title: Anti-CD8, replicate 2

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting were made using the Cell Ranger software v7.1.0.
Assembly: GRCm39
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
To prepare the cell suspension for 3’ 10X genomic single cell RNA sequencing, mice were anaesthetized (80 mg of ketamine and 10 mg of xylazine per kilogram of body weight via i.p. injection) and transcardially perfused with 20 ml of oxygenated cold artificial cerebrospinal fluid (CSF) solution (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20mM HEPES, 25mM glucose, 5 mM Sodium Ascorbate, 2 mM Thiourea, 0.5 mM CaCl2, and 10 mM MgSO4).2mm spinal cord including the lesion site or the corresponding location in the naïve spinal cord segment was immediately dissected. After, spinal cord tissues were processed using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) following the manufacturer’s protocol combined with some modifications as described previously (Milich et al., 2021). The dissociated cells were incubated with 20ul of myelin removal beads (Miltenyi Biotec, 130-096-433) to remove myelin debris following the manufacturer’s protocol. After centrifugation, cell pellets were resuspended in 1X PBS (Thermo Fisher Scientific, 14190250) + 0.04%BSA (Jackson Immuno Research, 001-000-162). An aliquot of cells was stained with Acridine Orange/Propidium Iodide dye (AO/PI Cell Viability Kit, Labtech, F23001). Cell concentration and viability were measured using the LUNA-FL Dual Fluorescence Cell Counter (Logos, L20001-LG). Cells were immediately proceeded to the 10X single cell RNA sequencing procedures.
Library was performed according to the manufacturer’s instructions (single cell 3’ V2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for the subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: biol rep 3 of City of Haarlem inner perianth lobes at green-bud stage

status: Public on Jan 12 2025

type: SRA

city: Shatin

first: Kwan-Ho

last: WONG

address: The Chinese University of Hong Kong, Ma Liu Shui

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: CH3nB

library_source: transcriptomic

data_processing:
After removal of adaptor trimming and quality trimming, the qualified sequences were adopted for mRNA de novo assembly using Trinity software. The gene expressions were then quantification into read counts by mapping the reads to a set of reference transcript sequences using RNA-Seq by Expectation Maximization (RSEM), and calculated the relative abundance of unigene based on the alignment of reads against the reference transcript using Bowtie. The read counts were then normalized into Fragments Per Kilobase of transcript sequence per Millions (FPKM) value.
Assembly: Absence of reference genome.
Supplementary files format and content: Excel Binary File Format (XLS) file containing raw read counts for each sample
Supplementary files format and content: Excel Binary File Format (XLS) file containing FPKM values for each sample

molecule: total RNA

organism: Hyacinthus orientalis

source_name: Inner perianth lobes

growth_protocol: The bulbs were imported from the Netherlands (Simple Pleasures Flowerbulbs & Perennials Inc.) in September 2022. They were firstly immersed in tetrachlorophthalonitrile for 1 hour to prevent fungal infection. Air-dried bulbs were stored at 4 °C for three months. The vernalised bulbs were planted on 3rd January 2023, in an outdoor environment outside Li Dak Sum Yip Yio Chin R&D Centre for Chinese Medicine (GPS: 22.419292, 114.210200) with natural sunlight. Perianth were collected during 16th January to 4th February 2023.

extract_protocol:
The collected tissues were immediately immersed in RNAlater™ Stabilization Solution and stored at appropriate conditions before RNA extraction. Total RNA was extracted using Qiagen RNeasy Plant Mini Kit (Qiagen Co., Hilden, Germany) following the instructions of manufacturer. The quality and quantity of extracted RNA were assessed by 1.5% agarose gel electrophoresis and Nanodrop Lite Spectrophotometer (Thermo Fisher Scientific, MA, USA), respectively.
Libraries of mRNA with poly-A enrichment were sequenced on Illumnia NovaSeq X Plus platform, with paired-end sequencing of 150 nucleotides. About 6 Gb data were targeted for each sample.

tag: tissue

value: Inner perianth lobes

tag: cultivar

value: City of Haarlem

tag: developmental stage

value: Green flower buds


title: biol rep 1 of City of Haarlem perianth tube at green-bud stage

description: Library name: CH1tB

source_name: Perianth tube

value: Perianth tube


title: Anti-CD8, replicate 1

city: London

first: Guiping

last: Kong

address: 55-96, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description: 10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

source_name: Spinal cord

value: Spinal cord

tag: strain

tag: treatment


title: biol rep 2 of City of Haarlem perianth tube at green-bud stage

description: Library name: CH2tB


title: IgG, replicate 2

description: 10x Genomics

value: IgG


title: biol rep 2 of City of Haarlem inner perianth lobes at green-bud stage

description: Library name: CH2nB


title: Old-naive_GEX, replicate 2

description: GEX (5' mRNA) library, 10X Genomic

data_processing:
The demultiplexing, barcode processing, 5’ gene counting, and V(D)J transcript sequence assembly were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

extract_protocol:
To prepare the cell suspension for 5’ 10X genomic single cell RNA sequencing, mice were anaesthetized (80 mg of ketamine and 10 mg of xylazine per kilogram of body weight via i.p. injection) and transcardially perfused with 20 ml of cold 1XPBS (Thermo Fisher Scientific, 14287080). 4mm spinal cord including the lesion site or the corresponding location in the naive spinal cord segment was immediately dissected. After, spinal cord tissues were processed using the Multi Tissue Dissociation Kit 1 (Miltenyi Biotec, 130-110-201) following the manufacturer’s protocol. The dissociated cells were incubated with 40ul of myelin removal beads (Miltenyi Biotec, 130-096-433) to remove myelin debris following the manufacturer’s protocol. After centrifugation of the final step in the myelin removal procedures, cell pellets were resuspended in 50ul 1X MojoSort Buffer (Biolegend, 480017) and 0.5ul of TruStain FcX PLUS anti-mouse CD16/32 antibody (Biolegend, 156604) was added to the cell suspension to block Fc receptors for 10 min on ice. Antibody cocktails were prepared in 50ul Brilliant Stain Buffer (Thermo Fisher Scientific, 00-4409-42). Antibodies used for sorting were: APC anti-CD45 (30-F11, 2 µg/ml, 103111, Biolegend), Brilliant Violet 711 anti-CD8a (53-6.7, 2 µg/ml, 100759, Biolegend), Brilliant Violet 605 anti-CD4 (RM4-5, 2 µg/ml, 100547, Biolegend), FITC anti-TCR β (H57-597, 5 µg/ml, 109205, Biolegend) and LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific, L34966, 1:1000). Cells were stained with the antibody cocktails in the dark at 4°C for 20 min followed by two times washing with 1X MojoSort Buffer. Cell sorting was conducted using BD FACSAria III flow cytometer. After FACS, cells were washed twice with 1XPBS+0.04%BSA and immediately proceeded to the 10X TCR single cell RNA sequencing procedures.
Library was performed according to the manufacturer’s instructions (single cell 5’ V2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, and amplified by PCR for the subsequent V(D)J library and 5ʹ gene expression (GEX) library construction. For the V(D)J library construction, full-length V(D)J segments were amplified via PCR from the full-length cDNA using primers specific to the TCR. The appropriated sized V(D)J fragments were selected with SPRIselect reagent and used for the library construction. Full length of amplified and purified cDNA was used for the 5ʹ gene expression (GEX) library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample dual index were added.

tag: cell type

value: CD8+ and CD4+ T cells

tag: age

value: 20-24 months old

value: Naive


title: biol rep 1 of City of Haarlem inner perianth lobes at coloured-bud stage

description: Library name: CH1nC

value: Coloured flower buds


title: biol rep 3 of City of Haarlem outer perianth lobes at green-bud stage

description: Library name: CH3oB

source_name: Outer perianth lobes

value: Outer perianth lobes


title: biol rep 1 of City of Haarlem inner perianth lobes at green-bud stage

description: Library name: CH1nB


title: biol rep 1 of City of Haarlem outer perianth lobes at coloured-bud stage

description: Library name: CH1oC


title: LEE62A17

first: James

last: Turner

address: The Francis Crick Institute, 1 Midland Road

institute: The Francis Crick Institute

library_source: genomic

data_processing:
Read trimming was performed with TrimGalore v0.6.0 using these parameters: --clip_R1 6 --3_prime_clip_R1 6
Mapping was performed with Bismark v0.18.0 using these parameters: --non_directional --un --ambiguous
SNP splitting was performed with SNPsplit v0.3.4 using these parameters: --bisulfite –conflicting
Methylation analysis was performed with R v3.4.3 using the methylKit v1.4.1 package
Plotting was performed with R v3.4.3 using the ggplot2 v3.2.0 and Gviz v1.22.3 packages
Assembly: MonDom5

molecule: genomic DNA

organism: Monodelphis domestica

source_name: Spleen

extract_protocol:
PureLink Genomic DNA Mini kit
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

value: Spleen

tag: genotype

value: WT

tag: stock

tag: Sex

value: Female


title: IgG, replicate 1

description: 10x Genomics


title: biol rep 3 of Gipsy Queen perianth tube at full-anthesis stage

description: Library name: GQ3tA

value: Gipsy Queen

value: In full anthesis


title: biol rep 2 of City of Haarlem outer perianth lobes at green-bud stage

description: Library name: CH2oB


title: LEE62A16

source_name: Liver

value: Liver


title: LEE62A13

value: Male


title: LEE62A15

source_name: Brain

value: Brain


title: biol rep 2 of Gipsy Queen perianth tube at full-anthesis stage

description: Library name: GQ2tA


title: Caenorhabditis elegans, YA Males, Neurons, rep 6

city: Rehovot

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Males_batch_4_sample_4
10x Genomics
Combined_features.tsv.gz

data_processing:
Demultiplexing, barcode processing, gene counting, and data aggregation were carried out using Cell Ranger software versions v3.0.2, v4.0.0 and 5.0.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: WBcel235 release WS276
Supplementary files format and content: Tab-seperated values files and matrix files

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: rab-3::tagRFP+ neurons

growth_protocol: C. elegans strains used in this study OH10690 and MOS264 were cultivated at 15oC on 15 cm nematode growth media (NGM) plates seeded with NA22 bacteria. Embryos were isolated by hypochlorite treatment of adult hermaphrodites and were age-synchronised 14-16 hours on a foodless NGM plate at 25°C. L1 larvae were collected and were placed on a food NGM plates approximately 1.5 cm from the food on NGM plates and were allowed to crawl towards food for 1-2 hours at RT. Using a scalpel, the area where L1/embryos were initially placed was removed. L1 worms were collected and washed with M9 buffer and were incubated at 20oC until adulthood (45-48 hours).

