transposon-mediated de novo murine glioblastomas. The tumor tissues were minced with scalpels and digested with accutase at 37℃ for 20-30 min, then washed and incubated with serum free neural stem cell culture medium of Neurobasal Medium with B27 and N2 supplements (Gibco, Grand Island, NY, USA) and 10 ng/ml of EGF and bFGF (Minneapolis, MN, USA). The neurospheres were dissociated with accutase (Innovative Cell Technologies, San Diego, CA, USA) and maintained with the neural stem cell culture medium at 37 ºC in 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells lysed with Trizol (Thermo Fisher Scientific, Waltham, MA) and purified with the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Stably Gli2-knockdown glioblastoma stem cells were established via lentiviral-mediated shRNA. The cells were transducted with lentiviral non-target (control) or Gli2 shRNA.

value: glioblastoma stem cell line

tag: shRNA

value: non-target control


title: P14_OIR_Rod_depleted_rep1

description:
Drop-seq data
Gael_181114_R2_CD73FT_P14_OIR_2000ST
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: P14_NORM_whole_retina_rep1

description:
Drop-seq data
Gael_20170413_R1_2800STAMPS
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: P14_NORM_Rod_depleted_rep1

description:
Drop-seq data
Gael-181212-2000_STAMPS_NORM_CD73FT_P14
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD007_indexed


title: GSC-Gli2-knockdown


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD006_indexed


title: RNA-Pool-9

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

data_processing:
RNA-seq reads in fastq files were aligned to mm10 using Subread aligner
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCm38 gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: Podocytes

growth_protocol: To elucidate the transcriptomic differences between young and aged podocytes, inducible NPHS2-rtTA|tetO-cre|tdTomato mice were generated. The podocin-tetracycline-controlled transactivator protein (rtTA) mice, generously provided by Dr. Jeffrey Kopp (National Institutes of Health, Bethesda, MD), and previously described by Shigehara et al., were crossed with commercially available tetO-cre mice (Stock#: 006234) and tdTomato (Stock #: 007914) mice from The Jackson Laboratory (Bar Harbor, ME). Triple transgenic mice of both sexes were identified by genotyping for the presence of each transgene.  To achieve specific and permanent labeling of podocytes, three-week old animals received doxycycline hydrochloride via feed, at 625 mg/kg, for 21 days ad libitum (HarlanTD.01306). Medicated feed was changed weekly, and at the end of the labeling period, animals were returned to their standard diet, then randomized into a young cohort (defined as mice sacrificed at 3-4 months of age, n = 15 females, 11 males) or an aged cohort (defined as mice sacrificed at 22-23 months of age, n = 5 females, 3 males).  Control animals included those lacking the NPHS2-rtTA transgene and triple-transgenic animals not provided doxycycline chow.  Mice were housed in the animal care facility of the University of Washington under specific pathogen-free conditions with ad libitum access to food and water. Animal protocols were approved (2968-04) by the University of Washington Institutional Animal Care and Use Committee.. Mice were sacrificed at the ages described above by cervical dislocation.

extract_protocol:
The purification of total and RNA was performed using the miRNeasy micro kit (Qiagen, Germantown, MD).  Flow sorted cells were homogenized with the addition of 700 ul of QIAzol Lysis Reagent. After addition of chloroform, the homogenate was separated into aqueous and organic phases by centrifugation.  The upper, aqueous phase was extracted.  On-column DNAse digestion was also performed to remove any residual genomic DNA contamination followed by additional washes.  High quality RNA was then eluted in 18 ul of RNase-free water.  Quantitative assessment of the purified total RNA was accomplished by using a Qubit Broad Range RNA kit (Thermo Fisher, Waltham, MA).  The RNA was further evaluated qualitatively by a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Sequencing libraries were prepared using the TrueSeq Stranded mRNA Kits (Illumina Inc., San Diego, CA) according to the manufacturer’s instructions. Sequencing was performed using NextSeq 500/550 v2.5 sequencing reagent kits and The NextSeq 550Dx instrument (Illumina Inc.)
Paired-end RNA-Seq

treatment_protocol: The kidney capsule and surrounding fat were dissected away and the kidney tissue was placed into ice cold RPMI 1640 medium, without L-glutamine or phenol red (GE Healthcare Bio-Sciences, Pittsburgh, PA). Kidney medulla was dissected away and the remaining kidney cortex was minced into fine pieces. Kidney cortex was digested in 0.2mg/ml Liberase™ TL (Sigma-Aldrich, St. Louis, MO), 100 U/ml DNAse I (Sigma-Aldrich, St. Louis, MO) in RPMI 1640 medium, without L-glutamine or phenol red by shaking in a 37oC water bath for 30 minutes. The digest was passed through an 18G needle (Becton Dickenson, Franklin Lakes, NJ) 10 times to further dissociate the tissue. The enzymes were inactivated by combining the digest with 5ml of in media consisting of RPMI 1640 medium, without L-glutamine or phenol red (GE Healthcare Bio-Sciences, Pittsburgh, PA) supplemented with 1mM sodium pyruvate (ThermoFisher Scientific, Waltham, MA), 9% Nu-Serum™ IV Growth Medium Supplement (Corning Incorporated - Life Sciences, Durham, NC) and 100U/ml Penicillin-Streptomycin (ThermoFisher Scientific, Waltham, MA). The suspension was passed through a 100µm, then a 40 µm cell strainer (BD Biosciences, San Jose, CA), to clear debris, then pelleted by centrifugation at 200G at 4oC for 5 minutes. The cells were re-suspended in the media described above, counted and isolated using multi-color fluorescence-activated cell sorting (FACS) on a BD FACS Aria II (BD Biosciences, San Jose, CA) housed within a BSL1/2 approved biosafety cabinet. Sorted cells were pelleted by centrifugation and snap frozen and stored at -80oC until RNA isolation. The entire isolation procedure took 6-7 hours per animal. Samples were then shipped on dry ice to Roswell Park Cancer Institute for further processing.

