title: sart3_mutant_1

city: Guangzhou

first: Mei

last: Wu

state: Guangdong

address: Waihuan Dong Road

department: School of Medicine

country: China

institute: South China University of Technology

data_processing:
Reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads mapped to each gene.
rMATS(3.2.5) software was used to analysis the AS event.
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw gene counts and  FPKM values for sart3 mutants and WT siblings
Supplementary_files_format_and_content: Splicing genes of different splicing events for sart3 mutants

organism: Danio rerio

source_name: Whole embryos

extract_protocol:
The sart3 mutant and the WT sibling were generated from sart3+/- intercross embryos by high-resolution melting genotyping. Then, RNA from sart3 mutant and the WT sibling  embryos was extracted with TRIzol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer’s recommendations

value: Whole embryos

tag: developmental stage

value: 4 dpf


title: sart3_mutant_2

status: Public on Sep 08 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: Veh_r2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
SM3030
Sample_3030
processed data file: RNAseq_RAW_CT_rat_hepa.txt

data_processing:
RNA-seq and ChIP-seq sequencing data was aligned to mm10 or rn5 using STAR
RNAseq data was quantified by HOMER and normalised using DESeq2
GR ChIPseq peaks and bedgraph files were generated using HOMER
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text files with DESeq2 normalised RNAseq data

molecule: polyA RNA

organism: Rattus norvegicus

source_name: primary hepatocyte

growth_protocol: Mice were housed at 12 hour light/dark cycles and trained to night restricted feeding. Primary hepatocytes were isolated from Male Sprague Dawley rats and seeded on collagen coated plates in Gibo Medium 199 + GlutaMAX (Gibco life technologies, cat: 41150-020) supplemented with 100 nM.  Decadron (dex), 1 % P/S, 4 % FCS and 1 nM human insulin. 2-3 hours after isolation, the medium was changed to Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S, 0.1 % FCS, 1 nM human Insulin and kept overnight.

extract_protocol:
RNA_seq: Primary hepatocytes: Cells were lysed in TRIzol-RNA lysis reagent  (ThermoFisher). Liver tissue: Approximately 5 mg of liver tissues were homogenized using Ultra-Thorax in TRIzol-RNA lysis reagent. RNA was purified using  EconoSpin columns (Epoc Life) according to manufacturer’s instructions.
ChIP-seq: Chromatin was prepared from 100-150mg formaldehyde crosslinked liver tissu. Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
Libraries from ChIP'ed DNA were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions. Total RNA (1000 ng) was prepared for sequencing using ribosome depletion followed by random primed cDNA synthesis or polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina.

treatment_protocol: Nr3c1fl/fl mice were injected with AAV-tbg-GFP or AAV-tbg-CRE ten days before sacrifice. The primary hepatocytes were serum depleted in Gibo Medium 199 + GlutaMAX supplemented with 1 % P/S and 0.1 % HAS for 4 hours before cells were stimulated with 500 nM dex for 2.5 hours, human insulin for 2 hours or in a combination and RNA was harvested.

tag: strain

value: Sprague Dawley

tag: aav injection

value: non treated

tag: treatment

value: vehicle

tag: tissue/cell type

value: primary hepatocyte


title: SM-GE8YP_S122_E1-50

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

organism: Macaca fascicularis

source_name: Macaque LGN Parvocellular

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: age

value: 10 yrs

value: PC

tag: facs gating

value: NeuN-positive

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster

value: P


title: WT_Sibling_Control_3

value: WT


title: 2686-6

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description:
microRNA
MicroRNAseq library prep.
validation_mature_normalized_CPM.tsv

data_processing:
Cutadapt preprocesssing was performed to remove the first three bases and adapter sequences with the parameters "cutadapt -a TCTGGAATTCTCGGGTGCCAAGGAACTCC -m 16 -u 3"; fastqs in this submission from validation cohort timepoint 5 have already been trimmed.
Cutadapt trimmed reads were processed with the nf-core smRNASeq pipeline version 1.0 using the GRCm38 genome reference (with the parameter --genome GRCm38) and adapters for the Illumina small RNA protocol (by setting --protocol Illumina). Briefly, trimmed reads were mapped using bowtie to miRBase mature miRNAs (using the parameters -k 50 --best --strata), and the number of reads mapping to each was counted using samtools stats and miRTOP. Each library was also subjected to extensive quality control, including estimation of library complexity, contamination, sequence quality, read length and depth, among other metrics detailed in the pipeline repository. Mapped reads were merged into a matrix of counts per gene for each sample at each timepoint and normalized to counts per million (CPM) reads mapped, as implemented in edgeR. Surrogate variable analysis was used to check for confounding experimental effects and none were apparent.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Expression matrices of miRNAs in rows and samples in columns.

organism: Mus musculus

source_name: PBMC

growth_protocol: The expression of the leukemogenic fusion gene Cbfb-MYH11 (CM) in conditional CM knock-in mice (Cbfb56M/+/Mx1-Cre) leads to development of AML with a median survival of approximately 4 months after induction of CM. This model recapitulates the human inv(16) AML, one of the common subsets of AML characterized by the rearrangement of chromosome 16 at bands p13 and q22, which at the molecular level creates the chimeric fusion gene CBFB-MYH11. To induce CM expression, 6-8 weeks old CM knock-in mice were injected intraperitoneally with polyinosinic–polycytidylic acid [poly (I:C)] (InvivoGen, tlrl-picw-250) at 14 mg/kg/dose every other day for a total of 7 doses. Age-matched littermates lacking the transgene were similarly treated and used as control. All mice were maintained in an Association for Assessment and Accreditation of Laboratory Animal Care–accredited animal facility and all experimental procedures were performed in accordance with federal and state government guidelines and established institutional guidelines and protocols approved by the Institutional Animal Care and Use Committee at City of Hope.

extract_protocol:
Total RNA was isolated from PBMC using AllPrep DNA/RNA Kit (Qiagen).
Testing cohort samples were allocated to randomized batches for library preparation, such that samples from each timepoint were distributed evenly over all sequencing runs. Validation cohort samples were processed in batches as collected. All libraries were prepared using the Illumina TruSeq Small RNA protocol with minor modification following the manufacturer’s instructions. Briefly, for each sample, 280 ng of total RNA was ligated to the sRNA 3′ adaptor (5’-TCTGGAATTCTCGGGTGCCAAGGAACTCC-3’) with T4 RNA Ligase 2, truncated (New England BioLabs) for 1 h at 22°C, and subsequently ligated to a 5′ adaptor: 5’-GUUCAGAGUUCUACAGUCCGACGAUCNNN-3’) with T4 RNA ligase 1 (New England BioLabs) for 1 h at 20°C. The constructed small RNA library was first reverse-transcribed using GX1 (5′- GGAGTTCCTTGGCACCCGAGA) as the RT primer then subjected to PCR amplification for 13 cycles, using the primers GX1 (5′-CAAGCAGAAGACGGCATACGAGAT[NNNNNN]GTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’) and GX2 (5′- AATGATACGGCGACCACCGAGATCTACAC[NNNNNNNN]CGACAGGTTCAGAGTTCTACAGTCCGA-3’), followed by 6% TBE PAGE gel purification with size selection (for targeted small RNAs of 17–35 nt). Individual libraries were prepared using a unique index primer (NNNNNNNN in the GX1 and GX2 primer) in order to allow for pooling of multiple samples prior to sequencing.

value: PBMC

tag: timepoint

value: CM

value: CHW

tag: Sex

value: Male


title: 2689-6

value: Ctrl

value: CW

value: Female


title: SM-GE8YP_S120_E1-50

source_name: Macaque LGN Magnocellular

value: MC

value: M


title: 2702-6


title: iCLIP_SRSF4_4

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

data_processing:
libraries sequenced usign Illumina HiSeq 2000 single end 75nt
Adapters and barcodes were removed from all iCLIP reads before mapping to the mouse mm9 genome assembly (Ensembl59 annotation) using Bowtie software (version 0.10.1).
statistically significant cross-link events (X-links), all uniquely mapping reads were used, PCR duplicates were removed using the random barcodes within the 3’adapter, X-link sites were extracted (1st nucleotide of the read) and randomized within co-transcribed regions.
Significant X-links (false discovery rate [FDR] <0.05) were calculated using normalized numbers of input X-links
Genome_build: Ensembl59
Supplementary_files_format_and_content: Significant X-links (false discovery rate [FDR] <0.05) in BED format grouped for all samples

source_name: Neonatal cardiomyocytes

growth_protocol: Neonatal cardiomyocytes were extracted from C57BL/6 mice at P0 or P1.23 A total of 8 million cells were plated in 10 cm2 plates

extract_protocol:
Mice were sacrificed with carbon dioxide, hearts were extracted, perfused with PBS and tissue was inmediatly freezed in liquid nitrogen. Total RNA was purified using RNeasy Mini Kit (Qiagen).
Briefly, crosslinked RNA was digested to lengths of 80-200 nucleotides using RNaseI (Ambion) and RNA-protein complexes were immunopurified using Protein G Dynabeads® (ThermoFisher Scientific) coupled with a goat anti-GFP antibody (D. Drechsel, MPI-CBG, Dresden). Isolated and purified RNA fragments were ligated to pre-adenylated DNA 3’ adapters (IDT) and reverse-transcribed using barcoded RT-primers and SuperscriptIV (ThermoFisher Scientific). cDNA fragments were size-selected, circularized using CircLigaseTM (Epicentre) and re-linearized by BamHI (NEB). The final cDNA libraries now containing 5’ and 3’ adapters were amplified using AccuPrime (ThermoFisher Scientific)

treatment_protocol: The following day, cells were transfected with 15 μg of SRSF4-GFP modRNA using 21 μL Lipofectamine 2000. At 48 h post-transfection, cells were irradiated once with 100 mJ UV light (254 nm)

tag: Stage

value: Neonatal cardiomyocytes


title: SM-GE8YP_S118_E1-50


title: plt1 2 C6 2

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.5.0,  including removing bases with low quality score (<20)  and cutting sequencing adaptors followed by filtering short reads.
For bulk RNA-seq, the paired-end reads of RNA-seq data were mapped to Arabidopsis thaliana genome (TAIR10) using STAR v2.7.2b. Gene abundance was determined using STAR v2.7.2b . Differentially expressed genes were detected by DESeq2.
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana hypocotyl derived callus

growth_protocol: Arabidopsis seeds were sterilized by 75% ethanol and stratified at 4℃ for 3 days. Seeds were germinated vertically and grown on 1/2 Murashige &Skoog basal (MS) medium without sucrose at 22°C under darkness for 9 d.

