title: Fesource_NP_rep3

type: RNA

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Array 4x44K (GPL22578) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Mycroarray Scanner System (Agilent) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (GE1_105_Dec08 and Grid: 076115_D_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Zea mays

source_name: root

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Zea mays L. inbred line PR33T56 (Pioneer) were germinated on paper soaked with 1 mM CaSO4 in dark at 25°C. Six seedlings have been transferred in one pot filled with 1.8 L of nutrient solution (NS) maintained continuously aerated. For each treatments was set-up one pot. The  growth and treatment experiment was repeated three indipendent times (biological replicates).
Plants were grown into a 16/8 day/light photoperiod at 25°C and at 200 μmol m-2 sec-1 PPFD (Photosynthetic Photon Flux Density). The roots of three seedlings of each pot (treatment) were sampled after 24 h and pooled (one biological replicate).

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol:
C (control): plant grown in NS with the following composition: 0.7 mM K2SO4, 2 mM Ca(NO3)2, 0.5 mM MgSO4, 0.1 mM KH2PO4, 0.1 mM KCl, 100 μM FeNaEDTA, 10 μM H3BO3, 0.5 μM MnSO4, 0.5 μM ZnSO4, 0.2 μM CuSO4 and 0.01 μM (NH4)6Mo7O24; -P: plants grown in NS without KH2PO4; PNP: plants grown in the NS without KH2PO4 and supplied with FePO4 NPs as P source;
PB: plants grown in the NS without KH2PO4 and supplied with non-nano FePO4 (bulk) as source of P; -Fe: plants grown in the NS without FeNaEDTA; FeNP: plants grown in the NS without FeNaEDTA and supplied with FePO4 NPs as Fe source; FeB: plants grown in the NS without FeNaEDTA and supplied with non-nano FePO4 (bulk) as source of Fe.

value: root

value: Roots of plants grown for 24 h in a NS without FeNaEDTA and supplied with FePO4 NPs as Fe source.


title: Fe-deficient_rep3

status: Public on Mar 21 2025

molecule: total RNA

tag: tissue

tag: treatment

value: Roots of plants grown for 24 h in a NS without FeNaEDTA.


title: R2T

type: SRA

city: Leioa

first: Iraia

middle: Maialen

last: Muñoa Hoyos

state: Bizkaia

address: Barriso Sarriena S/N

country: Spain

institute: Universidad del País Vasco

description: Library name: Sample4

library_source: genomic

data_processing:
FASTQC Report (v.0.11.6) was used to assess  the quality of the FASTQ files. Sequenced reads were trimmed for adaptor sequence with TrimGalore! (v.0.6.2), and mapped to mm10 whole genome usin Bismark (v.0.22.1). Differential expressed methylation sites were called using MethylKit (v.1.16.1) and EdgeR (v.3.32.1)
Assembly: mm10
Supplementary files format and content: Raw counts files
Supplementary files format and content: Methylation sites file

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embrionic Stem Cells

growth_protocol: Mouse (Oct4-GFP) embryonic stem cells (mESCs) were cultured feeder-free in 0.1% gelatin coated dishes.  For all conditions cells were passaged in 48h intervals, using trypsin  for detachment.

extract_protocol:
DNA was extracted using classic phenol-chloroform/isoamyl method.
DNA methylation library was prepared for sequencing using standard Illumina protocols

treatment_protocol: For drug treatment, mESCs were grown in respective medium supplemented with %0.9 (p/v) NaCl and 10uM morphine for 24 h, for control and treatment condition respectively and collected for further experimentation (P1). After treatment removal, mESCs were seeded and maintained in culture for 48h and 96h and collected (P2 and P3) for experimentation.

tag: cell line

value: Mouse Embrionic Stem Cells

tag: cell type

value: mESCs

tag: genotype

value: WT

value: YES


title: R2C

description: Library name: Sample 2

value: NO


title: Fe-deficient_rep2


title: Psource_NP_rep2

value: Roots of plants grown for 24 h in a NS without KH2PO4 and supplied with FePO4 NPs as P source.


title: Fe-deficient_rep1


title: Fesource_NP_rep2


title: Fesource_bulk_rep3

value: Roots of plants grown for 24 h in a NS without FeNaEDTA and supplied with non-nano FePO4 (bulk) as source of Fe.


title: Psource_bulk_rep2

value: Roots of plants grown for 24 h in a NS without KH2PO4 and supplied with non-nano FePO4 (bulk) as source of P.


title: p65Chip_Th2_ns_rep2

city: NEW YORK

first: Sankar

last: Ghosh

state: NY

department: Microbiology & Immunology

country: USA

institute: Columbia University

description: Library name: p65Chip_Th2_ns_rep2

data_processing:
RNA-Seq: Raw FASTQ reads were initially removed of adaptor and low base quality contamination using Trim Galore v0.6.7, which implements cutadapt as the underlying base removal algorithm. The reads were then aligned with STAR v2.7.10b to the mouse genome mm10, and genes were quantified with featureCounts v2.0.6. Normalization and differential expression were done with the Bioconductor package DESeq2
ATAC-Seq/p65Chip-Seq: Raw FASTQ reads were initially removed of adaptor and low base quality contamination and further align to the mouse genome mm10 by using Bowtie2. Post-alignment preprocessing was performed with the Picard tool, MarkDuplicates, samtools, and deeptools. Unique aligned reads with MAPQ >=30 were retained in BAM format and used in peaks calling to identify open chromatin (ATAC-Seq) or binding (ChIP-Seq) region with MACS v2.2.7.1 using a q-value threshold of 0.05. Only regions called in at least two of the three replicates for each sample were used in downstream analysis. For Th2 samples in ChIP-Seq data, only regions called in both replicates were used. Differential peak analysis was performed with the Bioconductor package Diffbind. Bam files from replicates were merged with samtools and then converted into bigwig files using deeptools.
Assembly: mm10
Supplementary files format and content: Raw count for RNA-Seq, bigwig files for ATAC-Seq and p65Chip-Seq

source_name: Lymphe node

growth_protocol: ILC2 isolation: Lung tissue was disrupted into small pieces and digested with 1.5 mg/mL Collagenase IV (Worthington Biochemical) plus 100 μg/mL DNase I (Sigma) and 0.5U Dispase (Corning) for 45 min at 37 °C in HBBS medium (Gibco) containing 5% fetal bovine serum (FBS, Gibco). Tissue pieces were strained into single-cell suspension followed by treatment with Red Blood Cell Lysing Buffer (RBC-LB; Sigma). The suspension was separated by a 40/80% Percoll (Cytiva) gradient with centrifugation at 1,000g for 20 min at 22 °C before processing. After staining, ILC2 were sorted as live Lin-CD45+CD127+ST2+KLRG1+. In Krlg1Cre-NF-kBfl/fl mice, ILC2s were further sorted as ST2+GFP+ to select NF-kB-KO cells. Lin antibody cocktail included CD3, CD5, CD19, B220, CD11b, CD11c, TCRγδ, Gr-1, FcεR1 and CD8α. Th2 generation: Naïve CD4+ T (CD4n) cells were isolated from peripheral lymph nodes and by first enriching the cell suspension in naïve CD4+ T cells by using MojoSort™ Mouse CD4 Naïve T Cell Isolation Kit (BioLegend). CD4n were then sorted as live CD4+ CD44Low/- and then differentiated into Th2 cells on plates coated with 1 mg/mL anti-CD3/anti-CD28 antibodies in the presence of 1 mg/mL anti-IFNg (eBioscience) and 10 ng/mL IL-2/IL-4 (Peprotech) for 4 days, and then expanded for 3 days in the presence of IL-2 and IL-4 (10 ng/mL). To delete NF-kB subunit alleles, Th2 cells were incubated for 45 min at 37 °C in HBSS medium containing the TAT-CRE recombinase (50 mg/mL) (Merck Millipore). Transduction was stopped by washing cells in growth media before returning to culture. After 2 days, Th2 NF-kB-KO cells were sorted by FACS as CD4+GFP+ and cultured for 2 more days with IL-2 10 mg/mL before stimulation. Culture condition: All cells were maintained at 37 °C in RPMI medium (Gibco) containing 10% FBS, 100 U/mL penicillin (Gibco), 0.1 mg/mL streptomycin (Gibco), 50mg/mL Gentamicin (Invitrogen), 1mM sodium pyruvate (Invitrogen), 1X MEM on-Essential Amino Acids Solution (Gibco), 10mM HEPES buffer and 55mM b-mercaptoethanol (Gibco). Culture for RNA-Seq: Lung-isolated ILC2s were cultured overnight with 10 ng/mL IL-2, then stimulated with 50 ng/mL IL-33 for 3 hours. In vitro-differentiated Th2 cells were stimulated on plates pre-coated with 5 mg/mL anti-CD3/anti-CD28 antibodies for 3 hours. Culture for ATAC-Seq: Th2 cells were generated from CD4n and expanded for 2 days with 10 ng/mL IL-2/IL-4. Lung isolated ILC2s were expanded for 5 days with 10 ng/mL IL-2/IL-7 plus 20 ng/mL IL-25/IL-33 following by 2 days of resting with IL-2/IL-7 only. 50,000 ILC2 and Th2 cells were sorted as Live+ and cultured overnight with IL-2 (10 ng/mL) before stimulation. Th2 cells were stimulated on plates coated with 5 mg/mL anti-CD3/anti-CD28 antibodies and ILC2s were stimulated with 50 ng/mL IL-33 for 3 hours. Culture for p65Chip-Seq: In vitro-differentiated Th2 cells were expanded for a week with 10 ng/mL IL-2/IL-4 followed by 3 days of resting with IL-2 only. ILC2s were expanded for 3 weeks with 10 ng/mL IL-2/IL-7 and 20 ng/mL IL-25/IL-33 followed by 4 days of resting with IL-7 only. Th2 cells were stimulated on plates coated with 5 mg/mL anti-CD3/anti-CD28 antibodies and ILC2s were stimulated with 50 ng/mL IL-33 for 3h.