tag: Sex

value: Female

value: Young


title: RNA-Pool-14

value: Male


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD002_indexed


title: RNA-Pool-13


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD004_indexed


title: RNA-Pool-12


title: RNA-Pool-10


title: RNA-8

value: Aged


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A12_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A12_AD007_indexed


title: RNA-6


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A12_AD004_indexed


title: RNA-5


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A1_AD008_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD001_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A12_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD010_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD008_indexed


title: RNA-Pool-11


title: P17_OIR_whole_retina_rep1

description:
Drop-seq data
Sample_OIR-P17_R1
processed data file: retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD007_indexed


title: RNA-1


title: RNA-3


title: RNA-16


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD008_indexed


title: RNA-4


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A12_AD001_indexed


title: RNA-7


title: RNA-15


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD007_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A4_AD002_indexed


title: 7_h4E-BP1_hyper_+PP242

city: Beijing

first: Hua

last: Jin

state: Choose a State or Province

address: Rm 225-1, Bldg Qiushilou, Beijing Institute of Technology,

country: China

institute: Beijing Institute of Technology

description: TRIBE, RNA-seq

data_processing:
Library strategy: TRIBE
Trimmomatic-0.30/trimmomatic-0.30.jar SE -phred33 CROP:70 HEADCROP:6 LEADING:25 TRAILING:25 AVGQUAL:$avgquality MINLEN:19
Genome_build: Drosophila dm3 (BDGP Release 5); Human hg38 (GRCh38)
Supplementary_files_format_and_content: *.threshold.txt: Edited sites
Supplementary_files_format_and_content: *bw: bigWig files

organism: Homo sapiens

source_name: human prostate cancer cell PC3

growth_protocol: S2 cells were grown in Hyclone SFX-insect media with 10% of FBS. PC3 cells were grown in F-12K Medium (ATCC) with 10% of FBS.

extract_protocol:
GFP-positive cells were sorted and collected with a BD FACSAria II machine. Total RNA was extracted with TRIzol LS reagent.
TRIBE: Standard Illumina TruSeq RNA Library Kit.

tag: cell line

tag: transfected plasmids

tag: treatment

value: 2.5 μM of PP242 for 5 hrs


title: 5_h4E-BP1_hyper_+INK128_replicate1

description: TRIBE, RNA-seq

value: 200 nM of INK-128 for 5 hrs


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD006_indexed

value: MOs


title: 6_h4E-BP1_hyper_+INK128_replicate2

description: TRIBE, RNA-seq


title: 4_h4E-BP1_hyper_replicate2.

description: TRIBE, RNA-seq

value: DMSO for 5 hrs


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD006_indexed


title: 3_h4E-BP1_hyper_replicate1

description: TRIBE, RNA-seq


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD004_indexed


title: 2_Hyper_only_replicate2

description: TRIBE, RNA-seq

value: pAAV-CMV-eGFP3 and pCMV-hADAR2cd-E488Q


title: 1_Hyper_only_replicate1

description: TRIBE, RNA-seq


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD010_indexed


title: RNA-2


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD002_indexed


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD004_indexed


title: DEC.70818

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

address: 8700 Beverly Blvd

department: OB/GYN, Div REI

institute: Cedars Sinai Medical Center

description:
6
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx

data_processing:
Libraries were pooled at a 4 nM concentration and an average of 19.01 million 2 × 75 bp paired-end reads per sample were generated with Illumina NextSeq 500 using High Output 150-cycle flow cells. Reads were aligned to the human reference genome (build GRCh38 with Ensembl release version 82) using STAR. The DESeq2 Bioconductor package was used in the R statistical computing environment (http://www.R-project.org/) to normalize count data, estimate dispersion, and fit a negative binomial model for each gene. P-values were adjusted for multiple comparisons using the Benjamini-Hochberg False Discovery Rate procedure to generate FDR values. To describe tissue expression, we utilized both the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) value and a Z-score describing the position of a gene’s FPKM value compared to all other genes in a sample. The Z-score for a gene equals the number of standard deviations away from the mean FPKM of all genes (in a sample), such that a gene with Z-score of zero (0) has an FPKM equal to the mean FPKM of all genes (in that sample), and genes with a positive Z-score have an FPKM above the mean (in that sample). To determine which genes were expressed in each tissue type, we applied thresholds of mean FPKM>1 and mean Z-score>0 (n=4 per tissue). Consequently, “expressed genes” describes genes which are consistently expressed in decidua or placental tissue. Our criteria for defining differentially expressed genes (DEGs) is FDR<0.10, FPKM>1, and Z-score>0. This is similar to zFPKM method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized_counts_expression_matrix.xlsx: Excel table includes normalized count expression matrix.
Supplementary_files_format_and_content: Normalized_FPKM_expression_matrix.xlsx: Excel table includes FPKM.
Supplementary_files_format_and_content: bulkRNA_DE_expression_table.xlsx: Excel table contains all of DE analysis results and expression in count and FPKM.

source_name: decidua

extract_protocol:
Tissue samples (5-15 mg) were stored with 250 μl RNAlater RNA Stabilization Reagent (QIAGEN, Hilden, Germany) at -80°C in the CSMC Prenatal Repository until further processing. Briefly, tissue was thawed on ice with 600 μl of RLT Plus lysis buffer (QIAGEN) and 1% β-mercaptoethanol added to each sample. Tissue was homogenized by passing through increasingly thinner single-use needles (22G, 25G, 27G) attached to a 1 mL sterile, RNase-free syringe. The homogenates were loaded onto AllPrep spin columns and the remainder of the protocol was performed following manufacturer instructions for the AllPrep DNA/RNA Mini Kit (QIAGEN). The RNA elution was used for total RNA-sequencing.
RNA-seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT with Ribo-zero kits (Illumina, San Diego).

