title: GM12878-Pol2-total-50K-1

extract_protocol:
GM12878 protocol: Cells were centrifuged at 1,600 g for 5 min and resuspended in DPBS. Our experiments usually started with 4×10^5 cells/nuclei suspended in 100 µl of DPBS. 1 µl of PIC, 1 µl of 100 mM PMSF and 100 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and incubated at room temperature for 10 min. 10 µl of 100 mM CaCl2 and 2.5 µl 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 22 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing fragmented chromatin was collected into a new 1.5 ml tube and placed on ice. Chromatin volume equal to the stated number of cells per assay was taken and used for nMOWChIP, diluted to 60 µl loading volume with IP buffer if needed. Mouse protocol: A mouse brain was put on ice and PFC and cerebellum were dissected for nuclei isolation. The following steps are performed on ice and centrifugation performed at 4°C. Tissue was placed in 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use]. Tissue was homogenized in the grinder set (D9063, Sigma-Aldrich) by slowly douncing 15 times with pestle A and 25 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. The supernatant was removed and the pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by pipetting. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. If mixed nuclei (without separation of neurons and glia) were used for MOWChIP directly, the nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS). If nuclei labeling and FACS sorting were conducted, 500 µl of 2% normal goat serum (50062Z, Life Technologies) in DPBS was added to the nuclei pellet and incubated for 10 min before resuspending. Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was diluted with DPBS to 2 ng/µl. 8 µl of anti-NeuN was added to each 500 µl of nuclei suspension and incubated at 4°C for 1 h on a rotator. The labeled nuclei were then sorted using FACS (BD FACSAria, BD Biosciences). 8 µl of non-labeled nuclei were saved as unstained control prior to addition of anti-NeuN antobody. The concentration of nuclei suspension after FACS was typically low (~1.2×10^5/ml). The nuclei were re-concentrated by adding 200 µl of 1.8 M sucrose, 5 µl of 1M CaCl2 and 3 µl of 1M Mg(Ac)2 to 1 ml of the nuclei suspension. The mixture was incubated on ice for 15 min and centrifuged at 1800g for 15 min. Supernatant was removed and the nuclei pellet was resuspended in DPBS. Nuclei were digested using the same steps as GM12878 cells.
Libraries were constructed using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences) following the manufacturer’s instructions. 1× EvaGreen dye (Biotium) was added to the amplification mixture to monitor the PCR amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library fragment size was examined using TapeStation (Agilent) and the concentration was quantified with KAPA Library Quantification kit (Kapa Biosystems). Libraries were pooled accordingly for sequencing by Illumina HiSeq 4000 SR50 mode.


title: PB-05G

status: Public on Nov 05 2021

type: SRA

city: Seattle

first: Chengxiang

last: Qiu

state: WA

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

department: Genome Sciences

country: USA

institute: University of Washington

description: sci-RNA-seq3 library

library_source: transcriptomic

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file

molecule: polyA RNA

organism: Mus musculus

source_name: mouse embryos

growth_protocol: We set up C57BL/6J timed mouse breeding pairs; evidence of vaginal plug is counted as embryonic day 0.5. 16 days later, the dam was sacrificed. E16.5 embryos were then dissected and briefly rinsed in 1xPBS; the excess liquid was wicked away by Kimwipe before immediately flash freezing in LN2. Mice had ad libitum access to standard chow and water and were housed in the University of Washington Animal Research and Care Facility on a standard 12 hr light cycle. All procedures were approved by the UW IACUC (protocol number PROTO201800017). E16.5 embryos were stored in a foil pouch in LN2 storage tank until ready for dissociation.

extract_protocol:
Nuclei were isolated from a single E16.5 mouse with a hypotonic, phosphate-based, lysis buffer containing sucrose and DEPC, and fixed with a combination of DSP and methanol.
Nuclei were washed and resuspended in SPBSTM buffer. ~4 million of these nuclei were processed with 2 plates of RT indexes, 2 plates of ligation indexes, and 3.5 plates of PCR indexes, as per the protocol described above. About 2000 nuclei per well were distributed into the final PCR plates. All 3.5 plates of PCR reactions were pooled and sequenced on an Illumina NovaSeq 6000 with dual index reads using the S4-200 kit and standard primers (Read1 34 cycles, Index1 10 cycles, Index2 10 cycles, Read2 100 cycles), resulting in about 7.15 billion reads in total, or 4.34 billion after removal of PCR duplicates.

tag: developmental stage

value: mouse embryo (E16.5)

tag: strain


title: PB-05F

description: sci-RNA-seq3 library


title: PB-05E

description: sci-RNA-seq3 library


title: YH25005-1

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

country: China

institute: Northwest A&F University

data_processing:
Bcl2fastq Conversion software (v2.20) was used for basecalling.
The raw data was trimmed with strict standards as followsd:(1) Trimmed Reads with adapter seq;(2) Trimmed low quality bases(Reads would be discarded if percent of N base is greater than 10% or percent of low quality bases is greater than 50%).
We mapped the clean data against the reference genome of Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/). HISAT2 (https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download) is used as an alignment software for RNA-seq. Based on mapped data, we carried out library insert size check, sequencing randomness check, gene expression quantification analysis, alternative splicing analysis, novel genes detection and genes structure optimization.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis of two sample groups was performed using the DEseq2. Fold Change(FC)≥2 and FDR<0.01 were used as the screening criteria to identify differentially expressed genes.
Genome_build: Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/)
Supplementary_files_format_and_content: Tab-delimited text files include count number and fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample.

molecule: total RNA

organism: Brassica napus

source_name: Unmatured seeds

growth_protocol: The plants of the four genotypes were cultivated in the experimental field of Northwest A&F University.

extract_protocol:
The 24-days-old emboys of the four genotypes were collected and put into liquid nitrogen. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 (Agilent, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150. Raw Data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.

treatment_protocol: When the plants were flowering, the flowers opened in the same days were marked and the inflorescences were bagged to get selfing-pollinated seeds.

tag: tissue

value: Unmatured seeds

tag: development stage

value: 24 days old after pollination

tag: genotype


title: PB-05D

description: sci-RNA-seq3 library


title: PB-06F

description: sci-RNA-seq3 library


title: PB-05C

description: sci-RNA-seq3 library


title: PB-05B

description: sci-RNA-seq3 library


title: RGS16, biological replicate 4

type: RNA

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
RGS13-4
Gene expression data from cord blood CD34+ cells.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome Gene v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (EukGE-Ws2v4).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The digital data retrieved from the CEL files were processed by Partek Genomic Suite version 6.6 using modified RMA-algorithm.

label: Biotin

organism: Homo sapiens

source_name: Cord blood CD34+ cells, RGS16

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Two-Cycle cDNA Synthesis Kit and IVT labeling kit).

growth_protocol: Cord blood CD34+ cells were grown in Stemline II medium supplemented with TPO, SCF and Flt-3L, cells were subjected to 2 rounds of lentiviral transduction at MOI 4-8. Cells were harvested for gene expression profiling 24 hours after the last transduction.

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and RNeasy micro kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: GFP control, RGS1, RGS13 and RGS16 transduction.

tag: cell type

value: Cord blood CD34+ cells

tag: expression


title: GFP, biological replicate 4

description:
GFP-4
Gene expression data from cord blood CD34+ cells.

source_name: Cord blood CD34+ cells, GFP control

value: GFP control


title: RGS13, biological replicate 4

source_name: Cord blood CD34+ cells, RGS13


title: RGS1, biological replicate 4

description:
RGS1-4
Gene expression data from cord blood CD34+ cells.

source_name: Cord blood CD34+ cells, RGS1


title: RGS16, biological replicate 3

description:
RGS16-3
Gene expression data from cord blood CD34+ cells.


title: RGS1, biological replicate 3

description:
RGS1-3
Gene expression data from cord blood CD34+ cells.


title: PB-05A

description: sci-RNA-seq3 library


title: RGS16, biological replicate 2

description:
RGS16-2
Gene expression data from cord blood CD34+ cells.


title: GFP, biological replicate 3

description:
GFP-3
Gene expression data from cord blood CD34+ cells.


title: SW-2

value: SW


title: PB-04H

description: sci-RNA-seq3 library


title: SW-1


title: PB-04F

description: sci-RNA-seq3 library


title: PB-04G

description: sci-RNA-seq3 library


title: YH25005-2


title: R8Q10-3


title: PB-04D

description: sci-RNA-seq3 library


title: R8Q10-2


title: PB-04C

description: sci-RNA-seq3 library


title: SW-3


title: RGS13, biological replicate 3

description:
RGS13-3
Gene expression data from cord blood CD34+ cells.


title: PB-04B

description: sci-RNA-seq3 library


title: RGS13, biological replicate 2

description:
RGS13-2
Gene expression data from cord blood CD34+ cells.


title: PB-04A

description: sci-RNA-seq3 library


title: RGS1, biological replicate 2

description:
RGS1-2
Gene expression data from cord blood CD34+ cells.


title: RGS13, biological replicate 1

description:
RGS13-1
Gene expression data from cord blood CD34+ cells.


title: GFP, biological replicate 2

description:
GFP-2
Gene expression data from cord blood CD34+ cells.