extract_protocol:
RNA-Seq: Total RNA was prepared from approximately 50,000-100,000 cells using the RNeasy Mini Kit or RNeasy Plus Micro Kit (QIAGEN) and following the manufacturer’s protocol. RNA samples were quantified and quality checked by Bioanalyzer (Molecular Pathology core at Herbert Irving Comprehensive Cancer Center, Columbia University). mRNA was enriched from total RNA samples with Poly(A) mRNA isolation Kit (NEBNext) and libraries were prepared using the Ultra II RNA Library Prep Kit (NEBNExt) according to the manufacturer’s protocol. Libraries were sequenced by Novogene using Illumina NovaSeq 6000 for 150bp paired-end sequencing. ATAC-Seq: After stimulation, cells were washed twice with PBS and lysed in 50 ml lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) following a centrifugation at 600 g for 10 min at 4 °C. The pellets were resuspended in 50 ml transposition mix (25 ml TD buffer, 4 ml Tn5 transposase, 21 ml Nuclease free water; from Nextera DNA Library Preparation Kit, Illumina) and incubated in water bath at 37°C for 30min. Tagmented DNA was purified by using MinElute PCR Purification Kit (Qiagen) and amplified with 10 or 11 cycles of PCR based on the amplification curve. The libraries were purified by dual selection using AMPure XP beads and then sequenced by Novogene using Illumina NovaSeq 6000 for 150bp paired-end sequencing. p65Chip-Seq: At least 5 million cells were used for chromatin immunoprecipitation. After stimulation, cells were fixed with 1% formaldehyde (Sigma) for 10 min at room temperature followed by quenching with 0.125 M glycine (Sigma) for 10 min and PBS washing. Fixed cells were lysed in lysis buffer (10mM Tris pH8, 1mM EDTA pH8, 140mM NaCl, 1% Triton-X, 0.1% SDS, 0.1% Na-DOC) containing freshly added 1mM DTT and protease inhibitors (aprotinin, leupeptin, pepstatin, and PMSF) by incubating on ice for 10 min. Lysates were sonicated using the Q800R3 Sonicator (QSonica) and centrifuged to remove debris and to clear the lysate before immunoprecipitation with anti-p65 (Diagenode) overnight at 4 °C. IP samples were then washed and incubated with RNAse for 30 min at 37 °C followed by a proteinase K treatment for 2h at 37°C. Beads were then decrosslinked overnight at 65 °C and the DNA fragments were isolated using the AMPure XP beads (Beckman Coulter). Libraries were generated purified from purified DNA by using Ultra II DNA Library Prep Kit (NEBNExt) according to the manufacturer’s protocol. Libraries were sequenced by Novogene using Illumina NovaSeq 6000 for 150bp paired-end sequencing.
Other

value: Lymphe node

tag: strain

value: CD4+ T helper 2

value: Wild type


title: Psource_bulk_rep1


title: P-deficient_rep1

value: Roots of plants grown for 24 h in a NS without KH2PO4.


title: Fesource_bulk_rep1


title: Fesource_bulk_rep2


title: P-deficient_rep3


title: Fesource_NP_rep1


title: Psource_bulk_rep3


title: p65Chip_Th2_INPUT_rep1

description: Library name: p65Chip_Th2_INPUT_rep1


title: Control_rep3

value: Roots of plants grown fro 24 h in a complete NS.


title: P-deficient_rep2


title: R1T

description: Library name: Sample3


title: Psource_NP_rep1


title: p65Chip_Th2_ns_rep1

description: Library name: p65Chip_Th2_ns_rep1


title: Control_rep2


title: Control_rep1


title: p65Chip_Th2_INPUT_rep2

description: Library name: p65Chip_Th2_INPUT_rep2


title: p65Chip_Th2_CD3_28_rep2

description: Library name: p65Chip_Th2_CD3_28_rep2

value: 3h 5mg/ml aCD3/aCD28


title: p65Chip_Th2_CD3_28_rep1

description: Library name: p65Chip_Th2_CD3_28_rep1


title: p65Chip_ILC2_ns_rep3

description: Library name: p65Chip_ILC2_ns_rep3

source_name: Lung

value: Lung

value: Type 2 innate lymphoid cells


title: p65Chip_ILC2_INPUT_rep3

description: Library name: p65Chip_ILC2_INPUT_rep3


title: p65Chip_ILC2_INPUT_rep2

description: Library name: p65Chip_ILC2_INPUT_rep2


title: Psource_NP_rep3

value: root


title: R1C

description: Library name: Sample 1

value: Mouse Embrionic Stem Cells


title: p65Chip_ILC2_IL33_rep2

description: Library name: p65Chip_ILC2_IL33_rep2

value: 3h 50ng/ml IL-33


title: p65Chip_ILC2_INPUT_rep1

description: Library name: p65Chip_ILC2_INPUT_rep1


title: p65Chip_ILC2_IL33_rep3

description: Library name: p65Chip_ILC2_IL33_rep3


title: ATAC_Th2_CD3_28_rep3

description: Library name: ATAC_Th2_CD3_28_rep3


title: ATAC_Th2_ns_rep3

description: Library name: ATAC_Th2_ns_rep3


title: ATAC_Th2_ns_rep1

description: Library name: ATAC_Th2_ns_rep1


title: ATAC_Th2_ns_rep2

description: Library name: ATAC_Th2_ns_rep2


title: ATAC_Th2_CD3_28_rep2

description: Library name: ATAC_Th2_CD3_28_rep2


title: ATAC_ILC2_ns_rep3

description: Library name: ATAC_ILC2_ns_rep3


title: ATAC_ILC2_ns_rep1

description: Library name: ATAC_ILC2_ns_rep1


title: ATAC_Th2_CD3_28_rep1

description: Library name: ATAC_Th2_CD3_28_rep1


title: ATAC_ILC2_ns_rep2

description: Library name: ATAC_ILC2_ns_rep2


title: ATAC_ILC2_IL33_rep3

description: Library name: ATAC_ILC2_IL33_rep3


title: ATAC_ILC2_IL33_rep1

description: Library name: ATAC_ILC2_IL33_rep1


title: Soleus skeletal muscle, subject 7, after 21-day dry immersion

status: Public on Mar 22 2025

city: Moscow

first: Roman

middle: O.

last: Bokov

state: Moscow

address: Khoroshevskoye shosse, 76A

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

library_source: transcriptomic

data_processing:
Quality control of RNA sequencing data for each library was performed using the FASTQC program (version 0.12.1).
The tool Trimmomatic (Galaxy Version 0.38.1) was used to trim adapter sequences and low-quality readings.
The tool RNA STAR (Galaxy Version 2.7.10b+galaxy3) was used to map sequences to the Homo sapiens reference genome (version GRCh38.p14).
The read counts files were processed in the R (version 4.3.1). Normalization and differential gene expression analysis were performed using the R package «DESeq2» (analysis of paired samples with Benjamini-Hochberg correction).
Assembly: GRCh38.p14
Supplementary files format and content: One tab-delimited text file includes per gene read counts for each Sample

organism: Homo sapiens

source_name: Soleus skeletal muscle

extract_protocol:
Using the method of open-incision muscle biopsy under local anesthesia, samples of the soleus muscle were taken from all subjects 10-20 days before the start of the experiment (pre-immersion samples) and on the day of the end of the experiment (post-immersion samples). Soleus muscle samples were immediately frozen in liquid nitrogen and then stored in a low-temperature freezer at -80 °C. Total RNA was isolated from muscle tissue using the RNA isolation kit RNeasy Micro (Qiagen, Germany).
5 μg of purified total RNA from samples corresponding to 4 subjects (4 pre-DI samples and 4 post-DI samples) were concentrated in 5 μL of nuclease free water, using vacuum concentrator SpeedVac Savant SC210A (ThermoFisher Scientific, USA). Then this total RNA was used as a template for the synthesis of the first cDNA strand (nAnTiCAGE Library Preparation kit, DNAform, Japan and SuperScript III Reverse Transcriptase, Invitrogen, USA), which was then biotinylated at the 5’ end of using (nAnTiCAGE Library Preparation kit, DNAform, Japan). This allowed selection of 5’ cap contained RNAs using streptavidin beads (Dynabeads M270 Streptavidin, ThermoFisher Scientific, USA). At this stage, rRNA, truncated or not fully transcribed RNA was eliminated. For more efficient removal of nonspecific RNA strands, cDNA was treated by RNase I and H (nAnTiCAGE Library Preparation kit, DNAform, Japan) and then was purified using Agencourt AMPure XP (Beckman Coulter, USA). Next, linkers at the 5’and 3’ ends (nAnTiCAGE Library Preparation kit, DNAform, Japan) were sequentially ligated to the cap-trapped cDNA. The 5’ linker contains the XmaJI restriction endonuclease recognition and the MmeI class II restriction enzyme recognition site, as well as a barcode for multiplexing (nAnTiCAGE Library Preparation kit, DNAform, Japan). The 3’ linker contains an XbaI restriction enzyme recognition site. After treatment with restriction enzymes, short CAGE tags were obtained (nAnTiCAGE Library Preparation kit, DNAform, Japan). At the final stage, a second cDNA strand was synthesized (nAnTiCAGE Library Preparation kit, DNAform, Japan). The concentration of the libraries was validated using qPCR (KAPA Library Quantification Kits Illumina, KAPA Biosystems, South Africa) and sequenced on a HiSeq 2500 platform (Illumina, USA) using the HiSeq version 4 reagent kit (HiSeq SR Cluster Kit version 4 cBot and HiSeq SBS Kit version 4 50 cycles, Illumina, USA) in the 60 bp single end mode.

treatment_protocol: Under an immersion environment, the volunteer’s body is subjected to an impact of the buoyant force of water, and the support reactions are eliminated. The studies were carried out under standard conventional conditions, during which volunteer testers were placed one at a time in a pool measuring 200 x 100 x 100 cm, filled with water, in a horizontal position, the water temperature in the bath was maintained constant at +33 ± 0.5 °C. The daily routine in immersion was regulated by time intervals selected for examinations, preventive measures (if any), meals and sanitary and hygienic procedures. The daily routine was as close as possible to the onboard one, including 8 hours of sleep, 3 meals per day, a medical monitoring program and experimental studies. To carry out sanitary and hygienic measures, once a day the testers were removed from the bath for 15–20 minutes using a special lift.