value: Primary decidua tissue

tag: developmental stage

value: First trimester

tag: fetal sex


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A10_AD001_indexed


title: DEC.70792

description:
5
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx


title: DEC.70821

description:
8
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx


title: SL5_HS_mRNA

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description: mRNA-seq processed data

data_processing:
sRNA-Seq: Small RNA sequencing analysis was performed using the in-house ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

organism: Triticum turgidum subsp. durum

source_name: Flag leaf tissue

growth_protocol: Stress-tolerant genotype DBA Aurora and stress-sensitive genotype L6 (University of Adelaide breeding line, UAD1301020-8) were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). Briefly, the standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

extract_protocol:
Total RNA was extracted from a total of 120 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates) using the Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific). RNA concentration, quality and integrity was assessed by NanoDrop, gel electrophoresis and Bioanalyzer.
The 120 sRNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Kit. Eight transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit. For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.

treatment_protocol: Four treatment groups were: control group (CG), pre-anthesis water-deficit stress group (WS), post-anthesis heat stress group (HS) and water-deficit plus heat stress group (WH). All plants were well-watered from germination to booting. Water-deficit stress was applied to WS and WH by maintaining the soil water content at 6% (half of the field capacity) from booting until harvest (Liu et al., 2019). Heat stress was applied by placing plants in a growth chamber at 37°C/27°C with a 12h photoperiod. HS and WH plants were treated with heat for 24h at multiple reproductive time-points consecutively [5, 15, 25, 35, and 45 days post anthesis (DPA)] (Liu et al., 2019). After 24h, plants were moved back to the standard conditions and remained there between each treatment time-point. Flag leaf samples were collected at each DPA.

value: L6 (Stres-sensitive)

tag: treatment group

value: Heat stress (HS)

tag: time-point (dpa, days post anthesis)


title: DEC.70819

description:
7
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx


title: SL5_CG_mRNA

description: mRNA-seq processed data

value: Control group (CG)


title: Cmlc2OE_02

city: Shanghai

first: Tao

middle: Peter

last: Zhong

state: China

address: No.2005, Songhu Road

department: School of Life Sciences

institute: Fudan University

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data. Than, the data were aligned to zebrafish transcriptome (Ensembl genebuild GRCz10.86)  via software Hisat2 (v2.0.1). Gene expression qualified using HISeq (v0.6.1). Differential expression was called using DESeq.
Genome_build: GRCz10.86
Supplementary_files_format_and_content: all.fpkm_anno

organism: Danio rerio

source_name: ventricular apex of 8 hearts

growth_protocol: Adult zebrafish density was mantained at 5 fish per liter.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Constructed libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: Adult zebrafish were incubated daily with doxycycline from the day before heart injury, and tissue collected at 7 days post amputation.

value: Adult

value: AB

tag: time point

value: 7 days post amputation

tag: group

value: heart


title: Cmlc2OE_03

tag: strain


title: TL5_WS_mRNA

description: mRNA-seq processed data

value: DBA Aurora (Stress-tolerant)

value: Water-deficit plus heat stress (WH)


title: CVS.70818

description:
2
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx

source_name: chorionic villi

value: Primary placental tissue

value: Female


title: CVS.70792

description:
1
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx


title: 180322_CEMBA_mm_P56_P63_1A_CEMBA180226_1A_1_CEMBA180226_1A_2_A11_AD012_indexed

tag: brain region

tag: age


title: Cmlc2OE_01

source_name: ventricular apex of 6 hearts


title: MIA-PaCa-2_Untreated_rep6_J19638

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

description: Quant-seq

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was perform using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 script version 2.20.0 provided by Illumina.
Single-end sequencing reads from grafted samples were filtered into human and mouse reads using Disambiguate (v1.0.0). The filtered reads were then processed with a pipeline building upon upon the implementation of the ENCODE "Long RNA-seq" pipeline: Reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files contain sample-wise results procuded by FeaturesCounts and include raw count values for each gene.

source_name: MIA PaCa-2

growth_protocol: The cell lines were cultured with the media DMEM with 10% FCS at 37 degree Celsius incubators with 5% CO2.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Instead of chloroform, 10% volume 1-bromo-2-chloropropane (SigmaAldrich, # B9673) was added. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (# 015.96) according to manufacturer's instructions.

treatment_protocol: Not available

value: cell-line derived xenograft

tag: cell line used for xenograft

value: MIA PaCa-2

tag: cell type used for xenograft

value: pancreas carcinoma

value: Untreated

value: 0 h

tag: replicate


title: MIA-PaCa-2_Untreated_rep5_J19549

description: Quant-seq

tag: tissue


title: Ctrl_02

value: control


title: TL5_HS_mRNA

description: mRNA-seq processed data

tag: genotype


title: Ctrl_03


title: MIA-PaCa-2_Untreated_rep3_J19726

description: Quant-seq


title: MIA-PaCa-2_Untreated_rep2_J19639

description: Quant-seq


title: Ctrl_01


title: MIA-PaCa-2_Natrosol_4h_rep5_J19546

description: Quant-seq

treatment_protocol: Animals were treated p.o. with BI00923406 (qd)

value: Natrosol

value: 4 hr


title: TL5_CG_mRNA

description: mRNA-seq processed data

value: Control group (CG)