title: RGS16, biological replicate 1

description:
RGS16-1
Gene expression data from cord blood CD34+ cells.


title: R8Q10-1


title: PB-04E

description: sci-RNA-seq3 library


title: A28-3


title: A28-2


title: PB-03F

description: sci-RNA-seq3 library


title: PB-03H

description: sci-RNA-seq3 library


title: PB-03G

description: sci-RNA-seq3 library


title: PB-03C

description: sci-RNA-seq3 library


title: PB-03D

description: sci-RNA-seq3 library


title: A28-1


title: PB-03B

description: sci-RNA-seq3 library


title: N_Cat

city: Changchun

first: Xiaoyu

last: Yan

address: Xinmin street 126

institute: Jilin University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in text format

molecule: genomic DNA

source_name: hepatocellular carcinoma cells

growth_protocol: SNU-387 cells were cultured in 10cm  dish

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: cultured under 1% oxygen for 6h

tag: protocol

value: control (normoxia)

value: hepatocellular carcinoma cells

tag: cell line

tag: antibody

value: Beta Catenin (protentech, 51067-2-AP)


title: PB-02H

description: sci-RNA-seq3 library


title: PB-03A

description: sci-RNA-seq3 library


title: PB-02G

description: sci-RNA-seq3 library


title: PB-02F

description: sci-RNA-seq3 library


title: PB-02E

description: sci-RNA-seq3 library


title: PB-02D

description: sci-RNA-seq3 library


title: SP10_NT_r2

city: Bloomington

first: Daniel

last: Schwartz

state: IN

address: 1001 East 3rd Street

department: Biology

institute: Indiana University

data_processing:
Sequenced reads were adapter trimmed and quality filtered using Trimmomatic 0.38 with the cutoff threshold for average base quality score set at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded.
The cleaned reads were mapped to reference  using bowtie2 version 2.3.2
Read pairs mapping concordantly and uniquely to the annotated genes were counted using featureCounts  tool ver. 2.0.0 of subread package
Differential expression analysis was performed using DESeq2  ver. 1.24.0 from normalized read counts by comparing samples induced with IPTG to non-induced paired control samples, and the p-values were corrected for multiple-testing.
Genome_build: BsDelta6_pDR110_SigmaCDSappended.gb
Supplementary_files_format_and_content: Description of columns in CSV files is detailed in DEseq_descriptions.csv

organism: Bacillus subtilis

source_name: Bacilus subtilis culture

growth_protocol: We diluted overnight B. subtilis cultures (OD600 = 0.1) in fresh LB and grew them (37 °C, 200 RPM) to mid exponential phase (OD600 = 0.5)

extract_protocol:
Upon sampling, we immediately treated bacteria with the RNAprotect Bacteria reagent (Qiagen), and stored pellets at -80 °C for <1 week before RNA extraction using RNeasy Protect Bacteria Mini Kit (Qiagen) according to the manufacturer's instructions (protocol #5), including an on-column RNase-free DNase digestion.
Libraries were constructed using the Illumina TruSeq Stranded mRNA HT kit following depletion of rRNA using Illumina Ribo-Zero Plus kit.
RNAseq on Illumina NextSeq 500 platform as paired end reads (2 x 38 bp)

treatment_protocol: At mid-exponenial phase we split the cultures and added 1mM IPTG to one half to induce expression of the cloned gene (=IPTG). We added an equal volume of water to the other half of the split culture as a control (=NT). After induction, we returned incubated the cultures for 2 h before harvesting cells.

tag: induced gene

tag: treatment

value: NT

tag: replicate


title: SP10_NT_r1


title: RGS1, biological replicate 1

description:
RGS1-1
Gene expression data from cord blood CD34+ cells.


title: PB-03E

description: sci-RNA-seq3 library


title: RHP476: Peripheral blood granulocytes from heathy control

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.3
Mapped reads were summarized to gene level using featureCounts version 1.5 and with GENCODE GRCh38 v19 gene annotation
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Bioconductor edgeR package with normalized library sizes option and log2 transformation
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 transformed FPKM values for all samples

source_name: Blood

growth_protocol: Mononuclear cells and granulocytes were separated using a Ficoll gradient. PBMCs were collected from the Ficoll/PBS interphase, while granulocytes were recovered from the layer immediately above the RBC pellet. RBC lysis buffer was used to remove contaminating RBCs from the granulocyte fraction. The PBMCs were then fractionated into CD14-positive monocytes and CD14-negative leukocytes(a population mostly enriched in lymphocytes) using CD14+ immunomagnetic separation beads (MACS, Miltenyi).

extract_protocol:
The purified cells were lysed using mirVana total RNA isolation solution and stored at -80 °C until later RNA extraction following the manufacturer’s protocol (Ambion, CA).
All human RNAs were analyzed on Agilent Bioanalyzer for quality assessment with RNA Integrity Number (RIN) range from 7.1 to 10 and median RIN 9.5 (Agilent, Santa Clara, CA, USA). cDNA libraries were prepared using 300 ng of total RNA and 2ul of a 3:1000 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific, Waltham, MA, USA). The fragmented mRNA samples were subjected to cDNA synthesis using Illumina TruSeq® RNA sample preparation kit version 2 (Illumina, San Diego, CA, USA) according to manufacturer's protocol, except for the following modifications: 1. use of 12 PCR cycles, 2. two additional round of Agencourt Ampure XP SPRI beads (Beckman Courter) to remove >600bp double stranded cDNA. The length distribution of the cDNA libraries was monitored using DNA 1000 kits on the Agilent bioanalyzer (Agilent, Santa Clara, CA, USA). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) (3-4 samples/ lane). FASTQ files were mapped using STAR to the human genome build hg19. The mapped reads were then counted using featureCounts based on GENCODE V19 annotations to generate gene counts.

tag: individual

value: donor_id D010

value: Granulocyte

tag: disease state

value: Healthy control


title: RHP484: Peripheral blood monocytes from heathy control

value: Monocyte


title: RHP482: Peripheral blood monocytes from TB patient

value: donor_id A0029

value: TB


title: RHP478: Peripheral blood granulocytes from heathy control

value: donor_id D0022


title: SP10_IPTG_r3

value: IPTG


title: SP10_NT_r3


title: RHP475: Peripheral blood monocytes from heathy control


title: GFP, biological replicate 1

description:
GFP-1
Gene expression data from cord blood CD34+ cells.


title: PB-02B

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: PB-01G

description: sci-RNA-seq3 library


title: PB-01H

description: sci-RNA-seq3 library


title: SP10_IPTG_r1


title: RHP474: Peripheral blood granulocytes from TB patient


title: sigG_NT_r3

value: sigG


title: PB-01D

description: sci-RNA-seq3 library


title: PB-01E

description: sci-RNA-seq3 library


title: PB-01F

description: sci-RNA-seq3 library


title: H_Cat

value: hypoxia treatment


title: PB-01C

description: sci-RNA-seq3 library


title: RHP471: Peripheral blood monocytes from heathy control

value: donor_id D0021


title: sigG_NT_r2


title: PB-01B

description: sci-RNA-seq3 library


title: RHP469: Peripheral blood granulocytes from TB patient

value: donor_id A0024


title: PB-02C

description: sci-RNA-seq3 library


title: PB-01A

description: sci-RNA-seq3 library


title: PB-02A

description: sci-RNA-seq3 library


title: sigG_NT_r1


title: PA-12H

description: sci-RNA-seq3 library


title: RHP466: Peripheral blood granulocytes from heathy control


title: SP10_IPTG_r2


title: PA-12F

description: sci-RNA-seq3 library


title: RHP465: Peripheral blood monocytes from TB patient


title: sigG_IPTG_r3


title: sigG_IPTG_r2


title: PA-12G

description: sci-RNA-seq3 library


title: PA-12E

description: sci-RNA-seq3 library


title: PA-12D

description: sci-RNA-seq3 library


title: RHP257: Peripheral blood monocytes from TB patient

value: donor_id A0019


title: PA-12B

description: sci-RNA-seq3 library


title: sigG_IPTG_r1


title: PA-12C

description: sci-RNA-seq3 library


title: RHP254: Peripheral blood granulocytes from TB patient

value: donor_id A0018


title: PA-12A

description: sci-RNA-seq3 library


title: PA-11H

description: sci-RNA-seq3 library


title: sigF_NT_r2

value: sigF


title: sigF_NT_r3

value: NT


title: RHP253: Peripheral blood granulocytes from TB patient


title: PA-11F

description: sci-RNA-seq3 library


title: PA-11E

description: sci-RNA-seq3 library


title: PA-11G

description: sci-RNA-seq3 library


title: RHP252: Peripheral blood monocytes from heathy control

value: donor_id D0020


title: PA-11D

description: sci-RNA-seq3 library


title: sigF_NT_r1


title: RHP248: Peripheral blood granulocytes from heathy control

value: Granulocyte


title: PA-11C

description: sci-RNA-seq3 library


title: sigF_IPTG_r3


title: sigF_IPTG_r2


title: RHP246: Peripheral blood monocytes from TB patient


title: PA-11B

description: sci-RNA-seq3 library


title: PA-11A

description: sci-RNA-seq3 library


title: sigF_IPTG_r1


title: PA-10H

description: sci-RNA-seq3 library


title: PA-10G

description: sci-RNA-seq3 library


title: R379-26-SU-26(K2)