extract_protocol:
Samples were grind in liquid nitrogen and RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The hypocotyl explants (~1 cm in length) were detached and cultured on CIM (MS basal medium with vitamin, 2% w/v sucrose, 11 μM 2,4-Dichlorophenoxyacetic acid, 0.2 μM Kinetin) under 24-h light at 22℃ for 5-6 d.

value: CIM6d callus

value: plt1 plt2 double mutant


title: WT_Sibling_Control_2

value: Whole embryos

value: 4 dpf


title: SM-GE8YP_S117_E1-50

value: 10 yrs

value: NeuN-positive

value: Glut


title: SM-GE8YP_S119_E1-50


title: iCLIP_SRSF4_2


title: iCLIP_SRSF4_3


title: SM-GE67B_S051_E1-50

organism: Macaca nemestrina

value: 2.3 yrs


title: 2683-6

value: PBMC

value: WT


title: iCLIP_SRSF4_1


title: WT_Sibling_Control_1


title: 2720-5

value: HW

value: Male


title: 2685-6

value: CM

value: CHW


title: sart3_mutant_3


title: SM-GE8YP_S115_E1-50

value: MC


title: 2684-6


title: wt C6 2

value: wild type col-0


title: Control 3

data_processing:
libraries sequenced usign Illumina HiSeq 2000 pair end 125nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using TMM option from edgeR package
Genome_build: GRCm38 v84
Supplementary_files_format_and_content: RSEM estimated counts per sample per gene. Samples in columns, Genes in rows

source_name: Heart

extract_protocol:
Mice were sacrificed with carbon dioxide, hearts were extracted, perfused with PBS and tissue was inmediatly freezed in liquid nitrogen. Total RNA was purified using RNeasy Mini Kit (Qiagen).
A cDNA library was prepared with polyA positive selection according to Illumina protocol

value: Adult

value: Heart


title: 2718-5


title: SM-GE8YP_S114_E1-50


title: Control 2


title: SM-GE8YP_S116_E1-50

value: M


title: Callus_C6d

data_processing:
We applied fastp  with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. UMI-tools  was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to Arabidopsis thaliana genome (TAIR10) utilizing STAR  mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample.
Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 2.3.4, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction.
Supplementary_files_format_and_content: tab-delimited text files include UMI for each gene in each cell

extract_protocol:
For single-cell RNA-seq, ~150 callus at CIM 5-7 d were incubated in digest buffer (0.8 M sorbitol, 10 mM MES, 1.5% Cellulase RS, 1% Macerozyme R10, 1 mM CaCl2, 0.1% w/v BSA, 0.03% v/v β-mercaptoethanol, pH 5.7) for 1 h at room temperature and dissected under inverted microscope equipped with 10x objective lens to release the protoplast. The protoplast solution was strained through a 40-μm filter. The filtered solution was centrifuged at 500 g for 3 min, and then washed once with resuspension buffer (12% w/v sorbitol and 0.05% w/v BSA) at 4℃. The protoplast pellet was resuspended in 125 μl resuspension buffer. Cell viability of 99% was confirmed by AO/PI staining. The cell density was determined using a hemocytometer and the concentration was adjusted to 1000 protoplasts/μl.
BD Rhapsody system was used to capture the transcriptomic information of the single protoplast. Single-protoplast capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

treatment_protocol: The hypocotyl explants (~1 cm in length) were detached and cultured on CIM (MS basal medium with vitamin, 2% w/v sucrose, 11 μM 2,4-Dichlorophenoxyacetic acid, 0.2 μM Kinetin) under 24-h light at 22℃ for 6 d.

value: CIM6d callus


title: 2709-5

value: Female


title: SM-GE8YP_S112_E1-50

value: 10 yrs


title: SM-GE8YP_S113_E1-50

value: NeuN-positive


title: Control 1


title: 2705-5

value: Ctrl


title: dm_C6_2

value: wox5-1 wox7-1 double mutant


title: 2702-5

value: PBMC

value: CW


title: plt1 2 C6 1

value: plt1 plt2 double mutant


title: SRSF4_KO_3


title: dm_C6_1


title: SRSF4_KO_2


title: SM-GE8YP_S111_E1-50

value: GABA


title: SRSF4_KO_1


title: SM-GE8YP_S110_E1-50

value: Glut


title: wt_C6_2


title: 2700-5

value: CM

value: CHW


title: 453_45 °C sample 3

city: New York

first: Jonathan

middle: W.

last: Snow

address: 3009 Broadway

department: Biology

institute: Barnard College

description:
total RNA, polyA enriched
processed data file: C3v453

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera reference genome available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: comma-separated values, normalized read ouns for paired samples

organism: Apis mellifera

source_name: honey bee midgut_45 °C

extract_protocol:
Midguts were removed, stored in RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selectio
Llibrary preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

treatment_protocol: Honey bees were fed sucose solution Containing 0.5% DMSO) at either 35 °C  or 45 °C  for 4 hours.

tag: growth temperature

value: 45 °C

value: midgut


title: 2692-5


title: wt C6 1

value: wild type col-0


title: 2689-5


title: SM-GE8YP_S108_E1-50

value: MC


title: wt_C6_1

value: CIM6d callus


title: 2686-5

value: Male


title: 452_45 °C sample 2

description:
total RNA, polyA enriched
processed data file: C2v452


title: SM-GE8YP_S107_E1-50

value: 10 yrs

value: P


title: 451_45 °C sample 1

description:
total RNA, polyA enriched
processed data file: C1v451


title: SM-GE8YP_S105_E1-50

value: NeuN-positive

value: M


title: 2685-5

value: PBMC


title: 2684-5


title: wt_s5

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

description: Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v3.1 chemistry). BAM files and Feature-barcode matrices were generated using 10X Genomics Cellranger version 5.0.1

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to GRCz11 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: GRCz11
Supplementary_files_format_and_content: barcodes.tsv.gz, feature.tsv.gz, matrix.mtx.gz

source_name: wt reference hpf 10

extract_protocol: 10x Genomcis Chromium single cell preparation

value: WT

value: 10 hpf

tag: experiment

value: WT embryo


title: C2_35 °C sample 2 [re-analysis]

description:
total RNA, polyA enriched
This is duplicated sample record of GSM4138867 for the convenient retrieval of the complete raw data from SRA
processed data file: C2v452

source_name: honey bee midgut_35 °C

value: 35 °C

tag: tissue


title: C3_35 °C sample 3 [re-analysis]

description:
total RNA, polyA enriched
This is duplicated sample record of GSM4138868 for the convenient retrieval of the complete raw data from SRA
processed data file: C3v453


title: C1_35 °C sample 1 [re-analysis]

description:
total RNA, polyA enriched
This is duplicated sample record of GSM4138866 for the convenient retrieval of the complete raw data from SRA
processed data file: C1v451


title: wt_s6


title: SM-GE8YP_S106_E1-50

value: GABA


title: SM-GE8YP_S104_E1-50

value: Glut


title: wt_s4

source_name: wt reference hpf 8

value: 8 hpf


title: wt_s3


title: SM-GE8YP_S102_E1-50


title: SM-GE8YP_S109_E1-50


title: wt_s2

source_name: wt reference hpf 6

value: 6 hpf


title: 2683-5

value: Ctrl

tag: genotype


title: PC_3M_1E8_NC_2

city: Harbin

first: Yu

last: Mei

address: 92 West Dazhi Street,Nan Gang District

institute: Harbin Institute of Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（human） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

organism: Homo sapiens

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: prostate cancer cells

tag: genotype/variation

value: Mimic-negative control (NC)


title: tyr_6

source_name: tyr crispant

tag: strain

value: tyr crispant generated from wild type

value: Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo


title: SM-GE8YP_S101_E1-50

tag: donor

value: 10 yrs

value: MC

value: Low Quality


title: 2718-4

value: PBMC

tag: treatment

value: CM

value: CHW

value: Male


title: PC_3M_1E8_NC_1


title: wt_s1

value: WT

value: WT embryo


title: PC_3M_1E8_NC_3


title: tyr_7

value: 10 hpf


title: SM-GE8YP_S136_E1-50

tag: age

value: PC

tag: facs gating

value: NeuN-positive

value: Glut

value: P


title: SM-GE8YP_S100_E1-50

tag: sequencing batch

tag: cell class


title: PC_3M_1E8_3p_3

value: prostate cancer cells

value: mimic-miR-33b-3p (3p)


title: 2720-4

tag: timepoint

value: Ctrl

value: HW


title: 2708-4

tag: Sex

value: Female


title: SM-GE8YP_S103_E1-50

value: 10 yrs

value: MC

tag: cell cluster

value: M


title: 2702-4

value: PBMC

value: CW


title: 2705-4

value: Male


title: SM-GE8YP_S098_E1-50


title: SM-GE8YP_S096_E1-50

source_name: Macaque Pulvinar - Inferior

value: Pulv


title: tyr_4

value: tyr crispant generated from wild type

tag: Stage

value: 10 hpf

value: Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo


title: 2709-4

value: CM

value: CHW


title: PC_3M_1E8_3p_1

value: prostate cancer cells


title: SM-GE8YP_S099_E1-50

value: NeuN-positive

value: Glut


title: 2719-4


title: SM-GE8YP_S095_E1-50

value: GABA


title: SM-GE8YP_S097_E1-50


title: PC_3M_1E8_3p_2

value: mimic-miR-33b-3p (3p)