title: MIA-PaCa-2_Natrosol_4h_rep4_J19547

description: Quant-seq


title: CVS.70821

description:
4
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx

value: First trimester

value: Male


title: CVS.70819

description:
3
processed data file: Normalized_counts_expression_matrix.xlsx
processed data file: Normalized_FPKM_expression_matrix.xlsx
processed data file: bulkRNA_DE_expression_table.xlsx


title: MIA-PaCa-2_Natrosol_4h_rep3_J19725

description: Quant-seq


title: MIA-PaCa-2_Natrosol_4h_rep1_J19548

description: Quant-seq


title: MIA-PaCa-2_Natrosol_24h_rep5_J19540

description: Quant-seq

treatment_protocol: Animals were treated p.o. with Natrosol (bid, delta 6h)


title: sRNA -SL45_WH - Rep2

description:
DL119
sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)


title: sRNA -SL45_WH - Rep1

description:
DL118
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_Natrosol_24h_rep4_J19541

description: Quant-seq


title: TL5_WH_mRNA

description: mRNA-seq processed data

value: Water-deficit stress (WS)


title: MIA-PaCa-2_Untreated_rep4_J19550

description: Quant-seq


title: sRNA -SL45_HS - Rep2

description:
DL116
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: sRNA -SL45_HS - Rep3

description:
DL117
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_Natrosol_24h_rep1_J19542

description: Quant-seq


title: MIA-PaCa-2_Natrosol_24h_rep2_J19635

description: Quant-seq


title: MIA-PaCa-2_Natrosol_10h_rep5_J19543

description: Quant-seq


title: MIA-PaCa-2_Natrosol_24h_rep3_J19723

description: Quant-seq


title: sRNA -SL45_WS - Rep3

description:
DL114
sRNA-seq processed data.xlsx


title: sRNA -SL45_HS - Rep1

description:
DL115
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_Natrosol_10h_rep1_J19545

description: Quant-seq


title: MIA-PaCa-2_Natrosol_10h_rep3_J19724

description: Quant-seq


title: MIA-PaCa-2_Natrosol_10h_rep4_J19544

description: Quant-seq


title: sRNA -SL45_WH - Rep3

description:
DL120
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: SL5_WSdgd

description: degradome-seq processed data

data_processing:
Library strategy: degradome-seq
sRNA-Seq: Small RNA sequencing analysis was performed using the in-house ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)


title: MIA-PaCa-2_Natrosol_4h_rep2_J19637

description: Quant-seq


title: MIA-PaCa-2_BI00923406_50mgkg_4h_rep5_J19633

description: Quant-seq

value: 4 h


title: AsiDNA-treated, 3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: gene expression data from cells treated with AsiDNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

source_name: MDA-MB-231 cells AsiDNA-treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Cells were treated or not with AsiDNA during 6 total weeks before RNA extraction.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Cells were harvested and washed with PBS before RNA extraction from cell pellets.

value: breast cancer tumor cells


title: sRNA -SL45_WS - Rep2

description:
DL113
sRNA-seq processed data.xlsx


title: AsiDNA-treated, 2


title: Not treated, 3

description: gene expression data from MDA-MB-231 cells not treated

source_name: MDA-MB-231 cells not treated


title: Not treated, 2


title: SL5_WHdgd

description: degradome-seq processed data


title: MIA-PaCa-2_BI00923406_50mgkg_24h_rep5_J19627

description: Quant-seq

treatment_protocol: Animals were treated p.o. with BI00923406 (bid, delta 6h)

value: cell-line derived xenograft


title: AsiDNA-treated, 1


title: sRNA -SL45_WS - Rep1

description:
DL112
sRNA-seq processed data.xlsx


title: Not treated, 1


title: MIA-PaCa-2_BI00923406_50mgkg_24h_rep4_J19628

description: Quant-seq

value: MIA PaCa-2


title: MIA-PaCa-2_Natrosol_10h_rep2_J19636

description: Quant-seq

value: pancreas carcinoma


title: MIA-PaCa-2_BI00923406_50mgkg_24h_rep3_J19727

description: Quant-seq


title: SL5_CGdgd

description: degradome-seq processed data


title: SL5_HSdgd

description: degradome-seq processed data


title: sRNA -SL45_CG - Rep3

description:
DL111
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_BI00923406_50mgkg_24h_rep2_J19629

description: Quant-seq


title: MIA-PaCa-2_BI00923406_50mgkg_24h_rep1_J19536

description: Quant-seq


title: TL5_WSdgd

description: degradome-seq processed data

value: DBA Aurora (Stress-tolerant)


title: sRNA -SL45_CG - Rep1

description:
DL109
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_BI00923406_50mgkg_10h_rep5_J19630

description: Quant-seq


title: MIA-PaCa-2_BI00923406_50mgkg_10h_rep4_J19631

description: Quant-seq


title: sRNA -SL35_WH - Rep3

description:
DL108
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_BI00923406_50mgkg_10h_rep1_J19537

description: Quant-seq


title: MIA-PaCa-2_BI00923406_50mgkg_4h_rep3_J19722

description: Quant-seq


title: sRNA -SL35_WH - Rep2

description:
DL107
sRNA-seq processed data.xlsx


title: MIA-PaCa-2_BI00923406_50mgkg_10h_rep3_J19721

description: Quant-seq


title: TL5_HSdgd

description: degradome-seq processed data


title: TL5_CGdgd

description: degradome-seq processed data


title: MIA-PaCa-2_BI00923406_50mgkg_4h_rep2_J19634

description: Quant-seq


title: Dis3 P4 KO4

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: featurecounts output  and fastq files

source_name: P4 Testis

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Testes isolated from P4 aged control and knockout mice.