value: Soleus skeletal muscle

tag: subject

tag: Sex

value: male

tag: time point

value: after

tag: unloading model

value: 21-day dry immersion


title: RNA_Th2_WT_ns_rep2

description: Library name: RNA_Th2_WT_ns_rep2

molecule: polyA RNA


title: RNA_Th2_WT_CD3_28_rep2

description: Library name: RNA_Th2_WT_CD3_28_rep2


title: ATAC_ILC2_IL33_rep2

description: Library name: ATAC_ILC2_IL33_rep2


title: RNA_Th2_RelKO_ns_rep1

description: Library name: RNA_Th2_RelKO_ns_rep1

value: Relfl/fl C57BL/6

value: Rel KO


title: RNA_Th2_WT_CD3_28_rep1

description: Library name: RNA_Th2_WT_CD3_28_rep1

value: Lymphe node


title: RNA_Th2_RelKO_CD3_28_rep2

description: Library name: RNA_Th2_RelKO_CD3_28_rep2

value: CD4+ T helper 2


title: p65Chip_ILC2_ns_rep1

description: Library name: p65Chip_ILC2_ns_rep1

value: Wild type


title: RNA_Th2_RelKO_CD3_28_rep1

description: Library name: RNA_Th2_RelKO_CD3_28_rep1


title: RNA_Th2_WT_ns_rep1

description: Library name: RNA_Th2_WT_ns_rep1


title: RNA_Th2_p65KO_ns_rep2

description: Library name: RNA_Th2_p65KO_ns_rep2

value: p65fl/fl C57BL/6

value: p65 KO


title: RNA_Th2_p65KO_ns_rep1

description: Library name: RNA_Th2_p65KO_ns_rep1


title: RNA_Th2_RelKO_ns_rep2

description: Library name: RNA_Th2_RelKO_ns_rep2


title: p65Chip_ILC2_ns_rep2

description: Library name: p65Chip_ILC2_ns_rep2


title: RNA_Th2_DKO_ns_rep1

description: Library name: RNA_Th2_DKO_ns_rep1

value: p65Tr/Tr Relfl/fl C57BL/6

value: p65 Truncated - Rel KO


title: RNA_Th2_DKO_ns_rep2

description: Library name: RNA_Th2_DKO_ns_rep2


title: RNA_Th2_DKO_CD3_28_rep1

description: Library name: RNA_Th2_DKO_CD3_28_rep1

value: 3h 5mg/ml aCD3/aCD28


title: RNA_Th2_DKO_CD3_28_rep2

description: Library name: RNA_Th2_DKO_CD3_28_rep2


title: RNA_Th2_p65KO_CD3_28_rep2

description: Library name: RNA_Th2_p65KO_CD3_28_rep2


title: p65Chip_ILC2_IL33_rep1

description: Library name: p65Chip_ILC2_IL33_rep1

value: Lung

value: Type 2 innate lymphoid cells


title: RNA_Th2_p65KO_CD3_28_rep1

description: Library name: RNA_Th2_p65KO_CD3_28_rep1


title: RNA_ILC2_WT_ns_rep2

description: Library name: RNA_ILC2_WT_ns_rep2

value: KLRG1-Cre C57BL/6


title: RNA_ILC2_WT_IL33_rep3

description: Library name: RNA_ILC2_WT_IL33_rep3

value: 3h 50ng/ml IL-33


title: RNA_ILC2_RelKO_ns_rep3

description: Library name: RNA_ILC2_RelKO_ns_rep3

value: KLRG1-Cre Relfl/fl C57BL/6


title: RNA_ILC2_WT_IL33_rep1

description: Library name: RNA_ILC2_WT_IL33_rep1


title: RNA_ILC2_WT_IL33_rep2

description: Library name: RNA_ILC2_WT_IL33_rep2


title: RNA_ILC2_RelKO_ns_rep2

description: Library name: RNA_ILC2_RelKO_ns_rep2


title: RNA_ILC2_RelKO_ns_rep1

description: Library name: RNA_ILC2_RelKO_ns_rep1


title: RNA_ILC2_RelKO_IL33_rep3

description: Library name: RNA_ILC2_RelKO_IL33_rep3


title: RNA_ILC2_RelKO_IL33_rep2

description: Library name: RNA_ILC2_RelKO_IL33_rep2


title: RNA_ILC2_RelKO_IL33_rep1

description: Library name: RNA_ILC2_RelKO_IL33_rep1


title: RNA_ILC2_p65KO_IL33_rep3

description: Library name: RNA_ILC2_p65KO_IL33_rep3

value: KLRG1-Cre p65fl/fl C57BL/6


title: RNA_ILC2_p65KO_ns_rep3

description: Library name: RNA_ILC2_p65KO_ns_rep3


title: RNA_ILC2_p65KO_ns_rep2

description: Library name: RNA_ILC2_p65KO_ns_rep2


title: RNA_ILC2_p65KO_ns_rep1

description: Library name: RNA_ILC2_p65KO_ns_rep1


title: RNA_ILC2_p65KO_IL33_rep1

description: Library name: RNA_ILC2_p65KO_IL33_rep1


title: RNA_ILC2_WT_ns_rep3

description: Library name: RNA_ILC2_WT_ns_rep3


title: KP3

city: Shenyang

first: Lulu

last: Chen

address: No. 36, Sanhao Street, Heping District

country: China

institute: Shengjing Hospital of China Medical University

description:
Library name: sample6
KP-3_tpm

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: not provided
Supplementary files format and content: counts, tpm

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: liver

value: KPLA mouse model

value: infected with K. pneumoniae


title: KP1

description:
Library name: sample4
KP-1_tpm


title: C2

description:
Library name: sample2
C-2_tpm

value: control


title: KP2

description:
Library name: sample5
KP-2_tpm


title: C1

description:
Library name: sample1
C-1_tpm


title: C3

description:
Library name: sample3
C-3_tpm


title: RNA_ILC2_WT_ns_rep1

description: Library name: RNA_ILC2_WT_ns_rep1


title: Non-transfected, replicate 3

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

description: Library name: NT-REP3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore.
Reads were aligned against reference using STAR and quantified with Salmon.
Assembly: Quantified estimates were converted into normalized gene-level counts using R package tximport, and differential gene expression analysis was performed with R package DESeq2.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include normalized count matrix table from DESeq

source_name: Cultured astrocyte

extract_protocol:
48 hours after transfection, cells were harvested, and total RNA was extracted from astrocyte cell lysates.
Library was constructed using TruSeq stranded mRNA kit.

treatment_protocol: Cultured mouse cortical astrocytes were transfected with a plasmid expressing CMV-FLAG-BRAF KE.

value: Cultured astrocyte

value: naive

value: non-transfected


title: BRAF K499E-transfected, replicate 3

description: Library name: KE-REP3

value: BRAF K499E transfected


title: Non-transfected, replicate 1

description: Library name: NT-REP1


title: BRAF K499E-transfected, replicate 2

description: Library name: KE-REP2


title: BRAF K499E-transfected, replicate 1

description: Library name: KE-REP1


title: Microglia, eGFP

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description:
Library name: egfp
10X Genomics 3'GEX

data_processing:
The off-sequencer data was demultiplexed, aligned, and quantified with CellRanger v6.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: brain

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: brain

value: eGFP


title: Non-transfected, replicate 2

description: Library name: NT-REP2


title: Microglia, VEGFC

description:
Library name: vegfc
10X Genomics 3'GEX

value: VEGF-C


title: Li_78w_ATAC_XistBxC_-+_XX_2

city: Munich

first: Sarah

last: Hoelzl

state: Bavaria

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University of Munich

data_processing:
Alignment of ATAC-seq data was performed using the bowtie2 aligner.
To obtain high quality reads for downstream analysis, mitochondrial reads, mapping artifacts (≤ 38 bp or ≥ 2000 bp), low quality reads (MAPQ < 20), ENCODE blacklist genes (blacklist.v2.bed47) and duplicates (identified by GATK MarkDuplicates, version 4.2.2.0) were removed.
ATAC-seq peaks were called by MACS2 (version 2.1.0).
Allelic ratios of called ATAC-seq peaks were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Text file (.txt) reporting the calculated allelic ratios

source_name: Liver

growth_protocol: BL6 Xist -/+ females were purchased from Riken BRC Japan (RBRC02655: B6;129-Xist<tm5Sado>) and crossed with wild-type CAST males (JAX: Strain #000928) to obtain experimental F1 hybrids. At the according age, organs were harvested, flash-frozen in liquid nitrogen and stored at -80 °C for further use.

extract_protocol:
Nuclei from liquid nitrogen frozen organs were isolated using the Nuclei Extraction Buffer (Miltenyi) according to manufacturer’s instructions. For ATAC-sequencing, the integrity of isolated nuclei was assessed on the Countess™ II FL Automated Cell Counter equipped with the DAPI EVOS light cube. 50,000 nuclei were taken as input for Active Motif’s ATAC-Seq kit and libraries were generated according to manufacturer’s instructions.
ATAC-seq library was generated using the Active Motif’s ATAC-Seq kit.

value: Liver

tag: breed (mother_x_father)

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

value: female

tag: age

value: 78 weeks


title: Li_9w_ATAC_XistBxC_-+_XX_2

value: 9 weeks


title: Li_78w_ATAC_XistBxC_-+_XX_1


title: Li_9w_ATAC_XistBxC_-+_XX_1


title: Ki_9w_ATAC_XistBxC_-+_XX_2

source_name: Kidney

value: Kidney


title: Ki_78w_ATAC_XistBxC_-+_XX_2


title: RNA_ILC2_p65KO_IL33_rep2

description: Library name: RNA_ILC2_p65KO_IL33_rep2

value: Lung

value: KLRG1-Cre p65fl/fl C57BL/6

value: Type 2 innate lymphoid cells

value: p65 KO

value: 3h 50ng/ml IL-33


title: Ki_9w_ATAC_XistBxC_-+_XX_1


title: Ki_78w_ATAC_XistBxC_-+_XX_1


title: He_78w_snRNA_XistxC_++_XX

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment, and read count quantification of the raw sequencing data were performed using the cellranger multi pipeline (Cell Ranger 7.1.0 toolkit, 10x Genomics).
CellBender (version 0.3.0) was performed with default settings to eliminate technical artifacts such as ambient RNAs, which are common in single-nucleus data.
Processing of sample matrices was done using R and the Seurat 5.1.0 package
Allelic ratios of single cells and pseudobulk were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Text file (.txt) reporting the calculated allelic ratios of pseudobulk

source_name: Heart

extract_protocol:
Nuclei from liquid nitrogen frozen organs were isolated using the Nuclei Extraction Buffer (Miltenyi) according to manufacturer’s instructions. For snRNA-sequencing, nuclei of 1 replicate per time point (BL6xCAST females) were incubated with DRAQ7 for 5 min before sorting, staining the DNA of nuclei. Sorting the DRAQ7-positive population ensured a debris-free nuclei suspension, which was again assessed on the Countess™ II FL Automated Cell Counter equipped with the DAPI EVOS light cube.
Single-nucleus libraries were generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics) with a target of 10,000 nuclei per sample.

value: Heart


title: He_9w_snRNA_XistxC_++_XX


title: MP_9w_RNA_XistBxC_+y_XY_3

data_processing:
Paired-end RNA-seq data were aligned using STAR. Reads characterized by intron sizes exceeding 100000, multimappers, and alignments containing non-canonical junctions were removed prior to subsequent analysis. Uniquely aligned reads were quantified using htseq-count and the –stranded no flag.
Allelic ratios were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Text file including the raw read counts for each sample

source_name: Macrophages

growth_protocol: BL6 Xist -/+ females were purchased from Riken BRC Japan (RBRC02655: B6;129-Xist<tm5Sado>) and crossed with wild-type CAST males (JAX: Strain #000928) to obtain experimental F1 hybrids.

extract_protocol:
Single cell suspensions of hearts were obtained by performing an enzymatic retrograde perfusion. To do so, the heart was harvested and cannulated at the aorta. Coronary arteries were flushed briefly with 1ml Perfusion Buffer. Afterwards, the cannula with the heart was attached to the perfusion pump system, and the heart was perfused with Perfusion Buffer for 1min (4ml/min). Next, the heart was rinsed with a Digestion Buffer for 10min (recirculating, 4ml/min) to enzymatically dissociate the ventricular cells. Then, the heart was detached, atria were discarded, and the ventricles were roughly homogenized in 2.5ml Digestion Buffer by cutting with scissors shearing with a 1ml syringe 30 times. After adding 2.5ml Stop Buffer, the syringe sheared the liquid again for 30 times. Ultimately, the suspension was filtered through a 100µm strainer and put on ice. To separate cardiomyocytes from non-cardiomyocytes, the suspension was centrifuged at 100xg at 4°C for 1min and supernatant was transferred. This was repeated once and the sediment, containing cardiomyocytes, was resuspended in 500µl TRIzol, homogenized using a pellet pestle. After adding another 500µl TRIzol the cardiomyocytes were frozen at -80°C for further use. The supernatant, containing non-cardiomyocytes, was spinned down at 400xg 4 °C for 7min. After discarding the supernatant, the pellet was resuspended in RBC-Lysis-Buffer at room temperature for 0.5min. Next, 2ml PBS was added, and suspension was centrifuged at the same settings, followed by the filtering through a 70µm strainer. Cells were blocked with Fc-block at 4°C for 15min, before using CD45-conjugated microbeads (Miltenyi) to bind CD45-positive cells. Afterwards, the cell suspension was separated into a CD45-positive and CD45-negative fraction using the autoMACS Pro Separator by Miltenyi. Then, both fractions were stained with Zombie Green to detect dead cells, followed by the macrophage staining for the CD45-positive fraction (CD45-positive, CD11b, CD64, F4/80) and the endothelial staining (CD45-negative, CD105) and the fibroblast staining (CD45-negative, CD140a) for the CD45-negative fraction. After washing twice, 2,000 cells of each cell type were sorted, immediately frozen on dry ice, and stored at -80°C for further use. After thawing, sorted MCL were resuspended in 1ml TRIzol and RNA was isolated according to manufacturer’s instructions (Invitrogen, TRIzol Reagent, Cat. #15596018). Since the starting sample was small, 10μg of RNase-free glycogen was used as a carrier, and isopropanol precipitation was performed at -20°C overnight. RNA quality was measured on Agilent’s TapeStation System.
0,5-3ng of RNA were used to generate RNA-seq libraries using Takara’s SMART-Seq® v4 PLUS kit according to manufacturer’s instructions. A quarter of reaction volume per sample was pipetted by the MANTIS liquid handler. Concentration and fragment distribution of completed RNA-seq libraries was measured on Agilent’s TapeStation System.