extract_protocol:
To generate pure hermaphrodites populations C. elegans strain OH10690 with the genotype rab-3p(prom1)::2xNLS::TagRFP] IV was used. To generate male populations, C. elegans strain MOS264 with the genotype rab-3p(prom1)::2xNLS::TagRFP] IV; dpy-28(y1) III; him-8(e1489) IV was employed. This MOS264 strain harbors a temperature-sensitive mutation (y1) in the dosage compensation gene, dpy-28 along with him-8(e1489) mutation and a pan-neuronal RFP. This resulted in male population of ≥98% purity. After obtaining the worms of the sex and Young adult age, they were washed 10 times at 1300 rpm for 2 minutes with M9 buffer to get rid of any adhering bacteria. The worms were then washed with ddH2O. The worm pellets were then subjected to single cell dissociation using protocols described earlier with slight modifications. For every 0.5 ml of worm pellet 1 ml of freshly thawed sterile SDS-DTT solution (200 mM DTT, 0.25% SDS, 20 mM HEPES, 3% sucrose, pH 8.0, thawed freshly) was added and incubated at room temperature for 4 min with gentle mixing every 1 minute. Immediately after SDS-DTT treatment, worms were pelleted at 3,000 rpm for 1 min and washed 5 times with 10 ml egg buffer (118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES, pH 7.3). 0.5 ml aliquots of worm pellet were distributed to 1.6 mL microcentrifuge tubes. 1 mL freshly prepared 15 mg/mL Pronase-E was added to each tube and flicked to mix and then rotated at 20°C for 5 minutes. Using a glass pasteur pipette, worm suspensions were combined from multiple tubes and were transferred to a 7 mL dounce homogenizer (pestle clearance 0.02−0.056 mm, Kimble Chase). Pronase E was added to a final ratio of 4:1 relative to the worm pellet. If the worm pellet was smaller than 0.5 mL a 2mL glass homogenizer was used. The animals were disintegrated to single cells using type “B” plunger for 4-5 minutes at room temperature and then continued on ice gently. We note that homogenizing on ice increased cell survival. The status of dissociation was monitored under a dissecting microscope at 5-minute intervals. Dissociation was stopped when most of the animals were dissociated but a few whole or fragmented animals were still present. Using a glass pasteur pipette the cell suspension was aliquoted into 1.6 mL microcentrifuge tubes that were centrifuged at 5,000 x g for 5 minutes at 4 °C. Supernatant was removed and the cell pellet was washed 3 times with 1 mL ice-cold egg buffer per wash at 5,000 x g for 5 minutes at 4 °C. The cells pellet was resuspended in 1 ml ice-cold egg buffer and was passed through 5 μm syringe filter gently. Cell suspension was taken on ice to Fluorescence Activated Cell Sorting (FACS) sorting immediately. Single cell suspension from the desired strain were subjected to FACS on a BD FACSAria™ III Cell Sorter using a 70-micron nozzle. eFlour 450 dye (final concentration of 1 μl/mL) was used to discriminate live and dead cells. The cells were gated for side scatter (SSC)-Area vs forward scatter (FSC)-Area, then single cells were selected from doublet using FSC-Height vs FSC-Area. Finally, RFP+ cells were gated and sorted under the “4-way Purity” mask from this subpopulation. Wild-type him-5(e1490) without any RPF+ cells was used as control for gating. Sorted cells were collected in 1.6 mL microcentrifuge tube containing 500 µl L-15-20 (L-15 medium containing 20% fetal bovine serum). The suspension was centrifuged at 5,000 x g for 10 minutes at 4 °C, resuspended in 50-80 µl of L-15-20 and counted using a hemocytometer.
Single-cell capture and library preparation were performed following standard 10x Genomics protocols. A target of 10,000 cells per sample was set, and libraries were prepared using the Single Cell 3' v3 (Dual Index) chemistry kit.

value: rab-3::tagRFP+ neurons

tag: strain name

value: otIs355 [rab-3(prom1)::2xNLS-TagRFP] IV; dpy-28(y1) III; him-8(e1489) IV

value: Young Adult Males

tag: batch


title: biol rep 1 of Gipsy Queen perianth tube at full-anthesis stage

description: Library name: GQ1tA

value: Perianth tube


title: LEE62A12


title: LEE62A14


title: biol rep 3 of Gipsy Queen inner perianth lobes at full-anthesis stage

description: Library name: GQ3nA

value: Inner perianth lobes


title: biol rep 2 of Gipsy Queen inner perianth lobes at full-anthesis stage

description: Library name: GQ2nA


title: biol rep 3 of Gipsy Queen outer perianth lobes at full-anthesis stage

description: Library name: GQ3oA


title: biol rep 1 of Gipsy Queen inner perianth lobes at full-anthesis stage

description: Library name: GQ1nA


title: LEE62A10


title: Caenorhabditis elegans, YA Males, Neurons, rep 4

description:
Library name: Males_batch_3_sample_2
10x Genomics
Combined_features.tsv.gz


title: biol rep 2 of Gipsy Queen outer perianth lobes at full-anthesis stage

description: Library name: GQ2oA


title: Caenorhabditis elegans, YA Males, Neurons, rep 3

description:
Library name: Males_batch_3_sample_1
10x Genomics
Combined_features.tsv.gz


title: biol rep 1 of City of Haarlem outer perianth lobes at green-bud stage

description: Library name: CH1oB

value: City of Haarlem

value: Green flower buds


title: LEE62A9


title: biol rep 1 of Gipsy Queen outer perianth lobes at full-anthesis stage

description: Library name: GQ1oA


title: biol rep 2 of Gipsy Queen perianth tube at coloured-bud stage

description: Library name: GQ2tC

value: Coloured flower buds


title: biol rep 3 of Gipsy Queen perianth tube at coloured-bud stage

description: Library name: GQ3tC


title: biol rep 1 of Gipsy Queen perianth tube at coloured-bud stage

description: Library name: GQ1tC


title: Caenorhabditis elegans, YA Males, Neurons, rep 2

description:
Library name: Males_batch_2
10x Genomics
Combined_features.tsv.gz


title: LEE62A7


title: Caenorhabditis elegans, YA Males, Neurons, rep 1

description:
Library name: Males_batch_1
10x Genomics
Combined_features.tsv.gz


title: biol rep 2 of Gipsy Queen inner perianth lobes at coloured-bud stage

description: Library name: GQ2nC


title: biol rep 1 of Gipsy Queen inner perianth lobes at coloured-bud stage

description: Library name: GQ1nC


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 6

description:
Library name: Hermaphrodite_batch_3_Sample_4
10x Genomics
Combined_features.tsv.gz

value: otIs355 [rab-3(prom1)::2xNLS-TagRFP] IV

value: Young Adult Hermaphrodites


title: LEE62A6

value: Spleen

value: WT


title: biol rep 3 of Gipsy Queen inner perianth lobes at coloured-bud stage

description: Library name: GQ3nC

value: Gipsy Queen


title: biol rep 2 of Gipsy Queen outer perianth lobes at coloured-bud stage

description: Library name: GQ2oC

value: Outer perianth lobes


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 5

description:
Library name: Hermaphrodite_batch_3_Sample_3
10x Genomics
Combined_features.tsv.gz


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 4

description:
Library name: Hermaphrodite_batch_3_Sample_2
10x Genomics
Combined_features.tsv.gz


title: biol rep 3 of Gipsy Queen outer perianth lobes at coloured-bud stage

description: Library name: GQ3oC


title: LEE62A11


title: Caenorhabditis elegans, YA Males, Neurons, rep 5

description:
Library name: Males_batch_4_sample_3
10x Genomics
Combined_features.tsv.gz


title: LEE62A4


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 3

description:
Library name: Hermaphrodite_batch_3_Sample_1
10x Genomics
Combined_features.tsv.gz


title: biol rep 3 of Gipsy Queen inner perianth lobes at green-bud stage

description: Library name: GQ3nB


title: biol rep 1 of Gipsy Queen outer perianth lobes at coloured-bud stage

description: Library name: GQ1oC


title: LEE62A5

value: Liver

value: Female


title: biol rep 3 of Gipsy Queen perianth tube at green-bud stage

description: Library name: GQ3tB


title: biol rep 1 of Gipsy Queen perianth tube at green-bud stage

description: Library name: GQ1tB


title: LEE62A8

value: Brain


title: GE-T0

type: other

city: Montreal

first: Alain

last: Moreau

state: QC

address: 3175 Côte-Ste-Catherine

country: Canada

institute: CHU Sainte-Justine

description: Plasma_Baseline_Healthy Control

hyb_protocol: For hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used. For example, labelled miRNA is hybridised on 8x60K microarrays at 55C for at least 20 hours using Agilent's recommended hybridisation chamber and oven. Afterwards, microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for five minutes at ambient temperature followed by a second wash with preheated (37 C) Gene Expression Wash Buffer 2 for five minutes.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for 8x60K and 5 micron for 8x15K SurePrint G3 Gene Expression Microarrays, generating a 20 bit TIFF  file.

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files. Prior to normalisation of the background substracted signals, the following processing steps are performed: removal of signals from control probes; mean of signals from replicate probes; mean of signals from all probes of a target. For processing of raw data signals, intensities below 0.1 were set to 0.1 according to Agilent's recommendation. Data of all samples are quantile normalised using the ranked mean quantiles according to Bolstad et al. A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias", Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets. The ranked signal value is replaced with the mean quantile value of the same rank. Thus, the highest value in all samples becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on.

molecule: other

organism: Homo sapiens

source_name: Human Plasma, Baseline, Healthy Control

label_protocol: For labelling, the miRNA Labeling Kit (Agilent Technologies) is used to generate fluorescent miRNA. This end-labelling method involves a dephosphorylation step and subsequent ligation of one Cyanine 3-pCp molecule to the 3'end of a miRNA molecule.

extract_protocol: Biobanked plasma samples were thawed and centrifugated at 17,000 x g for 15 minutes at 4°C. The RNA was extracted using the NucleoSpin miRNA Plasma kit (MACHEREY-NAGEL GmbH & Co. KG, Düren,Germany) according to the manufacturer's instructions.