extract_protocol:
Testess were isolated, total RNA was isolated using a RNeasy Micro Kit.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

value: B6D2F1 inbred

value: Testis

value: Dis3 KO

value: postnatal day 4 (P4)


title: TL5_WHdgd

description: degradome-seq processed data


title: sRNA -SL35_WH - Rep1

description:
DL106
sRNA-seq processed data.xlsx


title: Dis3 P4 KO5


title: Dis3 P4 KO2


title: sRNA -SL35_HS - Rep3

description:
DL105
sRNA-seq processed data.xlsx


title: sRNA -SL45_CG - Rep2

description:
DL110
sRNA-seq processed data.xlsx

value: Control group (CG)


title: Dis3 P4 WT5

value: Dis3 WT


title: Dis3 P4 WT3


title: Dis3 P4 KO3


title: Dis3 P4 WT4


title: sRNA -SL35_HS - Rep2

description:
DL104
sRNA-seq processed data.xlsx


title: Dis3 P4 WT2


title: Dis3 P4 KO1


title: sRNA -SL35_HS - Rep1

description:
DL103
sRNA-seq processed data.xlsx


title: Dis3 P4 WT1


title: prg-1_ergo-1_mRNA_1

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Bioinformatic analysis. Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2(Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts. Reads per million were plotted along the WS258 genome using Integrative Genomics Viewer 2.3.68(Robinson et al., 2011). Gene ontology analysis was performed using the Enrichment Analysis Tool on WormBase(Angeles-Albores, RY, Chan, & Sternberg, 2016). Gene enrichment analysis was performed using reference gene lists from WormExp(Yang et al., 2016).
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to each gene

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1s of ergo-1(tm1860) and prg-1(n4357) worms were plated on enriched peptone plates and cultured at 20°C.

extract_protocol:
8,000 animals per sample were harvested as adults (~64hrs at 20°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
mRNA-seq library preparation. Nuclease-free H2O was added to 7.5μg of each RNA sample, extracted from whole animals, to a final volume of 100μL. Samples were incubated at 65°C for 2 minutes then incubated on ice. The Dynabeads mRNA Purification Kit (ThermoFisher 61006) was used according to the manufacturer’s protocol. 20μL of Dynabeads was used for each sample. 100ng of each mRNA sample was used to prepare libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) according to the manual, using NEBNext multiplex oligos for Illumina (NEB E7335S). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q33231). Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.Small RNA library preparation. Small RNAs (18- to 30- nt) were size selected on denaturing 15% polyacrylamide gels (Criterion 3450091) from total RNA samples. Libraries were prepared as previously described(Montgomery et al., 2012). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

tag: Stage

value: Day 1 Adult

tag: molecule subtype

value: mRNA selected from total RNA


title: prg-1_ergo-1_mRNA_2


title: sRNA -SL35_WS - Rep3

description:
DL102
sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)

value: Water-deficit stress (WS)


title: sRNA -SL35_WS - Rep2

description:
DL101
sRNA-seq processed data.xlsx


title: 4C_PESix3VP_del36

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
library strategy: 4C-seq
Reads were assigned to samples based on the first 10 bases of the read. Subsequently, the primer sequence was removed from the read and the remaining sequence starting before the restriction site for NlaIII (CATG) was trimmed to 41 bases. These 41 bases were aligned to the mouse reference genome (mm10) using HISAT2 (Kim et al., 2015). From these alignments, RPM (reads per million) normalized bedgraph files were generated for downstream visualization and analysis (Thongjuea et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: rpm normalized bed/bedGraph

source_name: mouse embryonic stem cells

growth_protocol: mESC (E14) were cultured on gelatine-coated plates using Knock-out DMEM (KO-DMEM, Life Technologies) supplemented with 15% FBS (Life Technologies) and LIF. For the diffentiation into AntNPC, these mESC lines were plated at a density of 12.000 cells/cm2 on gelatin-coated plates and grown for three days in N2B27 medium supplemented with 10 ng/ml bFGF (Life Technologies) and without serum or LIF. N2B27 medium contains: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies) and Neurobasal medium (Life Technologies) (1:1), supplemented with 1x N2 (Life Technologies), 1x B27 (Life Technologies), 2 mM L-glutamine (Life Technologies), 40 mg/ml BSA (Life Technologies), 0.1 mM 2-mercaptoethanol (Life Technologies)). Subsequently, cells were grown for another two days in N2B27 medium without bFgf (D3–D5). To improve the homogeneity of the differentiation, from D2-D5 the N2B27 medium was also supplemented with 5 mM Xav939, a potent WNT inhibitor.

extract_protocol:
Circular Chromatin Conformation Capture (4C) followed by sequencing were performed as previously described (Cruz-molina et al., 2017). Briefly, cells grown to confluence in 10 cm dishes were crosslinked with 1% formaldehyde for 10 min, quenched with 0.125 M glycine, washed with PBS and incubated in lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and 1x protease inhibitor) on ice for 10 min. Nuclei were then re-suspended in 0.5 mL 1.2x CutSMART buffer (NEB) with 0.3% SDS and incubated at 37°C with constant shaking for 1h. Then, Triton X-100 was added to a final concentration of 2%, followed by 1h incubation at 37°C with constant shaking. Next, 600 U of NlaIII (NEB) were added to digest chromatin overnight at 37°C with constant shaking (900 rpm). NlaIII was inactivated by adding SDS to a final concentration of 1.6% and incubating the mixture for 20 min at 65°C. The digested chromatin was transferred to 50 mL tubes and 1x ligation buffer (50 mM Tris-HCl pH 7.6, 10 mM MgCl2, 1 mM ATP, 1mM DTT) was added up to a final volume of 7 ml. Triton X-100 was added to a final concentration of 1% and the solution was incubated for 1h at 37°C and 300 rpm. Afterwards, the digested chromatin was ligated using 100 U of T4 DNA ligase (Life Technologies) for 4 hours at 16°C, followed by RNase A treatment (300 μg total, Peqlab) for 45 min at 37°C. Subsequently, chromatin was de-crosslinked by treating with Proteinase K (300 μg total, Peqlab) and incubating at 65°C overnight. DNA was purified by phenol/chloroform extraction followed by ethanol precipitation and re-suspended in 100 μL of water. The purified DNA was digested with 50 U of DpnII (NEB) in 500 μL of 1x NEBuffer at 37°C overnight. DNA samples were again purified (phenol/chloroform extraction and ethanol precipitation), re-suspended in 500 μL of water and ligated with 200 U of T4 DNA Ligase in a final volume of 14 mL 1x ligation buffer overnight at 16°C. DNA samples were subjected to another round of phenol/chloroform extraction and ethanol precipitation, re-suspended in 150 μL of water and purified by QIAquick PCR Purification Kit (QIAGEN).
4C samples were amplified by inverse PCR using specific primers for each viewpoint. The primer included illumina adaptor sequences and short barcodes. The inverse PCRs were performed with the expand long template PCR system and 30 amplification cycles (94°C 2 min, 30x [94°C 10 sec, 60°C 1 min, 68°C 3 min], 68°C 5 min). The inverse PCR primers were designed as previously described (Stadhouders et al., 2013). Once amplified, 4C-seq libraries were sequenced on the HiSeq2500.