value: Macrophages

value: male


title: EC_9w_RNA_XistBxC_+y_XY_3

source_name: Endothelial cells

value: Endothelial cells


title: EC_9w_RNA_XistBxC_+y_XY_2


title: EC_9w_RNA_XistBxC_+y_XY_1


title: MP_9w_RNA_XistBxC_-+_XX_1


title: MP_9w_RNA_XistBxC_-+_XX_3


title: EC_9w_RNA_XistBxC_-+_XX_1


title: CM_9w_RNA_XistBxC_+y_XY_3

source_name: Cardiomyocytes

value: Cardiomyocytes


title: WT myotube, nucleus fraction, cell culture 4, replicate 3 (miRNAseq)

city: Oxford

first: David

last: Seoane Miraz

address: IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Headington

department: Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Single-end reads from miRNA library were cleaned from adaptors using Trimmomatic (Bolger et al., 2014) and quality checked with FastQC application to remove from the dataset those reads with low quality values (Phred score threshold below 20)
Follow-up analysis were computed through webserver sRNAtoolbox (Aparicio-Puerta et al., 2022) including reads assembling, reads mapping on human reference genome, reads annotation based on miRBase reference database, reads count, and differential expression analysis were carried out in DEseq2
Assembly: hg17
Supplementary files format and content: Processed data files in .csv format content show read counts for expression levels of miRNA between nuclei and cytoplasms of DM1 and control (WT) skeletal muscle cells

molecule: nuclear RNA

source_name: Ctrl muscle cells

growth_protocol: Myoblasts were cultivated in Skeletal Muscle Cell Growth Medium (PromoCell) supplemented with 1% penicillin/ streptomycin/ amphotericin B in an incubator at 37ºC and an atmosphere of 5% CO2, until cell confluence reached approximately 80%, changing the media on alternate days. Then, myoblast differentiation into myotubes was induced by replacing growth media to Skeletal Muscle Cell Differentiation Medium (PromoCell) for 5 to 8 days, changing the media on alternate days.

extract_protocol:
Wild-type control and DM1 myotubes were split out into nucleus and cytoplasm fractions using PARIS kit (Invitrogen), and total RNA was isolated by RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. RNA quality and concentration was determined using a NanoDrop 2000 (Thermo Scientific) spectrophotometer.
cDNA libraries were prepared using a TruSeq Small RNA Library Preparation Kit (Illumina) following manufacturer’s instructions. Sequencing was performed using rapid mode in a HiSeq 2500 System (Illumina)

treatment_protocol: No treatment

value: Ctrl muscle cells

value: primary myoblasts

value: No treated


title: EC_9w_RNA_XistBxC_-+_XX_2

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

value: female


title: CM_9w_RNA_XistBxC_+y_XY_2


title: CM_9w_RNA_XistBxC_+y_XY_1


title: MP_9w_RNA_XistBxC_+y_XY_2


title: MP_9w_RNA_XistBxC_+y_XY_1


title: WT myotube, nucleus fraction, cell culture 4, replicate 1 (miRNAseq)


title: WT myotube, nucleus fraction, cell culture 3, replicate 3 (miRNAseq)


title: MP_9w_RNA_XistBxC_-+_XX_2


title: CM_9w_RNA_XistBxC_-+_XX_2


title: WT myotube, nucleus fraction, cell culture 3, replicate 1 (miRNAseq)


title: CM_9w_RNA_XistBxC_-+_XX_1


title: CF_9w_RNA_XistBxC_+y_XY_3

source_name: Cardiac fibroblasts

value: Cardiac fibroblasts


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 3 (miRNAseq)

molecule: cytoplasmic RNA


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 2 (miRNAseq)


title: CF_9w_RNA_XistBxC_+y_XY_1


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 1 (miRNAseq)


title: CF_9w_RNA_XistBxC_+y_XY_2


title: CF_9w_RNA_XistBxC_-+_XX_3


title: EC_9w_RNA_XistBxC_-+_XX_3


title: CM_9w_RNA_XistBxC_-+_XX_3


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 1 (miRNAseq)


title: CF_9w_RNA_XistBxC_-+_XX_1


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 2 (miRNAseq)


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 1 (miRNAseq)

source_name: DM1 muscle cells

value: DM1 muscle cells

value: mutation with 2,600 CTG repeats


title: Sp_78w_RNA_XistBxC_-+_XX_2

data_processing:
Paired-end RNA-seq data were aligned using STAR. Reads characterized by intron sizes exceeding 100000, multimappers, and alignments containing non-canonical junctions were removed prior to subsequent analysis. Uniquely aligned reads were quantified using htseq-count and the –stranded reverse flag.
Allelic ratios were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Text file including the raw read counts for each sample

source_name: Spleen

extract_protocol:
Frozen organs of 4w-, 9w-, 1.5y-week old mice were homogenized in appropriate amounts of TRIzol reagent (1 ml TRIzol reagent per 50-100 mg tissue) using the GentleMACSTM Dissociator RNA_02_01 program. 1 ml of homogenized organs was used for RNA isolation. Frozen organs of E14.5 embryos were thawed in 500 µl TRIzol reagent. Embryonic organs were homogenized using a pellet pestle. Another 500 µl TRIzol reagent was added, and RNA isolation was performed for all time points according to manufacturer’s instructions (Invitrogen, TRIzol Reagent, Cat. #15596018). RNA concentration was measured by the NanoDrop Microvolume Spectrophotometer.
100 ng of RNA were used to generate poly-A captured RNA-seq libraries using lllumina’s Stranded mRNA Prep, Ligation kit according to manufacturer’s instructions. An eighth of reaction volume per sample was pipetted by the MANTIS liquid handler. Concentration and fragment distribution of completed RNA-seq libraries was measured on Agilent’s TapeStation System.

value: Spleen


title: Sp_78w_RNA_XistBxC_-+_XX_3


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 3 (miRNAseq)


title: Sp_78w_RNA_XistBxC_+y_XY_1


title: WT myotube, nucleus fraction, cell culture 3, replicate 2 (miRNAseq)


title: Sp_78w_RNA_XistBxC_+y_XY_2


title: Sp_9w_RNA_XistBxC_+y_XY_3


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 2 (miRNAseq)


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 1 (miRNAseq)


title: Sp_9w_RNA_XistBxC_-+_XX_3


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 3 (miRNAseq)


title: Sp_9w_RNA_XistBxC_+y_XY_1


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 2 (miRNAseq)


title: Sp_9w_RNA_XistBxC_-+_XX_2


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 3 (miRNAseq)


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 2 (miRNAseq)


title: CF_9w_RNA_XistBxC_-+_XX_2


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 3 (miRNAseq)


title: Sp_78w_RNA_XistBxC_+y_XY_3


title: Sp_9w_RNA_XistBxC_-+_XX_1


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 1 (miRNAseq)


title: WT myotube, nucleus fraction, cell culture 4, replicate 3 (mRNAseq)

data_processing:
Data processed by Novogene Ltd. according to its analysis pipeline and quality standards
Assembly: hg17
Supplementary files format and content: Processed data files in Excel format (.xls) content show log2 fold change of different expression levels of both mRNA and lncRNA between nuclei and cytoplasms of DM1 and control (WT) skeletal muscle cells

extract_protocol:
Wild-type control and DM1 myotubes were split out into nucleus and cytoplasm fractions using PARIS kit (Invitrogen), and total RNA was isolated by RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. RNA quality and concentration was determined using a NanoDrop 2000 (Thermo Scientific) spectrophotometer.
cDNA libraries were prepared using an Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina), according to manufacturer recommendations. The total RNA was ribodepleted and this fraction was converted to cDNA. A second strand cDNA synthesis incorporated dUTP. Then, the cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion and prepared libraries were size selected, multiplexed and quality checked before sequencing. Pair-end sequencing was performed in a HiSeq 4000 System (Illumina).

value: No treatment


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 1 (miRNAseq)


title: WT myotube, nucleus fraction, cell culture 4, replicate 2 (mRNAseq)


title: Sp_4w_RNA_XistBxC_+y_XY_3


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 3 (miRNAseq)


title: Sp_4w_RNA_XistBxC_+y_XY_2


title: Sp_9w_RNA_XistBxC_+y_XY_2


title: WT myotube, nucleus fraction, cell culture 4, replicate 2 (miRNAseq)


title: Sp_4w_RNA_XistBxC_-+_XX_3


title: WT myotube, nucleus fraction, cell culture 3, replicate 2 (mRNAseq)


title: Sp_4w_RNA_XistBxC_-+_XX_2


title: WT myotube, nucleus fraction, cell culture 4, replicate 1 (mRNAseq)


title: WT myotube, nucleus fraction, cell culture 3, replicate 3 (mRNAseq)


title: Sp_4w_RNA_XistBxC_+y_XY_1


title: Sp_4w_RNA_XistBxC_-+_XX_1


title: Sp_78w_RNA_XistBxC_-+_XX_1


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 2 (mRNAseq)


title: Mu_78w_RNA_XistBxC_+y_XY_2

source_name: Muscle

value: Muscle


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 3 (mRNAseq)


title: Mu_78w_RNA_XistBxC_-+_XX_3


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 3 (mRNAseq)


title: WT myotube, cytoplasm fraction, cell culture 4, replicate 1 (mRNAseq)


title: Mu_78w_RNA_XistBxC_-+_XX_2


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 2 (mRNAseq)


title: WT myotube, cytoplasm fraction, cell culture 3, replicate 1 (mRNAseq)


title: Mu_78w_RNA_XistBxC_-+_XX_1


title: Mu_9w_RNA_XistBxC_+y_XY_3


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 3 (mRNAseq)


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 1 (mRNAseq)


title: Mu_9w_RNA_XistBxC_-+_XX_3


title: Mu_9w_RNA_XistBxC_+y_XY_2


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 2 (mRNAseq)


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 2 (mRNAseq)


title: Mu_9w_RNA_XistBxC_-+_XX_1


title: Mu_9w_RNA_XistBxC_+y_XY_1


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 3 (mRNAseq)