value: plasma

tag: disease status

value: Healthy control (HC)

value: F

tag: age (years)

tag: cobb angle (°)

tag: final cobb (°) age (years)

tag: functional group (used for different studies)

tag: timepoints (used for different studies)


title: biol rep 1 of Gipsy Queen inner perianth lobes at green-bud stage

description: Library name: GQ1nB

tag: tissue

tag: cultivar


title: PBS_21d_Col1A2_fibroblast

city: Saskatoon

first: Andrew

last: Leask

state: Saskatchewan

address: 105 Wiggins

department: College of Dentistry

institute: University of Saskatchewan

data_processing:
The data quality for fastq was checked using FastQC
Cell ranger count pipeline was executed to align reads in fastq files to the reference transcriptome
The generated counts for the samples were group based on the condition and  then the conditions were aggregated to perform the downstream analysis for the the conditions simultaneously
Assembly: mm10
Supplementary files format and content: PBS_barcodes.tsv.gz, PBS_features.tsv.gz, PBS_matrix.mtx.gz

source_name: Skin

growth_protocol: At 3-week-old, mice were treated with tamoxifen (10 mg/mL) or corn oil (vehicle control) every day for 5 days. Six weeks later, mice were euthanized, and skin collected

extract_protocol:
Skin was then digested with 2mg/ml Collagenase type IV (Life Technologies, 17104019) for 3h at 37°C. Digested skin was smashed and filtered through a 70mm strainer. Cells were pelleted (450g x 5 min) and resuspended in RBC lysis buffer (Invitrogen, 00-4333-57) for 3 min before being pelleted (450g x 5 min). Finally, cells were brought into single cell suspension for FACS sorting by filtering through a 40mm strainer. GFP-tagged Col1A2-Cre-fibroblasts were then isolated using BD FACSMelody (BD Biosciences, Franklin Lakes, NJ) and a 488nm blue laser with a BP/527/32/LP/507/5 filter
Approximately 5000 cells were captured for GEM generation, Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) used for library construction.
Libraries were diluted and pooled to 4 nM and spiked with 1% Phix control before sequencing.Pooled library was sequenced using Illumina HO 150 cycle kit with following sequencing configuration: 28 l 10 l 10l 90

value: Skin

value: single-cells

value: Col1A2-Cre(ER)T/0; ROSA26mTmG

value: PBS


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 2

description:
Library name: Hermaphrodite_batch_2
10x Genomics
Hermaphrodite_batch_2_features.tsv.gz

value: rab-3::tagRFP+ neurons


title: 993-T90

source_name: Humam Plasma,post 90min stimulation, AIS, progressor

value: Progressor (P)


title: biol rep 3 of Gipsy Queen outer perianth lobes at green-bud stage

description: Library name: GQ3oB

tag: developmental stage

value: Green flower buds


title: LEE62A1

value: Spleen


title: biol rep 3 of Pink Pearl perianth tube at full-anthesis stage

description: Library name: PP3tA

value: Perianth tube

value: Pink Pearl

value: In full anthesis


title: biol rep 1 of Gipsy Queen outer perianth lobes at green-bud stage

description: Library name: GQ1oB

value: Outer perianth lobes

value: Gipsy Queen


title: LEE62A3

value: Liver

value: WT

value: Male


title: 864-T90

source_name: Human Plasma, Post 90min stimulation, AIS, non-progressor

value: plasma

value: Non-progressor (NP)

value: F


title: biol rep 2 of Gipsy Queen outer perianth lobes at green-bud stage

description: Library name: GQ2oB


title: LEE307A97

source_name: embryo

extract_protocol:
direct lysis
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

tag: inferred sex

value: male


title: biol rep 1 of Pink Pearl perianth tube at full-anthesis stage

description: Library name: PP1tA


title: 993-T0

source_name: Humam Plasma, Baseline, AIS, progressor


title: biol rep 3 of Pink Pearl inner perianth lobes at full-anthesis stage

description: Library name: PP3nA

value: Inner perianth lobes


title: biol rep 2 of Pink Pearl perianth tube at full-anthesis stage

description: Library name: PP2tA


title: LEE307A96


title: LEE307A98

value: female


title: LEE62A2


title: 864-T0

source_name: Human Plasma, Baseline, AIS, non-progressor


title: biol rep 2 of Pink Pearl inner perianth lobes at full-anthesis stage

description: Library name: PP2nA


title: biol rep 2 of Gipsy Queen inner perianth lobes at green-bud stage

description: Library name: GQ2nB


title: biol rep 1 of Pink Pearl inner perianth lobes at full-anthesis stage

description: Library name: PP1nA


title: biol rep 2 of Gipsy Queen perianth tube at green-bud stage

description: Library name: GQ2tB


title: biol rep 3 of Pink Pearl outer perianth lobes at full-anthesis stage

description: Library name: PP3oA


title: 849-T90

value: M


title: LEE307A94


title: 849-T0


title: biol rep 2 of Pink Pearl outer perianth lobes at full-anthesis stage

description: Library name: PP2oA


title: LEE307A93


title: biol rep 1 of Pink Pearl outer perianth lobes at full-anthesis stage

description: Library name: PP1oA


title: 827-T90


title: biol rep 2 of Pink Pearl perianth tube at coloured-bud stage

description: Library name: PP2tC

value: Coloured flower buds


title: biol rep 3 of Pink Pearl perianth tube at coloured-bud stage

description: Library name: PP3tC


title: LEE307A92


title: biol rep 1 of Pink Pearl perianth tube at coloured-bud stage

description: Library name: PP1tC


title: biol rep 3 of Pink Pearl inner perianth lobes at coloured-bud stage

description: Library name: PP3nC


title: LEE307A91


title: 827-T0


title: 6017-T90


title: biol rep 2 of Pink Pearl inner perianth lobes at coloured-bud stage

description: Library name: PP2nC


title: biol rep 1 of Pink Pearl inner perianth lobes at coloured-bud stage

description: Library name: PP1nC


title: biol rep 3 of Pink Pearl outer perianth lobes at coloured-bud stage

description: Library name: PP3oC


title: LEE307A90


title: LEE307A9


title: 6017-T0


title: biol rep 2 of Pink Pearl outer perianth lobes at coloured-bud stage

description: Library name: PP2oC


title: LEE307A89


title: 4283-T90

description: Plasma_Post-stimulation_Healthy Control

source_name: Human Plasma, Post 90min stimulation, Healthy Control

value: Healthy control (HC)


title: 4283-T0

description: Plasma_Baseline_Healthy Control


title: LEE307A88


title: biol rep 2 of Pink Pearl perianth tube at green-bud stage

description: Library name: PP2tB

value: Perianth tube

value: Green flower buds


title: biol rep 1 of Pink Pearl perianth tube at green-bud stage

description: Library name: PP1tB

value: Pink Pearl


title: biol rep 2 of Pink Pearl inner perianth lobes at green-bud stage

description: Library name: PP2nB


title: LEE307A85


title: 4217-T0

description: Plasma_Baseline_Healthy Control


title: biol rep 1 of Pink Pearl inner perianth lobes at green-bud stage

description: Library name: PP1nB


title: LEE307A84


title: 4216-T0

description: Plasma_Baseline_Healthy Control


title: biol rep 3 of Pink Pearl outer perianth lobes at green-bud stage

description: Library name: PP3oB

value: Outer perianth lobes


title: biol rep 2 of Pink Pearl outer perianth lobes at green-bud stage

description: Library name: PP2oB


title: LEE307A82


title: biol rep 1 of Pink Pearl outer perianth lobes at green-bud stage

description: Library name: PP1oB


title: 4214-T90

description: Plasma_Post-stimulation_Healthy Control


title: biol rep 3 of Jan Bos perianth tube at full-anthesis stage

description: Library name: JB3tA

value: Jan Bos

value: In full anthesis


title: LEE307A81

value: WT


title: biol rep 2 of Jan Bos perianth tube at full-anthesis stage

description: Library name: JB2tA


title: biol rep 1 of Jan Bos perianth tube at full-anthesis stage

description: Library name: JB1tA


title: biol rep 1 of Pink Pearl outer perianth lobes at coloured-bud stage

description: Library name: PP1oC


title: LEE307A80


title: 4214-T0

description: Plasma_Baseline_Healthy Control


title: biol rep 3 of Jan Bos inner perianth lobes at full-anthesis stage

description: Library name: JB3nA


title: LEE307A8


title: biol rep 1 of Jan Bos inner perianth lobes at full-anthesis stage

description: Library name: JB1nA


title: biol rep 3 of Pink Pearl perianth tube at green-bud stage

description: Library name: PP3tB


title: biol rep 2 of Jan Bos inner perianth lobes at full-anthesis stage

description: Library name: JB2nA


title: LEE307A79


title: 4211-T0

description: Plasma_Baseline_Healthy Control


title: 3268-T90

description: Plasma_Post-stimulation_Healthy Control


title: biol rep 2 of Jan Bos outer perianth lobes at full-anthesis stage

description: Library name: JB2oA


title: LEE307A78


title: biol rep 1 of Jan Bos outer perianth lobes at full-anthesis stage

description: Library name: JB1oA


title: 3268-T0

description: Plasma_Baseline_Healthy Control


title: biol rep 3 of Pink Pearl inner perianth lobes at green-bud stage

description: Library name: PP3nB


title: biol rep 3 of Jan Bos outer perianth lobes at full-anthesis stage

description: Library name: JB3oA


title: 1729-T90

value: Progressor (P)


title: biol rep 2 of Jan Bos perianth tube at coloured-bud stage

description: Library name: JB2tC


title: biol rep 3 of Jan Bos perianth tube at coloured-bud stage

description: Library name: JB3tC


title: 1729-T0

value: plasma


title: LEE307A74


title: biol rep 1 of Jan Bos perianth tube at coloured-bud stage

description: Library name: JB1tC


title: 1691-T90


title: LEE307A73


title: biol rep 3 of Jan Bos inner perianth lobes at coloured-bud stage

description: Library name: JB3nC


title: Biosolids Male 8770

city: Ann Arbor

first: Vasantha

last: Padmanabhan

state: MI

address: 1150, W. Medical Centre Drive

country: USA

institute: university of Michigan

data_processing:
The adapters and over-represented sequences from the sequencing reads were removed using Trimmomatic.
FastQC was used to validate the quality of the raw data and trimmed data summarized using MultiQC.
The paired end reads were aligned to the sheep reference genome (ARS-UI_Ramb_v3.0) using Spliced Transcripts Alignment to a Reference (STAR) aligner (v2.6.0c).
FeatureCounts (v1.5.0-p3) was used to count the number of reads mapped to each gene.
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: tab delimited text file includes raw counts for all the samples

organism: Ovis aries

extract_protocol:
RNA isolation was carried out using the Qiagen RNeasy mini kit following manufacturer’s instructions, using 30mg of frozen liver tissue. RNA was quantified using the Qubit BR dsDNA kit, and quality assessed on the TapeStation 4200.
Library preparation was done using TruSeq RNA library prep kit. Multiplexed samples were sequenced at 50 cycles using NovaSeq S4 flowcell.