title: tyr_1

tag: experiment


title: sebox_3

source_name: sebox crispant

value: sebox crispant generated from wild type


title: tyr_5


title: 2692-4

tag: tissue

value: Ctrl

value: Female


title: 2690-4

value: PBMC

tag: genotype


title: tyr_3


title: SM-GE8YP_S092_E1-50

value: 10 yrs


title: 2700-4


title: SM-GE8YP_S091_E1-50


title: 2689-4

value: CW


title: sebox_2


title: 2684-4

value: Male


title: SM-GE8YP_S094_E1-50

value: Pulv


title: SM-GE8YP_S093_E1-50


title: noto_3

source_name: noto crispant

value: noto crispant generated from wild type

value: 10 hpf


title: SM-GE8YP_S088_E1-50


title: lhx1a_3

source_name: lhx1a crispant

value: lhx1a crispant generated from wild type

value: Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo


title: noto_1


title: tyr_2

value: tyr crispant generated from wild type


title: 2683-4

value: WT


title: noto_2


title: SM-GE8YP_S086_E1-50

value: NeuN-positive

value: Glut


title: 2685-4

value: CM

value: CHW


title: 2705-3

value: Ctrl

value: HW


title: SM-GE8YP_S089_E1-50

value: GABA


title: SM-GE8YP_S085_E1-50

value: 10 yrs


title: 2720-3

value: PBMC


title: lhx1a_4


title: 2686-4

value: Male


title: SM-GE8YP_S087_E1-50

value: Pulv


title: lhx1a_2


title: irx3a_2

source_name: irx3a crispant

value: irx3a crispant generated from wild type


title: SM-GE8YP_S084_E1-50


title: 2718-3


title: 2700-3

value: Female


title: lhx1a_1

value: lhx1a crispant generated from wild type

value: 10 hpf


title: irx3a_3

value: Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo


title: SM-GE8YP_S081_E1-50


title: SM-GE8YP_S083_E1-50


title: SM-GE8YP_S090_E1-50


title: 2719-3


title: flh_control_2

source_name: control of flh mutant

value: floating head mutant, +/+ and +/n1

value: Control embryos were generated by crossing heterozygotes and selecting mutants based on their morphology at 10 hpf.


title: 2731-3

source_name: PBMC


title: 2709-3


title: SM-GE8YP_S082_E1-50

value: NeuN-positive

value: Glut


title: SM-GE8YP_S079_E1-50


title: sebox_1

value: sebox crispant generated from wild type


title: flh_mut_2

source_name: flh mutant

value: floating head mutant, n1/n1

value: Mutant embryos were generated by crossing heterozygotes and selecting mutants based on their morphology at 10 hpf.


title: 2708-3

value: CM

value: CHW


title: 2689-3

value: PBMC

value: Ctrl

value: CW


title: flh_mut_1


title: 2690-3


title: 2686-3

value: Male


title: SM-GE8YP_S078_E1-50

value: 10 yrs

value: Pulv


title: 2692-3

value: Female


title: 2811Hom

city: Bethesda

first: Guohao

last: Wang

state: MD

address: 35 3c1004 Convent Dr.

department: NINDS

institute: NIH

data_processing:
8 mRNA-Seq samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing. The samples have 63 to 85 million pass filter reads with more than 90% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt software before alignment with the reference genome (Mouse - mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 97%. Unique alignment is above 82%. There are 1.47 to 7.64% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.47% ribosomal bases. Percent coding bases are between 41-48%. Percent UTR bases are 44-48%, and mRNA bases are between 89-93% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 71-76% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools. Both the normalized count and the raw count are provided as part of the data delivery.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, RawCountFile_rsemgenes, RPKMCountFile_genes_filtered

source_name: Nervous system Spinal Cord

growth_protocol: All the experimental process and research complies with NIH ethics program, policies, and guidelines. The rodent animal study protocol was approved by the Animal Care and Use Committee (ACUC) of NCI and NINDS in National Institutes of Health (NIH). All rodent breeding and maintenance were handled in accordance with the guidelines of the Animal Care and Use Committee of NCI and NINDS in NIH. All mice were bred in the animal facility at the National Cancer Institute (NCI) at Frederick and National Institute of Neurological Disorders and Stroke (NINDS) under specific pathogen-free conditions in a temperature-controlled environment with a 12-hour day/night light cycle. The 2 to10-month-old mice were used in this study and the house temperature was 75°F (23°C) with 40% humidity. Mice diet were used NIH07 rodent diet formulation (Rodent NIH-07 22.5-5) made by ZeiGLeR Bros. Inc. in Pennsylvania, U.S.A. Mice drinking water can be always accessible

extract_protocol:
Total mouse spinal cord mRNA purification was performed using Monarch® Total RNA Miniprep Kit (New England Biolabs, T2010S).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When ablation of Arf1, mice will be injected tamoxifen (100mg/kg by IP injection) for deletion of Arf1.

value: Homozygous

value: Spinal cord


title: 2700Hom


title: flh_control_1

value: floating head mutant, +/+ and +/n1

value: 10 hpf

value: Control embryos were generated by crossing heterozygotes and selecting mutants based on their morphology at 10 hpf.


title: SM-GE8YP_S072_E1-50

value: NeuN-positive

value: Glut


title: 2702-3


title: 2808Het

value: heterozygous


title: 2847Hom


title: SM-GE8YP_S071_E1-50

value: GABA


title: irx3a_1

value: irx3a crispant generated from wild type

value: Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo


title: SM-GE8YP_S077_E1-50


title: SM-GE8YP_S070_E1-50


title: SM-GE8YP_S080_E1-50


title: 2831Het


title: 2812Hom


title: SM-GE8YP_S075_E1-50


title: 2718-2

value: PBMC

value: CM

value: CHW


title: PND56 Adipocyte_5 Bulk RNAseq

city: Detroit

first: James

middle: G.

last: Granneman

state: mi

address: 6135 Woodward

department: CMMG

institute: Wayne State University

description: Lexogen 3'FWD mRNA-seq

data_processing:
Bulk-RNAseq libraries were sequenced using Illumina HiSeq 4000 with a single-end read format.  Sequencing reads were aligned to the mouse chromosome (mm10) with STAR (v 2.5.2a), and read counts were quantified with HTSeq-count using the Bluebee platform (https://www.bluebee.com).
Single cell (sc) and nuclei (sn)-RNAseq libraries were sequenced using Nextseq500.  Libraries were demultiplexed then processed using 10X Genomics Cellranger (3.0.2) pipeline.  Ambient RNA was cleaned using SoupX R package, and a corrected gene matrix generated (processed file).
Single nuclei (sn) ATAC-seq libraries were sequenced using Nextseq500. Reads were demultiplexed and further processed with the Cellranger ATAC v1.2 pipeline.  Custom peaks were called using the SnapATAC vignette  (https://github.com/r3fang/SnapATAC) using the commands --nomodel --shift 100 --ext 200 --qval 5e-2.  The custom peaks  were used to create a cell-peak matrix using the Cellranger-ATAC reanalyze pipeline (10X Genomics, v 1.2) on aggregated libraries without depth correction.  For each aggregated library, PND06 (gemwell-1), PND18 (gemwell-2), and PND56 (gemwell-3) (processed file).
Genome_build: mm10
Supplementary_files_format_and_content: Bulk RNA-seq: tab-delimited text files
Supplementary_files_format_and_content: scRNA-seq: Matrix table with gene counts
Supplementary_files_format_and_content: snATAC-seq: Aggregated HDF5 Feature Barcode Matrix Format

source_name: Adipocyte (iWAT)

extract_protocol: Lexogen mRNA 3'FWD kit from total RNA were used to generate libraries.

value: inguinal white adipose tissue

tag: developmental age

value: Postnatal day 56

value: Adipocyte

value: Male


title: SM-GE8YP_S076_E1-50

value: 10 yrs

value: Pulv


title: SM-GE8YP_S074_E1-50


title: 2807Het

value: Spinal cord


title: 2685-3


title: 2521-AN-4: S1P

city: Nashville

first: Dylan

last: Burnette

state: TN

address: 465 21st Avenue S.

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Cutadapt was used to trim adapters.
STAR was used to map reads to the human reference genome hg19.
DESeq2 was used to detect differential expression between conditions.
Genome_build: hg19
Supplementary_files_format_and_content: A count table that provides complete data with values for all features and all samples

source_name: iPSC-derived human cardiac myocytes

growth_protocol: Purchased frozen differentiated cardiac myocytes from Cellular Dynamics and thawed as per manufacturer's instructions

extract_protocol:
Cells were trypsinized and pelleted on day 9 post-thaw and RNA extraction was performed using RNAeasy extraction kit.
Stranded mRNA (polyA-selected) Library prep

treatment_protocol: Cells were treated with 1 uM of each compound or DMSO control on days 4, 6, and 8 post-thaw

tag: cell type

value: iPSC-derived human cardiac myocytes

tag: dataset name

tag: density

value: sparse (6250 cells/well)

value: S1P 1 uM


title: 2553-AN-5: XS

value: XS

value: XMU-MP-1 0.1 uM and S1P 0.1 uM


title: 2553-AN-4: S1P


title: 2719-2

tag: strain


title: 2696Het

value: heterozygous


title: 2720-2

tag: treatment

value: Ctrl

value: HW


title: 2553-AN-2: Sparse Control

value: Sparse Control

value: DMSO


title: 2553-AN-3: XMU

value: XMU

value: XMU-MP-1 1 uM


title: SM-GE8YP_S069_E1-50

tag: donor

tag: age

value: NeuN-positive

value: Glut


title: 2553-AN-1: Dense Control

value: Dense Control

value: dense (50000 cells/well)


title: PND56 Adipocyte_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue

value: Postnatal day 56

value: Adipocyte

value: Male


title: 2684-3

value: PBMC

value: CM

value: CHW


title: 2708-2

value: Female


title: PND56 Adipocyte_4 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq


title: 2521-AN-5: XS

value: iPSC-derived human cardiac myocytes

value: XS

value: sparse (6250 cells/well)

value: XMU-MP-1 0.1 uM and S1P 0.1 uM


title: SM-GE8YP_S067_E1-50

value: 10 yrs

value: Pulv

tag: facs gating

tag: sequencing batch

value: GABA


title: 2683-3

tag: timepoint

value: Ctrl

value: WT


title: SM-GE8YP_S065_E1-50

value: NeuN-positive

tag: cell class


title: 2709-2

tag: Sex


title: PND56 Adipocyte_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue

value: Postnatal day 56


title: 2521-AN-1: Dense Control

value: Dense Control

value: dense (50000 cells/well)