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 3 (mRNAseq)


title: Mu_78w_RNA_XistBxC_+y_XY_1


title: WT myotube, nucleus fraction, cell culture 3, replicate 1 (mRNAseq)


title: DM1 myotube, nucleus fraction, cell culture 2, replicate 2 (miRNAseq)


title: Mu_78w_RNA_XistBxC_+y_XY_3


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 1 (mRNAseq)


title: DM1 myotube, cytoplasm fraction, cell culture 2, replicate 2 (mRNAseq)


title: Mu_4w_RNA_XistBxC_+y_XY_2


title: Mu_4w_RNA_XistBxC_+y_XY_3


title: Mu_4w_RNA_XistBxC_+y_XY_1


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 3 (mRNAseq)


title: Lu_78w_RNA_XistBxC_+y_XY_3

value: Lung


title: Mu_4w_RNA_XistBxC_-+_XX_2


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 2 (mRNAseq)


title: Mu_4w_RNA_XistBxC_-+_XX_3


title: Mu_4w_RNA_XistBxC_-+_XX_1


title: DM1 myotube, cytoplasm fraction, cell culture 1, replicate 1 (mRNAseq)


title: Mu_9w_RNA_XistBxC_-+_XX_2


title: OE Re watered replicate 3

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Library name: OE_R_4
OE Re watered replicate 3

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped to Arabidopsis thaliana TAIR10 reference genome using STAR.
Reads quantification was performed by Salmon.
Normalized counts were obtained from R tximport and DESeq2 package.
Assembly: TAIR10 reference genome
Supplementary files format and content: Matrix table files include normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis seeds were surface sterilized in 70% (vol/vol) ethanol for 2 min and then washed three times in sterile deionized water. Sterilized seeds were incubated in 1.5 ml centrifuge tubes with clean sterile-deionized water at 4-8 °C for 3 d. Vernalized seeds were spread on ½ MS growth medium in agar (Murashige and Skoog [MS] Basal medium, 0.22% MS salts; 1% Sucrose; 0.8% plant agar) with 150 μg/ml of the antibiotic, timentin. Transformed lines were selected for resistance to 10 μg/mL of the herbicide, PPT (phosphinothricin). Arabidopsis plants were individually grown in plastic 4" pots (4-1/2" sq x 4" deep) in reach-in growth chambers with long-day (16 h 22 °C: 8 h 20°C, light: dark cycle) or short-day (8 h 22 °C: 16 h 20°C, light: dark cycle) conditions. Long-day growth conditions were used for Agrobacterium-mediated plant transformation and for whole plant phenotypic analyses where we could visually compare leaf, floral stem and roots of WT and AtTOR transgenic lines.

extract_protocol:
RNA was extracted from 0.1 g of each sample using a Qiagen RNeasy Mini Kit, and checked for quality using a Thermo Scientific NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer.
RNA-seq libraries were prepared using the Illumina TruSeq UD V1.5 Kit. Libraries were prepared by using RNA according to manufacturer's instruction and then loaded on an Illumina NovaSeq 6000 platform for pair-end sequencing with 150 cycles.

treatment_protocol: Under well-watered conditions, the consumed water was replenished to maintain the soil water content at a constant level for the whole process of assay (approx. 60% of full water holding capacity). Under drought challenged conditions, water was withheld for the 11-day time period between 27 DAG until 38 DAG. Subsequently, the plants were rewatered for 4 days and long-term WUE measured at the end of the recovery period.

value: Leaf

value: Re watered

tag: batch


title: OE Re watered replicate 2

description:
Library name: OE_R_2
OE Re watered replicate 2


title: DM1 myotube, nucleus fraction, cell culture 1, replicate 1 (mRNAseq)


title: OE Re watered replicate 1

description:
Library name: OE_R_1
OE Re watered replicate 1


title: Lu_78w_RNA_XistBxC_-+_XX_3

source_name: Lung


title: GC Re watered replicate 3

description:
Library name: GC_R_3
GC Re watered replicate 3


title: GC Re watered replicate 1

description:
Library name: GC_R_1
GC Re watered replicate 1


title: GC Re watered replicate 2

description:
Library name: GC_R_2
GC Re watered replicate 2


title: Lu_9w_RNA_XistBxC_+y_XY_3

value: male


title: Lu_78w_RNA_XistBxC_-+_XX_1


title: Lu_9w_RNA_XistBxC_+y_XY_2


title: WT Re watered replicate 3

description:
Library name: WT_R_4
WT Re watered replicate 3


title: OE Drought treated replicate 3

description:
Library name: OE_D_4
OE Drought treated replicate 3

value: Drought treated


title: WT Re watered replicate 2

description:
Library name: WT_R_3
WT Re watered replicate 2


title: Lu_9w_RNA_XistBxC_-+_XX_3


title: Lu_9w_RNA_XistBxC_+y_XY_1


title: WT Re watered replicate 1

description:
Library name: WT_R_2
WT Re watered replicate 1


title: Lu_9w_RNA_XistBxC_-+_XX_2


title: OE Drought treated replicate 2

description:
Library name: OE_D_2
OE Drought treated replicate 2


title: Lu_78w_RNA_XistBxC_+y_XY_2


title: OE Drought treated replicate 1

description:
Library name: OE_D_1
OE Drought treated replicate 1


title: Lu_9w_RNA_XistBxC_-+_XX_1


title: Lu_78w_RNA_XistBxC_+y_XY_1


title: Lu_4w_RNA_XistBxC_+y_XY_3


title: Lu_4w_RNA_XistBxC_+y_XY_2


title: GC Drought treated replicate 3

description:
Library name: GC_D_4
GC Drought treated replicate 3


title: Lu_4w_RNA_XistBxC_+y_XY_1


title: Lu_4w_RNA_XistBxC_-+_XX_3


title: WT Drought treated replicate 2

description:
Library name: WT_D_3
WT Drought treated replicate 2


title: GC Drought treated replicate 1

description:
Library name: GC_D_2
GC Drought treated replicate 1


title: Lu_78w_RNA_XistBxC_-+_XX_2


title: WT Drought treated replicate 1

description:
Library name: WT_D_1
WT Drought treated replicate 1


title: GC Drought treated replicate 2

description:
Library name: GC_D_3
GC Drought treated replicate 2


title: Lu_4w_RNA_XistBxC_-+_XX_2


title: WT Drought treated replicate 3

description:
Library name: WT_D_4
WT Drought treated replicate 3


title: Lu_E14.5_RNA_XistBxC_-+_XX_2


title: OE Well watered replicate 3

description:
Library name: OE_4
OE Well watered replicate 3

value: Well watered


title: Lu_E14.5_RNA_XistBxC_-+_XX_1


title: Lu_E14.5_RNA_XistBxC_-+_XX_3


title: OE Well watered replicate 2

description:
Library name: OE_2
OE Well watered replicate 2


title: GC Well watered replicate 3

description:
Library name: GC_3
GC Well watered replicate 3


title: OE Well watered replicate 1

description:
Library name: OE_1
OE Well watered replicate 1


title: Li_78w_RNA_XistBxC_+y_XY_3

value: Liver


title: GC Well watered replicate 1

description:
Library name: GC_1
GC Well watered replicate 1


title: GC Well watered replicate 2

description:
Library name: GC_2
GC Well watered replicate 2


title: Li_78w_RNA_XistBxC_+y_XY_1


title: WT Well watered replicate 3

description:
Library name: WT_4
WT Well watered replicate 3


title: Li_78w_RNA_XistBxC_-+_XX_2


title: Li_78w_RNA_XistBxC_-+_XX_3


title: WT Well watered replicate 2

description:
Library name: WT_2
WT Well watered replicate 2


title: WT Well watered replicate 1

description:
Library name: WT_1
WT Well watered replicate 1


title: Rat, placenta, PolyI:C, Female, Rep 4

city: London

first: Stephen

middle: J

last: Renaud

state: Ontario

address: 1151 Richmond St, MSB428

institute: University of Western Ontario

data_processing:
Raw fastq data files were analyzed using Partek Flow
After importation, data was aligned to the Rattus norvegicus genome using STAR 2.7.3a and annotated using rn7, resulting in 18,951 genes.
Features with less than 23 reads were filtered out, leaving 15,134 genes.
Normalization was done using DESeq2 (median ratio) with a lowest average coverage filter of 1.0 applied, resulting in 14,949 genes
Assembly: rn7
Supplementary files format and content: tab delimited txt file which contains raw counts (DeSeq2) for each sample

organism: Rattus norvegicus

source_name: Placenta GD18.5

growth_protocol: When female rats were in proestrus, they were caged with a fertile male. After pairing overnight, vaginal smears were assessed under a light microscope. If spermatozoa were present, the rat was considered pregnant and that day was counted as gestational day 0.5 (GD0.5). Pregnant females were then separated from bucks and left undisturbed for 18 days.

extract_protocol:
RNA was extracted from male and female placental tissues by homogenizing in TRIzol (ThermoFisher Scientific). After adding chloroform, the aqueous phase was collected and diluted 1:1 with 70% ethanol, placed on RNeasy columns (Qiagen Inc), treated with DNase I, and RNA purified.
Libraries were generated using the NEBNext directional library prep kit for Illumina (New England Biolabs) at Génome Québec

treatment_protocol: Pregnant females were intravenously administered sterile saline (0.9% NaCl), or an equal volume of sterile saline containing 4 mg/kg of PolyI:C sodium salts (Sigma-Aldrich). Intravenous injections were performed under isoflurane anesthesia (5% induction, 2% maintenance).

value: Sprague-Dawley

value: Placenta GD18.5

value: Female


title: Li_78w_RNA_XistBxC_-+_XX_1

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

value: female


title: Li_9w_RNA_XistBxC_+y_XY_2


title: Rat, placenta, PolyI:C, Female, Rep 3


title: Lu_4w_RNA_XistBxC_-+_XX_1


title: Rat, placenta, PolyI:C, Female, Rep 2


title: Li_9w_RNA_XistBxC_-+_XX_3


title: Li_9w_RNA_XistBxC_+y_XY_1


title: Rat, placenta, PolyI:C, Female, Rep 1


title: Li_4w_RNA_XistBxC_+y_XY_2


title: Rat, placenta, PolyI:C, Male, Rep 3

value: Male


title: Rat, placenta, PolyI:C, Male, Rep 4


title: Li_9w_RNA_XistBxC_-+_XX_2


title: Li_9w_RNA_XistBxC_-+_XX_1


title: Li_4w_RNA_XistBxC_+y_XY_3


title: Rat, placenta, PolyI:C, Male, Rep 2


title: Li_4w_RNA_XistBxC_-+_XX_3


title: Rat, placenta, Saline, Female, Rep 3

value: Saline


title: Li_9w_RNA_XistBxC_+y_XY_3


title: Li_4w_RNA_XistBxC_-+_XX_2


title: Li_78w_RNA_XistBxC_+y_XY_2


title: Rat, placenta, Saline, Female, Rep 1


title: Rat, placenta, PolyI:C, Male, Rep 1


title: Li_4w_RNA_XistBxC_+y_XY_1


title: Rat, placenta, Saline, Male, Rep 4


title: Rat, placenta, Saline, Female, Rep 4


title: Li_E14.5_RNA_XistBxC_-+_XX_2


title: Li_4w_RNA_XistBxC_-+_XX_1


title: Rat, placenta, Saline, Male, Rep 2


title: Rat, placenta, Saline, Male, Rep 3


title: Phaeobacter inhibens DSM 17395 chpT::Tn B

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

description:
Library name: JP119
chpT_B

data_processing:
Reads were mapped to reference genomes using bowtie2 in end-to-end mode with default parameters. A table with reads per protein-coding sequence was generated from each indexed bam file using featureCounts with default parameters.
Assembly: GCA_000154765.2
Supplementary files format and content: table with read counts per gene (identified by locus_tag)

organism: Phaeobacter inhibens DSM 17395

source_name: whole cells

growth_protocol: strains were grown in marine broth until mid-exponential phase

extract_protocol:
Total RNA was isolated with the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturers protocol and including the optional DNase digestion step. Depletion of rRNA was performed with the mRNA Ribo-Zero magnetic kit (Epicentre, Madison, WI, USA) according to the manufacturer’s instructions.
The library was prepared from ribosomally depleted total RNA using the Scriptseq v2 RNA-seq (RNA sequencing) library preparation kit (Epicentre, Madison, WI, USA) according to the manufacturer’s protocol.