city: Houston

first: Yalan

last: Deng

state: Texas

address: MD Anderson Cancer Center, Zayed Building, Z7.2036, 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

data_processing:
The quality of fastq files was determined by Fastqc (V0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The pair-ended reads were mapped to mouse mm10 (Feb 2009, UCSC) genome using Tophat (V2.1.1, https://github.com/infphilo/tophat); only uniquely mapped reads were extracted using SAMtools (V1.5, http://samtools.sourceforge.net/) as inputs for differential gene expression analysis.
The results from RSeQC (V2.6.4, http://rseqc.sourceforge.net/) also indicated high data quality. Cufflinks (V2.2.1, http://cole-trapnell-lab.github.io/cufflinks) was used to assemble the transcriptome using RefSeq (Sep 7, 2015) annotation file and quantitate the gene expression level with reads per kb per million (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: excel file including FPKM values for all Samples

source_name: liver

extract_protocol:
Total RNA was extracted using the PuroLink RNA Mini Kit (Invitrogen, 12183018A)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: age

value: 12 weeks

value: Lifrfl/fl;Crealb/alb


title: pDR110_NT_r3


title: R379-28-SU-27(K3)


title: RHP245: Peripheral blood granulocytes from heathy control

value: donor_id D0018

value: Healthy control


title: RHP244: Peripheral blood monocytes from heathy control

value: donor_id D009

value: Monocyte


title: RHP242: Peripheral blood granulocytes from TB patient

value: donor_id A0016

value: TB


title: PA-10F

description: sci-RNA-seq3 library

value: mouse embryo (E16.5)


title: R379-24-SU-24(C3)

value: Lifrfl/fl


title: R379-25-SU-25(K1)


title: pDR110_NT_r2


title: R379-23-SU-23(C2)


title: PA-10E

description: sci-RNA-seq3 library


title: PA-10D

description: sci-RNA-seq3 library


title: pDR110_IPTG_r3

value: IPTG


title: PA-10C

description: sci-RNA-seq3 library


title: RHP237: Peripheral blood monocytes from heathy control


title: RNA_Ring1b_cKO_pESC

city: Vancouver

first: Kentaro

last: Mochizuki

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
Reads were aligned to the mouse genome (mm10) and transcripts using STAR (Dobin et al., 2013) with --sjdbGTFfile and --twopassMode Basic options.
Aligned reads were converted to bigWig format using bedtools (Quinlan et al., 2010) and bedGraphToBigWig (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: pESC

extract_protocol:
pESCs were cultured in DMEM (Kohjin-bio) with 20% fetal bovine serum (Sigma), MEM nonessential amino acids, L-glutamine, 2-mercaptoethanol, and LIF on mitomycin C-treated (Sigma) primary MEF feeder layers. For cKO, 4OHT was added to the medium to a final concentration of 800 nM.
Total RNA was prepared from cultured cells using the Allprep DNA/RNA mini kit (Qiagen) following vendor’s instructions. Each RNA-seq library was prepared from 1 μg of total RNA, using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), following the supplier’s instructions. Libraries were quantified with the KAPA Library Quantification Kit (Illumina). Samples were multiplexed and adjusted to 2 nM concentration, followed by Illumina HiSeq2000 sequencing. Reads were generated by 50 bp single end sequencing.

value: pESC

value: Ring1b cKO

tag: chip antibody


title: RHP238: Peripheral blood monocytes from TB patient


title: RHP236: Peripheral blood granulocytes from heathy control


title: pDR110_IPTG_r2


title: RHP233: Peripheral blood monocytes from heathy control

value: donor_id D0017


title: pDR110_IPTG_r1


title: RNA_Ring1b_WT_pESC

tag: developmental stage

value: Ring1b WT


title: RHP227: Peripheral blood monocytes from TB patient

value: donor_id A0012


title: PA-10A

description: sci-RNA-seq3 library

tag: strain


title: PA-10B

description: sci-RNA-seq3 library


title: RHP225: Peripheral blood granulocytes from heathy control

value: Granulocyte


title: Goe3_NT_r3

value: NT


title: CNO2d_2

first: Robert

last: Krencik

state: TX

address: 6670 Bertner Ave.

department: Neurosurgery

institute: Houston Methodist

description: Day14 Astrostim Cells + 2day CNO Rep2

data_processing:
DESeq2
Genome_build: Homo sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: Excel worksheet. Differential expression analysis, Read Count, FPKM

source_name: Day14 Astrostim Cells + 2day CNO Rep2

growth_protocol: Cells attached as monolayer to matrigel and fed with Neural Media

extract_protocol:
Direct-zol RNA kit (Zymo) with on-column Dnase treatment
Novogene Eukaryotic RNA-seq (cDNA library), NEB poly-A selected

treatment_protocol: With or without doxycycline (dox) and with or without clozapine N-oxide (CNO)

value: Astrostim Cells

value: Dox+CNO

tag: timepoint


title: CNO2d_1

description: Day14 Astrostim Cells + 2day CNO Rep1

source_name: Day14 Astrostim Cells + 2day CNO Rep1


title: CNO2d_3

description: Day14 Astrostim Cells + 2day CNO Rep3

source_name: Day14 Astrostim Cells + 2day CNO Rep3


title: pDR110_NT_r1


title: RHP223: Peripheral blood granulocytes from TB patient


title: PA-09G

description: sci-RNA-seq3 library


title: RHP221: Peripheral blood monocytes from heathy control

value: donor_id D0016

value: Healthy control


title: PA-09F

description: sci-RNA-seq3 library


title: Goe3_IPTG_r3


title: PA-09E

description: sci-RNA-seq3 library


title: Goe3_IPTG_r2


title: RHP219: Peripheral blood granulocytes from TB patient

value: donor_id A0030


title: CNO2hr_2

description: Day14 Astrostim Cells + 2hr CNO Rep2

source_name: Day14 Astrostim Cells + 2hr CNO Rep2


title: CNO2hr_1

description: Day14 Astrostim Cells + 2hr CNO Rep1

source_name: Day14 Astrostim Cells + 2hr CNO Rep1


title: PA-09D

description: sci-RNA-seq3 library


title: RHP215: Peripheral blood monocytes from TB patient

value: Monocyte


title: Goe3_IPTG_r1


title: Ctrl_3

description: Day 14 Astrostim Cells Rep3

source_name: Day 14 Astrostim Cells Rep3

value: Dox


title: RHP214: Peripheral blood granulocytes from TB patient

value: donor_id A0010

value: TB


title: PA-09C

description: sci-RNA-seq3 library

source_name: mouse embryos

value: mouse embryo (E16.5)