tag: cell line

tag: cell type

value: 2i+LIF ESC

tag: genotype/variation

value: deletion of TAD boundary between Six3 and Six2


title: prg-1_hrde-1_mRNA_3


title: prg-1_hrde-1_mRNA_2


title: prg-1_hrde-1_mRNA_1


title: 4C_Six2promVP_WT

value: wild type


title: 4C_PESix3VP_WT


title: 4C_Six2promVP_del36


title: 4C_Gria1-insVP_TFBS+CGI_ESC

value: Knock-in in Gria1 TAD


title: sRNA -SL35_WS - Rep1

description:
DL100
sRNA-seq processed data.xlsx

tag: treatment group


title: prg-1_ergo-1_mRNA_3


title: 4C_Gria1-insVP_CGI_ESC


title: sosi-1_eri-6[e-f]_mut-16_mRNA_3


title: sRNA -SL35_CG - Rep3

description:
DL99
sRNA-seq processed data.xlsx

tag: time-point (dpa, days post anthesis)


title: HNhx/mAB-PN9cx3_rep3

city: Yangling

first: Yuchen

state: Shaanxi

address: No.22 XinongLu

institute: Northwest A&F University

description: piglets infected with PRRSV-HNhx with treatment of Mab-PN9cx3

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 1, fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples.

organism: Sus scrofa

source_name: porcine alveolar macrophages

extract_protocol:
Bronchoalveolar lavage fluid (BALF) from piglets experimental infected by PRRSV with or without mAB treatment was collected by lung lavation with sterilized PBS.PAMs from BALF were harvested by centrifugation at 300 g for 10 min and viability of PAMs was evaluated by stained cells with trypan blue. Totally 1× 107 viable PAMs were harvested using 1 mL TRizol Reagent
For RNA-seq, mRNA was purified and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit (non-strand specific).

treatment_protocol: The 4-week-old piglets  were divided into seven groups,  Among these seven groups, two groups received a HP-PRRSV-JXA1 or NADC30-like HNhx challenge, two groups were Mab-PN9cx3 treatment groups followed by challenging with HP-PRRSV-JXA1 or NADC30-like HNhx, two groups were treated with isotype Mab (2G8) followed by challenging with two PRRSV isolates, and the remaining group was included as negative control (MOCK). At minus 2-day (-2 day) -post inoculation (d.p.i.), an intravenous (I.V.) administration with 10mg of mAb-PN9cx3 or mAb-2G8 (2mg/mL in PBS) was conducted in the lateral auricular vein of each piglet in indicated groups. In all PRRSV challenge only groups, a same volume of PBS was administrated in the same route as well. All piglets except negative control were challenged at 0 d.p.i with 2 ml of the HP-PRRSV-JXA1 or NADC30-like HNhx virus stock. One day later (1 d.p.i), additional 10mg of mAb-PN9cx3 or mAb-2G8 was administrated via auricular vein for Mab-treated groups. All animals were euthanized and subjected to necropsy andPAMs harvesting at 21 d.p.i.

tag: cell-type

value: PAMs collected from 8-week-old  pigs

tag: infection

value: PRRSV-HNhx with treatment of Mab-PN9cx3

tag: days post infection

value: 21 dpi


title: sosi-1_eri-6[e-f]_mut-16_mRNA_2

tag: strain


title: 4C_Gria1-insVP_WT_ESC


title: sosi-1_eri-6[e-f]_mut-16_mRNA_1


title: HNhx/mAB-PN9cx3_rep2


title: 4C_Gria1-promVP_TFBS+CGI_ESC


title: HNhx/mAB-PN9cx3_rep1


title: sRNA -SL35_CG - Rep2

description:
DL98
sRNA-seq processed data.xlsx


title: sosi-1_eri-6[e-f]_mRNA_3

value: USC1338 - sosi-1{delta} eri-6[e-f]{delta}(cmp263) I


title: sRNA -SL35_CG - Rep1

description:
DL97
sRNA-seq processed data.xlsx


title: 4C_Gria1-promVP_CGI_ESC


title: HNhx_rep3

description: piglets infected with PRRSV-HNhx

value: PRRSV-HNhx


title: sRNA -SL25_WH - Rep3

description:
DL96
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: sRNA -SL25_WH - Rep2