value: DMSO


title: SM-GE8YP_S068_E1-50

value: Glut

tag: cell cluster


title: SM-GE8YP_S063_E1-50

value: Low Quality


title: 2731-2

value: PBMC

value: CM

value: CHW

value: Female


title: 2391-AN-5: XS

value: iPSC-derived human cardiac myocytes

value: XS

value: sparse (6250 cells/well)

value: XMU-MP-1 0.1 uM and S1P 0.1 uM


title: 2692-2

value: Ctrl

value: CW


title: 2521-AN-3: XMU

value: XMU

value: XMU-MP-1 1 uM


title: PND56 LinNeg SVC_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

source_name: Lineage negative stromal cells (iWAT)

value: inguinal white adipose tissue

value: Postnatal day 56

value: Lineage Negative Stromal Cells

value: Male


title: 2705-2

value: HW


title: SM-GE8YP_S066_E1-50

value: 10 yrs

value: Pulv

value: NeuN-positive

value: GABA


title: SM-GE8YP_S064_E1-50

value: Glut


title: PND56 Adipocyte_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: Adipocyte


title: 2521-AN-2: Sparse Control

value: iPSC-derived human cardiac myocytes

value: Sparse Control

value: sparse (6250 cells/well)

value: DMSO


title: 2690-2

value: PBMC

value: CM

value: CHW

value: Female


title: 2702-2

value: Ctrl

value: CW


title: PND56 LinNeg SVC_5 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue

value: Postnatal day 56

value: Lineage Negative Stromal Cells

value: Male


title: 2700-2


title: SM-GE8YP_S062_E1-50

value: 10 yrs

value: Pulv

value: NeuN-positive


title: 2689-2


title: PND56 LinNeg SVC_4 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq


title: PND56 LinNeg SVC_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq


title: 2686-2


title: SM-GE8YP_S060_E1-50

value: Glut


title: SM-GE8YP_S059_E1-50


title: 2391-AN-2: Sparse Control

value: iPSC-derived human cardiac myocytes

value: Sparse Control


title: 2391-AN-1: Dense Control

value: Dense Control

value: dense (50000 cells/well)

value: DMSO


title: 2391-AN-3: XMU

value: XMU

value: sparse (6250 cells/well)

value: XMU-MP-1 1 uM


title: SM-GE8YP_S061_E1-50


title: PND18 Adipocyte_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: Postnatal day 18

value: Adipocyte


title: PND18 Adipocyte_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue


title: PND56 LinNeg SVC_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: Postnatal day 56

value: Lineage Negative Stromal Cells


title: Day10 EPS-blastoids

city: beijing

first: zheying

last: min

address: Yiheyuan road NO.5

institute: Peking University

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters, based on 10x Genomics pre-built hg20 reference genome. EPS-blastoids on day 6 were recovered about 10,000 cells, and blastoids IVC structures on day 8 and day 10 were recovered 6156 and 4348 cells, respectively.
The R package Seurat 3.0.12 was used to analyze feature-barcode matrix as following steps: 1, Cells whose gene numbers were less than 200, or unique features counts over 9000, or gene numbers ranked in the top 1%, or mitochondrial gene ratio was more than 20% according to quality control matrix plots, were regarded as abnormal and filtered out.
2, UMI counts were normalized with NormalizeData function by default settings. A non-linear dimensionality reduction was performed using PCA, clustered with resolution setting at 0.5-2, and visualized by TSNE and UMAP.
3, Differentially expressed genes (DEGs) in clusters were determined by the FindAllMarkers function. For the DEGs, the GO terms in biological process were enriched using DAVID. Heatmap of DEGs between clusters was performed with R package pheatmap.
Genome_build: hg20
Supplementary_files_format_and_content: processed datat files included the tsv files containing information on barcodes and gene annotations, and the mtx files containing gene umi counts.

source_name: Blastoids generated from EPS cells

growth_protocol: The cells culturing conditions were as follows: 37°C, 5% CO2 and saturated humidity. Human EPS cells were differentiated with BMP4 for 3-4 days. On day 0, the cultured EPS cells were digested into single cells by TrypLE, and the feeder was removed by pasting twice on 0.5% gelatin for 15-20 minutes each time. The EPS cells were collected, centrifuged and seeded into BMP4 differentiation medium. After 3 days of differentiation, cells were dissociated into single cells with 0.05% trypsin. Mix the BMP4 treated cells (1×10e5 cells) and EPS cells (2×10e4 cells) together following 5:1 ratio to total 1.2×10e5 cells per well with 0.5 ml culture medium, and then seeded into one well of 24-well aggreWell400 culture plate pretreated with anti-adherence rinsing solution following instruction (Stem Cell Technologies, #07010). The culture medium was slightly changed without disturbing aggregates in the V-shape bottom every day and aggregates were collected on day 6. The culture medium of human EPS-blastoids is composed of EPS medium and IVC1 medium in a ratio of 1.5:1 (v/v).  The blastoids were collected on day 6, and transferred to the 8-well plate (treated with Matrigel 30 minutes in advance), and cultured with IVC1 for 2 days. On day8, observe whether blastoid was adherent to the bottle of the dish or not, and replace the culture medium with IVC2 for further culture if the blastoid which was adherent to the wall till to day 10. IVC1 medium is composed of Advanced DMEM/F12, 20% Heat-inactivated FBS, 2mM L-glutamine, 100U/mL penicillin and streptomycin, 1% ITS-X, 1% sodium pyruvate，8nM β-estradiol, 200ng/mL progesterone, 2 μM Y27632 and 25 μM N-Acetyl-L-cysteine. IVC2 medium is composed of Advanced DMEM/F12, 30% Knockout serum, 2mM L-glutamine, 100U/mL penicillin and streptomycin, 1% ITS-X, 1% sodium pyruvate，8nM β-estradiol, 200ng/mL progesterone, 2 μM Y27632 and 25 μM N-Acetyl-L-cysteine.

extract_protocol:
EPS-blastoids were picked up by mouth pipette and washed with PBS containing 0.05% BSA. About 200 blastoids on day 6, 40 blastoids IVC structures on day 8 and 20 blastoids IVC structures on day 10 were collected for single-cell RNA-seq. Samples on day 6 were dissociated with enzyme mix composed of 0.5×Versene (Lonza, 17711E), 0.5×Accumax (STEMCELL Technologies, 07921) and 0.05×DNaseI (STEMCELL Technologies, 07900) at 37°C for 30 min with agitation and terminated by 5% BSA in PBS. Samples on day 8 or 10 were dissociated with enzyme mix composed of 0.25% Trypsin (Thermo Fisher Scientific, 25200056), and 0.05×DNaseI (STEMCELL Technologies, 07900) at 37°C for 15 min with agitation and terminated by 5% BSA in PBS. Dissociated cells were repeated pipetting and washed with PBS containing 0.05% BSA.
Dissociated cells were repeated pipetting and washed with PBS containing 0.05% BSA. Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3(10×Genomics, 1000075). The cell suspension (300-600 living cells per microliter determined by Count Star, about 20,000 dissociated cells each sample) were loaded onto the Chromium Single Cell B Chip (10×Genomics, 1000074) and processed in the Chromium single cell controller (10×Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.  Finally, sequencing was performed on the Illumina Novaseq6000 sequencer with a sequencing depth of at least 60,000 reads per cell and 150 bp (PE150) paired-end reads (performed by Novogene, Tianjin).

tag: type

value: synthetic embryos

tag: developmental stage

value: female


title: PND18 Adipocyte_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: tissue

value: Male


title: 2684-2

value: PBMC

value: CM

tag: genotype

value: CHW


title: 2685-2


title: Day8 EPS-blastoids


title: 2683-2

value: Ctrl

value: WT


title: 2391-AN-4: S1P

tag: cell type

value: iPSC-derived human cardiac myocytes

value: S1P 1 uM


title: PND18 LinNeg SVC_4 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: developmental age


title: SM-GE8YP_S056_E1-50

source_name: Macaque LGN Parvocellular

value: 10 yrs

value: PC

value: NeuN-positive

value: Glut

value: P


title: SM-GE8YP_S058_E1-50

value: Pulv


title: E440-Rib

city: Edmonton

first: Fred

last: Berry

state: AB

address: 3002D Li Ka Shing Centre, University Of Alberta, University Of Alberta

country: Canada

institute: University of Alberta

data_processing:
Read were aligned to mouse reference genome GRCm38 using HISAT2 (version 2.1.0) and STAR (version 2.7.6) after quality check
After genome index was generated, STAR was used to align the reads to the genome with the parameters --runThreadN 32 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMstrandField intronMotif --chimSegmentMin 20 --chimOutType   SeparateSAMold --quantMode TranscriptomeSAM GeneCounts
For HISAT2, genome index was build and reads were aligned to the genome after extracting the splice sites from hisat2_extract_splice_sites.py script on M25 release from gencode with the parameters  -x M25_index --known-splicesite-infile M25_splice_sites.txt -p 16
RSEM (version 1.2.31) was used to quantify STAR's output using the parameters --bam -p 16 --paired-end
featureCounts (version 1.6.0) was used to quanify HISAT2's output using the parameters  -t exon -g gene_id
DESeq2 (version 1.26.0) was used for the differential gene expression analysis from RSEM and featureCounts output. The final output was a list of genes with significant p-value (<0.05) after correction for multiple testing with a false discovery rate of less than 0.1. A combined list of common genes was obtained by averaging the genes with a filtered log2 fold change ± 1
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM tab-limited results files with FPKM and TPM values for each sample
Supplementary_files_format_and_content: featureCounts tab-limited count data file for each sample
Supplementary_files_format_and_content: A comma separated file with a list of differentialy expressed genes from RSEM-DESeq2 workflow with log2FoldChange values with gene annotation for each sample
Supplementary_files_format_and_content: A comma separated file with a list of differentialy expressed genes from featureCounts-DESeq2 workflow with log2FoldChange values with gene annotation for each sample
Supplementary_files_format_and_content: An excel file of common genes with consistent differential expression log2 fold change values between both the pipelines

source_name: Rib

extract_protocol:
Rib cages from 16.5 dpc embryos were dissected and cleaned of connective tissue before freezing in liquid nitrogen. RNA was isolated using QIAgen RNeasy Mini kits.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rib