value: Liver

tag: prenatal exposure

value: Biosolids

value: Male


title: 1691-T0

value: F


title: Biosolids Male 8762


title: 1681-T90


title: biol rep 1 of Jan Bos inner perianth lobes at coloured-bud stage

description: Library name: JB1nC

value: Inner perianth lobes


title: Biosolids Male 8735


title: LEE307A7

value: female


title: 1681-T0


title: biol rep 3 of Jan Bos outer perianth lobes at coloured-bud stage

description: Library name: JB3oC

value: Coloured flower buds


title: LEE307A68


title: Biosolids Male 8695


title: Biosolids Male 8690


title: 1680-T90


title: biol rep 2 of Jan Bos outer perianth lobes at coloured-bud stage

description: Library name: JB2oC


title: 1680-T0


title: LEE307A67

value: male


title: biol rep 1 of Jan Bos outer perianth lobes at coloured-bud stage

description: Library name: JB1oC


title: GE-T90

description: Plasma_Post-stimulation_Healthy Control

source_name: Plasma_Post-stimulation_Healthy Control

value: Healthy control (HC)


title: Biosolids Male 8778


title: Biosolids Female 8775

value: Female


title: LEE307A65


title: LEE307A63


title: LEE307A71


title: Biosolids Male 8764


title: Biosolids Female 8733


title: 954-T90

value: Non-progressor (NP)


title: LEE307A60


title: Biosolids Female 8731


title: biol rep 2 of Jan Bos inner perianth lobes at coloured-bud stage

description: Library name: JB2nC

source_name: Inner perianth lobes


title: biol rep 2 of Jan Bos perianth tube at green-bud stage

description: Library name: JB2tB

source_name: Perianth tube

value: Perianth tube

value: Green flower buds


title: LEE307A70


title: 954-T0


title: biol rep 1 of Jan Bos perianth tube at green-bud stage

description: Library name: JB1tB

value: Jan Bos


title: LEE307A59

value: WT


title: 853-T90


title: LEE307A56


title: biol rep 3 of Jan Bos inner perianth lobes at green-bud stage

description: Library name: JB3nB


title: Biosolids Female 8668


title: 853-T0


title: biol rep 3 of Jan Bos perianth tube at green-bud stage

description: Library name: JB3tB


title: 844-T0


title: 844-T90


title: biol rep 1 of Jan Bos inner perianth lobes at green-bud stage

description: Library name: JB1nB


title: biol rep 2 of Jan Bos inner perianth lobes at green-bud stage

description: Library name: JB2nB


title: Biosolids Female 8653


title: Biosolids Female 8714


title: Biosolids Female 8649


title: LEE307A54


title: 793-T90

value: Progressor (P)


title: LEE307A52


title: Biosolids Female 8647


title: 793-T0

value: plasma


title: Control Male 8428

value: Liver

value: Control


title: biol rep 3 of Jan Bos outer perianth lobes at green-bud stage

description: Library name: JB3oB

value: Outer perianth lobes


title: 4217-T90

description: Plasma_Post-stimulation_Healthy Control

value: F


title: biol rep 1 of Jan Bos outer perianth lobes at green-bud stage

description: Library name: JB1oB


title: biol rep 2 of Jan Bos outer perianth lobes at green-bud stage

description: Library name: JB2oB


title: Caenorhabditis elegans, YA hermaphrodites, Neurons, rep 1

description:
Library name: Hermaphrodite_batch_1
10x Genomics
Combined_features.tsv.gz

value: rab-3::tagRFP+ neurons

tag: cell type

value: otIs355 [rab-3(prom1)::2xNLS-TagRFP] IV

tag: treatment

value: Young Adult Hermaphrodites


title: LEE307A44

tag: genotype

value: female


title: Control Male 8425

tag: Sex

value: Male


title: Control Male 8408


title: LEE307A45


title: 4216-T90

description: Plasma_Post-stimulation_Healthy Control

value: Healthy control (HC)


title: LEE163A4

data_processing:
Read trimming was performed with TrimGalore v0.6.0 using these parameters: --clip_R1 6 --3_prime_clip_R1 6
Mapping was performed with Bismark v0.18.0 using these parameters: --non_directional --un --ambiguous
SNP splitting was performed with SNPsplit v0.3.4 using these parameters: --bisulfite –conflicting
Methylation analysis was performed with R v3.4.3 using the methylKit v1.4.1 package
Plotting was performed with R v3.4.3 using the ggplot2 v3.2.0 and Gviz v1.22.3 packages
Assembly: mm10

organism: Mus musculus x Mus spretus

extract_protocol:
PureLink Genomic DNA Mini kit for gDNA extraction from adult tissues. Direct lysis for low-input sperm and blastocyst samples
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

value: Brain

tag: strain

value: C57BL/6J x Mus spretus

value: Female


title: LEE307A55


title: 4211-T90

description: Plasma_Post-stimulation_Healthy Control


title: LEE307A42

value: male


title: LEE307A53

value: WT


title: Control Male 8382


title: Control Male 8364


title: 392-T0

value: Non-progressor (NP)


title: LEE73A11


title: LEE307A40


title: LEE73A12


title: LEE307A41


title: LEE307A4


title: LEE73A10


title: 1695-T90

source_name: Human Plasma, Post 90min stimulation, AIS, progressor

value: plasma

value: Progressor (P)


title: 1695-T0


title: 392-T90


title: LEE73A9


title: LEE73A8

value: Liver


title: 1693-T90


title: Control Female 8360

value: Control


title: LEE307A37


title: Control Female 8353


title: Control Male 8394


title: LEE307A36


title: LEE73A7


title: 1693-T0

value: F


title: 1690-T90


title: LEE307A34


title: LEE73A6


title: Control Female 8322


title: LEE307A33


title: LEE73A5


title: Control Female 8313


title: 1690-T0


title: Control Male 8351


title: LEE73A4


title: LEE307A32


title: LEE73A3


title: 4155

description: Plasma_Baseline_Healthy Control


title: Control Female 8269


title: 4124

description: Plasma_Baseline_Healthy Control


title: Control Female 8263


title: Control Female 8378


title: Control Female 8245


title: LEE307A3


title: LEE307A38


title: 4119

description: Plasma_Baseline_Healthy Control

value: M


title: LEE73A2


title: LEE307A29


title: LEE307A26


title: LEE73A1


title: 4113

description: Plasma_Baseline_Healthy Control


title: K1-DT

city: Los Angeles

first: youssef

last: errami

state: CA

address: 650 Charles E Young Dr S

department: MIMG

institute: University of California Los Angeles

description: Library name: Sample 8

data_processing:
The CRISPR/Cas9 screening data were performed by MAGeCK and MAGeCK-VISPR algorithms. MAGeCK-VISPR calculated the beta score for each gene. The differential beta scores between the BRAFi treatment and DMSO treatment were compared using MAGeCKFlute, which was designed to perform quality control, normalization, and downstream analysis of the functional CRISPR screens.
Assembly: Human GRCh38
Supplementary files format and content: tab delimited txt files normalized count contains median-normalized values to adjust for the effect of library sizes and read count distributions
Supplementary files format and content: tab delimited txt files contains raw count for each samples
Library strategy: CRISPR Screen

growth_protocol: K1 and 8505c were purchased from Millipore-Sigma Cat. No. 92030501, and Cat. No. 94090184. Cells were cultured according to provider instructions.

extract_protocol:
After harvesting the cells from different groups, we extracted the genomic DNA. Library construction for NGS was performed by two-step PCR. The PCR products were purified and then sequenced on a HiSeq 2500 by Azenta Next Generation Sequencing Services. Each library was sequenced at 30–40 million reads to achieve ∼300 × average coverage over the CRISPR library.
Library construction for NGS was performed by two-step PCR. The PCR products were purified and then sequenced on a HiSeq 2500 by Azenta Next Generation Sequencing Services. Each library was sequenced at 30–40 million reads to achieve ∼300 × average coverage over the CRISPR library.

treatment_protocol: Human Brunello CRISPR knockout pooled library was a gift from David Root and John Doench (Addgene #73178). lentiCas9-Blast was a gift from Feng Zhang (Addgene plasmid # 52962). pLenti-U6sgbbBsmbI-puro-2A-Fluc was a gift from Sidi Chen (Addgene plasmid # 100277). The standard protocols to anneal and clone the sgRNA oligos into the lentiCRISPR v2 vector. For the pooled CRISPR screen, a total of 1×108 cells were infected with the pooled lentiviral library at a multiplicity of infection (MOI) of 0.3. After puromycin selection, the cells were divided into two groups (Day 0 and treatment). The cell pellet of Day 0 group was stored at −80 °C. For the treatment groups, the cells were cultured for 21 days or until confluency was reached and treated with 10 μM of Dabrafenib+ 10nM of Trametinib. Media was replaced with fresh media every 3-4 days.

tag: cell line

value: Thyroid gland papillary carcinoma

value: Cas9+Brunello library

value: Dabrafenib+Trametinib

tag: batch


title: LEE307A25

value: female


title: liver cell

city: Chengdu

first: yuan

last: Yang

country: China

institute: Sichuan Agricultural University

description: Library name: HepG2

library_source: other

data_processing:
java -jar /data/Yangyuan/software/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -threads 10
Assembly: hg38
Supplementary files format and content: remove adapt for each fq.gz and get each clean.pair.fq.gz

source_name: liver

extract_protocol:
The RNA3' end was labeled with pCp-biotin
Transformed into strand-specific libraries for sequencing

value: liver

value: liver cell


title: K1-TRA

description: Library name: Sample 7

value: Trametinib


title: 4108

description: Plasma_Baseline_Healthy Control

tag: disease status

value: Healthy control (HC)

tag: age (years)


title: LEE307A24

value: male


title: Ovaries, 10 weeks, req3

first: XingYu

last: Wang

state: Sichuan

address: No.211 Huimin Road

description:
Girl-10w-3-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m33G), overcoming the hindrance these modifications pose to reverse transcriptase activity.

data_processing:
Small RNA sequences were annotated using the software SPORTS1.1 (updated from SPORTS1.0) with one mismatch tolerance (SPORTS1.1 parameter setting: -M 1). Reads were mapped to the following individual non-coding RNA databases sequentially: (1) the miRNA database miRBase 21; (2) the genomic tRNA database GtRNAdb; (3) the mitochondrial tRNA database mitotRNAdb; (4) the rRNA and YRNA databases assembled from the National Center for Biotechnology Information nucleotide and gene database; (5) the piRNA databases, including piRBase and piRNABank; and (6) the non-coding RNAs defined by Ensembl and Rfam 12.3. The tsRNAs were annotated based on both pre-tRNA and mature tRNA sequences. Mature tRNA sequences were derived from the GtRNAdb and mitotRNAdb sequences using the following procedures: (1) predicted introns were removed; (2) a CCA sequence was added to the 3′ ends of all tRNAs; and (3) a G nucleotide was added to the 5′ end of histidine tRNAs. The tsRNAs were categorized into four types based on the origin of the tRNA loci: 5′ tsRNA (derived from the 5′ end of pre-/mature tRNA); 3′ tsRNA (derived from the 3′ end of pre-tRNA); 3′ tsRNA-CCA end (derived from the 3′ end of mature tRNA); and internal tsRNAs (not derived from 3′ or 5′ loci of tRNA). For the rsRNA annotation, we mapped the small RNAs to the parent rRNAs in an ascending order of rRNA sequence length to ensure a unique annotation of each rsRNA (for example, the rsRNAs mapped to 5.8S rRNA would not be further mapped to the genomic region overlapped by 5.8S and 45S rRNAs). Differentially expressed sncRNA analysis was performed using the R package DESeq2.
Assembly: mm10
Supplementary files format and content: The small RNA types and reads aligned for each sample

source_name: Ovaries

extract_protocol:
Testicular tissues from male mice and ovarian tissues from female mice were collected into cryotubes and rapidly frozen in liquid nitrogen, followed by storage at -80°C until further use.Total RNA was extracted using TRIzol Reagent (1 ml; Invitrogen; 15596018). Small RNAs of 15–50 nucleotides was selected.
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m22G), overcoming the hindrance these modifications pose to reverse transcriptase activity.