title: Goe3_NT_r2


title: ELDg169_NT_r3


title: Ctrl_2

description: Day 14 Astrostim Cells Rep2

source_name: Day 14 Astrostim Cells Rep2


title: PA-09H

description: sci-RNA-seq3 library


title: PA-09B

description: sci-RNA-seq3 library


title: RHP213: Peripheral blood granulocytes from heathy control


title: ELDg169_NT_r2


title: ELDg169_NT_r1


title: RHP210: Peripheral blood monocytes from TB patient


title: Goe3_NT_r1


title: Ctrl_1

description: Day 14 Astrostim Cells Rep1

source_name: Day 14 Astrostim Cells Rep1


title: CNO2hr_3

description: Day14 Astrostim Cells + 2hr CNO Rep3

source_name: Day14 Astrostim Cells + 2hr CNO Rep3


title: PA-09A

description: sci-RNA-seq3 library


title: iChR2_3

description: Day 14 OptoNeurons Rep3

source_name: Day 14 OptoNeurons Rep3

value: OptoNeurons


title: RHP209: Peripheral blood granulocytes from heathy control

value: donor_id D0015


title: ELDg169_IPTG_r3

value: IPTG


title: RHP208: Peripheral blood granulocytes from heathy control

value: donor_id D0014


title: iChR2_2

description: Day 14 OptoNeurons Rep2

source_name: Day 14 OptoNeurons Rep2


title: PA-08H

description: sci-RNA-seq3 library


title: PA-08G

description: sci-RNA-seq3 library


title: ELDg169_IPTG_r2


title: RHP206: Peripheral blood monocytes from TB patient

value: donor_id A0007


title: iChR2_1

description: Day 14 OptoNeurons Rep1

source_name: Day 14 OptoNeurons Rep1


title: D12Dox_3

description: Day 12 iAstros Rep3

source_name: Day 12 iAstros Rep3

value: iAstros


title: RHP205: Peripheral blood monocytes from heathy control

source_name: Blood


title: ELDg169_IPTG_r1

source_name: Bacilus subtilis culture


title: ELDg168_IPTG_r3


title: PA-08E

description: sci-RNA-seq3 library


title: D12Dox_2

description: Day 12 iAstros Rep2

source_name: Day 12 iAstros Rep2


title: D12Dox_1

description: Day 12 iAstros Rep1

source_name: Day 12 iAstros Rep1


title: PA-08D

description: sci-RNA-seq3 library


title: ELDg168_IPTG_r1


title: PA-08C

description: sci-RNA-seq3 library


title: RHP198: Peripheral blood granulocytes from TB patient

value: Granulocyte


title: NoDox_3

description: Day 12 Neural Progenitor Cells Rep3

source_name: Day 12 Neural Progenitor Cells Rep3

value: Neural Progenitor Cells


title: RHP204: Peripheral blood monocytes from heathy control


title: PA-08B

description: sci-RNA-seq3 library


title: ELDg168_NT_r3

value: NT


title: NoDox_2

description: Day 12 Neural Progenitor Cells Rep2

source_name: Day 12 Neural Progenitor Cells Rep2


title: ELDg168_NT_r2


title: RHP193: Peripheral blood monocytes from heathy control

value: donor_id C0003


title: RHP194: Peripheral blood granulocytes from TB patient

value: donor_id A0004


title: ELDg168_IPTG_r2


title: PA-08A

description: sci-RNA-seq3 library


title: NoDox_1

description: Day 12 Neural Progenitor Cells Rep1

source_name: Day 12 Neural Progenitor Cells Rep1


title: PA-08F

description: sci-RNA-seq3 library


title: ELDg168_NT_r1


title: PA-02E

description: sci-RNA-seq3 library


title: healthy 9

city: Tokyo

first: Koji

last: Yahara

address: Aoba-cho 4-2-1, Higashimurayama-shi

country: Japan

institute: National Institute of Infectious Diseases

description: whole blood RNA of a healthy control

data_processing:
Data QC & trimming reads (FastQC, trimmomatic)
Mapping reads to the human reference genome (HISAT2)
Counting reads mapped to each gene (featureCounts)

source_name: blood

extract_protocol:
RNA was extracted from the blood samples using the PAXgene Blood RNA Kit
library preparation and RNA-Seq were conducted by Novogen Inc.. Globin mRNA was removed from the total RNA using the GlobinClear Kit. mRNA was enriched using oligo(dT) beads, and rRNA was removed using the Ribo-Zero kit. First, the mRNA was fragmented randomly by adding fragmentation buffer, and cDNA was synthesized using an mRNA template and random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repairs, A ligation, and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

tag: disease status

value: Healthy

tag: tissue

value: whole blood


title: healthy 8

description: whole blood RNA of a healthy control


title: PA-02D

description: sci-RNA-seq3 library


title: RHP185: Peripheral blood granulocytes from heathy control

value: donor_id C0002

value: Healthy control


title: L5B5 NB-Glycerol death phase

city: Seville

first: Jose Luis

last: Gonzalez-Pimentel

address: Av. Reina Mercedes 10

country: Spain

institute: IRNAS-CSIC

data_processing:
Raw reads were rRNA removal with SORTMERNA and subsequently trimmed for low-quality and adaptor sequences using Trimmomatic. Mapping to whole genome sequence was done with STAR. Htseq-count was used to count the mapped reads.
Genome_build: CP084742
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Pseudomonas sp. L5B5

source_name: Bacterium

extract_protocol:
Biomass from every condition was harvested using TRIsure reagent and Direct-zol RNA Miniprep kit (Zymo). Library type: TruSeq Stranded Total RNA (NEB Microbe)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phase

value: Death 72 hours


title: RHP182: Peripheral blood monocytes from TB patient

value: donor_id A0001

value: Monocyte

value: TB


title: healthy 7

description: whole blood RNA of a healthy control


title: L5B5 NB-Fructose stationary phase

value: Stationary 24 hours


title: PA-02C

description: sci-RNA-seq3 library

source_name: mouse embryos

value: mouse embryo (E16.5)


title: RHP181: Peripheral blood monocytes from heathy control


title: L5B5 NB-Mannose stationary phase


title: L5B5 NB-Glucose stationary phase


title: healthy 5

description: whole blood RNA of a healthy control


title: healthy 6

description: whole blood RNA of a healthy control


title: RHP178: Peripheral blood granulocytes from TB patient


title: RHP175: Peripheral blood monocytes from TB patient

value: donor_id A0002


title: healthy 4

description: whole blood RNA of a healthy control


title: RHP186: Peripheral blood monocytes from TB patient


title: RHP189: Peripheral blood granulocytes from heathy control


title: PA-02A

description: sci-RNA-seq3 library


title: RHP072: Peripheral blood monocytes from TB patient

value: donor_id A0008


title: PA-02B

description: sci-RNA-seq3 library


title: RHP179: Peripheral blood granulocytes from TB patient

value: Granulocyte


title: PA-02F

description: sci-RNA-seq3 library


title: L5B5 NB-Glycerol stationary phase


title: L5B5 NA-Glycerol exponential phase

value: Exponential 6 hours


title: healthy 2

description: whole blood RNA of a healthy control


title: healthy 1

description: whole blood RNA of a healthy control


title: CNO 11

description: whole blood RNA of a CNO patient

value: Chronic non-bacterial osteomyelitis (CNO)


title: RHP069: Peripheral blood granulocytes from TB patient


title: SA47_S1_L001

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
For each sample, the raw UMI (unique molecular index) counts of each gene in each cell were generated using cellRanger count (cellranger 5.0.0 http:// 10xgenomics.com) with mm10 as reference genome.
Genes expressed in less than 3 cells and cells expressing less than 200 genes were removed, while cells expressing more than 5000 genes were considered as potential doublets and removed. Cells were considered as injured or apoptotic and removed when 50% of the expression were from mitochondrial genes, similar as other renal single cell study in which renal tubular cell were found with high mitochondrial contents
Genome_build: mm10
Supplementary_files_format_and_content: Gene-Cell expression matrix of raw counts

source_name: whole kidney

extract_protocol:
The mice were anesthetized and perfused with chilled 1×PBS via the left heart. Kidneys were removed, minced into 1 mm3 pieces with a razor blade, and incubated in 2 ml of digestion buffer containing 1mg/ml collagenase type II (Sigma), 1 mg/ml Pronase E (Boster), and 50μg/ml DNase I ( Roche) at 37℃ for 10 minutes. The partially digested tissue was then passed through a 100-μm cell strainer (Falcon) into HBSS (Hank’s Balanced Salt Solution) twice on ice and pelleted by centrifugation (200g for 5mins). Then, the pellet was resuspended with HBSS and sheared with a 27G needle to remove large clumps. They were further filtered through a 40-μm cell strainer (Falcon) to get single cell solution. After centrifugation, the cell pellets were incubated with 3ml of RBC lysis buffer (TIANGEN, RT122-02) to remove red blood cells at room temperature for 3 minutes. Finally, cells were washed and resuspended in HBSS for three times to remove debris or cell aggregates. Cell viability and number was determined using Countess® II Automated Cell Counter (Invitrogen, C10227) after stained with Trypan blue. Using this method, we were able to generate single cell suspensions with > 80% viability.
Single cells were resuspended with HBSS to a suitable concentration (1600,000-7000,000 cells/ml). The viable cells were then loaded into Chromium microfluidic chips with 3’ (Gel Bead Kit version 2) chemistry and barcoded with a 10x Chromium Controller (10xGenomics). RNA from the barcoded cells was subsequently reverse-transcribed to generate cDNA and sequencing libraries constructed with reagents from a Chromium Single Cell 3’v2 reagent kit (10x Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaSeq 6000) using 150bp paired-end sequencing.

treatment_protocol: mice were treated with ARB and SGLT2i for 8 weeks


title: SA46_S1_L004


title: CNO 10

description: whole blood RNA of a CNO patient


title: RHP068: Peripheral blood granulocytes from heathy control

value: donor_id D007


title: healthy 3

description: whole blood RNA of a healthy control


title: FGR male 1

city: Manchester

first: Bernadette

middle: Carolyn

last: Baker

state: Lancashire

address: Oxford Road

department: Maternal and Fetal Health Research Centre

country: United Kingdom

institute: University of Manchester

description:
Test
PPO 3

data_processing:
Amplification curves were analysed using the Roche LC software for determination of Cq (by 2nd derivative method) and for melt curve analysis. ND denotes not detected.
For normalisation the NormFinder program was used and found the global mean of 194 microRNAs detected in all samples was optimal. Target miRNA signal normalised to global mean using formula 2^-dCq where dCq= Cq target - Cq global mean.
Fold change calculations used the formula 2^ddCq where ddCq = dCq Test - dCq Control

label: SYBR Green

source_name: Maternal serum 36 week gestation

label_protocol: 19µl RNA was reverse transcribed in 95µl reactions using miRCURY LNA Universal miRNA RT kit as per manufacturers protocol. Amplification performed in Roche Lightcycler 480 system with 40 cycles of 95°C for 10s followed by 1min at 60°C.

extract_protocol: Total RNA isolated from maternal serum (200 microlitres starting material) using miRCURY RNA Isolation kit for Biofluids (Exiqon) following manufacturers protocol with on-column DNAse digestion step and addition of MS2 phage carrier RNA (Roche).