value: embryonic day 16.5


title: E433-Rib


title: SM-GE8YP_S057_E1-50


title: PND18 LinNeg SVC_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue

value: Postnatal day 18

value: Lineage Negative Stromal Cells


title: Day6 EPS-blastoids

value: synthetic embryos

value: female


title: SM-GE8YP_S053_E1-50


title: Crypto 3

city: Münster

first: Nina

last: Neuhaus

address: Albert-Schweitzer-Campus 1

department: Centre of Reproductive Medicine and Andrology

country: Germany

institute: University Hospital of Münster

data_processing:
True Cellular Barcode identification and read quantification with Alevin (0.13.1), with a the flags "--chromium", "--useCorrelation", "-l ISR" and "--expectCells 6000" and providing lists of mitochondrail and ribosomal genes. The index was created on "gencode.v30.transcripts.fa", providing the "--gencode" option.
Counts were imported into Seurat (3.0.2),  cells were filtered which had a total expressed gene count less than 200.
Normalization was carried out with sctransform (0.2.0), while regressing for mitochondrial gene count content and total RNA count. A increased number of variable features (5000) was used in this process.
Sample Integration was performed with Seurats Anchor Integration technique, using 5000 features for the anchor finding process.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab separated matrix of the raw Alevin gene counts per cell for each sample
Supplementary_files_format_and_content: Tab separated matrix of the integrated, normalized counts per cell
Supplementary_files_format_and_content: Metadata table with additional information for each cell

source_name: Testicular tissue

extract_protocol:
Adult human testis biopsies were obtained from three normal and three cryptozoospermic patients undergoing therapeutic testicular sperm extraction. For each patient, a single cell suspension was obtained using a two-step enzymatic digestion.
12.000 cells per patient (normal=3; crypto=3) were resuspended in MEMα at a concentration of 500 cells/μl and loaded onto the Chromium Single Cell A Chip. The library preparation was performed following the kit instructions (Chromium Single Cell Kit [v2 chemistry]). Briefly ~6.000 cells per patient were captured by the 10x Genomics Chromium controller, after cDNA synthesis, 12-14 cycles were used for library amplification. The resulting libraries were quantified using the Lab901 TapeStation system (Agilent) before proceeding with shallow sequencing on a NextSeq-550 sequencer (Illumina) as a quality control measure. The final, deep sequencing was performed on a NovaSeq 6.000 sequencer (Illumina), using 2 × 150 bp paired-end sequencing.

tag: diagnosis

value: Cryptozoospermia

tag: age (years)

tag: ejaculate volume (ml)

tag: total sperm count (millions)

tag: sperm concentration (million/ml)

tag: total testosterone (>12 nmol/l)

tag: shbg (11-71 nmol/l)

tag: free testosterone (>250 pmol/l)

tag: prolactin (<500 mu/l)

tag: estradiol (<250 pmol/l)

tag: testicular volume (ml)

tag: bergmann-kliesch score

tag: % tubules with elongated spermatids

tag: % tubules with round spermatids

tag: % tubules with spermatocytes

tag: % tubules with spermatogonia

tag: % tubules sertoli cell only

tag: % tubular shadows

tag: retrieval of sperm from the tese

value: Yes

tag: karyotype

tag: cftr deletion

value: Not available

tag: azf deletion

value: No deletion


title: PND18 LinNeg SVC_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: strain

tag: tissue

tag: developmental age

tag: cell type

tag: Sex

value: Male


title: SM-GE8YP_S051_E1-50

tag: donor

tag: age

value: 10 yrs

value: PC

tag: facs gating

tag: sequencing batch

tag: cell class

tag: cell cluster


title: SM-GE8YP_S055_E1-50

value: NeuN-positive

value: GABA


title: Crypto 1

tag: diagnosis

tag: age (years)

tag: ejaculate volume (ml)

tag: total sperm count (millions)

tag: sperm concentration (million/ml)

tag: total testosterone (>12 nmol/l)

tag: shbg (11-71 nmol/l)

tag: free testosterone (>250 pmol/l)

tag: prolactin (<500 mu/l)

tag: estradiol (<250 pmol/l)

tag: testicular volume (ml)

tag: bergmann-kliesch score

tag: % tubules with elongated spermatids

tag: % tubules with round spermatids

tag: % tubules with spermatocytes

tag: % tubules with spermatogonia

tag: % tubules sertoli cell only


title: SM-GE8YP_S052_E1-50

tag: donor

tag: age

tag: facs gating

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster


title: PND18 LinNeg SVC_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: strain

tag: tissue

tag: developmental age

tag: cell type

tag: Sex


title: Normal 1

tag: diagnosis

value: Obstructive azoospermia

tag: age (years)

tag: ejaculate volume (ml)

tag: total sperm count (millions)

tag: sperm concentration (million/ml)

tag: total testosterone (>12 nmol/l)

tag: shbg (11-71 nmol/l)

tag: free testosterone (>250 pmol/l)

tag: prolactin (<500 mu/l)

tag: estradiol (<250 pmol/l)

tag: testicular volume (ml)

tag: bergmann-kliesch score

tag: % tubular shadows

tag: retrieval of sperm from the tese

tag: karyotype

tag: cftr deletion

tag: azf deletion


title: SM-GE8YP_S040_E1-50

tag: donor

tag: age

tag: facs gating

tag: sequencing batch

tag: cell class

tag: cell cluster

value: P


title: PND06 LinNeg SVC_4 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: strain

tag: tissue

value: inguinal white adipose tissue

tag: developmental age

value: Postnatal day 06

tag: cell type

tag: Sex


title: E423-Rib

value: Rib

value: embryonic day 16.5

tag: genotype


title: EU236

city: Pontedera (PI)

first: Gianni

last: Ciofani

address: Viale Rinaldo Piaggio 34

country: Italy

institute: Istituto Italiano di Tecnologia

description: polyadenylated RNA

data_processing:
Sequencing was done on a HiSeq 2500 (Illumina) sequencer, in 2x250 bp paired-end configuration.  Illumina CASAVA was used for base-calling. Raw sequence data generated from the sequencer were converted to FASTQ files.
Low-quality data were removed, and reads were trimmed to remove possible adapter sequences by using Trimmomatic v.0.36.29. For small RNA samples, only trimmed reads with a length comprised between 15 and 31 nucleotides were retained.
Polished sequences from standard (polyadenylated RNA) libraries were mapped to the reference mouse genome (GRCm38.p6) found at Ensembl30 with STAR aligner31 v.2.5.2b, and BAM files were thus generated.
Unique gene hit counts for genes were computed via featureCounts32 from the Subread package33 v.1.5.2. Only unique reads falling within exon regions were counted.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: featureCounts output files containing unique gene hit counts for polyadenylated RNAs.

source_name: C2C12 proliferating myoblasts

growth_protocol: C2C12 myoblasts (ATCC CRL-1772) at passage 6-10 were seeded at a density of 1,500 cells/cm2 on Thermanox coverslips (1.05 x 2.20 cm2) positioned at the bottom of ad hoc-prepared polydimethylsiloxane multiwell plates at L-96 h (where “L” stands for launch time). At L-72 h, samples were transferred to twelve experiment units (EUs, KEU-ST developed by Kayser Italia and qualified for flight to the ISS) loaded with cell culture medium (100 μg/ml FBS-coated NC dispersion in reservoir M1 of six EUs, whereas the remaining ones did not contain nanoparticles), saline solution (Dulbecco’s phosphate buffered saline with Ca2+/Mg2+, Gibco 14040141 in reservoir S) for cell rinse prior to fixation, and a fixative solution (RNAlater, Ambion AM7020 in reservoir F) for nucleic acid preservation. EUs (n=3 for each experimental class) were enclosed in experiment containers (ECs, KIC-SL developed by Kayser Italia and qualified for flight to the ISS) ensuring second-level containment and interface with the European Space Agency (ESA) Kubik incubator facility on board the ISS. Passive conditioned temperature (25-30°C) was kept from handover until hardware installation in Kubik incubator (set at 37°C) on board the ISS. Temperature was recorded with iButton data loggers every minute from completion of hardware assembly and verification (L-38 h, t=0 dd in Figure 1) until experiment end. Upload occurred with a Dragon/Falcon 9 vector (SpaceX CRS-17 mission). At L+81 h, ECs were placed in the Kubik incubator set at 37°C, and five fluidic activations were automatically performed at days 3, 5, 7, and 9 post launch. Activations 4 and 5 were in particular performed at day 9 (activation 5 with 5 min delay). After 2 h from fixation, the ECs were transferred to the MELFI refrigerator and stowed at -80°C until re-entry. Once the space experiment flight time and temperature profiles were known, the whole experiment was repeated on ground in the KEU-ST and KIC hardware with the support of a Kubik Interface Simulation Station (KISS) module, placed inside a laboratory tissue culture incubator.

extract_protocol:
Cell cultures were transferred to 2 ml test tubes, covered with their supernatant (containing over 70% of RNAlater) and centrifuged at 16,000 g for 15 min at 4°C. The supernatant was carefully removed leaving a volume of 100 μl to prevent cell loss. MirVana PARIS kit (Ambion AM1556) was used for cell lysis, as well as for following RNA extraction and purification procedures. Cell lysis was performed by pipetting ice-cold cell disruption buffer (300 μl) on the cell culture-bearing support, by vortexing for 30 s and by placing samples on ice every 10 s. A 1.5% β-mercaptoethanol denaturing solution (400 μl) was added to each tube; after a 5 min incubation on ice, an acid-phenol:chloroform solution (800 μl) was added to the lysate. After a 30 s agitation with vortex, the support was removed and samples were centrifuged at 10,000 g for 20 min. The aqueous phase (700 μl) from each sample was transferred to another clean tube, and 1.25 volumes of 99.9% ethanol (875 μl) were added. Each solution was then loaded twice on a filter column in a collection tube, and centrifuged at 15,000 g for 70 s. The eluate was discarded, and complete miRNA Wash Solution 1 (700 μl) was added for centrifugation at 15,000 g for 1 min. The eluate was again discarded, and complete Wash Solution 2/3 (500 μl) was added twice for centrifugation at 15,000 g for 1 min. The eluate was again discarded, and the filter column was fully dried prior to transfer to a clean collection tube. RNAse-free water (40 μl) was deposited in each filter column and incubated for 10 min, and then total RNA (including small RNAs) was eluted by centrifugation at 15,000 g for 5 min.
Standard libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, polyadenylated fractions were enriched, fragmented and reverse-transcribed (first and second strand cDNAs). Ends were repaired, 5’-phosphorilated and poly(A)-tailed. Resulting sequences were ligated to universal adapters and polymerase chain reaction (PCR)-amplified. Small RNA (chiefly miRNA) libraries were prepared aside, by ligating adapters selectively to those 5’- and 3’-ends processed by the endoribonuclease Dicer; resulting sequences were also reverse-transcribed and amplified by PCR.
Ultra-Low Input RNA-Seq (GeneWiz) pipeline

treatment_protocol: See "growth protocol".