treatment_protocol: no treatment

value: whole cells

tag: replicate

value: B


title: Li_E14.5_RNA_XistBxC_-+_XX_1


title: Rat, placenta, Saline, Male, Rep 1


title: Phaeobacter inhibens DSM 17395 chpT::Tn A

description:
Library name: JP118
chpT_A

value: A


title: Ki_78w_RNA_XistBxC_+y_XY_3

value: Kidney


title: right hemisphere tissures of MCAO rat

city: Harbin

first: Pan

last: yujun

state: Heilongjiang Province

address: No. 23, Youzheng Street, Nangang District

institute: the First Clinical College of Harbin Medical University

data_processing:
Basecalls performed using bc12fastq V2.19
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: Rattus norvegicus ensembl 92
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: right hemisphere tissues

extract_protocol:
The fresh rat brain tissues were stored in the GEXSCOPE Tissue Preservation Solution (Singleron Biotechnologies) and transported to the Singleron lab on ice as soon as possible. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for 3 times and minced into 1~2 mm pieces. Then the tissue pieces were digested with 2ml GEXSCOPE Tissue Dissociation Solution (Singleron Biotechnologies) at 37℃ for 15min in 15ml centrifuge tube with sustained agitation. After digestion, using 40-micron sterile strainers to filter the samples and centrifuging the samples at 1000 rpm for 5min. Then the supernatant was discarded, and the sediment was resuspended in 1ml PBS. To remove the red blood cells, 2 ml GEXSCOPE red blood cell lysis buffer (Singleron Biotechnologies) was added at 25°C for 10min. The solution was then centrifuged at 1000 rpm for 5min and suspended in PBS. The sample was stained with trypan blue (Sigma) and microscopically evaluated. We mixed 5 samples per group into one cell suspension pool as previous described
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: Sprague Dawley

value: brain

value: treated with MCAO


title: w_Te_3

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description:
Library name: w_Te_3
w_Te_3

data_processing:
RNA-seq: RNA-seq libraries were made using the Illumina Truseq Total RNA library Prep Kit LT. Sequencing was performed on the Illumina Hiseq2500 platform. Following the trimming of adapter sequences with Trimmomatic, RNA-seq reads from replicated wild type (x3) and mutant samples (x3) were aligned to the Drosophila melanogaster (dm6) genome assembly utilizing HISAT2. Gene annotations were sourced from UCSC. The DESeq2 Bioconductor package was employed to identify differentially expressed mRNAs between w1118 and the hamPR/hamPR mutant, as well as between +/Df and hamSK1/Df mutant, with a subsequent estimation of the false discovery rate (FDR). Genes with an FDR < 10% and absolute Log2FC>0 were considered differentially expressed.
CUT&Tag: We mapped the CUT&TAG samples of w1118 and pBAC_ham_sfGFP in TE and TG tissues to the dm6 genome assembly using Bowtie2 with the following parameters: bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The coverage for these samples was generated using bedtools genomeCoverageBed and normalized to library depth to yield reads per million per base (RPM).
Assembly: dm6
Supplementary files format and content: bigwig
Supplementary files format and content: RNAseq counts matrix

organism: Drosophila melanogaster

source_name: Testis

growth_protocol: Standard Drosophila melanogaster culture condition

extract_protocol:
Total RNA was extracted from finely dissected genital discs or testis samples from 18-25h APF animals using Trizol reagent (Invitrogen). Standard protocol was used for CUT&Tag.
RNA-seq libraries were made using the Illumina Truseq Total RNA library Prep Kit LT. CUT&Tag libraries were generated by PCR using a Universal i5 primer, a uniquely barcoded i7 primer, and PCR master mix (NEB Phusion® High-Fidelity PCR Master Mix with HF Buffer, M0531).

value: Testis

value: wt


title: Ki_78w_RNA_XistBxC_+y_XY_2

value: male


title: Phaeobacter inhibens DSM 17395 cckA::Tn A

description:
Library name: JP116
cckA_A


title: w_Te_2

description:
Library name: w_Te_2
w_Te_2


title: w_Te_1

description:
Library name: w_Te_1
w_Te_1


title: Rat, placenta, Saline, Female, Rep 2

value: Sprague-Dawley


title: Ki_78w_RNA_XistBxC_+y_XY_1


title: w_GD_3

description:
Library name: w_GD_3
w_GD_3

source_name: Genital disc

value: Genital disc


title: Li_E14.5_RNA_XistBxC_-+_XX_3

source_name: Liver

value: Liver


title: Ki_78w_RNA_XistBxC_-+_XX_3

source_name: Kidney

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ


title: w_GD_1

description:
Library name: w_GD_1
w_GD_1


title: w_GD_2

description:
Library name: w_GD_2
w_GD_2


title: Phaeobacter inhibens DSM 17395 ctrA:Tn B

description:
Library name: JP115
ctrA_B


title: w_Df_Te_3

description:
Library name: w_Df_Te_3
w_Df_Te_3

value: wt/Df


title: Ki_78w_RNA_XistBxC_-+_XX_2

value: female


title: Ki_78w_RNA_XistBxC_-+_XX_1


title: Phaeobacter inhibens DSM 17395 ctrA::Tn A

description:
Library name: JP114
ctrA_A


title: w_Df_Te_2

description:
Library name: w_Df_Te_2
w_Df_Te_2


title: Phaeobacter inhibens DSM 17395 wild_type B

description:
Library name: JP113
wildtype_B

value: wild type


title: w_Df_Te_1

description:
Library name: w_Df_Te_1
w_Df_Te_1


title: w_Df_GD_2

description:
Library name: w_Df_GD_2
w_Df_GD_2


title: Phaeobacter inhibens DSM 17395 wild_type A

description:
Library name: JP112
wildtype_A

value: whole cells


title: Ki_9w_RNA_XistBxC_+y_XY_3


title: right hemisphere tissures of Sham rat

value: untreated


title: w_Df_GD_3

description:
Library name: w_Df_GD_3
w_Df_GD_3


title: Phaeobacter inhibens DSM 17395 cckA::Tn B

description:
Library name: JP117
cckA_B

value: B


title: Ki_9w_RNA_XistBxC_+y_XY_2

value: Kidney


title: Patient_3_slice2

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: spatial transcriptome sequencing

data_processing:
The Visium sequencing data were processed by Space Ranger.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: ovarian cancer

extract_protocol:
The frozen tissues were embedded in the OCT compound, and the tissues were cryosectioned and placed on the Visium Spatial Slides.
Library construction was performed according to the standard Visium workflow.

value: ovarian cancer

tag: subject status

value: patient with SCC-MT


title: sk1_Df_Te_1

description:
Library name: sk1_Df_Te_1
sk1_Df_Te_1


title: sk1_Df_Te_3

description:
Library name: sk1_Df_Te_3
sk1_Df_Te_3


title: Patient_3_slice1

description: spatial transcriptome sequencing


title: w_Df_GD_1

description:
Library name: w_Df_GD_1
w_Df_GD_1


title: sk1_Df_GD_3

description:
Library name: sk1_Df_GD_3
sk1_Df_GD_3


title: sk1_Df_GD_2

description:
Library name: sk1_Df_GD_2
sk1_Df_GD_2


title: Patient_2

description: spatial transcriptome sequencing


title: sk1_Df_GD_1

description:
Library name: sk1_Df_GD_1
sk1_Df_GD_1


title: Ki_9w_RNA_XistBxC_-+_XX_3


title: Ki_9w_RNA_XistBxC_+y_XY_1


title: dPR_Te_3

description:
Library name: dPR_Te_3
dPR_Te_3

value: hamPRdel


title: Patient_1

description: spatial transcriptome sequencing


title: Ki_9w_RNA_XistBxC_-+_XX_2


title: dPR_Te_2

description:
Library name: dPR_Te_2
dPR_Te_2

value: Testis


title: dPR_Te_1

description:
Library name: dPR_Te_1
dPR_Te_1


title: 5hmC_Tumor_F75

city: Springfield

first: Shannon

last: Kinney

state: MA

address: 1215 Wilbraham Road Center for Sciences and Pharmacy

department: Pharmaceutical and Administrative Sciences

institute: Western New England University

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (GRCm38-MM10) using BOWTIE software (V2.1.0).
hMeDIP peaks were identified by MACS2 and differentially hydroxymethylated regions (DhMRs) were identified by diffReps by comparing all samples to each other (e.g. normal sample 1 versus normal sample 2, or normal sample 1 versus tumor sample 1).
Final WIG files of hMeDIP-seq signal densities were generated.
Assembly: GRCm38-MM10
Supplementary files format and content: hMeDIP density represented by WIG file at 50 bp fixed step intervals.
Library strategy: hMeDIP-seq

source_name: F75 TRAMP Mouse Prostate Tumor tissue

extract_protocol:
All prostate and tumor tissues were microdissected at necropsy, flash frozen in liquid nitrogen, and stored at -80°C
Total DNA was purified from TRAMP tumor samples that were also evaluated through RNA-seq as there was sufficient tissue for both DNA and RNA extraction from the tumors.
To obtain sufficient total DNA for normal mouse prostate hMeDIP-seq analysis, only RNA or DNA could be extracted from a single normal mouse prostate due to their small size.
hMeDIP-seq was performed as a fee for service by Arraystar Inc. (Rockville, MD www.arraystar.com).
Genomic DNA was sonicated to ~200 - 900bp with a Bioruptor sonicator (Diagenode).
800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol.
Adaptor-ligated DNA was used for immunoprecipitation using a Rat monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode).
To recover the immunoprecipitated DNA fragments, 100 uL of protein G magnetic beads (Life Technologies) were added and incubated for an additional 2 hours at 4°C with agitation.
hMeDIP and supernatant DNA were purified using Qiagen MinElute columns.
14 cycles of PCR were performed on 5 ?L of the immunoprecipitated DNA using the single-end Illumina PCR primers.
Libraries were quality controlled by Agilent 2100 Bioanalyzer.
The library was denatured with 0.1 M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8 pM concentration, amplified in situ using TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 2000 according to the manufacturer's instructions.

treatment_protocol:
Normal prostate samples were obtained from adult f1 males generated by crosses of C57BL/6 and FVB strain mice.
TRAMP prostate tissues were obtained from 24-28 week old f1 Probasin-SV40 transgene heterozygous males generated by crosses of C57BL/6 TRAMP males (homozygous for the transgene) with wildtype FVB females.