tag: infant sex

value: Male

tag: maternal age

tag: maternal bmi

tag: gestation of delivery (days)

tag: individualised birthweight centile

tag: birthweight (g)


title: CNO 9

description: whole blood RNA of a CNO patient


title: RHP063: Peripheral blood granulocytes from TB patient

value: donor_id A0009


title: FGR female 1

description:
Test
PPO 1

value: Female


title: SA39_S1_L004

tag: treatment


title: L5B5 NA-Glycerol stationary phase


title: RHP060: Peripheral blood monocytes from TB patient

tag: individual

value: donor_id A0003


title: CNO 7

description: whole blood RNA of a CNO patient

value: whole blood


title: CNO 8

description: whole blood RNA of a CNO patient


title: FGR female 2

description:
Test
PPO 2


title: RHP059: Peripheral blood granulocytes from heathy control

value: donor_id D006

tag: disease state

value: Healthy control


title: SA47_S1_L004


title: NewSGLT219_S1_L004


title: Control male 2

description:
Control
CON 4


title: NewSGLT219_S1_L001


title: RHP071: Peripheral blood monocytes from heathy control

value: Monocyte


title: FGR male 2

description:
Test
PPO 4

source_name: Maternal serum 37 week gestation


title: CNO 6

description: whole blood RNA of a CNO patient


title: SA39_S1_L001


title: Control male 1

description:
Control
CON 3


title: RHP056: Peripheral blood monocytes from heathy control


title: CNO 5

description: whole blood RNA of a CNO patient


title: RHP054: Peripheral blood granulocytes from TB patient

value: TB


title: Control female 2

description:
Control
CON 2


title: SA46_S1_L001


title: NewSGLT216_S1_L004


title: Control female 1

description:
Control
CON 1


title: CNO 4

description: whole blood RNA of a CNO patient


title: RHP053: Peripheral blood monocytes from heathy control

value: donor_id D008


title: RHP051: Peripheral blood granulocytes from TB patient

value: donor_id A0013


title: CNO 3

description: whole blood RNA of a CNO patient


title: NewSGLT2_9_S1_L004


title: CNO 2

description: whole blood RNA of a CNO patient


title: NewSGLT2_9_S1_L001


title: NewSGLT216_S1_L001


title: RHP048: Peripheral blood monocytes from TB patient


title: RHP047: Peripheral blood granulocytes from heathy control


title: db_dbSGLT259_S1_L004


title: CNO 1

description: whole blood RNA of a CNO patient


title: RHP038: Peripheral blood monocytes from heathy control

value: donor_id D004


title: U2F-V4

city: Hengyang

first: Qingtuan

last: Meng

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

data_processing:
RNA-seq reads were filtered to get clean reads using FastQ (v0.20.0).
The clean reads were aligned to the human genome GRCh38.p13 using STAR (v2.7.6a)
Transcript Per Million was calculated by RSEM (1.3.3)
Differential gene expression analysis was done using limma package in R (v3.7)
P value was adjusted using the Benjamini–Hochberg method
Genome_build: hg38
Supplementary_files_format_and_content: Processed_data.csv (TPMs for all samples)

source_name: U2F organoid

growth_protocol: Human forebrain organoids were cultured in media reported in published protocols

extract_protocol:
Qiagen miRNeasy Mini Kit was used to extract total RNA
Sequencing libraries were prepared for RNA-seq using standard Illumina protocols

treatment_protocol: VPA (final concentration is 1 mM) was added to the organoid culture media. 72 hours later, total RNA was extracted.

value: forebrain organoids

tag: tissue derived from

value: U2F iPS cell line

value: VPA


title: db_dbSGLT259_S1_L003


title: ARB_29_S1_L004

value: ARB


title: RHP034: Peripheral blood monocytes from TB patient

value: donor_id A0011


title: RHP036: Peripheral blood granulocytes from TB patient

value: Granulocyte


title: ARB_29_S1_L001


title: ARB_28_S1_L004


title: RHP031: Peripheral blood granulocytes from heathy control


title: RHP029: Peripheral blood monocytes from TB patient

value: donor_id A0005


title: U2F-NC2

value: control


title: ARB_28_S1_L001


title: RHP026: Peripheral blood granulocytes from heathy control

value: donor_id D003


title: ARB_27_S1_L004


title: U1M-V3

source_name: U1M organoid

value: U1M iPS cell line


title: RHP022: Peripheral blood granulocytes from TB patient


title: U2F-V3


title: U2F-V2


title: U1M-V2


title: tumor tissue with DSF and anti-PD-1 treatment_3

city: Wuhan

first: Xin

last: Zheng

address: 1095 Jiefang Avenue, Qiaokou District

department: Union Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads   containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper(https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Supplementary_files_format_and_content: gene_expression.xls: All_sample_gene_expression
Supplementary_files_format_and_content: rna_expression.xls: All_rna_expression
Supplementary_files_format_and_content: GO.rar: GO_result
Supplementary_files_format_and_content: KEGG_PATHWAY.rar: KEGG_PATHWAY_result
Supplementary_files_format_and_content: All_samples.CorrelationHeatmap.xls: CorrelationHeatmap
Supplementary_files_format_and_content: PCA_all_sample.xls: PCA_result
Supplementary_files_format_and_content: GroupPlan.xls: GroupPlan

source_name: tumor

growth_protocol: 4T1 cells (1 × 106) were subcutaneously transplanted into the right flank of mice. The tumor-bearing mice were randomly categorized into 4 groups

extract_protocol:
Total RNA was isolated from the 4T1 xenografted tumors tissue sample using TRIZOL Reagent (Invitrogen, USA), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
The total RNAs were subjected to RNA deep sequencing with BGISEQ-500 platform at Beijing Genomics Institute (BGI, China)

treatment_protocol: The tumor-bearing mice were randomly categorized into 4 groups (n=5/group):control; anti-PD-1 blocking Ab i.p.; DSF p.o; anti-PD-1 blocking Ab + DSF.

tag: straub

value: BALB/c

value: DSF and anti-PD-1 treatment

tag: cell type


title: RHP021: Peripheral blood monocytes from heathy control

value: Monocyte

value: Healthy control


title: U2F-NC4


title: tumor tissue with DSF and anti-PD-1 treatment_2


title: tumor tissue with DSF and anti-PD-1 treatment_1


title: Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 94-2094 (tolerant) - biological replicate

city: Ribeirão Preto

first: Danyel

last: Contiliani

address: Av. Bandeirantes, 3900

country: Brazil

institute: University of Sao Paulo

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Feature Extraction 9.5.3.1 software (Agilent Technologies) was used to extract data using as reference the benchmark for Two-Color microarray from Agilent—February 2007 version (protocol GE2-v5_95_Feb07) with minor adjustments. After background signal correction, we conducted the normalization across the entire range of array data (a linear normalization method). LOWESS normalization was used to correct the intensity-dependent dye biases. Then, the outlier genes were identified using the HTself method (with minor adjustments) adapted for the Agilent Platform with 90% confidence.

organism: Saccharum officinarum

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

extract_protocol: Total RNA extraction from leaves and internodes were performed using the protocol described by LOGEMANN, J. et al. Analytical Biochemistry, v. 163, p. 16-20, 1987. The RNA samples were treated with DNase in solution and puriﬁed on-column using the RNase-Free DNase Set (Qiagen, Hilden, Germany), according to the manufacturer.

treatment_protocol: 7065: IACSP 97-7065 plants; D1: Droghut; L1: leaf+1; 4C: collection 4 (10 months of growth); B2: biological replicate 2

value: leaves

tag: variety


title: Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible) - biological replicate

value: IACSP 97-7065 drought susceptible


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible) - biological replicate


title: Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible)


title: Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 94-2094 (tolerant)


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible)_N


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible) - biological replicate2


title: U1M-V1


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible)


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 94-2094 (tolerant) - biological replicate


title: U2F-NC3


title: Drought 7 months (irrigated as control) - Leaf +1 - Variety IACSP 94-2094 (tolerant)


title: U1M-NC3


title: RHP018: Peripheral blood granulocytes from TB patient

value: donor_id A0022

value: TB


title: dbdbctrl12_S1_L004

value: db/db


title: tumor tissue with anti-PD-1 treatment_2

value: anti-PD-1 treatment


title: RHP016: Peripheral blood monocytes from TB patient


title: ARB_27_S1_L001

value: ARB


title: dbdbctrl15_S1_L001


title: dbdbctrl12_S1_L001


title: U1M-NC1

value: forebrain organoids


title: dbdbctrl15_S1_L004


title: RHP013: Peripheral blood granulocytes from heathy control

value: donor_id D002

value: Granulocyte


title: tumor tissue with anti-PD-1 treatment_1


title: db_dbCtrl12_S1_L003


title: U1M-NC2

value: control


title: RHP009: Peripheral blood granulocytes from heathy control

value: donor_id C0001


title: db_db_28_S1_L004


title: RHP020: Peripheral blood monocytes from heathy control


title: db_dbCtrl12_S1_L002


title: GM12878-HDAC2-100K-2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: nMOWChIP-seq data. Name format: Sample-target-cell/nuclei number-replicate number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools55 and bedtools56 to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: GM12878 cell line

growth_protocol: GM12878 cells were obtained from Coriell Institute for Medical Research. Cells were cultured in RPMI-1640 medium (30-2001, ATCC) with 15% fetal bovine serum (16000-044, Gibco) and 1% pen-strep (Invitrogen) at 37°C, 5% CO2. Cells were subcultured every 3 d to maintain exponential growth. C57BL/6J mice were purchased from Jackson Laboratory and maintained in the animal facility with 12-h light/12-h dark cycles and food and water ad libitum. 8-week old male mice were sacrificed by compressed CO2 followed by cervical dislocation. Mouse brains were rapidly dissected, frozen on dry ice and stored at -80°C. This study was approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech.