tag: experimental class type

value: F

tag: treatment

value: with nanoceria

tag: regime

value: on land


title: SM-GE8YP_S054_E1-50


title: PND06 Adipocyte_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: Adipocyte


title: Crypto 2

tag: diagnosis

value: Cryptozoospermia

tag: age (years)

tag: ejaculate volume (ml)

tag: total sperm count (millions)

tag: sperm concentration (million/ml)

tag: total testosterone (>12 nmol/l)

tag: shbg (11-71 nmol/l)

tag: free testosterone (>250 pmol/l)

tag: prolactin (<500 mu/l)

tag: estradiol (<250 pmol/l)

tag: testicular volume (ml)

tag: bergmann-kliesch score

tag: % tubules with elongated spermatids

tag: % tubules with round spermatids

tag: % tubules with spermatocytes

tag: % tubules with spermatogonia

tag: % tubules sertoli cell only

tag: % tubular shadows

tag: retrieval of sperm from the tese

value: Yes

tag: karyotype

tag: cftr deletion

value: Not available

value: No deletion


title: SM-GE8YP_S049_E1-50

tag: donor

tag: age

value: 10 yrs

value: PC

tag: facs gating

value: NeuN-positive

tag: sequencing batch

tag: cell class

tag: cell cluster


title: Normal 3

tag: diagnosis

value: Obstructive azoospermia

tag: age (years)

tag: ejaculate volume (ml)

tag: total sperm count (millions)

tag: sperm concentration (million/ml)

tag: total testosterone (>12 nmol/l)

tag: shbg (11-71 nmol/l)

tag: free testosterone (>250 pmol/l)

tag: prolactin (<500 mu/l)

tag: estradiol (<250 pmol/l)

tag: testicular volume (ml)

tag: azf deletion


title: Interacting S.co ΔcvnD8 -rep3 (2020)

city: Berkeley

first: Matthew

middle: F

last: Traxler

state: CA

address: 311 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
Reads were cleaned and trimmed using trimmomatic version 0.33.0
mapping to the genome was done using bowtie2 version 2.2.4.1
reads were counted with HTSeq version 0.11.3
differential expression was tested using DESeq2 version 1.26.0 on R version 3.6.3
Genome_build: Streptomyces coelicolor A3(2) complete genome AL645882
Supplementary_files_format_and_content: tab-delimited text file with the read counts for each gene

organism: Streptomyces coelicolor

source_name: Bacterial patches

growth_protocol: 0.5ul of a 2x10^8 cfu/ml Streptomyces coelicolor spore stock was spotted on ~2mm think  ISP2 agar plates and grown at 30C for 4 days

extract_protocol:
Biomass was scraped off agar plates and frozen in liquid nitrogen followed by grinding with mortar and pestle and addition of trizol. The Zymogen Direct-zol RNA miniprep kit (R2051) was used to purify the RNA, with the optional DNase treatment step included
RNA preparation was done by the UC Berkeley Functional Genomics Laboratory. Briefly, rRNA was removed using the Illumina Ribo-Zero rRNA removal kit (bacteria) and the remaining RNA was prepared with a Wafergen PrepX RNA library prep kit for Illumina. Indexing PCR was performed using in-house dual indexed primers and 14 cycles.

treatment_protocol: Interacting patches had 0.5ul of a 8x10^8 Amycolatopsis sp. AA4 stock spotted 0.75cm away

tag: strain

value: {delta}SCO6940 (cvnD8)

tag: treatment

value: interacting


title: Normal 2

tag: bergmann-kliesch score

tag: % tubules with elongated spermatids

tag: % tubules with round spermatids

tag: % tubules with spermatocytes

tag: % tubules with spermatogonia

tag: % tubules sertoli cell only

tag: % tubular shadows

tag: retrieval of sperm from the tese

tag: karyotype

tag: cftr deletion

value: p.Phe508del +   Variant with variable penetrance p.(Arg117His)


title: E435-Rib

tag: tissue

value: Rib

tag: age

tag: genotype

value: wild type


title: E434-Rib

value: embryonic day 16.5


title: PND06 Adipocyte_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: inguinal white adipose tissue

tag: developmental age

value: Postnatal day 06

tag: cell type

tag: Sex

value: Male


title: SM-GE8YP_S038_E1-50

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: mm10, Mmul_10

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

tag: facs gating

tag: sequencing batch

tag: cell class

value: Glut

tag: cell cluster

value: P


title: PND06 Adipocyte_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

tag: strain

value: Adipocyte


title: EU236-smallRNA

description: Dicer-cut small RNA

tag: experimental class type

value: F

tag: treatment

value: with nanoceria

tag: regime

value: on land


title: Interacting S.co ΔcvnD8 -rep1 (2020)


title: SM-GE8YP_S037_E1-50

value: 10 yrs

value: PC

value: NeuN-positive


title: EU228

description: polyadenylated RNA


title: EU228-smallRNA

description: Dicer-cut small RNA


title: SM-GE8YP_S039_E1-50


title: PND06 LinNeg SVC_3 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq

value: Lineage Negative Stromal Cells


title: Interacting S.co ΔcvnD8 -rep2 (2020)

value: {delta}SCO6940 (cvnD8)

value: interacting


title: SM-GE8YP_S036_E1-50


title: SM-GE8YP_S035_E1-50


title: PND06 LinNeg SVC_1 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq


title: RV_8h rep3

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

data_processing: The transcript abundance is quatifiy using Kallisto.

source_name: heart

extract_protocol:
Heart is isolated from 12 weeks old mice. 10 mL HTK solution was infused for preservation. Isolated hearts are then stored in ice-cold HTK for 0, 4, and 8hs, then connect to ex vivo perfusion system. After 1h of perfusion in Krebs buffer, the LV and RV was harvested and snap-freezed in liquid nitrogen. Total RNA from LV and RV was then isolated using Trizol followed by on column DNAse I digestion using qiagen RNeasy Mini kit.
1 µg total RNA was used for RNA library construction using NEB ultraII directional kit.

value: 12 weeks

tag: time point


title: PND06 LinNeg SVC_2 Bulk RNAseq

description: Lexogen 3'FWD mRNA-seq


title: Interacting S.co ΔcvnC8 -rep3 (2020)

value: {delta}SCO6941 (cvnC8)


title: E420-Rib

value: Rib

value: embryonic day 16.5

value: wild type


title: EU226-smallRNA

description: Dicer-cut small RNA


title: Interacting S.co ΔcvnC8 -rep2 (2020)


title: RV_8h rep2


title: SM-GE8YP_S034_E1-50

value: Glut


title: EU231

description: polyadenylated RNA

value: E

value: without nanoceria


title: Interacting S.co ΔcvnC8 -rep1 (2020)


title: RV_8h rep1


title: Interacting S.co ΔcvnB8 -rep3 (2020)

value: {delta}SCO6942 (cvnB8)


title: SM-GE8YP_S033_E1-50

value: P


title: EU226

description: polyadenylated RNA

value: F

value: with nanoceria

value: on land


title: EU231-smallRNA

description: Dicer-cut small RNA


title: RV_4h rep3


title: Interacting S.co WT -rep3 (2020)

value: WT


title: RV_4h rep2


title: EU230-smallRNA

description: Dicer-cut small RNA


title: SM-GE8YP_S031_E1-50

value: 10 yrs

value: PC

value: NeuN-positive


title: Interacting S.co ΔcvnB8 -rep1 (2020)

value: interacting


title: SM-GE8YP_S032_E1-50


title: RV_0h rep3

value: 12 weeks


title: EU229

description: polyadenylated RNA


title: EU229-smallRNA

description: Dicer-cut small RNA


title: RV_4h rep1


title: SM-GE8YP_S030_E1-50


title: EU189-smallRNA

description: Dicer-cut small RNA

value: D

value: in space with gravity


title: SM-GE8YP_S029_E1-50


title: EU190-smallRNA

description: Dicer-cut small RNA


title: Interacting S.co WT -rep1 (2020)


title: Interacting S.co WT -rep2 (2020)


title: RV_0h rep2


title: RV_0h rep1


title: SM-GE8YP_S025_E1-50


title: LV_8h rep1


title: SM-GE8YP_S027_E1-50

value: GABA


title: EU190

description: polyadenylated RNA


title: Isolated S.co ΔcvnD8 -rep2 (2020)

value: {delta}SCO6940 (cvnD8)

value: isolated


title: SM-GE8YP_S028_E1-50

value: Glut


title: LV_8h rep2


title: SM-GE8YP_S024_E1-50

source_name: Macaque LGN Magnocellular

value: MC


title: SM-GE8YP_S026_E1-50

value: P


title: Isolated S.co ΔcvnD8 -rep3 (2020)


title: LV_8h rep3


title: EU188

description: polyadenylated RNA


title: SM-GE8YP_S023_E1-50


title: Isolated S.co ΔcvnD8 -rep1 (2020)


title: Isolated S.co ΔcvnC8 -rep1 (2020)

value: {delta}SCO6941 (cvnC8)


title: EU230

description: polyadenylated RNA

value: E

value: without nanoceria


title: Isolated S.co ΔcvnC8 -rep3 (2020)


title: LV_4h rep2


title: EU187-smallRNA

description: Dicer-cut small RNA

value: C


title: EU188-smallRNA

description: Dicer-cut small RNA

value: with nanoceria


title: Interacting S.co ΔcvnB8 -rep2 (2020)

value: {delta}SCO6942 (cvnB8)