value: TRAMP Tumor

value: C57BL/6:FVB TRAMP SV40 L Tag

tag: Stage

value: Late Stage 24 Weeks

value: TRAMP SV40 Tag, Rat probasin Promoter

value: Tumor


title: dPR_GD_3

description:
Library name: dPR_GD_3
dPR_GD_3

value: Genital disc


title: 5hmC_Tumor_F15

source_name: F15 TRAMP Mouse Prostate Tumor tissue


title: dPR_GD_2

description:
Library name: dPR_GD_2
dPR_GD_2


title: dPR_GD_1

description:
Library name: dPR_GD_1
dPR_GD_1


title: Ki_4w_RNA_XistBxC_+y_XY_3

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

value: male


title: 5hmC_Normal_SM501

source_name: SM501 Normal Mouse Prostate

value: Normal Mouse Prostate

value: Adult Male 22 Weeks

value: WT

value: Normal


title: Ki_9w_RNA_XistBxC_-+_XX_1

value: Kidney

value: female


title: hMAIT_perfusate, enriched  MAIT cells from perfusate from donors,biol rep2

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: MAIT cells

extract_protocol:
Total RNAs were extracted from sorted cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MAIT cells


title: 5hmC_Normal_SM500

source_name: SM500 Normal Mouse Prostate


title: hMAIT_perfusate, enriched  MAIT cells from perfusate from donors,biol rep3


title: hMAIT_perfusate, enriched  MAIT cells from perfusate from donors,biol rep1


title: sk1_Df_Te_2

description:
Library name: sk1_Df_Te_2
sk1_Df_Te_2


title: Ki_4w_RNA_XistBxC_+y_XY_1


title: hMAIT_LF, enriched hepatic MAIT cells from HBV infected liver failure patients,biol rep3

tag: disease state

value: HBV infected liver failure


title: 293FT cells transfected with BLU-VIPR containing NEAT1 gRNA (replicate 2) (Light)

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
CRISPResso2
Assembly: hg38
Supplementary files format and content: A table showing the number reads for each nucleotide at each position in the NEAT1 amplicon.
Library strategy: Sequencing of PCR amplicon.

source_name: Human embryonic kidney

growth_protocol: 293FT cells were maintained in DMEM supplemented with 10% fetal bovine serum at 37C in a humidified incubator with 5% CO2.

extract_protocol:
Genomic DNA was extracted from cells exposed to light, and from cells kept in the dark, using the Monarch Genomic DNA Purification Kit following the manufacturer’s protocol (New England Biolabs).
A pooled sequencing librarry was generated by equimolar pooling of indexed genomic PCR products of endogenous NEAT1. The PCR products were isolated using QIAquick Gel Extraction Kit (Qiagen) and quality control was performed with the Agilent High Sensitivity D1000 ScreenTape System (Agilent Technologies).

treatment_protocol: Twenty-four hours post-transfection, cells were exposed to pulses (20 seconds ON, 60 seconds OFF) of 1 mW/cm2 of 470 nm light for 48 hours or kept in the dark.

tag: tissue

value: Human embryonic kidney

value: BLU-VIPR NEAT1

value: Light


title: 293FT cells transfected with BLU-VIPR containing NEAT1 gRNA (replicate 1) (Light)

tag: treatment


title: hMAIT_LF, enriched hepatic MAIT cells from HBV infected liver failure patients,biol rep2


title: Ki_4w_RNA_XistBxC_-+_XX_3


title: Ki_4w_RNA_XistBxC_-+_XX_2


title: 293FT cells transfected with BLU-VIPR containing NEAT1 gRNA (replicate 2) (Dark)

tag: cell line

value: Dark


title: hMAIT_Comp, enriched hepatic MAIT cells from HBV infected patients with compensated liver function,biol rep4


title: hMAIT_HBVN, enriched hepatic MAIT cells from HBV negative patients with compensated liver function,biol rep2

value: HBV infected patients with compensated liver function


title: Ki_4w_RNA_XistBxC_-+_XX_1


title: hMAIT_HBVN, enriched hepatic MAIT cells from HBV negative patients with compensated liver function,biol rep1


title: 293FT cells transfected with BLU-VIPR containing NEAT1 gRNA (replicate 1) (Dark)


title: Ki_E14.5_RNA_XistBxC_-+_XX_3


title: hMAIT_Comp, enriched hepatic MAIT cells from HBV infected patients with compensated liver function,biol rep2


title: hMAIT_Comp, enriched hepatic MAIT cells from HBV infected patients with compensated liver function,biol rep3


title: eMAIT_LT, expanded MAIT cells from HBV-related liver failure patients received liver transplantation,biol rep4


title: Ki_4w_RNA_XistBxC_+y_XY_2


title: eMAIT_LT, expanded MAIT cells from HBV-related liver failure patients received liver transplantation,biol rep3


title: Ki_E14.5_RNA_XistBxC_-+_XX_2


title: 293FT cells transfected with BLU-VIPR containing NTC gRNA (replicate 2) (Light)

value: BLU-VIPR NTC


title: 293FT cells transfected with BLU-VIPR containing NTC gRNA (replicate 1) (Light)


title: eMAIT_LT, expanded MAIT cells from HBV-related liver failure patients received liver transplantation,biol rep2


title: eMAIT_LT, expanded MAIT cells from HBV-related liver failure patients received liver transplantation,biol rep1


title: Ki_E14.5_RNA_XistBxC_-+_XX_1


title: eMAIT_LF, expanded MAIT cells from HBV-related liver failure patients,biol rep3

value: HBV-related liver failure


title: He_78w_RNA_XistBxC_+y_XY_3

source_name: Heart

value: Heart

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ


title: eMAIT_LF, expanded MAIT cells from HBV-related liver failure patients,biol rep2


title: hMAIT_LF, enriched hepatic MAIT cells from HBV infected liver failure patients,biol rep1


title: 293FT cells transfected with BLU-VIPR containing a non-targeting control (NTC) gRNA (replicate 1) (Dark)


title: He_78w_RNA_XistBxC_+y_XY_2

value: male


title: eMAIT_HD, expanded MAIT cells from healthy donor ,biol rep4

value: healthy


title: eMAIT_HD, expanded MAIT cells from healthy donor ,biol rep3


title: eMAIT_LF, expanded MAIT cells from HBV-related liver failure patients,biol rep1


title: eMAIT_HD, expanded MAIT cells from healthy donor ,biol rep2


title: hMAIT_Comp, enriched hepatic MAIT cells from HBV infected patients with compensated liver function,biol rep1


title: He_78w_RNA_XistBxC_-+_XX_3


title: He_78w_RNA_XistBxC_+y_XY_1


title: cMAIT_LF, circulating MAIT cells from HBV-related liver failure patients ,biol rep3


title: cMAIT_LF, circulating MAIT cells from HBV-related liver failure patients ,biol rep1


title: He_78w_RNA_XistBxC_-+_XX_2


title: 293FT cells transfected with BLU-VIPR containing NTC gRNA (replicate 2) (Dark)


title: He_78w_RNA_XistBxC_-+_XX_1


title: eMAIT_HD, expanded MAIT cells from healthy donor ,biol rep1


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep5


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep6


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep4


title: He_9w_RNA_XistBxC_+y_XY_3


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep2


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep1


title: cMAIT_HD, circulating MAIT cells from healthy donor ,biol rep3


title: He_9w_RNA_XistBxC_+y_XY_2


title: He_9w_RNA_XistBxC_+y_XY_1


title: cCD8+T_HD, circulating conventional CD8+T cells from healthy donor ,biol rep3


title: cCD8+T_HD, circulating conventional CD8+T cells from healthy donor ,biol rep2


title: He_9w_RNA_XistBxC_-+_XX_3


title: cCD8+T_HD, circulating conventional CD8+T cells from healthy donor ,biol rep1


title: PL, puncture liver tissue from liver tissue of LF patients received liver transplantation,biol rep4

source_name: Liver tissue

extract_protocol:
Total RNAs were extracted from liver tissue using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver tissue


title: PL, puncture liver tissue from liver tissue of LF patients received liver transplantation,biol rep3


title: PL, puncture liver tissue from liver tissue of LF patients received liver transplantation,biol rep2


title: cMAIT_LF, circulating MAIT cells from HBV-related liver failure patients ,biol rep2


title: PL, puncture liver tissue from liver tissue of LF patients received liver transplantation,biol rep1


title: He_9w_RNA_XistBxC_-+_XX_1


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep9


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep8


title: He_9w_RNA_XistBxC_-+_XX_2


title: 7509-JF-2

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 7509-JF-2

data_processing:
“BCL Convert Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices.”
Assembly: hg19
Supplementary files format and content: cellranger output format

source_name: femoral artery

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: femoral artery

value: mixed (single cell)

tag: cell type

value: human arterial


title: He_4w_RNA_XistBxC_+y_XY_3

tag: genotype


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep7


title: 3467-AB-2

description: Library name: 3467-AB-2


title: He_4w_RNA_XistBxC_+y_XY_2


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep6


title: 7509-JF-1

description: Library name: 7509-JF-1


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep5


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep4


title: 3467-AB-1

description: Library name: 3467-AB-1


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep3


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep2


title: He_4w_RNA_XistBxC_+y_XY_1


title: He_4w_RNA_XistBxC_-+_XX_3

value: female


title: LF,Liver tissue, liver tissue from HBV-related liver failure patients, biol rep1


title: HBVP,Liver tissue, HBV infected tissue with compensated liver function, biol rep5


title: He_4w_RNA_XistBxC_-+_XX_2


title: HBVP,Liver tissue, HBV infected tissue with compensated liver function, biol rep4


title: HBVP,Liver tissue, HBV infected tissue with compensated liver function, biol rep3


title: HBVP,Liver tissue, HBV infected tissue with compensated liver function, biol rep2


title: IMPACT_WID_29

city: New York

first: Simon

last: Powell

address: 1250 1st Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: IMPACT_WID_29

data_processing:
RNA sequencing reads were first examined using FASTQC, then Illumina universal adapters were trimmed by cutadapt. The trimmed reads were aligned to the GRCh37 human genome using STAR RNA-Seq aligner, and then mapped single-end reads from transcripts were counted using the GenomicAlignments package in Bioconductor.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include gene read counts for each sample
Supplementary files format and content: tab-delimited text files include gene TPM values for each sample

source_name: Abdominal Wall

extract_protocol:
Following Institutional Review Board (IRB) approval, formalin-fixed paraffin-embedded (FFPE) tissues of 10 cases were retrieved from the pathology archives of Memorial Sloan Kettering Cancer Center (MSK). Two pathologists (F.P. and T.V.) reviewed cases and included tumors arising from different anatomic locations. Cases were microdissected from ten eight-micron-thick histologic sections under a stereomicroscope (Olympus SZ61) to ensure a tumor content ≥80%. RNA was extracted using the RNAeasy FFPE kit (Qiagen) and subjected to RNA-sequencing at MSK Integrated Genomics Operation (IGO).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.5-1 µg of total RNA with DV200 percentages varying from 17-38% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE150 run, using the NovaSeq 6000 S4 Reagent Kit (300 Cycles) (Illumina).