description:
DL95
sRNA-seq processed data.xlsx


title: sosi-1_eri-6[e-f]_mRNA_2


title: 4C_Gria1-promVP_TFBS_ESC


title: sosi-1_eri-6[e-f]_mRNA_1


title: sosi-1_mut-16_mRNA_3


title: sRNA -SL25_WH - Rep1

description:
DL94
sRNA-seq processed data.xlsx


title: 4C_Gria1-promVP_WT_ESC


title: JAX1/mAB-PN9cx3_rep3

description: piglets infected with PRRSV-JXA1 with treatment of Mab-PN9cx3

value: PRRSV-JXA1 with treatment of Mab-PN9cx3


title: 4C_Gata6-promVP_TFBS+CGI_AntNPC

source_name: mouse anterior neural progenitor cells

value: AntNPC

value: Knock-in in Gata6 TAD


title: HNhx_rep1

description: piglets infected with PRRSV-HNhx


title: 4C_Gria1-insVP_TFBS_ESC


title: sosi-1_mut-16_mRNA_2

value: Day 1 Adult


title: sRNA -SL25_HS - Rep2

description:
DL92
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: 4C_Gata6-promVP_CGI_AntNPC


title: JAX1/mAB-PN9cx3_rep2


title: sosi-1_mut-16_mRNA_1

value: mRNA selected from total RNA


title: 4C_Gata6-promVP_TFBS_AntNPC


title: sosi-1_mRNA_3

value: USC1335 - sosi-1{delta}(cmp262) I


title: 4C_Gata6-promVP_WT_AntNPC


title: sRNA -SL25_HS - Rep1

description:
DL91
sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)


title: JAX1_rep3

description: piglets infected with PRRSV-JXA1


title: sRNA -SL25_WS - Rep3

description:
DL90
sRNA-seq processed data.xlsx

value: Water-deficit stress (WS)


title: 4C_Gata6-insVP_TFBS+CGI_ESC

value: 2i+LIF ESC


title: sosi-1_mRNA_2


title: sRNA -SL25_WS - Rep2

description:
DL89
sRNA-seq processed data.xlsx


title: JAX1_rep2

description: piglets infected with PRRSV-JXA1


title: sRNA -SL25_HS - Rep3

description:
DL93
sRNA-seq processed data.xlsx


title: sosi-1_mRNA_1


title: JAX1_rep1

description: piglets infected with PRRSV-JXA1


title: sRNA -SL25_WS - Rep1

description:
DL88
sRNA-seq processed data.xlsx


title: sRNA -SL25_CG - Rep3

description:
DL87
sRNA-seq processed data.xlsx

value: Control group (CG)


title: 4C_Gata6-insVP_TFBS_ESC


title: eri-6[e-f]_mut-16_mRNA_3


title: HNhx_rep2

description: piglets infected with PRRSV-HNhx

value: PAMs collected from 8-week-old  pigs


title: Mock_rep3

description: No PRRSV infection, No Mab treatment

value: Non


title: eri-6[e-f]_mut-16_mRNA_2


title: 4C_Gata6-insVP_WT_ESC

value: wild type


title: sRNA -SL25_CG - Rep2

description:
DL86
sRNA-seq processed data.xlsx


title: eri-6[e-f]_mut-16_mRNA_1


title: Mock_rep2

description: No PRRSV infection, No Mab treatment

value: 21 dpi


title: JAX1/mAB-PN9cx3_rep1


title: 4C_Gata6-promVP_TFBS+CGI_ESC


title: sRNA -SL25_CG - Rep1

description:
DL85
sRNA-seq processed data.xlsx


title: Mock_rep1

description: No PRRSV infection, No Mab treatment


title: eri-6[e-f]_mRNA_3

value: USC1332 - eri-6[e-f]{delta}(cmp261) I


title: sRNA -SL15_WH - Rep3

description:
DL84
sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: 4C_Gata6-promVP_CGI_ESC


title: sRNA -SL15_WH - Rep2

description:
DL83
sRNA-seq processed data.xlsx


title: eri-6[e-f]_mRNA_1


title: 4C_Gata6-promVP_TFBS_ESC


title: 4C_Gata6-insVP_CGI_ESC


title: 4C_Gata6-promVP_WT_ESC


title: Input 3 [2893_1_F]

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by novoalign (versoin 3.04.06)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

source_name: HPC input

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

value: Hematopoietic Progenitor Cell


title: sRNA -SL15_HS - Rep3

description:
DL81
sRNA-seq processed data.xlsx


title: prg-1_ergo-1_small_RNA_3


title: Fetal HPC H3K27me3-2 [2893_1_E]

description:
processed data in series file:
fetal_HPC_k27_2893.fc.signal.bigwig
fetal_HPC_k27_2893.filt.narrowPeak.gz

source_name: Fetal HPC H3K27me3

tag: age


title: sRNA -SL15_HS - Rep2

description:
DL80
sRNA-seq processed data.xlsx


title: prg-1_ergo-1_small_RNA_1

value: size selected RNA from total RNA


title: Adult HPC H3K27me3-2 [2893_1_B]

description:
processed data in series file:
adult_HPC_k27_2893.fc.signal.bigwig
adult_HPC_k27_2893.filt.narrowPeak.gz

source_name: Adult HPC H3K27me3

value: 8 week old


title: Adult HPC H3K27me3-3 [2893_1_C]


title: sRNA -SL15_WS - Rep3

description:
DL78
sRNA-seq processed data.xlsx


title: prg-1_hrde-1_small_RNA_3

value: Day 1 Adult


title: sRNA -SL15_HS - Rep1

description:
DL79
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: prg-1_ergo-1_small_RNA_2


title: prg-1_hrde-1_small_RNA_2


title: Fetal HPC H3K27me3-1 [2893_1_D]


title: prg-1_hrde-1_small_RNA_1


title: Adult HPC H3K27me3-1 [2893_1_A]