extract_protocol:
GM12878 protocol: Cells were centrifuged at 1,600 g for 5 min and resuspended in DPBS. Our experiments usually started with 4×10^5 cells/nuclei suspended in 100 µl of DPBS. 1 µl of PIC, 1 µl of 100 mM PMSF and 100 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and incubated at room temperature for 10 min. 10 µl of 100 mM CaCl2 and 2.5 µl 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 22 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing fragmented chromatin was collected into a new 1.5 ml tube and placed on ice. Chromatin volume equal to the stated number of cells per assay was taken and used for nMOWChIP, diluted to 60 µl loading volume with IP buffer if needed. Mouse protocol: A mouse brain was put on ice and PFC and cerebellum were dissected for nuclei isolation. The following steps are performed on ice and centrifugation performed at 4°C. Tissue was placed in 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)¬2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use]. Tissue was homogenized in the grinder set (D9063, Sigma-Aldrich) by slowly douncing 15 times with pestle A and 25 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. The supernatant was removed and the pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by pipetting. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. If mixed nuclei (without separation of neurons and glia) were used for MOWChIP directly, the nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS). If nuclei labeling and FACS sorting were conducted, 500 µl of 2% normal goat serum (50062Z, Life Technologies) in DPBS was added to the nuclei pellet and incubated for 10 min before resuspending. Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was diluted with DPBS to 2 ng/µl. 8 µl of anti-NeuN was added to each 500 µl of nuclei suspension and incubated at 4°C for 1 h on a rotator. The labeled nuclei were then sorted using FACS (BD FACSAria, BD Biosciences). 8 µl of non-labeled nuclei were saved as unstained control prior to addition of anti-NeuN antobody. The concentration of nuclei suspension after FACS was typically low (~1.2×10^5/ml). The nuclei were re-concentrated by adding 200 µl of 1.8 M sucrose, 5 µl of 1M CaCl2 and 3 µl of 1M Mg(Ac)2 to 1 ml of the nuclei suspension. The mixture was incubated on ice for 15 min and centrifuged at 1800g for 15 min. Supernatant was removed and the nuclei pellet was resuspended in DPBS. Nuclei were digested using the same steps as GM12878 cells.
Libraries were constructed using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences) following the manufacturer’s instructions. 1× EvaGreen dye (Biotium) was added to the amplification mixture to monitor the PCR amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library fragment size was examined using TapeStation (Agilent) and the concentration was quantified with KAPA Library Quantification kit (Kapa Biosystems). Libraries were pooled accordingly for sequencing by Illumina HiSeq 4000 SR50 mode.

tag: cell line

tag: chip antibody


title: tumor tissue with DSF treatment_2

value: DSF treatment


title: RHP007: Peripheral blood monocytes from heathy control

source_name: Blood


title: GM12878-MEF2C-100K-2


title: RHP008: Peripheral blood granulocytes from TB patient

value: donor_id A0006


title: tumor tissue with DSF treatment_1

value: BALB/c


title: GM12878-MEF2C-100K-1


title: db_db_28_S1_L001


title: GM12878-HDAC2-100K-1


title: tumor tissue with anti-PD-1 treatment_3


title: tumor tissue control_3


title: RHP003: Peripheral blood monocytes from TB patient

value: Monocyte


title: dbm2_S1_L001

value: db/m


title: GM12878-HDAC2-50K-2

extract_protocol:
GM12878 protocol: Cells were centrifuged at 1,600 g for 5 min and resuspended in DPBS. Our experiments usually started with 4×10^5 cells/nuclei suspended in 100 µl of DPBS. 1 µl of PIC, 1 µl of 100 mM PMSF and 100 µl lysis buffer [4% Triton X-100, 100 mM tris-HCl, 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and incubated at room temperature for 10 min. 10 µl of 100 mM CaCl2 and 2.5 µl 100U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 22 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The solution was centrifuged at 16,100g for 5 min at 4°C. Supernatant containing fragmented chromatin was collected into a new 1.5 ml tube and placed on ice. Chromatin volume equal to the stated number of cells per assay was taken and used for nMOWChIP, diluted to 60 µl loading volume with IP buffer if needed. Mouse protocol: A mouse brain was put on ice and PFC and cerebellum were dissected for nuclei isolation. The following steps are performed on ice and centrifugation performed at 4°C. Tissue was placed in 3 ml of ice-cold nuclei extraction buffer [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1% Triton X-100, with 30 µl of PIC (P8340, Sigma-Aldrich), 3 µl of 100 mM PMSF, and 3 µl of 1 M dithiothreitol added before use]. Tissue was homogenized in the grinder set (D9063, Sigma-Aldrich) by slowly douncing 15 times with pestle A and 25 times with pestle B. Homogenate was filtered through a 40 µm cell strainer into a 15 ml tube and centrifuged at 1000g for 10 min. The supernatant was removed and the pellet was resuspended in 500 µl nuclei extraction buffer and transferred to a 1.5 ml tube. 750 µl of 50% iodixanol, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1M dithiothreitol were added and mixed by pipetting. The mixture was centrifuged at 10,000g for 20 min and the supernatant was removed. If mixed nuclei (without separation of neurons and glia) were used for MOWChIP directly, the nuclei pellet was resuspended in 200 µl of Dulbecco's phosphate-buffered saline (DPBS). If nuclei labeling and FACS sorting were conducted, 500 µl of 2% normal goat serum (50062Z, Life Technologies) in DPBS was added to the nuclei pellet and incubated for 10 min before resuspending. Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was diluted with DPBS to 2 ng/µl. 8 µl of anti-NeuN was added to each 500 µl of nuclei suspension and incubated at 4°C for 1 h on a rotator. The labeled nuclei were then sorted using FACS (BD FACSAria, BD Biosciences). 8 µl of non-labeled nuclei were saved as unstained control prior to addition of anti-NeuN antobody. The concentration of nuclei suspension after FACS was typically low (~1.2×10^5/ml). The nuclei were re-concentrated by adding 200 µl of 1.8 M sucrose, 5 µl of 1M CaCl2 and 3 µl of 1M Mg(Ac)2 to 1 ml of the nuclei suspension. The mixture was incubated on ice for 15 min and centrifuged at 1800g for 15 min. Supernatant was removed and the nuclei pellet was resuspended in DPBS. Nuclei were digested using the same steps as GM12878 cells.
Antibody information: anti-Pol II-total (Abcam, ab817, lot GR3271868-2),anti-Pol II-S5 (Abcam, ab5131, lot GR3202335-5), anti-EGR1 (Santa Cruz, sc-101033, lot A1618), anti-MEF2C (Santa Cruz, sc-365862, lot B0818), anti-HDAC2 (Abcam, ab124974, lot GR97402-7)
Libraries were constructed using Accel-NGS 2S Plus DNA Library kit (Swift Biosciences) following the manufacturer’s instructions. 1× EvaGreen dye (Biotium) was added to the amplification mixture to monitor the PCR amplification. Library was eluted to 7 µl of low EDTA TE buffer. Library fragment size was examined using TapeStation (Agilent) and the concentration was quantified with KAPA Library Quantification kit (Kapa Biosystems). Libraries were pooled accordingly for sequencing by Illumina HiSeq 4000 SR50 mode.


title: RHH031: Peripheral blood monocytes from TB patient

value: donor_id A0009


title: tumor tissue control_2


title: GM12878-HDAC2-50K-1


title: ST3

status: Public on Nov 04 2021

city: NANJING

first: LIUYANG

last: Du

state: JIANGSU

address: WEIGANG NO.1

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
Control
processed data file: novel_circRNA_TPM.xls

data_processing:
Poly-N, adapter and low-quality were removed by in-house perl scripts. Quality control analysis was performed by ng_qc.
Clean reads were aligned to the Sus scrofa Ensembl 76 using Tophat v2.0.9 with the following configurations two passMode Basic --hhlibraryhtypecfrhfirststrand.
circRNAs were identified using find-circ and CIRI as a supplement. The back-spliced reads with at least two supporting reads were annotated as circRNAs.
Expression level of circRNAs was normalized by TPM (transcript per million) through the following criteria: Normalized expression = (mapped reads) / (total reads) * 1000000.
Genome_build: Sus scrofa Ensembl 76
Supplementary_files_format_and_content: novel_circRNA_TPM.xls: Excel file includes normalized values for each Sample.
Supplementary_files_format_and_content: novel_circRNA_gtf.txt
Supplementary_files_format_and_content: novel_circRNA_seq_merged.fa.txt

organism: Sus scrofa

source_name: swine testicular cells

extract_protocol:
Total RNA was isolated from uninfected or infected ST cells using SuPerfecTRITM Total RNA Isolation Reagent (Pufei) according to the manufacturer.
A total amount of 5 µg RNA per sample was used as input material for RNA sample preparation. Firstly, ribosomal RNAs were depleted by using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) to get rRNA-depleted RNAs. rRNA-depleted RNAs were further treated with RNase R (Epicentre, USA) and then were subjected to Trizol extraction. Subsequently, sequencing libraries were generated using the rRNA-depleted and RNase R digested RNAs by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: ST cells were uninfected or infected with PDCoV at a multiplicity of infection (MOI) of 10 and harvested at 11 hour post infection or without, respectively.