value: Abdominal Wall


title: IMPACT_WID_36

description: Library name: IMPACT_WID_36

source_name: GE Junction

value: GE Junction


title: HBVP,Liver tissue, HBV infected tissue with compensated liver function, biol rep1


title: He_E14.5_RNA_XistBxC_-+_XX_3


title: HBVN,Liver tissue, HBV negative tissue, biol rep4


title: IMPACT_WID_18

description: Library name: IMPACT_WID_18

source_name: Lung

value: Lung


title: HBVN,Liver tissue, HBV negative tissue, biol rep2


title: He_E14.5_RNA_XistBxC_-+_XX_2


title: HBVN,Liver tissue, HBV negative tissue, biol rep3


title: IMPACT_WID_14

description: Library name: IMPACT_WID_14

source_name: Esophagus

value: Esophagus


title: He_E14.5_RNA_XistBxC_-+_XX_1


title: IMPACT_WID_13

description: Library name: IMPACT_WID_13


title: Br_78w_RNA_XistBxC_+y_XY_2

source_name: Brain

value: Brain


title: Nebulized_FLAMOD_Trachea3_biol_rep3

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

description:
Library name: Library-411
RnaSeq Illumina NovaSeq (2x150)

data_processing:
STAR-2.7.10a
Genome index was generated using the annotation file Macaca_fascicularis_6.0.110.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (-quantMode using bidirectional input (R1/R2))
_ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Assembly: Macaca_fascicularis_6.0.110
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

organism: Macaca fascicularis

source_name: Trachea

growth_protocol: Experiments were conducted in female (n=11) cynomolgus macaques (Macaca Fascicularis, Vietnam), 3-3.5 kg, obtained from Bioprim® (Baziege, France).

extract_protocol:
Nasal, tracheal, bronchial, lung tissues and blood samples were collected for RNA extraction and sequencing. For Nasal, tracheal, bronchial and lung tissue RNA extraction, tissue was collected and preserved in NucleoProtect® RNA (Macherey-Nagel, Duren, Germany) at -80°C until ready for processing. Tissue was dried on paper towels and any visible cartilage was removed. The remaining tissue was added to 1 ml RA1 lysis buffer (Macherey-Nagel) supplemented with 2% TCEP (Sigma) and disintegrated with an UltraTurrax homogenizer (IKA-Werke, Staufen, Germany). For nasal, bronchial and tracheal samples, a pretreatment with proteinase K was performed to remove collagen. Briefly, 700 μl of undiluted lysate (nasal) or diluted lysate 1:1 (bronchial, tracheal) was added to 1190 μl water substituted with 20 μl proteinase K (20 mg/ml) and incubated at room temperature for 10 min, followed by a 10 min incubation at 55 °C and centrifugation at 10,000 rpm for 3 min. The supernatant was then mixed with equal parts volume of 100% ethanol and the mixture was loaded onto the NucleoSpin RNA Plus extraction kit columns, and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel). Extracts were eluted in 20 μl (nasal) or 30 μl (bronchial, tracheal and lung) RNAse-free water. Blood samples (3 ml) were collected in TempusTM blood RNA tubes (Thermofisher Scientific) and stored at -20 °C. Tubes were thawed and the stabilized blood was diluted up to 12 ml with D-PBS (Gibco) and vortexed vigorously for 30 seconds followed by centrifugation at 4 °C, for 30 min at 3000 rcf. The pellet was dissolved in 1 ml RA1 buffer + 2% TCEP and 500 μl was loaded onto the NucleoSpin RNA Plus extraction kit columns and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel). Extracts were eluted in 40 μl RNAse-free water. RNA quality was checked by spectrophotometry (Nanodrop), the molecular integrity was assessed with the TapeStation 4200 (Agilent Technologies), and the quantification was done using QuantiFluor RNA System (Promega).
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen) as well as QIAseq FastSelect-Globin Kit for blood samples (Qiagen). 200 ng of total RNA.

treatment_protocol: For intravenous route (I.V.), macaques (n=3) were sedated (3 mg/kg ketamine, 125 µg/kg medetomidine), then anaesthetized with isoflurane 2%, intubated and maintained under mechanical ventilation as described for inhalation route. Then 100 µg of FLAMOD in 100 µL were rapidly injected in the saphenous vein. For the kinetic analyses, blood samples were collected at 0h, 1h15m, 3h, 6h and 24h. After a washout period, these same three macaques were nebulized with 1mg/ml of FLAMOD. One hour post-nebulization nasal, tracheal, bronchial and lung samples were collected. All samples were subjsected to RNA extraction and sequencing. For the high (n=3) and low dose  (n=5) FLAMOD nebulization experiments, macaques were administered xx mg/ml and xx mg/ml FLAMOD, respectively. For the kinetic analyses, blood samples were collected ay 0h, 1h15m or 1h30m, 3h, 6h and 24h post administration  and processed for RNA extraction and sequencing.

value: Trachea


title: Nebulized_FLAMOD_Bronchus3_biol_rep3

description:
Library name: Library-413
RnaSeq Illumina NovaSeq (2x150)

source_name: Bronchus

value: Bronchus


title: Nebulized_FLAMOD_Bronchus2_biol_rep2

description:
Library name: Library-412
RnaSeq Illumina NovaSeq (2x150)


title: He_4w_RNA_XistBxC_-+_XX_1


title: Nebulized_FLAMOD_Trachea1_biol_rep1

description:
Library name: Library-409
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_Naive_Lung2_biol_rep2

description:
Library name: Library-408
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_Trachea2_biol_rep2

description:
Library name: Library-410
RnaSeq Illumina NovaSeq (2x150)


title: IMPACT_WID_01

description: Library name: IMPACT_WID_01

source_name: Esophagus tumor

value: Esophagus tumor


title: Br_78w_RNA_XistBxC_+y_XY_1


title: Nebulized_Naive_Bronchus3_biol_rep3

description:
Library name: Library-407
RnaSeq Illumina NovaSeq (2x150)


title: Br_78w_RNA_XistBxC_-+_XX_3


title: Br_78w_RNA_XistBxC_-+_XX_2


title: Nebulized_FLAMOD_Bronchus1_biol_rep1

description:
Library name: Library-403
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_Naive_Trachea2_biol_rep2

description:
Library name: Library-415
RnaSeq Illumina NovaSeq (2x150)


title: HBVN,Liver tissue, HBV negative tissue, biol rep1


title: Caco-2, CBS KO-2

city: Beijing

first: Xuan

last: He

address: Xishiku street, Xicheng, Beijing

department: Department of Gastrointestinal Surgery

institute: Peking University First Hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38 ensemble v107
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Colon adenocarcinoma tissue

growth_protocol: Caco-2 cells were cultivated in a 10%FBS high glucose DMEM medium, and the environment is 37 ° C containing 5%CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Colon adenocarcinoma tissue

value: Tumor cell

value: CBS knockout


title: Nebulized_Naive_Bronchus2_biol_rep2

description:
Library name: Library-400
RnaSeq Illumina NovaSeq (2x150)


title: IMPACT_WID_08

description: Library name: IMPACT_WID_08

source_name: Bone

value: Bone


title: Br_78w_RNA_XistBxC_-+_XX_1

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ


title: Br_78w_RNA_XistBxC_+y_XY_3

value: male


title: Caco-2, CBS KO-1


title: Nebulized_Naive_Lung1_biol_rep1

description:
Library name: Library-396
RnaSeq Illumina NovaSeq (2x150)


title: Br_9w_RNA_XistBxC_+y_XY_3


title: Caco-2, WT-3

value: WT


title: IMPACT_WID_06

description: Library name: IMPACT_WID_06

source_name: Bladder

value: Bladder


title: Nebulized_Naive_Nose3_biol_rep3

description:
Library name: Library-395
RnaSeq Illumina NovaSeq (2x150)

source_name: Nose

value: Nose


title: Nebulized_Naive_Nose2_biol_rep2

description:
Library name: Library-393
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_Naive_Nose1_biol_rep1

description:
Library name: Library-391
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_Nose3_biol_rep3

description:
Library name: Library-389
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_Naive_Trachea1_biol_rep1

description:
Library name: Library-406
RnaSeq Illumina NovaSeq (2x150)


title: Caco-2, CBS KO-3


title: Nebulized_Naive_Nose4_biol_rep4

description:
Library name: Library-405
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_Lung3_biol_rep3

description:
Library name: Library-388
RnaSeq Illumina NovaSeq (2x150)


title: Caco-2, WT-1


title: Nebulized_FLAMOD_Nose2_biol_rep2

description:
Library name: Library-387
RnaSeq Illumina NovaSeq (2x150)


title: Caco-2, WT-2


title: Nebulized_Naive_Bronchus1_biol_rep1

description:
Library name: Library-399
RnaSeq Illumina NovaSeq (2x150)


title: Br_9w_RNA_XistBxC_-+_XX_3

value: female


title: Nebulized_FLAMOD_Nose1_biol_rep1

description:
Library name: Library-385
RnaSeq Illumina NovaSeq (2x150)


title: Br_9w_RNA_XistBxC_-+_XX_2


title: Nebulized_FLAMOD_L5_24h_biol_rep5

description:
Library name: Library-383
RnaSeq Illumina NovaSeq (2x150)

source_name: Blood

value: Blood


title: Br_9w_RNA_XistBxC_-+_XX_1


title: Nebulized_FLAMOD_L5_3h_biol_rep5

description:
Library name: Library-381
RnaSeq Illumina NovaSeq (2x150)


title: Br_4w_RNA_XistBxC_+y_XY_3


title: Nebulized_FLAMOD_L5_1h30_biol_rep5

description:
Library name: Library-380
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L5_0h_biol_rep5

description:
Library name: Library-379
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L4_24h_biol_rep4

description:
Library name: Library-378
RnaSeq Illumina NovaSeq (2x150)


title: Br_9w_RNA_XistBxC_+y_XY_2


title: Br_4w_RNA_XistBxC_+y_XY_2


title: Nebulized_FLAMOD_L4_6h_biol_rep4

description:
Library name: Library-377
RnaSeq Illumina NovaSeq (2x150)


title: Br_9w_RNA_XistBxC_+y_XY_1


title: Nebulized_FLAMOD_L4_1h30_biol_rep4

description:
Library name: Library-375
RnaSeq Illumina NovaSeq (2x150)


title: Br_4w_RNA_XistBxC_-+_XX_3


title: Br_4w_RNA_XistBxC_-+_XX_2


title: Nebulized_FLAMOD_L3_3h_biol_rep3

description:
Library name: Library-371
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_Lung1_biol_rep1

description:
Library name: Library-384
RnaSeq Illumina NovaSeq (2x150)

value: Lung


title: Nebulized_FLAMOD_L3_1h30_biol_rep3

description:
Library name: Library-370
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L5_6h_biol_rep5

description:
Library name: Library-382
RnaSeq Illumina NovaSeq (2x150)


title: Br_E14.5_RNA_XistBxC_-+_XX_3


title: Nebulized_FLAMOD_L2_6h_biol_rep2

description:
Library name: Library-367
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L2_3h_biol_rep2

description:
Library name: Library-366
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L4_0h_biol_rep4

description:
Library name: Library-374
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L2_24h_biol_rep2

description:
Library name: Library-368
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L3_0h_biol_rep3

description:
Library name: Library-369
RnaSeq Illumina NovaSeq (2x150)


title: Br_E14.5_RNA_XistBxC_-+_XX_1


title: Nebulized_FLAMOD_L4_3h_biol_rep4

description:
Library name: Library-376
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L3_24h_biol_rep3

description:
Library name: Library-373
RnaSeq Illumina NovaSeq (2x150)


title: Br_4w_RNA_XistBxC_+y_XY_1


title: Nebulized_FLAMOD_Lung2_biol_rep2

description:
Library name: Library-386
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L2_0h_biol_rep2

description:
Library name: Library-364
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L1_24h_biol_rep1

description:
Library name: Library-363
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L2_1h30_biol_rep2

description:
Library name: Library-365
RnaSeq Illumina NovaSeq (2x150)