value: Ovaries


title: K1-DAB

description: Library name: Sample 6

value: Dabrafenib


title: Ovaries, 10 weeks, req2

description:
Girl-10w-2-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m32G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: LEE307A23

value: WT


title: 3098

value: plasma

value: Non-progressor (NP)

tag: cobb angle (°)

tag: final cobb (°) age (years)


title: K1-C

description: Library name: Sample 5

value: DMSO


title: 3080

value: F

tag: functional group (used for different studies)

tag: timepoints (used for different studies)


title: Ovaries, 10 weeks, req1

description:
Girl-10w-1-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m31G), overcoming the hindrance these modifications pose to reverse transcriptase activity.

tag: tissue


title: LEE307A21

tag: developmental stage


title: 8505c-TRA

description: Library name: Sample 3

value: Anaplastic thyroid carcinoma


title: 8505c-DT

description: Library name: Sample 4


title: 3062

value: M


title: LEE307A2

tag: inferred sex


title: Ovaries, 4 weeks, req3

description:
Girl-4w-3-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m30G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: Ovaries, 4 weeks, req2

description:
Girl-4w-2-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m29G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: Ovaries, 4 weeks, req1

description:
Girl-4w-1-O
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m28G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: LEE307A192


title: 8505c-DAB

description: Library name: Sample 2

value: Cas9+Brunello library


title: LEE307A184


title: 1595

source_name: Human Plasma, Baseline, AIS, progressor

value: Progressor (P)


title: Testes, 10 weeks, req2

description:
Boy-10w-2-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m26G), overcoming the hindrance these modifications pose to reverse transcriptase activity.

source_name: Testes

value: Testes


title: 8505c-C

description: Library name: Sample 1


title: LEE307A183

value: female


title: Testes, 10 weeks, req3

description:
Boy-10w-3-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m27G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: iPSC, Han Chinese, normoxia, ind10

city: Chicago

first: Anna

last: Di Rienzo

state: IL

department: Human Genetics

institute: University of Chicago

data_processing:
The bulk RNAseq reads were aligned with the STAR aligner and read counts performed with RSEM using default settings.
Assembly: Gencode 2019-09-05 transcriptome (GRCh38)
Supplementary files format and content: Bulk RNAseq: tab separated values files.

growth_protocol: For the Tibetan samples, peripheral whole blood samples were collected by venipuncture, and LCLs were generated using a standard protocol (Coriell Institute) for establishment of lymphoblastoid cell cultures from peripheral blood mononuclear cells (PBMCs). All Han Chinese samples used in the study were obtained from Coriell in the form of LCLs. Reprogramming of LCLs to iPSCs was performed in accordance with Thomas et al., 2015. All generation and maintenance of iPSCs were performed in atmospheric oxygen concentration. Cells were grown in culture at 37°C, 5% CO2 in a standard incubator. iPSCs were then differentiated into vascular endothelium. Our panel of TAC-CHB iPSCs were grown to confluence in batches of 4-8 lines (balanced for population and sex). On day 0 cells were detached using Cell Release, an EDTA-based solution, counted, and replated at a density of ~50,000 cells/cm2 in Essential 8 media supplemented with Rho-associated kinase (ROCK) inhibitor Y27632 (BioVision, 1994-1). On day 1, medium was replaced with N2B27 medium – a 1:1 mixture of DMEM:F12 (Life technologies, 11320-033) and Neurobasal media (Life technologies, 21103049) with glutaMAX (Life technologies, 35050038), β-Mercaptoethanol (0.097%) ( Life technologies, 21985023), N2(Life technologies, 17502048), and B27 minus vitamin A (Life technologies, 12587010)] this was supplemented with 8uM CHIR (Tocris, 4953) and 25ng/ml hBMP4 (PeproTech, 120-05ET) and added to the cells at high volume (i.e. 15 mL in 22.1cm dish). The cells were left undisturbed for 3 days. On day 4, media was exchanged for EC Induction Medium - StemPro-34 SFM medium (Life technologies, 10639-011) supplemented with 200 ng/mL VEGF165 (PeproTech, 100-20) and 2μM forskolin (Abcam, ab120058), and penicillin-streptomycin]. EC Induction Medium was refreshed on day 5, and on day 6 CD144+ cells were either isolated via pulldown or replated for subsequent single-cell sequencing.

extract_protocol:
RNA extraction was performed in 5 balanced batched of 8 (balanced for population, sex, and treatment) in a Qiagen Qiacube (9001292) using the Rneasy Plus Mini Kit. RNA was assessed for concentration prior to library preparation
500ng of each sample was used for library prep using Illumina TruSeq2 RNA-seq library prep kit and set A indexes (RS-122-2001). All libraries were assessed via bioanalyzer to be of sufficient quality, concentration, and fragment size for further processing.

treatment_protocol: For the population-wide bulk RNA sequencing, bead-purified iPSC-derived endothelial cells were washed and lysed in-plate using RLT Plus buffer from the Qiagen Rneasy Plus Mini Kit (74134). Cell culture replicates in hypoxia were lysed and harvested in the hypoxia box with no exposure to normoxia prior to lysis. Lysates were flash frozen and stored at -80C degrees until all batches were complete.

value: LCL-iPS

value: iPSC

value: wild type

value: normoxia


title: 1519


title: iPSC, Han Chinese, normoxia, ind9


title: Testes, 10 weeks, req1

description:
Boy-10w-1-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m25G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: 4103

description: Plasma_Baseline_Healthy Control

value: Healthy control (HC)


title: LEE307A182


title: LEE307A181


title: 967


title: iPSC, Han Chinese, normoxia, ind8


title: iPSC, Han Chinese, normoxia, ind7


title: Testes, 3 weeks, req3

description:
Boy-3w-3-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m24G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: 3030


title: LEE307A19

value: male


title: iPSC, Han Chinese, normoxia, ind6


title: LEE307A180

value: WT


title: 1692

value: plasma


title: Testes, 3 weeks, req1

description:
Boy-3w-1-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m22G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: 946

value: Non-progressor (NP)


title: iPSC, Han Chinese, normoxia, ind5


title: LEE307A179


title: 917


title: 907


title: LEE307A178


title: iPSC, Han Chinese, normoxia, ind3


title: iPSC, Han Chinese, normoxia, ind4


title: 952


title: NL106_Tcells

type: RNA

city: Stanford

first: Yury

last: Goltsev

address: 3220 CCRS, Baxter lab,

department: Department of Microbiology and Immunology

institute: Stanford Medical School

description: RNA from fixed and permeabilized AML patient T cells sorted from PBMC after staining

hyb_protocol: Following fragmentation, 5 ug of amplified DNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: standard Affymetrix scan protocol

data_processing: The data were analyzed by RMA-express software based on remapped custom ENSENG .cdf files (hgu133plus2hsensgcdf version 13.0.0; http://brainarray.mbni.med.umich.edu/Brainarray).

label: biotin

label_protocol: Biotinylated amplified cDNA was prepared according to Ovation Pico WTA kit (NuGEN)

extract_protocol: Following treatment  with G-CSF (20 ng/ml for 15 min at 37 °C) cells were fixed for 10 min at room temperature (RT) by adding 16% formaldehyde (100 µL/mL) directly into tubes with media (RPMI, 10% FCS). A stock of fixed cells was pelleted by centrifugation at 500 g for 5 min and was re-suspended in a residual volume by vortexing. Ice-cold methanol was added, and cells were either kept on ice for 10 min prior to analysis or stored at -80 °C. Cells in methanol were spun and resuspended in 1:1 mixture of methanol with 10% formaldehyde in PBS, 0.1% Tween 20 (PBST), kept for 5 min on ice, then spun and resuspended in 10% formaldehyde in PBST and kept for 20 min at RT. Following this post-fixation, cells were washed twice with PBST/RNasin (40 units/ml) and stained with an antibody cocktail in the presence of RNasin (800 units/ml). Following staining, cells were washed twice with PBST/RNasin (40 units/ml) and stored until sorting in PBST/RNasin (800 units/ml). Cells were sorted into PBST/RNasin (80 units/ml) and RNA was isolated using the RecoverAll kit (Ambion). It was crucial to add 1 μl of RNasin (40 units/ul) to the 60 μl DNase digestion mix

value: AML patient T cells sorted from PBMC

tag: rna preparation protocol

value: RecoverALL (Ambion)

value: G-CSF (20 ng/ml for 15 min at 37 °C)


title: 894

value: F


title: LEE307A176


title: Testes, 3 weeks, req2

description:
Boy-3w-2-T
Pandora-seq (Panoramic RNA Display by Overcoming RNA modification Aborted sequencing) addresses the issue of adapter ligation caused by terminal modifications in small RNAs (ranging from 15-50 nt) through enzymatic treatments (T4PNK, AlkB). This method converts 3' phosphate groups or 2',3' cyclic phosphate groups into 3'-OH groups, and 5'-OH groups into 5' phosphate groups. Additionally, it removes specific RNA methyl modifications (m1A, m1G, m3C, m23G), overcoming the hindrance these modifications pose to reverse transcriptase activity.


title: 892

value: M


title: iPSC, Han Chinese, normoxia, ind1

tag: cell type


title: 896

value: Progressor (P)


title: LEE307A174


title: LEE307A175


title: 884


title: iPSC, Han Chinese, normoxia, ind2

tag: treatment


title: LEE307A177

tag: genotype


title: NL102_Tcells

source_name: RNA from fixed and permeabilized AML patient T cells sorted from PBMC after staining


title: NL103_Tcells


title: NL105_Tcells


title: LEE307A173


title: PDN, rat, rep2

city: Beijing

first: Jing

address: No. 49, North Garden Street, Haidian District, Beijing

institute: Peking University Third Hospital

description: Library name: DD2

data_processing:
RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
Assembly: rattus_norvegicus_Ensembl_97
Supplementary files format and content: mRNA_gene.FPKM.xls
Supplementary files format and content: mRNA_genes.readcount.xls

organism: Rattus norvegicus

source_name: sensory neuron

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 1 µg total RNA per sample was used as input material for the lncRNA library preparation. Strand-specific libraries were generated using NEBNext® UltraTM

value: sensory neuron

tag: gender


title: PDN, rat, rep3

description: Library name: DD3


title: NL101_Tcells


title: 786

tag: Sex


title: PDN, rat, rep1

description: Library name: DD1


title: NL027_Tcells


title: LEE307A17


title: NL023_Tcells


title: 745


title: 733


title: control, rat, rep3

description: Library name: DV3


title: LEE307A163

source_name: sperm

value: sperm


title: LEE307A161


title: control, rat, rep1

description: Library name: DV1


title: control, rat, rep2

description: Library name: DV2


title: LEE307A141


title: NL019_Tcells


title: NL010_Tcells


title: cruabc_DAF10_R3

city: Columbia

first: Ruthie

last: Angelovici

state: MO

address: 371D Christopher S. Bond Life Sciences Center, 1201 Rollins St

department: Division of Biological Sciences

institute: University of Missouri

description: Developmental stage

data_processing:
FASTQC version 0.11.7
STAR version 2.7.10a
Assembly: Arabidopsis Thaliana TAIR10 reference genome
Supplementary files format and content: tab delimited file that contains the raw counts output by STAR aligner with --quantMode GeneCounts
Supplementary files format and content: combined raw counts

organism: Arabidopsis thaliana

source_name: cruabcabc 10 days after flowering

growth_protocol: Seeds from Col-0 and cruabc were grown in growth chambers at 22°C/24°C (day/night) under long-day conditions (16 h of light/8 h of dark) and watering was provided to keep plants hydrated at all times. Seeds were harvested at 10, 12, 14, 16, 18, and 20 days after flowering (DAF).