value: swine testicular cells

value: uninfected


title: dblmA132_S1_L004


title: ST1


title: tumor tissue control_1


title: tumor tissue with DSF treatment_3


title: PS2

description:
Infected at MOI=10 and harvested at 11 hour post infection.
processed data file: novel_circRNA_TPM.xls

value: infected by PDCoV

tag: pdcov strain


title: PS3


title: PS1


title: ST2


title: microRNA-seq from left cerebral cortex (ENCLB538JYJ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR919OSV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR919OSV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB538JYJ
size range: <30

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6CASTF1/J male adult (18-20 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

tag: description

value: B6Cast F1 DPN18-20months

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 18-20 month

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS972OCB at ENCODE; https://www.encodeproject.org/ENCBS972OCB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from layer of hippocampus (ENCLB844LMN)

description:
https://www.encodeproject.org/experiments/ENCSR744JYO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR744JYO
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB844LMN
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: unknown

value: 25 day

value: ENCBS049EMJ at ENCODE; https://www.encodeproject.org/ENCBS049EMJ/


title: microRNA-seq from left cerebral cortex (ENCLB652SRR)

description:
https://www.encodeproject.org/experiments/ENCSR919OSV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR919OSV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB652SRR
size range: <30

value: ENCBS321KXV at ENCODE; https://www.encodeproject.org/ENCBS321KXV/


title: microRNA-seq from gastrocnemius (ENCLB158BDW)

description:
https://www.encodeproject.org/experiments/ENCSR781NKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR781NKQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB158BDW
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (2 months) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND 2 months Female 03 gastrocnemius for Wold core

value: female

value: 2 month

value: ENCBS821KNX at ENCODE; https://www.encodeproject.org/ENCBS821KNX/


title: microRNA-seq from gastrocnemius (ENCLB230CET)

description:
https://www.encodeproject.org/experiments/ENCSR781NKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR781NKQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB230CET
size range: <30

value: tissue

value: B6Cast F1 PND 2 months Female 04 gastrocnemius for Wold core

value: ENCBS523ZPG at ENCODE; https://www.encodeproject.org/ENCBS523ZPG/


title: microRNA-seq from heart (ENCLB813XXE)

description:
https://www.encodeproject.org/experiments/ENCSR485TDS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR485TDS
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB813XXE
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (2 months) heart tissue

value: heart

value: B6Cast F1 PND 2 months Female 04 heart for Wold biobank

value: Barbara Wold, Caltech

value: ENCBS353NKX at ENCODE; https://www.encodeproject.org/ENCBS353NKX/


title: microRNA-seq from layer of hippocampus (ENCLB115WYH)

description:
https://www.encodeproject.org/experiments/ENCSR730GFX/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR730GFX
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB115WYH
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (36 days) layer of hippocampus tissue

value: layer of hippocampus

value: 36 day

value: The Jackson Laboratory

value: ENCBS574NYN at ENCODE; https://www.encodeproject.org/ENCBS574NYN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from layer of hippocampus (ENCLB907PGW)

description:
https://www.encodeproject.org/experiments/ENCSR730GFX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR730GFX
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB907PGW
size range: <30

value: unknown

value: ENCBS151TGO at ENCODE; https://www.encodeproject.org/ENCBS151TGO/


title: microRNA-seq from heart (ENCLB269TEH)

description:
https://www.encodeproject.org/experiments/ENCSR878DFT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR878DFT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB269TEH
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue

value: B6Cast F1 PND 2 months Male 04 heart for Wold biobank

value: male

value: ENCBS297GPP at ENCODE; https://www.encodeproject.org/ENCBS297GPP/


title: microRNA-seq from layer of hippocampus (ENCLB129YHM)

description:
https://www.encodeproject.org/experiments/ENCSR964USQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR964USQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB129YHM
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (14 days) layer of hippocampus tissue

value: tissue

value: 14 day

value: ENCBS299AJA at ENCODE; https://www.encodeproject.org/ENCBS299AJA/


title: microRNA-seq from heart (ENCLB748TNC)

description:
https://www.encodeproject.org/experiments/ENCSR485TDS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR485TDS
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB748TNC
size range: <30

value: heart

value: B6Cast F1 PND 2 months Female 03 heart for Wold biobank

value: female

value: 2 month

value: ENCBS759GYL at ENCODE; https://www.encodeproject.org/ENCBS759GYL/


title: microRNA-seq from layer of hippocampus (ENCLB581YTD)

description:
https://www.encodeproject.org/experiments/ENCSR744JYO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR744JYO
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB581YTD
size range: <30

value: layer of hippocampus

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS609MWU at ENCODE; https://www.encodeproject.org/ENCBS609MWU/


title: microRNA-seq from gastrocnemius (ENCLB649FXE)

description:
https://www.encodeproject.org/experiments/ENCSR658KLA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND25 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR658KLA
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB649FXE
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (25 days) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND25 Male 04 gastrocnemius for Wold core

value: unknown

value: The Jackson Laboratory

value: ENCBS737XNU at ENCODE; https://www.encodeproject.org/ENCBS737XNU/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from gastrocnemius (ENCLB549ZPI)

description:
https://www.encodeproject.org/experiments/ENCSR658KLA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND25 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR658KLA
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB549ZPI
size range: <30

value: tissue

value: B6Cast F1 PND25 Male 03 gastrocnemius for Wold core

value: male

value: ENCBS404WDD at ENCODE; https://www.encodeproject.org/ENCBS404WDD/


title: microRNA-seq from heart (ENCLB859GVG)

description:
https://www.encodeproject.org/experiments/ENCSR878DFT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR878DFT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB859GVG
size range: <30

value: heart

value: B6Cast F1 PND 2 months Male 03 heart for Wold biobank

value: ENCBS154PWG at ENCODE; https://www.encodeproject.org/ENCBS154PWG/


title: microRNA-seq from layer of hippocampus (ENCLB737FDP)

description:
https://www.encodeproject.org/experiments/ENCSR657KLT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND10 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR657KLT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB737FDP
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (10 days) layer of hippocampus tissue

value: layer of hippocampus

value: female

value: 10 day

value: ENCBS739AAH at ENCODE; https://www.encodeproject.org/ENCBS739AAH/


title: microRNA-seq from gastrocnemius (ENCLB976CMU)

description:
https://www.encodeproject.org/experiments/ENCSR656EWH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR656EWH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB976CMU
size range: <30

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: Barbara Wold, Caltech

value: ENCBS619XVK at ENCODE; https://www.encodeproject.org/ENCBS619XVK/


title: microRNA-seq from left cerebral cortex (ENCLB702VAN)

description:
https://www.encodeproject.org/experiments/ENCSR857OZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR857OZQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB702VAN
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (2 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND 2 months Male 04 left cerebral cortex for Wold biobank

value: unknown

value: 2 month

value: The Jackson Laboratory

value: ENCBS790MBN at ENCODE; https://www.encodeproject.org/ENCBS790MBN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from left cerebral cortex (ENCLB546ZKW)

description:
https://www.encodeproject.org/experiments/ENCSR857OZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR857OZQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB546ZKW
size range: <30

value: B6Cast F1 PND 2 months Male 03 left cerebral cortex for Wold biobank

value: male

value: ENCBS350BQS at ENCODE; https://www.encodeproject.org/ENCBS350BQS/


title: microRNA-seq from gastrocnemius (ENCLB084KSV)

description:
https://www.encodeproject.org/experiments/ENCSR656EWH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR656EWH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB084KSV
size range: <30

value: gastrocnemius

value: female

value: ENCBS138KFH at ENCODE; https://www.encodeproject.org/ENCBS138KFH/


title: microRNA-seq from layer of hippocampus (ENCLB217ETR)

description:
https://www.encodeproject.org/experiments/ENCSR642MUL/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR642MUL
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB217ETR
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (14 days) layer of hippocampus tissue

value: layer of hippocampus

value: 14 day

value: ENCBS229LCL at ENCODE; https://www.encodeproject.org/ENCBS229LCL/


title: microRNA-seq from layer of hippocampus (ENCLB638TNX)

description:
https://www.encodeproject.org/experiments/ENCSR642MUL/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR642MUL
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB638TNX
size range: <30

value: Barbara Wold, Caltech

value: ENCBS708FHL at ENCODE; https://www.encodeproject.org/ENCBS708FHL/


title: microRNA-seq from layer of hippocampus (ENCLB786KZK)

