title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-M-spleen-95_GT18-00076_TCCTGAGC-TATGCAGT_S3


title: B6-3mo-M-naive-3_GT18-04705_CGATGT_S4

status: Public on Dec 01 2021

type: SRA

city: Farmington

first: Duygu

last: Ucar

state: Connecticut

address: 10 Discovery Drive

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Libraries were pooled and sequenced 75 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 40 million reads per sample.
Single-end RNA-seq reads were aligned to the mouse genome (mm10) with Bowtie 2 and counts were generated with RSEM.
To normalize the raw counts count-per-million (cpm) function from edgeR package is used and the genes that are log(cpm)<1 and expressed less than 2 samples were excluded from rest of the analyses.
For differential analysis pipeline, however, raw counts are used with the default options of edgeR package, and via TMM normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Count Files for B6/NZO

molecule: total RNA

organism: Mus musculus

extract_protocol:
Data is obtained from spleen and peripheral blood lymphocytes (PBLs) of C57BL/6J and NZO/HILtJ mouse strains, hereafter B6 and NZO, respectively, at ages 3, 12, and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq, remaining cells collected for other RNA preparations.
30 ng of total RNA, with the addition of 6 µl ERCC Spike-In Control Mix 1 (Ambion Thermo Fisher) diluted 1:10,000, was used for library construction. Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 assay on the TapeStation (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturer's instructions.

tag: strain

tag: age

tag: Sex

value: male

tag: tissue

value: naive


title: K5 +Igf1 3h rep1

type: RNA

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 3h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Igf1 (3.26 pM).

hyb_protocol: Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies, Palo Alto, CA).

scan_protocol: Arrays were then scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System (Agilent Technologies, Palo Alto, CA).

data_processing: Raw microarray data were acquired and analyzed using Agilent’s Feature Extraction v.12.1 software to assess the array spot quality, as well as to check signal and background intensity statistics in the default setting. Raw signal values were thresholded to 1, log2 transformed, normalized to the 75th percentile, and baselined to the median of all samples using GeneSpringGX v.14.9 (Agilent Technologies). Then, to identify genes with significant temporal expression changes and evaluate trend differences in CGNs undergoing apoptosis (K5 vs K25) and exposed to SP, PACAP or IGF1 treatment with respect to untreated (K5), pre-processed normalized array data were analyzed by using the R package maSigPro (microarray Significant Profiles). Genes whose expression levels varied in a statistically significant way along time were detected using the linear step-up Benjamini-Hochberg false discovery rate (FDR) procedure setting a corrected p-value ≤ 0.05.

organism: Rattus norvegicus

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 3h, replicate 1

label_protocol: Aliquots (750 ng) of Cy3‐labeled cRNA targets were hybridized on arrays using the SurePrint G3 Rat Gene Expression 8x60K microarray kit (Agilent Technologies, Palo Alto, CA).

growth_protocol: Primary cultures of CGNs were prepared from 8-day-old Wistar rats (Charles River, Calco, Italy) and were cultured as previously described (ins ref). In brief, cerebella were sliced and tissue was dissociated through trypsinization in 0.025% trypsin solution (15 min at 37 °C) and trituration in presence of DNase (0.01%) and trypsin inhibitor (0.05%). Dissociated cells were collected through centrifugation and resuspended in basal Eagle’s medium supplemented with 10% fetal calf serum, 25 mm KCl, 2 mm glutamine and 100 μg/ml gentamycin. Cytosine arabinofuranoside (10 μM) was added after 18 h of culture to inhibit the growth of non-neuronal cells. After 6 days ‘in vitro’, extracellular KCl was shifted from 25 to 5 mm for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mm KCl, neurons were incubated with the same medium up to 48 h (K5), whereas control neurons were incubated with a serum-free medium supplemented with 25 mm KCl (K25).

extract_protocol: Total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates for each experimental condition (K25, K5, K5+SP, K5+Pacap, K5+Igf1). RNA quantity and quality were assessed using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, MA, USA) and a 2100 Bioanalyzer microfluidic electrophoresis platform (Agilent Technologies, Palo Alto, CA), respectively, according to the manufacturer's instructions. Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA), following the manufacturer's protocol.

treatment_protocol: K5 neurons were also treated with a maximal effective dose of SP (200 nM), Pacap (100 nM) or Igf1 (3.26 pM). All the substances were obtained from Sigma-Aldrich (Milano, Italy), unless otherwise specified.

value: Wistar

value: Cerebella

tag: cell type

value: Cerebellar Granule Neurons (CGNs) primary culture

value: 8-day-old (P8)


title: K5 + Igf1 1h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 1h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Igf1 (3.26 pM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 1h, replicate 4


title: B6-3mo-M-naive-2_GT18-04704_ATCACG_S12


title: K5 + Igf1 1h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 1h, replicate 3


title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-F-spleen-94_GT18-00075_AGGCAGAA-CTCCTTAC_S6

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
trimmed reads were aligned to mouse genome (mm10) using BWA
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the samples of the same tissue were merged to generate one consensus peak set by using R package DiffBind.
Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized using the cpm function via the log option turned on from edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: Atacseq consensus peaks per tissue/cell type, Normalized Count Files

molecule: genomic DNA

extract_protocol:
Data is obtained from spleen and peripheral blood lymphocytes (PBLs) of C57BL/6J and NZO/HILtJ mouse strains, hereafter B6 and NZO, respectively, at ages 3, 12, and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq
ATAC-seq libraries were prepared using 50,000 cells, as previously described (Buenrostro et al, 2015), with the following modifications: digitonin was added to the transposition reaction at a final concentration of 0.01%; the transposition reaction was purified using the Genomic DNA Clean & Concentrator-10 kit (Zymo Research Corporation); PCR amplification was carried out using the Nextera DNA Library Prep (Illumina) Index Adapters, Nextera PCR Master Mix, and PCR Primer Cocktail for 10 cycles of PCR; PCR reaction was purified using 1.7x SPRI beads (Agencourt AMPure XP, Beckman Coulter). Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies) and quantitative  PCR (KAPA Biosystems), according to the manufacturer's instructions. Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 reagents (Illumina).