extract_protocol:
Total RNA extracted from dry and developing seeds was isolated using a hot borate method (Birtić & Kranner, 2006) and purified using Direct-zol RNA Miniprep Plus filter columns (Zymo Research).
RNA samples were subject to sequencing using the Illumina NoavSeq 6000 sequencing platform (2-3 samples per treatment), resulting in library sizes of approximately 50 million, 100-bp paired-end reads (per sample). RNA sequencing data quality was checked using MultiOC (Ewels et al., 2016) and reads were trimmed for quality control before analyses. In short, reads whose 3' ends overlapped with the adapter for a minimum of 3 bases with 90% identity were trimmed at the 3’ end for Illumina adapters, for ambiguous nucleotides (N’s) and for poly-G artifacts arising from Illumina two-color chemistry using Cutadapt version 1.18 (Martin, 2011). After trimming, reads shorter than 10 bp were discarded (with their associated paired read).

treatment_protocol: The treatment consists of comparing the triple mutant cruabc (T-DNA insertions targeting CRUA (At5g44120.3), CRUB (At1g03880.1), and CRUC (At4g28520.1)) with Col-0 during seed maturation and normal growth conditions

value: Seed

value: cruabc

value: triple seed storage protein mutant

tag: time (days_after_flowering)

tag: round


title: 693

tag: disease status


title: 692

tag: age (years)


title: LEE307A140


title: 630

tag: cobb angle (°)


title: ND3_Tcells_fixed

description: RNA from fixed and permeabilized Normal Donor T cells sorted from PBMC

extract_protocol: Sorted live T cells (CD3+) from PBMC of a normal donor 3, ND3, were fixed for 10 min at room temperature (RT) by adding 16% formaldehyde (100 µL/mL) directly into tubes with media (RPMI, 10% FCS). A stock of fixed cells was pelleted by centrifugation at 500 g for 5 min and was re-suspended in a residual volume by vortexing. Ice-cold methanol was added, and cells were either kept on ice for 10 min prior to analysis or stored at -80 °C. Cells in methanol were spun and resuspended in 1:1 mixture of methanol with 10% formaldehyde in PBS, 0.1% Tween 20 (PBST), kept for 5 min on ice, then spun and resuspended in 10% formaldehyde in PBST and kept for 20 min at RT. Following this post-fixation, cells were washed twice with PBST/RNasin (40 units/ml) and stained in the presence of RNasin (800 units/ml) with antibodies (p-Stat3 and p-Stat5) that in other experiments were to be used to enrich for AML cell subsets based on their G-CSF-mediated Stat signaling responses . Following staining, cells were washed twice with PBST/RNasin (40 units/ml) and stored until sorting in PBST/RNasin (800 units/ml).  To mimic the “sorting after staining” scenario cells were re-sorted into PBST/RNasin (80 units/ml) and RNA was isolated using the RecoverAll kit (Ambion).

value: Normal Donor T cells sorted from PBMC


title: 622

tag: final cobb (°) age (years)


title: LEE307A14


title: cruabc_DAF12_R3

description: Developmental stage

source_name: cruabcabc 12 days after flowering


title: cruabc_DAF10_R1

description: Developmental stage


title: cruabc_DAF12_R1

description: Developmental stage


title: LEE307A138


title: 621

tag: functional group (used for different studies)


title: NL009_Tcells


title: ND1_Tcells_live

description: RNA from live Normal Donor T cells sorted from PBMC

extract_protocol: RNA was isolated by standard protocols (without fixation steps) from viable Monocytes (CD33+) sorted from PBMC of Normal Donor

value: trizol followed by RNAeasy purification


title: ND2_Tcells_live

source_name: RNA from live Normal Donor T cells sorted from PBMC


title: 714

tag: timepoints (used for different studies)


title: LEE307A16

source_name: embryo

value: female


title: 600

tag: tissue


title: NL106_RC

description: RNA from fixed and permeabilized AML blast cells sorted based on positive response to G-CSF induction (high phospho-Stat5/3)

value: sorted AML blast cells  responding to G-CSF induction (high phospho-Stat5/3)


title: LEE307A13

tag: developmental stage

value: WT


title: 593

value: plasma


title: cruabc_DAF14_R1

description: Developmental stage

source_name: cruabcabc 14 days after flowering


title: NL001_Tcells

value: AML patient T cells sorted from PBMC


title: 592

source_name: Human Plasma, Baseline, AIS, non-progressor

value: Non-progressor (NP)


title: LEE307A114

tag: inferred sex


title: NL105_RC

source_name: RNA from fixed and permeabilized AML blast cells sorted based on positive response to G-CSF induction (high phospho-Stat5/3)

tag: rna preparation protocol

value: RecoverALL (Ambion)

value: G-CSF (20 ng/ml for 15 min at 37 °C)


title: cruabc_DAF16_R3

description: Developmental stage

source_name: cruabcabc 16 days after flowering


title: cruabc_DAF16_R1

description: Developmental stage


title: 590

value: F


title: NL103_RC

tag: cell type


title: 572

value: M


title: LEE307A112

source_name: oocyte

value: oocyte


title: LEE307A134

value: sperm


title: cruabc_DAF18_R1

description: Developmental stage

source_name: cruabcabc 18 days after flowering

value: Seed

tag: treatment


title: NL101_RC


title: cruabc_DAF18_R3

description: Developmental stage

tag: genotype

value: cruabc


title: cruabc_DAF14_R3

description: Developmental stage

value: triple seed storage protein mutant


title: LEE307A111


title: cruabc_DAF20_R3

description: Developmental stage

source_name: cruabcabc 20 days after flowering


title: NL027_RC


title: 502

value: Progressor (P)


title: NL023_RC


title: LEE307A109


title: LEE307A110


title: cruabc_DAF20_R1

description: Developmental stage


title: NL019_RC


title: 492


title: LEE307A108


title: 484


title: Col-0_DAF10_R3

description: Developmental stage

source_name: Col-0 10 days after flowering

value: Control


title: NL010_RC


title: LEE307A113


title: NL102_RC


title: Col-0_DAF10_R2

description: Developmental stage


title: 477


title: LEE307A107


title: LEE307A106


title: 463

source_name: Human Plasma, Baseline, AIS, progressor


title: Col-0_DAF10_R1

description: Developmental stage


title: 536


title: 453


title: NL009_RC


title: NL001_RC


title: Col-0_DAF12_R3

description: Developmental stage

source_name: Col-0 12 days after flowering


title: LEE307A102

value: male


title: Col-0_DAF12_R2

description: Developmental stage


title: ND1_CD34plusCD38plus

description: RNA from live Normal Donor circulating CD34plusCD38plus cells sorted from PBMC

extract_protocol: RNAqueous (Ambion)

value: Normal Donor CD34plusCD38plus cells sorted from PBMC

value: RNAqueous (Ambion)


title: 435

value: plasma


title: 433


title: NL106_NRC

description: RNA from fixed and permeabilized AML blast cells sorted based on the absence of response to G-CSF induction (low phospho-Stat5/3)

value: sorted AML blast cells not responding to G-CSF induction (low phospho-Stat5/3)


title: Col-0_DAF12_R1

description: Developmental stage


title: LEE307A10

value: WT


title: 422

value: Non-progressor (NP)


title: NL105_NRC

source_name: RNA from fixed and permeabilized AML blast cells sorted based on the absence of response to G-CSF induction (low phospho-Stat5/3)

value: RecoverALL (Ambion)

value: G-CSF (20 ng/ml for 15 min at 37 °C)


title: LEE307A1


title: Col-0_DAF14_R3

description: Developmental stage

source_name: Col-0 14 days after flowering


title: Col-0_DAF14_R2

description: Developmental stage


title: HCT116, DON, rep3

city: shanghai

first: tan

last: zizheng

address: songhu road

institute: Fudan university

description:
Library name: Sample6
case1-3

data_processing:
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases. The clean reads obtained were then aligned to the hg19 human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie. Differentially expressed genes (DEGs) were identified by Deseq2 (for sample with replications) with a cut-off value of log2 |fold change| >1 and p-adjust < 0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules based on gene ontology (GO) and KEGG pathway categories. Terms with pvalue<0.05 were considered significant. Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: hg19
Supplementary files format and content: Excel files includes FPKM for each Sample.
Supplementary files format and content: allgenes_sample_FPKM.xls

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12310ES, China) following manufacturer’s recommendations. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

tag: cell line

value: diazo-5-oxo-L-norleucine (DON)


title: HCT116, DON, rep2

description:
Library name: Sample5
case1-2


title: 393

tag: Sex

value: M


title: LEE307A105

value: oocyte


title: Col-0_DAF14_R1

description: Developmental stage

value: Seed

tag: time (days_after_flowering)


title: NL102_NRC


title: NL103_NRC


title: Col-0_DAF16_R3

description: Developmental stage

source_name: Col-0 16 days after flowering

tag: round


title: 409

tag: disease status

value: F


title: NL101_NRC


title: 381

tag: age (years)


title: 332

tag: cobb angle (°)


title: NL027_NRC


title: Col-0_DAF16_R2

description: Developmental stage


title: HCT116, DMSO, rep2

description:
Library name: Sample2
control1-2

value: control


title: Col-0_DAF16_R1

description: Developmental stage


title: NL019_NRC


title: HCT116, DMSO, rep1

description:
Library name: Sample1
control1-1


title: NL023_NRC


title: Col-0_DAF18_R3

description: Developmental stage

source_name: Col-0 18 days after flowering


title: 326

tag: final cobb (°) age (years)


title: 315

tag: functional group (used for different studies)


title: NL010_NRC


title: Col-0_DAF18_R2

description: Developmental stage


title: 288

tag: timepoints (used for different studies)


title: PLC, shRBBP5, RNA-seq

city: Hefei

first: Ling

last: Ye

address: 443 Huangshan Road

institute: University of Science and technology of China

data_processing:
Reads were aligned to the human genome hg19 using Hisat2 (v 2.2.1).
Transcripts were assembled with Stringtie (v 1.3.4).
Gene differential expression analysis was carried out with the DESeq2 (v 1.28.1).
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: PLC