title: eri-6[e-f]_mRNA_2

value: mRNA selected from total RNA


title: sRNA -SL15_WS - Rep2

description:
DL77
sRNA-seq processed data.xlsx


title: P0 Ifnar ko HPC-4 [s4545_3018_1_R]

description: processed data file: gene_level_read_counts.2nd_submission.txt.gz

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: P0 Ifnar ko HPC

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: Ifnar -/-

value: Hematopoietic progenitor cell


title: sosi-1_eri-6[e-f]_mut-16-small-RNA-3


title: sRNA -SL15_WS - Rep1

description:
DL76
sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)

value: Water-deficit stress (WS)


title: sRNA -SL15_CG - Rep3

description:
DL75
sRNA-seq processed data.xlsx

value: Control group (CG)


title: sosi-1_eri-6[e-f]_mut-16-small-RNA-2


title: sRNA -SL15_CG - Rep2

description:
DL74
sRNA-seq processed data.xlsx


title: sosi-1_eri-6[e-f]_mut-16-small-RNA-1


title: P0 Ifnar ko HPC-2 [s4545_3018_1_O]


title: S2_MGAS_PVC

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads from each sample were aligned on gender specific hg19 reference genome (pseudoautosomal region was masked on the chromosome Y for males) using the STAR aligner (v2.5.0) with the following parameters: --alignIntronMax 1, --outFilterMismatchNmax 100, --alignEndsType EndToEnd, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads. We excluded reads that: (1) mapped to more than one locus; (2) were duplicated; and (3) mapped to the mitochondrial genome. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads.
Genome_build: hg19

source_name: primary visual cortex

extract_protocol:
50mg of frozen brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Magnesium acetate, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Magnesium acetate, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to ultracentrifugation at 24,000 rpm for 1 hour at 4°C. Pellets were resuspended in 500µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore Cat #MAB377X), anti-SOX67 and anti-SOX108 as previously described4 Prior to FANS sorting, DAPI (Thermoscientific) was added to a final concentration of 1µg/ml. GABAergic neurons (DAPI+ NeuN+ SOX6+), Glutamatergic neurons (DAPI+ NeuN+ SOX6-), oligodendrocytes (DAPI+ NeuN- SOX10+) and microglia/astrocytes (DAPI+ NeuN- SOX10-) nuclei were sorted into individual tubes (pre-coated with 5% BSA) using a FACSAria flow cytometer (BD Biosciences).
ATAC-seq reactions were performed on the 48 samples using an established protocol51 with minor modifications. In brief, 75,000 sorted nuclei were centrifuged at 500 g
for 10 min at 4°C. Pellets were re-suspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Reactions were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204), eluting in 10µL of buffer EB. Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011) under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute for a total of 5 cycles. To prevent saturation due to over-amplification, a 5 µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 µL reaction. The additional number of cycles was determined by first plotting linear Rn vs. Cycle
 and secondly calculating the cycle number corresponding to 1⁄4 of maximum fluorescence intensity. In general, adding 2-4 cycles to this estimate was found to yield optimal libraries, as evidenced by analysis on Tapestation D5000 ScreenTapes (Agilent technologies Cat# 5067-5588). Following amplification, libraries were resolved on 2% agarose gels and fragments ranging in size from 100-1000bp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Prior to sequencing, libraries were quantified with the Qubit dsDNA HS assay kit (Invitrogen Cat#Q32851) and by quantitative PCR (KAPA Biosystems Cat#KK4873). Fragment sizes were estimated using Tapestation D5000 ScreenTapes (Agilent technologies Cat# 5067-5588) and libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

value: primary visual cortex

value: microglia and astrocytes

tag: gender

value: Male

tag: age of death

tag: postmortem interval (hours)

tag: heart weight (grams)

tag: alcohol toxicology

value: negative

tag: Cause of death

value: sudden cardiac death


title: S4_MGAS_PVC

tag: tissue

value: Female


title: sosi-1_eri-6[e-f]_small_RNA_3

value: USC1338 - sosi-1{delta} eri-6[e-f]{delta}(cmp263) I

tag: Stage

tag: molecule subtype


title: sRNA -SL15_WH - Rep1

description:
DL82
sRNA-seq processed data.xlsx

source_name: Flag leaf tissue

tag: genotype

value: Water-deficit plus heat stress (WH)


title: P0 Ifnar ko HPC-1 [s4545_3018_1_N]

tag: cell type


title: P0 Ifnar ko HPC-3 [s4545_3018_1_P]


title: S3_MGAS_PVC


title: P0 wild type HPC-4 [s4545_3018_1_M]

source_name: P0 wild type HPC

value: wild type


title: sosi-1_eri-6[e-f]_small_RNA_2

value: Day 1 Adult

value: size selected RNA from total RNA


title: P0 wild type HPC-3 [s4545_3018_1_K]


title: S1_MGAS_PVC


title: sosi-1_mut-16-small-RNA-3


title: sosi-1_eri-6[e-f]_small_RNA_1


title: P0 wild type HPC-2 [s4545_3018_1_J]


title: sRNA -SL5_WH - Rep2

description:
DL71
sRNA-seq processed data.xlsx

tag: treatment group

tag: time-point (dpa, days post anthesis)


title: sRNA -SL5_HS - Rep3

description:
DL69
sRNA-seq processed data.xlsx

value: Heat stress (HS)


title: S3_MGAS_DLPFC

source_name: dorsolateral prefrontal cortex

value: dorsolateral prefrontal cortex


title: S2_MGAS_DLPFC


title: sRNA -SL5_HS - Rep2

description:
DL68
sRNA-seq processed data.xlsx


title: P0 wild type HPC-1 [s4545_3018_1_I]

value: Hematopoietic progenitor cell


title: sosi-1_mut-16-small-RNA-2