title: EU189

description: polyadenylated RNA


title: Isolated S.co ΔcvnC8 -rep2 (2020)


title: LV_4h rep3


title: LV_4h rep1


title: SM-GE8YP_S021_E1-50

value: 10 yrs

value: NeuN-positive


title: Isolated S.co ΔcvnB8 -rep1 (2020)


title: EU187

description: polyadenylated RNA


title: LV_0h rep3

value: 12 weeks


title: LV_0h rep2


title: Isolated S.co ΔcvnB8 -rep3 (2020)


title: SM-GE8YP_S018_E1-50


title: LV_0h rep1


title: SM-GE8YP_S020_E1-50


title: EU186-smallRNA

description: Dicer-cut small RNA


title: Isolated S.co ΔcvnB8 -rep2 (2020)


title: Isolated S.co WT -rep1 (2020)

value: WT


title: SM-GE8YP_S017_E1-50


title: Isolated S.co WT -rep2 (2020)


title: EU186

description: polyadenylated RNA

value: in space with gravity


title: EU185-smallRNA

description: Dicer-cut small RNA


title: Isolated S.co WT -rep3 (2020)


title: nRnY

city: Austin

first: Yu Jin

last: Jang

state: Texas

address: 2506 Speedway, NMS 4.246

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Droplet-based sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.0.2, 10x Genomics Inc) using the Mus musculus genome (mm9,GRCm38) (official Cell Ranger reference, version 1.2.0).  Cells were filtered by custom cutoff (more than 500 and less than 7000 detected genes, more than 2000 UMI count) to remove potential empty droplets and doublets.
Downstream analysis included data normalisation, highly variable gene detection, log transformation, principal component analysis, neighbourhood graph generation and Louvain graph-based clustering, which was done by python package scanpy (version 1.3.6) using default parameters.
Genome_build: Mus musculus, mm9/GRCm38
Supplementary_files_format_and_content: raw fastq files and  mtx/tsv format for matrix, barcode, and genes

source_name: Non_lineage labelled cells collected at day 28 post injury

growth_protocol: Mice for the lineage tracing and injury experiments were  bred and maintained under specific-pathogen-free conditions at the Cambridge Stem Cell Institute and Gurdon Institute of University of Cambridge.

extract_protocol:
For lineage-labeled cells from Red2-NotchN1ICD mice, YFP+CD45-CD31-EpCAM+ or RFP+CD45-CD31-EpCAM+ cells were sorted at day 28 post bleomycin injury (4 mice were pooled for each experiment). For non-lineage-labeled cells isolated from Red2-NotchN1ICD mice in parallel with experiment of lineage-labeled cells, we combined the cells of EpCAM+RFP-RFP- and EpCAM- population with a ratio of 1:1, respectively. The resulting cell suspension (~110,000 cells each) were submitted as separate samples to be barcoded for the droplet-encapsulation single-cell RNA-seq experiments using the Chromium Controller (10X Genomics). Single cell cDNA synthesis, amplification, and sequencing libraries preparation were performed using the Single Cell 3' Reagent Kit as per the 10x Genomics protocol. Libraries were multiplexed so that 2 libraries were sequenced per single lane of HiSeq 4000 using the following parameters: Read1: 27 cycles, i7: 9 cycles, i5: 0 cycles; Read2: 100 cycles to generate 150bp paired end reads.
The resulting cell suspension (~110,000 cells each) were submitted as separate samples to be barcoded for the droplet-encapsulation single- cell RNA-seq experiments using the Chromium Controller (10X Genomics). Single cell cDNA synthesis, amplification and sequencing libraries were generated using the Single Cell 3' Reagent Kit as per the 10x Genomics protocol.
10x libraries were multiplexed so that 2 libraries were sequenced per single lane of HiSeq 4000

treatment_protocol:
0.2mg/g body weight tamoxifen was given via intraperitoneal (IP) injection.
1.25U/kg of bleomycin were delivered intratracheally.

value: Lung

value: lung pogenitor cells


title: EU184-smallRNA

description: Dicer-cut small RNA

value: B

value: in space without gravity


title: EU185

description: polyadenylated RNA


title: RFP

source_name: Lineage labelled RFP+ cells collected at day 28 post injury


title: YFP

source_name: Lineage labelled YFP+ cells collected at day 28 post injury


title: EU184

description: polyadenylated RNA


title: SM-GE8YP_S015_E1-50

city: Seattle

first: Bosiljka

last: Tasic

address: 615 Westlake Ave N.

institute: Allen Institute for Brain Science

value: MC

value: Glut


title: SM-GE8YP_S016_E1-50

value: GABA


title: C2

city: Pontevedra

first: Pilar

last: Soengas

state: Pontevedra

address: Palacio de Salcedo

department: Brassica Genetic and Biochemistry

country: Spain

institute: CSIC

data_processing:
HCS from Illumina HiSeq 2000
The reads were de novo assembled using “Cap3” and the contigs were then BLASTed vs the bacterial uniprot database (ENSEMBL).
Differential expression analysis was performed with the R package DESeq (Anders and Huber 2010) with the standard parameters
Genome_build: Bacterial uniprot database (ENSEMBL)
Supplementary_files_format_and_content: Tab-delimited text files including Gene annotation, Expression values, logFC and FDR

organism: Xanthomonas campestris pv. campestris

source_name: Colonies

growth_protocol: Bacteria was grown in PDB medium supplemented with each isothiocyanate (100 µM).  After four hours of log-phase growing under agitation, bacteria were precipitated by centrifugation to perform RNA extractions. Each treatment was repeated two times.

extract_protocol:
RNA was extracted with RNAspin Mini RNA isolation Kit (GE Healthcare)
RNA-Seq. RNA-Seq libraries were created using the NEBNextUltra RNA Library Prep Kit for Illumina

treatment_protocol: Three different treatments were studied: allyl isothiocyanate (100 µM, Sigma-Aldrich, 36682), indol-3-carbinol (100 µM, Sigma-Aldrich, I7256-5G) and control.

value: control

tag: time of harvest

value: 4 hours


title: SM-GE8YP_S019_E1-50

value: M


title: C1


title: EU183-smallRNA

description: Dicer-cut small RNA

value: with nanoceria


title: SM-GE8YP_S013_E1-50


title: EU183

description: polyadenylated RNA


title: rAT2_ATACseq_rep2

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm10 genome using bowtie2 for ATAC-seq. STAR was used for mapping reads of RNA-seq.
Peaks of ATAC-seq were called using MACS2 peak caller. HTSeq was used for counting reads in exons for RNA-seq.
Genome_build: mm10
Supplementary_files_format_and_content: For ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as log2(FPKM+1) values for each genes.

molecule: genomic DNA

growth_protocol: Freshly sorted lineage-labeled cells from Scgb1a1-CreERTM;R26RtdTomato or Sftpc-CreERT2;R26RtdTomato mice were resuspended in basic medium (AdDMEM/F12 (Invitrogen) supplemented with B27, 1mM N-Acetylcysteine, 10 mM Nicotinamide). Then, cells were mixed with growth factor-reduced Matrigel at a ratio of 1:1. A 100μl mixture was placed in a 24-well Transwell insert with a 0.4-μm pore. Approximately 10×104 epithelial cells were seeded in each insert. After Matrigel formed a gel, 500μl of culture medium (basic medium supplemented with the growth factors: 50 ng/ml murine EGF, 100 ng/ml human FGF7/KGF, 100 ng/ml human FGF10, 50% WNT3A-conditioned media, 10% RSPO1-conditioned media, 100 ng/ml Noggin) was placed in the lower chamber. Medium was changed every other day and ROCK inhibitor Y27632 (10μM) was added in the medium for the first 2 days of culture. For passages, organoids were removed from the Matrigel by incubation with dispase (1mg/ml) for 40 mins at 37°C, followed by dissociation into single cells using trypLE treatment for 5 min at 37°C. 5~10×10^4 cells were transferred to fresh Matrigel in 24-well Transwell insert.

extract_protocol:
Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was performed in secretory cells and alveolar type 2 cells isolated from Scgb1a1-CreTM;R26RfGFP;Sftpc-dsRedIRES-DTR mice. Briefly, tagmentation reaction was performed with 50ng of target DNA, and then bPCR-compatible sites and barcode were added into the target DNA by PCR. After cleaning up the PCR products using Zymo DNA clean and concentrator-5 kit, the final product was sequenced using Illumina HiSeq 400 machine.  Global gene expression profiles using RNA-seq were performed in feeder-free cultured organoids derived from secretory cells and alveolar type 2 cells.  Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor, and amplified with PCR. Purified final PCR product was sequenced using Illumina NextSeq 500 machine.
ATAC-seq library was constructed using Nextera DNA library prep kit following the manufacturer’s protocol. RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7530S) according to manufacturer’s instruction.

treatment_protocol: DAPT (20μM) were treated every other day for 14 days.