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer’s instructions.
RNA libraries were prepared using the HiScript Ⅲ RT SuperMix (Vazyme).

value: PLC

value: Human liver cancer cell


title: PLC, shHKDC1, RNA-seq


title: HCT116, DON, rep1

description:
Library name: Sample4
case1-1


title: NL009_NRC


title: 267

extract_protocol: Biobanked plasma samples were thawed and centrifugated at 17,000 x g for 15 minutes at 4°C. The RNA was extracted using the NucleoSpin miRNA Plasma kit (MACHEREY-NAGEL GmbH & Co. KG, Düren,Germany) according to the manufacturer's instructions.

tag: tissue


title: Col-0_DAF20_R3

description: Developmental stage

source_name: Col-0 20 days after flowering

value: Control


title: PLC, NTC, RNA-seq


title: 240


title: PLC, shRBBP5, CUT&Tag

data_processing:
CUT&Tag reads were alligned to the UCSC hg19 gemone using Bowtie version 2.2.6.
Peaks were calle using MACS version 2.1.0.
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: Cell line

extract_protocol:
DNA was extracted using Hyperactive Universal CUT&Tag Assay Kit (TD903-01, Vazyme) according to the manufacturer’s instructions.
CUT&Tag libraries were prepared using the TruePrep® Index Kit V2 for Illumina.

value: Cell line


title: NL001_NRC


title: Col-0_DAF20_R2

description: Developmental stage


title: Col-0_DAF20_R1

description: Developmental stage


title: HCT116, DMSO, rep3

description:
Library name: Sample3
control1-3


title: 200


title: ND2_Monocytes_live

description: RNA from live Normal Donor Monocytes sorted from PBMC

value: Normal Donor Monocytes sorted from PBMC

value: trizol followed by RNAeasy purification


title: PLC, NTC, CUT&Tag

value: NTC


title: 165

value: plasma

value: Progressor (P)


title: ND1_Monocytes_live

source_name: RNA from live Normal Donor Monocytes sorted from PBMC


title: H295R cells, Forskolin 10uM treated, 48h, rep 4

city: Durham

first: Timothy

middle: E

last: Reddy

state: NC

address: 101 Science Dr

institute: Duke University

description:
Library name: H295R-forsk-4
Azenta RNA-Seq

data_processing:
RNA-Seq FASTQ from each samples was alignmed using STAR(PMID :  23104886) to hg38 . Transcript counts were determined using RSEM and differential gene expression analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: *.rsem.genes.results - contains the FPKM and TPM per sample

growth_protocol: NCI-H295R cells were cultured in DMEM/F-12 medium (Gibco #21041025) supplemented with 2.5% Nu-Serum (Corning #355100) and 1% ITS+Premix (Corning #354352) and grown as a monolayer at 37 °C, 5%CO2. COV434 cells were cultured in DMEM (Gibco #11965092) supplemented with 2 mM Glutamine and 10% Foetal Bovine Serum (FBS) and grown as a monolayer at 37 °C, 5%CO2. All experiments were performed between passages 5 and 12.

extract_protocol:
RNA extraction and RNA-seq was done using Azenta RNA-Sequencing.
Poly A RNA selection + RNA-seq

treatment_protocol: Cells were treated with 10uM Forskolin (Stemcell Tecnologies, #66575-29-9) or DMSO as control for 48 hours.

value: Adrenal cell

value: WT

value: 10uM Forskolin for 48hr

tag: batch


title: Col-0_DAF18_R1

description: Developmental stage


title: H295R cells, Forskolin 10uM treated, 48h, rep 3

description:
Library name: H295R-forsk-3
Azenta RNA-Seq


title: ND3_Monocytes_fixed

description: RNA from fixed and permeabilized Normal Donor Monocytes sorted from PBMC

extract_protocol: Sorted live monocytes (CD33+) from PBMC of a normal donor 3, ND3, were fixed for 10 min at room temperature (RT) by adding 16% formaldehyde (100 µL/mL) directly into tubes with media (RPMI, 10% FCS). A stock of fixed cells was pelleted by centrifugation at 500 g for 5 min and was re-suspended in a residual volume by vortexing. Ice-cold methanol was added, and cells were either kept on ice for 10 min prior to analysis or stored at -80 °C. Cells in methanol were spun and resuspended in 1:1 mixture of methanol with 10% formaldehyde in PBS, 0.1% Tween 20 (PBST), kept for 5 min on ice, then spun and resuspended in 10% formaldehyde in PBST and kept for 20 min at RT. Following this post-fixation, cells were washed twice with PBST/RNasin (40 units/ml) and stained in the presence of RNasin (800 units/ml) with antibodies (p-Stat3 and p-Stat5) that in other experiments were to be used to enrich for AML cell subsets based on their G-CSF-mediated Stat signaling responses . Following staining, cells were washed twice with PBST/RNasin (40 units/ml) and stored until sorting in PBST/RNasin (800 units/ml).  To mimic the “sorting after staining” scenario cells were re-sorted into PBST/RNasin (80 units/ml) and RNA was isolated using the RecoverAll kit (Ambion).

value: RecoverALL (Ambion)


title: HUVEC VEGFB6h rep3

city: Guangzhou

first: Yi

last: Liu

state: Guangdong

address: No.7 Jinsui Rd.

department: Vascular biology

institute: Zhongshan Ophthalmic Center Sun Yat-Sen University

data_processing:
The raw sequence reads that passed quality filters were aligned to human hg38 reference transcriptome with salmon (v0.11.3).
After alignment, tximport (v1.14.0) was used to generate read counts for gene-level expressions.
Differentially expressed genes were identified by DESeq2 (v1.22.2).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited gene expression matrix, each column denotes a sample, each row denotes a gene.

source_name: Human umbilical vein endothelial cell

extract_protocol:
Treated HUVECs were washed with PBS once and immediately extracted with TRNzol Universal Reagent for total RNA. Two ug of total RNA  was used for the construction of sequencing libraries.
Total RNA was send to Berry Genomics Co, Ltd (Beijing, China) for quality control, sample preparing, library construction and sequencing.

treatment_protocol: HUVECs were cultured in starvation medium (0.5% FBS in ECM medium, without ECGS) for 6 hours, futher treated with 100 ng/mL BSA or VEGF-B for 6 hours, and harvested for RNA extraction.

value: 100ng/mL VEGFB


title: 159


title: Old-14dpi, replicate 1

first: Guiping

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting were made using the Cell Ranger software v7.1.0.
Assembly: GRCm39
Supplementary files format and content: Cell Range output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Spinal cord

extract_protocol:
To prepare the cell suspension for 3’ 10X genomic single cell RNA sequencing, mice were anaesthetized (80 mg of ketamine and 10 mg of xylazine per kilogram of body weight via i.p. injection) and transcardially perfused with 20 ml of oxygenated cold artificial cerebrospinal fluid (CSF) solution (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20mM HEPES, 25mM glucose, 5 mM Sodium Ascorbate, 2 mM Thiourea, 0.5 mM CaCl2, and 10 mM MgSO4). 2mm spinal cord including the lesion site or the corresponding location in the naïve spinal cord segment was immediately dissected. After, spinal cord tissues were processed using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) following the manufacturer’s protocol combined with some modifications as described previously (Milich et al., 2021). The dissociated cells were incubated with 20ul of myelin removal beads (Miltenyi Biotec, 130-096-433) to remove myelin debris following the manufacturer’s protocol. After centrifugation, cell pellets were resuspended in 1X PBS (Thermo Fisher Scientific, 14190250) + 0.04%BSA (Jackson Immuno Research, 001-000-162). An aliquot of cells was stained with Acridine Orange/Propidium Iodide dye (AO/PI Cell Viability Kit, Labtech, F23001). Cell concentration and viability were measured using the LUNA-FL Dual Fluorescence Cell Counter (Logos, L20001-LG). Cells were immediately proceeded to the 10X single cell RNA sequencing procedures.
Library was performed according to the manufacturer’s instructions (single cell 3’ V2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for the subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample dual index were added.

value: Spinal cord

tag: strain


title: H295R cells, Forskolin 10uM treated, 48h, rep 2

description:
Library name: H295R-forsk-2
Azenta RNA-Seq


title: LEE163A3

first: James

source_name: E3.5 blastocyst

extract_protocol:
PureLink Genomic DNA Mini kit for gDNA extraction from adult tissues. Direct lysis for low-input sperm and blastocyst samples
EZ Methylation Kit (#D5020, Zymo)
post-bisulfite adapter tagging style whole-genome bisulfite sequencing libraries Clark et al 2017 Nature Protocols

value: E3.5 blastocyst

value: unknown


title: 123

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files. Prior to normalisation of the background substracted signals, the following processing steps are performed: removal of signals from control probes; mean of signals from replicate probes; mean of signals from all probes of a target. For processing of raw data signals, intensities below 0.1 were set to 0.1 according to Agilent's recommendation. Data of all samples are quantile normalised using the ranked mean quantiles according to Bolstad et al. A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias", Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets. The ranked signal value is replaced with the mean quantile value of the same rank. Thus, the highest value in all samples becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on.