description:
https://www.encodeproject.org/experiments/ENCSR532KTV/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR532KTV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB786KZK
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (36 days) layer of hippocampus tissue

value: tissue

value: 36 day

value: ENCBS421GWA at ENCODE; https://www.encodeproject.org/ENCBS421GWA/


title: microRNA-seq from layer of hippocampus (ENCLB736PFO)

description:
https://www.encodeproject.org/experiments/ENCSR532KTV/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR532KTV
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB736PFO
size range: <30

value: unknown

value: The Jackson Laboratory

value: ENCBS154RYV at ENCODE; https://www.encodeproject.org/ENCBS154RYV/


title: microRNA-seq from gastrocnemius (ENCLB910CBG)

description:
https://www.encodeproject.org/experiments/ENCSR590FZA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND36 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR590FZA
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB910CBG
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (36 days) gastrocnemius tissue

value: B6Cast F1 PND36 Male 03 gastrocnemius for Wold core

value: ENCBS182MGW at ENCODE; https://www.encodeproject.org/ENCBS182MGW/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from gastrocnemius (ENCLB634PUH)

description:
https://www.encodeproject.org/experiments/ENCSR590FZA/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND36 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR590FZA
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB634PUH
size range: <30

value: gastrocnemius

value: B6Cast F1 PND36 Male 04 gastrocnemius for Wold core

value: male

value: ENCBS458CJW at ENCODE; https://www.encodeproject.org/ENCBS458CJW/


title: microRNA-seq from layer of hippocampus (ENCLB646FEC)

description:
https://www.encodeproject.org/experiments/ENCSR964USQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR964USQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB646FEC
size range: <30

value: layer of hippocampus

value: 14 day

value: ENCBS642ONZ at ENCODE; https://www.encodeproject.org/ENCBS642ONZ/


title: microRNA-seq from layer of hippocampus (ENCLB241VFN)

description:
https://www.encodeproject.org/experiments/ENCSR657KLT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR657KLT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB241VFN
size range: <30

value: female

value: 10 day

value: Barbara Wold, Caltech

value: ENCBS286DXZ at ENCODE; https://www.encodeproject.org/ENCBS286DXZ/


title: microRNA-seq from left cerebral cortex (ENCLB537IVM)

description:
https://www.encodeproject.org/experiments/ENCSR521EUU/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR521EUU
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB537IVM
size range: <30

source_name: Mus musculus strain B6CASTF1/J female adult (18-20 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: ENCBS833RXG at ENCODE; https://www.encodeproject.org/ENCBS833RXG/


title: microRNA-seq from left cerebral cortex (ENCLB703UTU)

description:
https://www.encodeproject.org/experiments/ENCSR521EUU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months male left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR521EUU
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB703UTU
size range: <30

value: The Jackson Laboratory

value: ENCBS774TTB at ENCODE; https://www.encodeproject.org/ENCBS774TTB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from heart (ENCLB186QTQ)

description:
https://www.encodeproject.org/experiments/ENCSR252LYK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND4 female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR252LYK
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB186QTQ
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (4 days) heart tissue

value: heart

value: B6Cast F1 PND4 Female 03 heart for Wold biobank

value: unknown

value: 4 day

value: ENCBS502QND at ENCODE; https://www.encodeproject.org/ENCBS502QND/


title: microRNA-seq from heart (ENCLB098DTJ)

description:
https://www.encodeproject.org/experiments/ENCSR252LYK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND4 female heart microRNA-seq from Mortazavi
experiment encode accession: ENCSR252LYK
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB098DTJ
size range: <30

value: B6Cast F1 PND4 Female 04 heart for Wold biobank

value: female

value: ENCBS430MXC at ENCODE; https://www.encodeproject.org/ENCBS430MXC/


title: microRNA-seq from gastrocnemius (ENCLB094KKQ)

description:
https://www.encodeproject.org/experiments/ENCSR504LWH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR504LWH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB094KKQ
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (14 days) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND14 3x Males 03 gastrocnemius for Wold core

value: male

value: 14 day

value: Barbara Wold, Caltech

value: ENCBS340HGO at ENCODE; https://www.encodeproject.org/ENCBS340HGO/


title: microRNA-seq from layer of hippocampus (ENCLB895OKF)

description:
https://www.encodeproject.org/experiments/ENCSR370PLB/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR370PLB
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB895OKF
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (18-20 months) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: hippocampus_B6Cast F1_18 - 20 months_female_6_ENC4_cDNA513

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS528DMR at ENCODE; https://www.encodeproject.org/ENCBS528DMR/


title: microRNA-seq from left cerebral cortex (ENCLB985JFM)

description:
https://www.encodeproject.org/experiments/ENCSR340GMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR340GMJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB985JFM
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (2 months) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND 2 months Female 03 left cerebral cortex for Wold biobank

value: unknown

value: 2 month

value: ENCBS121OPX at ENCODE; https://www.encodeproject.org/ENCBS121OPX/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from gastrocnemius (ENCLB625GIK)

description:
https://www.encodeproject.org/experiments/ENCSR504LWH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 male gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR504LWH
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB625GIK
size range: <30

value: gastrocnemius

value: B6Cast F1 PND14 3x Males 04 gastrocnemius for Wold core

value: ENCBS368GVV at ENCODE; https://www.encodeproject.org/ENCBS368GVV/


title: microRNA-seq from layer of hippocampus (ENCLB346QGP)

description:
https://www.encodeproject.org/experiments/ENCSR373DYT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR373DYT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB346QGP
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (2 months) layer of hippocampus tissue

value: female

value: Barbara Wold, Caltech

value: ENCBS912RBR at ENCODE; https://www.encodeproject.org/ENCBS912RBR/


title: microRNA-seq from layer of hippocampus (ENCLB752LRT)

description:
https://www.encodeproject.org/experiments/ENCSR373DYT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR373DYT
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB752LRT
size range: <30

value: layer of hippocampus

value: tissue

value: ENCBS422YFH at ENCODE; https://www.encodeproject.org/ENCBS422YFH/


title: microRNA-seq from layer of hippocampus (ENCLB267KGY)

description:
https://www.encodeproject.org/experiments/ENCSR370PLB/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 18-20 months female hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR370PLB
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB267KGY
size range: <30

value: hippocampus_B6Cast F1_18 - 20 months_female_7_ENC4_cDNA514

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS953PDK at ENCODE; https://www.encodeproject.org/ENCBS953PDK/


title: microRNA-seq from left cerebral cortex (ENCLB984EET)

description:
https://www.encodeproject.org/experiments/ENCSR340GMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months female left cortex microRNA-seq from Mortazavi
experiment encode accession: ENCSR340GMJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB984EET
size range: <30

value: left cerebral cortex

value: B6Cast F1 PND 2 months Female 04 left cerebral cortex for Wold biobank

value: unknown

value: ENCBS235YYJ at ENCODE; https://www.encodeproject.org/ENCBS235YYJ/


title: microRNA-seq from gastrocnemius (ENCLB434CUL)

description:
https://www.encodeproject.org/experiments/ENCSR501DNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation mouse PND14 female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR501DNZ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB434CUL
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (14 days) gastrocnemius tissue

value: gastrocnemius

value: B6Cast F1 PND14 3x Females 03 gastrocnemius for Wold core

value: 14 day

value: ENCBS205QFK at ENCODE; https://www.encodeproject.org/ENCBS205QFK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: microRNA-seq from gastrocnemius (ENCLB404WYI)

description:
https://www.encodeproject.org/experiments/ENCSR501DNZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND14 female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR501DNZ
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB404WYI
size range: <30

value: B6Cast F1 PND14 Female 04 gastrocnemius for Wold core

value: female

value: Barbara Wold, Caltech

value: ENCBS838OKI at ENCODE; https://www.encodeproject.org/ENCBS838OKI/


title: microRNA-seq from gastrocnemius (ENCLB360HBV)

description:
https://www.encodeproject.org/experiments/ENCSR037MYU/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND10 female gastrocnemius microRNA-seq from Mortazavi
experiment encode accession: ENCSR037MYU
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB360HBV
size range: <30

source_name: Mus musculus strain B6CASTF1/J female (10 days) gastrocnemius tissue

value: tissue

value: B6Cast F1 PND10 Female 04 gastrocnemius for Wold core

value: 10 day

value: ENCBS900JGS at ENCODE; https://www.encodeproject.org/ENCBS900JGS/


title: microRNA-seq from layer of hippocampus (ENCLB230KPN)

description:
https://www.encodeproject.org/experiments/ENCSR060REO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation mouse PND 2 months male hippocampus microRNA-seq from Mortazavi
experiment encode accession: ENCSR060REO
assay title: microRNA-seq
assembly: mm10
encode release date: 2021-09-08
lab: Ali Mortazavi, UCI
library encode accession: ENCLB230KPN
size range: <30

source_name: Mus musculus strain B6CASTF1/J male (2 months) layer of hippocampus tissue

value: layer of hippocampus

value: male

value: 2 month

value: The Jackson Laboratory

value: ENCBS762CAG at ENCODE; https://www.encodeproject.org/ENCBS762CAG/