tag: tissue

value: lung

value: alveolar type 2 cells

value: untreated


title: SM-GE8YP_S022_E1-50

tag: age

value: 10 yrs

value: NeuN-positive


title: I3C2


title: rAT2_ATACseq_rep1


title: SM-GE8YP_S012_E1-50


title: sAT2_ATACseq_rep2


title: SM-GE8YP_S014_E1-50


title: I3C1


title: EU182

description: polyadenylated RNA


title: SM-GE8YP_S011_E1-50


title: AITC2

value: allyl-isothiocyanate


title: AITC1


title: EU192-smallRNA

description: Dicer-cut small RNA

value: A

value: without nanoceria


title: Spiroplasma-infected male replicate 4

city: New Haven

first: Jae Hak

last: Son

state: CT

address: 60 College St

institute: Yale School of Public Health

data_processing:
Basecalls using bcl2fastq2 v2.19.0
Sequenced reads were mapped to Glossina fuscipe fuscipe genome assembly (Yale_Gfus_2) using hisat2 in HISAT2 v2.2.1
The aligned reads were assigned to all annotated genes with htseq-count in HTSeq v0.13.5
The HTSeq output was used as input into DESeq2 v1.22.1 to identify differentially expressed genes with a model (Expression ~ sex + Spiroplasma infection status + sex*Spiroplasma infection status).
Genome_build: Glossina fuscipe fuscipe genome assembly (Yale_Gfus_2)
Supplementary_files_format_and_content: excel files that include sex and Spiroplasma infection staus comparisons, log2FoldChange, and FDR-corrected P value

organism: Glossina fuscipes fuscipes

source_name: reproductive tissues

extract_protocol:
Reproductive tracts of males and females were dissected in sterile 1x phosphate buffered saline (PBS) and flash frozen in liquid nitrogen. Total RNA was extracted according to TRIzol reagent manufacturer’s instructions (Thermo Fisher Scientific, USA).
the Ribo-Zero Gold rRNA removal kit (human/mouse/rat) MRZG12324
Ribosomal reduction libraries

value: male


title: SM-GE8YP_S008_E1-50


title: EU192

description: polyadenylated RNA

value: in space without gravity


title: Spiroplasma-infected male replicate 2


title: Testis, VC+MOP 2

city: Fuzhou

first: Lihong

last: Zhang

state: Fujian

address: No. 1 Xueyuan Road, Minhou County

institute: Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University

description:
Four3
lncRNA and mRNA

data_processing:
Basecalls performed using  Solexa pipeline v1.8.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5) software.
The transcript abundances for each sample was estimated with StringTie (1.3.1c).
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file.xlsx reports transcript abundances for each sample estimated with StringTie

source_name: Testis

growth_protocol: The rats used in this study were purchased and kept in the Laboratory Animal Center of Fujian Medical University. All the procedures conformed to Guidelines for the Care and Use of Laboratory Animals, which is established by Fujian Medical University and the Animal Approval Committee number is # SYXK-2012-0001.

extract_protocol:
Left testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment;2)Random primed first strand cDNA synthesis;3)dUTP based second strand cDNA synthesis; 4)Adaptor ligation and PCR amplification.

treatment_protocol: MOP, the polysaccharide in dried root (M. officinalis, Bajitian in Chinese) were extracted according to the specific protocol, the classical water extracting and alcohol precipitating method. In brief, after being grinded, the dried root was boiled in ethyl alcohol to remove oligosaccharide and lipid substance, then be extracted using deionized water, next be precipitated with 60% alcohol, the last Sevag reagent was added to remove protein. The experimental varicocele operation was done on the male rats to model varicocele by ligating the left vein of kidney partially. The same operation was conducted except the partial ligation on the rats in control group, and followed by 12 weeks conventional feeding. After the operation by 8 weeks, about 2 mL normal saline was administrated to the VC group rats daily for 4 weeks; 300 mg kg-1 MOP was given to VC+MOP group rats per day also lasting 4 weeks, and both by gavage. After being anesthetized (using 4–6 mg kg-1 chloral hydrat), the rats sacrificed to gain the left testicular tissue, and followed by being set into liquid nitrogen immediately. If the vascular dilation didn’t form or left kidney atrophy occurred in varicocele operation rats, the animals should be removed from the follow-up experiment.

value: Sprague Dawley

value: testis

value: 6-7 weeks

tag: condition

value: varicocele (VC)

value: Morinda officinalis polysaccharide (MOP)


title: Spiroplasma-infected male replicate 5


title: secretory_ATACseq_rep1

value: secretory cells


title: SM-GE8YP_S009_E1-50

value: MC

value: GABA


title: EU191-smallRNA

description: Dicer-cut small RNA


title: EU191

description: polyadenylated RNA


title: EU182-smallRNA

description: Dicer-cut small RNA

value: B

value: with nanoceria


title: Spiroplasma-uninfected male replicate 3


title: secretory_ATACseq_rep2

value: lung

value: untreated


title: Spiroplasma-uninfected male replicate 1


title: EU181

description: polyadenylated RNA


title: EU181-smallRNA

description: Dicer-cut small RNA


title: Spiroplasma-infected female replicate 5

value: female


title: Testis, VC 3

description:
Two8
lncRNA and mRNA

value: control


title: SM-GE8YP_S006_E1-50

value: 10 yrs

value: NeuN-positive


title: SM-GE8YP_S004_E1-50

value: Glut

value: M


title: SM-GE8YP_S007_E1-50


title: 5xFAD_9mo

city: Seoul

first: Hongyoon

last: Choi

state: Seoul Teugbyeolsi

address: Daehakro 101, Jongrogu

country: South Korea

institute: Seoul National University Hospital

data_processing:
scRNA-seq samples were pseudoaligned to the ENSEMBL GRCm38 Mus musculus transcriptome using Kallisto
Exonic counts for each barcode were estimated after the corrected BUS file with ‘bustools correct’ and ‘bustools sort’ using specifying “10× v2” chemistry as an option. After the estimation of gene counts using pseudoalignment, data were loaded using Seurat (version 3.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Approximately 1000-1500 cells from each dissected brain were directly loaded into each sample well following manufacturer instructions. All samples were combined into droplets with barcoded beads. Manufacturer specifications were followed for generation of the barcoded libraries and then the samples were sequenced to an average depth of 40,000-60,000 reads on an Illumina HiSeq 2500 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: 5xFAD; AD model

value: 9 months

value: Hippocampus


title: SM-GE8YP_S005_E1-50


title: Spiroplasma-infected female replicate 4

tag: Sex


title: Testis, VC 1

description:
Two1
lncRNA and mRNA

value: Sprague Dawley

value: testis

value: male

value: 6-7 weeks

value: varicocele (VC)


title: 5xFAD_6mo

value: 6 months


title: sAT2_ATACseq_rep1

value: lung

tag: cell type

value: alveolar type 2 cells


title: SM-GE8YP_S003_E1-50

tag: donor

value: MC

tag: facs gating

value: GABA


title: Spiroplasma-uninfected female replicate 2

value: female


title: Testis, Control  3

description:
One9
lncRNA and mRNA

value: control


title: 5xFAD_2mo

value: 2 months


title: Testis, VC+MOP 1

description:
Four1
lncRNA and mRNA

value: Morinda officinalis polysaccharide (MOP)


title: Testis, Control  1

description:
One2
lncRNA and mRNA


title: Spiroplasma-uninfected female replicate 3


title: SM-GE8YP_S010_E1-50

value: 10 yrs

value: NeuN-positive

tag: sequencing batch

tag: cell class


title: SM-GE8YP_S001_E1-50

value: Glut

tag: cell cluster

value: M


title: Testis, VC 2

description:
Two6
lncRNA and mRNA

tag: strain

value: Sprague Dawley

value: testis


title: Surface_2 [RNA-seq]

status: Public on Sep 07 2021

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Following sequencing, Illumina Real Time Analysis version 1.18.64 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
FASTQ files were aligned to astMex_2.0 using STAR under default parameters and --quantMode with gene models from Ensembl 96 to generate gene counts.
Genome_build: astMex_2.0
Supplementary_files_format_and_content: Tab-delimited text file of stranded Ensembl96 gene counts for each fish.

organism: Astyanax mexicanus

extract_protocol:
RNA was extracted from Liver tissue and purified using the Qiagen RNeasy kit.
Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina).

tag: morphotype/population

value: Surface

value: liver

tag: replicate


title: Tinaja_1 [RNA-seq]

source_name: Tinaja cave_liver

value: Tinaja cave


title: Tinaja_2 [RNA-seq]


title: Testis, VC+MOP 3

description:
Four5
lncRNA and mRNA

value: male

value: 6-7 weeks

value: varicocele (VC)

tag: treatment


title: SM-GE8YP_S002_E1-50

value: MC

value: GABA


title: Tinaja_H3K27me3_ip_2399_a

description: processed data file: tinaja_H3K27me3.bed

data_processing:
Following sequencing, Illumina Real Time Analysis version 1.18.64 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
FASTQ files for each chromatin mark were aligned to astMex_2.0 using bowtie2 under default parameters.
Reads mapping to the mitochondrial chromosome were filtered out using samtools prior to calling peaks with MACS2 under default parameters.
Overlapping peaks observed in at least 2 replicates were reduced using the GenomicRanges library in R.
Genome_build: astMex_2.0
Supplementary_files_format_and_content: BED files representing reproducible peak locations

source_name: Tinaja cave_liver_H3K27me3

extract_protocol:
Adult livers were dissected and fixed in 1% formaldehyde for 15 min. Chromatin was prepared using MAGnify Low Cell ChIP-Seq Kit (Thermo Fischer) and ChIP was done for H3K4me3 (Millipore, # 07-473), H3K27ac (Abcam, # ab4729), H3K27me3 (Abcam, # ab195477). 200,000 cells and 1ug of antibody was used for each sample.
Libraries were prepared using the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies).  Post amplification size selection was performed on all libraries using a Pippin Prep (Sage Science). Libraries were re-quantified, normalized, pooled and sequenced on Illumina Illumina HiSeq 2500 instrument as 50-bp single read.

tag: FISH type

tag: chip antibody

tag: sample type

value: ip

tag: background sample


title: Surface_1 [RNA-seq]

tag: tissue


title: Tinaja_tc_2399

source_name: Tinaja cave_liver_total chromatin

value: total chromatin


title: Surface_H3K27me3_ip_2399_b

description: processed data file: surface_H3K27me3.bed


title: Surface_tc_2399

source_name: Surface_liver_total chromatin


title: Tinaja_H3K4me3_ip_2005_B

description: processed data file: tinaja_H3K4me3.bed

source_name: Tinaja cave_liver_H3K4me3

value: H3K4me3 (Millipore, #07-473)


title: WT

tag: strain background

tag: genotype/variation

value: WT

tag: age

value: 2 months

value: Hippocampus


title: Pachon_tc_2399

source_name: Pachon cave_liver_total chromatin

value: Pachon cave


title: Pachon_H3K27me3_ip_2399_a

description: processed data file: pachon_H3K27me3.bed

source_name: Pachon cave_liver_H3K27me3


title: Spiroplasma-uninfected female replicate 1

tag: Sex

value: female


title: Surface_H3K27me3_ip_2399_a


title: Pachon_H3K4me3_1ug_ip_1934_b

description: processed data file: pachon_H3K4me3.bed

source_name: Pachon cave_liver_H3K4me3


title: Tinaja_tc_1934


title: Surface_H3K4me3_ip_1930_2

description: processed data file: surface_H3K4me3.bed


title: Surface_tc_1930