value: F


title: HUVEC VEGFB6h rep1


title: H295R cells, Forskolin 10uM treated, 48h, rep 1

description:
Library name: H295R-forsk-1
Azenta RNA-Seq


title: HUVEC VEGFB6h rep2


title: 95

description: Plasma_Baseline_Healthy Control

source_name: Human Plasma, Baseline, Healthy Control

value: Healthy control (HC)


title: Old-14dpi, replicate 2

description: 10x Genomics


title: PLC, shHKDC1, CUT&Tag

value: PLC

value: Human liver cancer cell


title: H295R Cells, DMSO treated 48h, rep 4

description:
Library name: H295R-ctrl-4
Azenta RNA-Seq

value: DMSO control for 48hr


title: 92

description: Plasma_Baseline_Healthy Control

value: M


title: LEE163A1


title: 176

source_name: Human Plasma, Baseline, AIS, non-progressor

value: Non-progressor (NP)


title: H295R Cells, DMSO treated 48h, rep 3

description:
Library name: H295R-ctrl-3
Azenta RNA-Seq


title: LEE307A191

source_name: Sperm

value: Sperm


title: 84

description: Plasma_Baseline_Healthy Control

value: plasma


title: H295R Cells, DMSO treated 48h, rep 2

description:
Library name: H295R-ctrl-2
Azenta RNA-Seq

value: Adrenal cell


title: 83

description: Plasma_Baseline_Healthy Control


title: HUVEC BSA6h rep1

value: 100ng/mL BSA


title: LEE307A190

value: WT


title: H295R Cells, DMSO treated 48h, rep 1

description:
Library name: H295R-ctrl-1
Azenta RNA-Seq


title: Liver from mice with childhood obesity, 2nd generation offspring (F2), replicate 3

status: Public on Jan 11 2025

type: genomic

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

country: Spain

institute: University of Barcelona

description: Biological replicate 3 of 3. Liver sample from SL mice; F2

hyb_protocol: Not provided

scan_protocol: Microarrays were scanned, using Agilent Microarray Scanner G2505 with a resolution of 2 μm

data_processing:
Agilent Feature Extraction Software (v.10.7) was used for background subtraction and LOWESS normalization.
Processed data matrix includes normalized log10 ratio (Cy5/Cy3) representing test/reference

source_name: Whole liver from neonates

label_protocol: 500 ng genomic DNA was divided into two fractions. One of them (250 ng) was subjected to immunoprecipitation with anti-cytosine antibodies. The DNA libraries of immuno-precipitated and non-precipitated samples were labeled (Cy3 and Cy5, respectively)

extract_protocol: Total genomic DNA extracted using DNAzol following manufacturer's instructions

tag: generation

value: Liver

tag: age

value: Postnatal day 7

tag: gender

value: Male

tag: molecule subtype

value: methylcytosine IP

value: Total DNA


title: Liver from mice with childhood obesity, 2nd generation offspring (F2), replicate 2

description: Biological replicate 2 of 3. Liver sample from SL mice, F2


title: Liver from mice with childhood obesity, 2nd generation offspring (F2), replicate 1

description: Biological replicate 1 of 3. Liver sample from SL mice, F2


title: Liver from Control mice, 2nd generation offspring (F2), replicate 1

description: Biological replicate 1 of 3. Liver sample from Control mice, F2


title: Sperm from mice with childhood obesity, 1st generation offspring (F1), replicate 3

description: Biological replicate 3 of 3. Sperm sample from SL mice; F1

source_name: Sperm from cauda epididymis

value: 4 months of age


title: Liver from Control mice, 2nd generation offspring (F2), replicate 3

description: Biological replicate 3 of 3. Liver sample from Control mice; F2


title: Sperm from mice with childhood obesity, 1st generation offspring (F1), replicate 2

description: Biological replicate 2 of 3. Sperm sample from SL mice, F1


title: LEE163A2

value: E3.5 blastocyst

tag: genotype

value: unknown


title: Sperm from mice with childhood obesity, 1st generation offspring (F1), replicate 1

description: Biological replicate 1 of 3. Sperm sample from SL mice, F1


title: Sperm from mice with childhood obesity, parental generation (F0), replicate 3

description: Biological replicate 3 of 3. Sperm sample from SL mice; F0


title: Sperm from mice with childhood obesity, parental generation (F0), replicate 2

description: Biological replicate 2 of 3. Sperm sample from SL mice, F0


title: Sperm from Control mice, first generation offspring (F1), replicate 2

description: Biological replicate 2 of 3. Sperm sample from Control mice, F1


title: Sperm from Control mice, first generation offspring (F1), replicate 3

description: Biological replicate 3 of 3. Sperm sample from Control mice; F1


title: HUVEC BSA6h rep3

tag: treatment


title: Sperm from Control mice, first generation offspring (F1), replicate 1

description: Biological replicate 1 of 3. Sperm sample from Control mice, F1


title: Sperm from mice with childhood obesity, parental generation (F0), replicate 1

description: Biological replicate 1 of 3. Sperm sample from SL mice, F0


title: Sperm from Control mice, parental generation (F0), replicate 2

description: Biological replicate 2 of 3. Sperm sample from Control mice, F0


title: HUVEC BSA6h rep2


title: Hues9_srNMPs_P8

city: Shanghai

first: Pingxin

last: Sun

address: 800 Xiangyin Road, Yangpu District

department: Department of Cell Biology

institute: Naval Medical University

data_processing:
The clean reads were then mapped to the reference genome using HISAT2.
Raw data were processed using Trimmomatic, and reads containing poly-N and low-quality reads were removed to obtain clean reads.
The clean reads were then mapped to the reference genome using HISAT2.
The FPKM value of each gene was calculated using Cufflinks, and the read counts of each gene were obtained with the HTSeq-count script.
Assembly: hg18
Supplementary files format and content: Tab-delimited taxt file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited taxt file includes RPKM value for each Sample

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen), and reverse transcription was performed with 1 μg of RNA using PrimeScriptTM RT Master Mix (TaKaRa).
For RNA-seq analysis, total RNA was extracted using a mirVana miRNA Isolation Kit (Ambion). Samples with an RNA integrity number (RIN) >7, as measured using an Agilent 2100 Bioanalyzer (Agilent Technologies), were subjected to sequencing analysis. cDNA libraries were constructed using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequenced with the Illumina NovaSeq 6000 system

tag: cell line

tag: cell type

value: neuromesodermal progenitors

value: neural induction


title: Hues9_ventral_neurons

value: neurons


title: Sperm from Control mice, parental generation (F0), replicate 1

description: Biological replicate 1 of 3. Sperm sample from Control mice, F0


title: Hues9_srNMPs_P25


title: Hues9_muscle_50D

value: skeletal muscle

value: skeletal muscle induction


title: Hues9_RASS_7D

value: neuron progenitors


title: Hues9_Dorsal_neurons


title: Hues9_RABC_7D


title: Liver from Control mice, 2nd generation offspring (F2), replicate 2

description: Biological replicate 2 of 3. Liver sample from Control mice, F2


title: Hues9_muscle_40D


title: Hues9

value: human embryonic stem cells

value: no induction


title: H1_ventral_neurons

value: WT


title: H1_srNMPs_P25


title: H1_RASS_7D


title: H1_RABC_7D


title: M79V3-LPS

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
RNA was sequenced using Illumina NextSeq (HO) 150 cycle Sequencing.
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Reference and Annotation: GRCh38 from ENSEMBL
Assembly: GRCh38 from ENSEMBL
Supplementary files format and content: tab delimited text file of Raw counts of each smples  Generated using Bioconductor R package Rsubread and featureCounts function
Supplementary files format and content: tab delimited text file of counts per million of each smples

source_name: Blood

extract_protocol:
Cells were lysed with RLT Plus Buffer (QIAGEN, Cat. No. 1053393)followed by RNA purifcationusing RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to manufacturer’s protocol.
RNA-seq libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen; Cat. No. 015) with the UMI add-on kit.

treatment_protocol: PBMC from PCSK9_inhibitor treated subjects (n = 3) and placebo controls (n = 3) and stimulated them with the TLR4 ligand LPS (1 ug /ml for 2 hours).TLR ligand (LPS) were obtained from InvivoGen

value: Blood

tag: patient visit

value: peripheral blood mononuclear cells

tag: sample type

value: LPS treatment(LPS)


title: M79V3-NT

value: NO treatment(NT)


title: M79V2-LPS


title: Sperm from Control mice, parental generation (F0), replicate 3

description: Biological replicate 3 of 3. Sperm sample from Control mice; F0

value: Sperm

value: Male

value: methylcytosine IP

value: Total DNA


title: M77V3-LPS

value: placebo


title: M79V2-NT


title: M77V3-NT


title: M77V2-NT


title: M75V3-LPS


title: M75V3-NT


title: M75V2-LPS


title: M75V2-NT


title: M73V3-LPS


title: M73V3-NT


title: M73V2-LPS


title: M73V2-NT


title: M72V3-NT


title: M71V3-LPS


title: H1_srNMPs_P8

value: neuromesodermal progenitors

value: neural induction


title: M72V3-LPS


title: M71V3-NT


title: M72V2-LPS


title: M70V3-LPS


title: M70V3-NT


title: H1_Dorsal_neurons

value: neurons


title: M70V2-LPS


title: M71V2-NT


title: M77V2-LPS


title: M70V2-NT


title: M71V2-LPS


title: M69V2-NT


title: M69V2-LPS


title: M68V3-LPS


title: M69V3-NT


title: M68V2-LPS


title: M69V3-LPS


title: M68V3-NT


title: M67V3-NT


title: M67V2-NT


title: M67V2-LPS


title: M67V3-LPS


title: M64V3-LPS


title: M64V3-NT


title: M72V2-NT


title: M64V2-LPS


title: M64V2-NT


title: M59V3-LPS


title: M59V3-NT


title: M59V2-LPS


title: M59V2-NT


title: M58V3-LPS


title: M58V3-NT


title: M56V2-LPS


title: M58V2-NT


title: M58V2-LPS


title: M56V3-LPS


title: M68V2-NT


title: M56V3-NT


title: M55V4-LPS


title: M54V2-LPS


title: M55V2-LPS


title: M55V4-NT


title: M56V2-NT


title: M54V4-NT


title: M54V4-LPS


title: M54V2-NT


title: M79V6-LPS


title: M80V6-NT


title: M79V6-NT


title: M17V6-LPS


title: M17V6-NT


title: M22V6-NT


title: M22V6-LPS


title: M14V6-LPS


title: M14V6-NT


title: M16V6-LPS


title: M16V6-NT


title: M55V2-NT


title: M26V6-LPS


title: M28V6-NT


title: M80V6-LPS


title: M42V6-NT


title: M77V6-LPS


title: M28V6-LPS


title: M45V6-NT


title: M72V6-LPS


title: M26V6-NT


title: M42V6-LPS


title: M51V6-LPS


title: M72V6-NT


title: M77V6-NT


title: M50V6-LPS


title: M51V6-NT


title: M49V6-LPS


title: M50V6-NT


title: M25V6-NT


title: M70V6-LPS


title: M75V6-LPS


title: M49V6-NT


title: M75V6-NT


title: M71V6-NT


title: M64V6-NT


title: M70V6-NT


title: M71V6-LPS


title: M20V6-NT


title: M27V6-LPS


title: M69V6-LPS


title: M73V6-NT


title: M73V6-LPS


title: M69V6-NT


title: M20V6-LPS


title: M31V6-NT


title: M27V6-NT


title: M64V6-LPS


title: M55V6-NT


title: M23V6-NT


title: M31V6-LPS


title: M68V6-LPS


title: M32V6-NT


title: M68V6-NT


title: M59V6-NT


title: M54V6-LPS


title: M67V6-NT


title: M55V6-LPS


title: M58V6-NT


title: M54V6-NT


title: M53V6-NT


title: M80V3-LPS


title: M53V6-LPS


title: M67V6-LPS


title: M23V6-LPS


title: M32V6-LPS


title: M80V2-LPS


title: M80V2-NT


title: M80V3-NT


title: M13V6-LPS


title: M53V3-NT


title: M13V6-NT


title: M53V2-NT


title: M53V2-LPS


title: M53V3-LPS


title: M51V3-LPS