value: NZO

value: Female

value: spleen


title: K5+Igf1 30' rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 0.5h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Igf1 (3.26 pM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 0.5h, replicate 4


title: B6-3mo-M-naive-1_GT18-04703_ATTCCT_S8


title: K5 + Igf1 1h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 1h, replicate 1


title: K5 + Igf1 1h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 1h, replicate 2


title: T71: Colon tumor from patient 71

type: genomic

city: Barcelona

first: Sara

last: Lahoz

address: Carrer del Rosselló, 149

country: Spain

institute: Institut D'Investigacions Sanitàries August Pi i Sunyer

description: Hybridized to Affymetrix Oncoscan SNP array for profiling copy-number alterations in tumor samples

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
raw SNP-array fluorescence intensity data (CEL files) were processed using SNP-FASST2 segmentation algorithm from Nexus  Copy  Number  software  version  9.0 (BioDiscovery,  El  Segundo,  CA,  USA) , achieving an estimate of the mean log2-ratio and B-allele frequency (BAF) values for each genome region. Major and minor allele numbers of each segment were inferred utilizing ASCAT R package version 2.5. For a chromosome region to be considered as carrying a CN gain or loss, log2-ratio cut-offs  were  set  on  0.18  and -0.18,  respectively;  and  to  be  considered  to  have  a  loss  of heterozygosity (LOH), BAF threshold was set on 0.3. Chromosomal regions showing a non-altered log2-ratio and BAF <0.3 were classified as copy-number neutral LOH (CNN-LOH).
Probe set values in OSCHP files include intensity values (column ‘Log2Ratio’) and frequency of the alternative allele (BAF) for each array-probe.

label: Biotin

organism: Homo sapiens

source_name: FFPE tumor

label_protocol: Affymetrix OncoScan FFPE Assay kit for staining with Biotin.

extract_protocol: DNA was extracted from each formalin-fixed paraffin-embedded (FFPE) tumor samples using the QIAmp DNA FFPE kit (Qiagen, Hilden, Germany) and then quantified using Qubit fluorometer assay (Thermo Fisher Scientific, MA, USA)

treatment_protocol: All patients were first-line treated with surgery, and none of them received adjuvant chemotherapy.

tag: disease state

value: Colon cancer

value: FFPE tumor


title: T68: Colon tumor from patient 68


title: T67: Colon tumor from patient 67


title: recovery ambulatory

city: Jupiter

first: Donald

middle: G.

last: Phinney

state: Florida

address: 130 Scripps Way Bldg A215

department: Molecular Medicine

institute: The Scripps Research Institute

data_processing:
Adapter sequences were removed using the cutadapt program
Sequences were aligned to the mouse genome via HISAT2
Alignments were mapped to gene transcripts using the featurecount program
Genome_build: mm9
Supplementary_files_format_and_content: csv file, raw transcript counts

source_name: flow sorted SSCs

extract_protocol:
Hind limbs bone marrow was flushed.  SSCs were isolated by FACS and RNA was isolated by mini-prep.  MSCs were derived by plating whole bone marrow and depletion before extraction by mini-prep.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Amb mice were ambulatory throughout the experimentation.  HU mice were tail suspended for the indicated duration.

value: limb bone marrow

value: flow sorted SSCs

tag: treatment

value: recovery AMB

tag: duration

value: Reloading control


title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-M-spleen-96_GT18-00077_GGACTCCT-TACTCCTT_S4

value: Male


title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-F-spleen-90_GT18-00074_CGTACTAG-TCTACTCT_S2


title: T70: Colon tumor from patient 70


title: B6-3mo-F-memory-5_GT18-04697_GTGAAA_S11

value: female

value: memory


title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-F-spleen-89_GT18-00073_TAAGGCGA-AGAGGATA_S5


title: B6-3mo-M-memory-2_GT18-04699_GTTTCG_S5

value: male


title: K5 +Pacap 3h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 3h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Pacap (100 nM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 3h, replicate 4

value: Wistar


title: B6-3mo-M-memory-3_GT18-04700_CGTACG_S6


title: K5+Igf1 30' rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 0.5h, replicate 3

value: Cerebella


title: T73: Colon tumor from patient 73


title: K5+Igf1 30' rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 0.5h, replicate 2

value: Cerebellar Granule Neurons (CGNs) primary culture


title: hindlimb unloaded+recovery

value: HU+recovery

value: 8 weeks + reloaded


title: K5 +Pacap 3h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 3h, replicate 2

value: 8-day-old (P8)


title: K5 +Pacap 3h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 3h, replicate 3


title: T64: Colon tumor from patient 64


title: B6-3mo-F-memory-4_GT18-04696_GTCCGC_S14


title: K5 +Pacap 3h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 3h, replicate 1


title: 14wk hindlimb unloaded SSC

value: HU

value: 14 weeks


title: B6-18mo-M-spleen-47_GT18-01795_CTTGTA_S58

value: spleen


title: 14wk ambulatory SSC

value: limb bone marrow

value: AMB


title: B6-3mo-M-memory-1_GT18-04698_GTGGCC_S2


title: 14wk ambulatory MSC

source_name: depleted MSCs

value: depleted MSCs


title: K5+Igf1 30' rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 0.5h, replicate 1


title: 14wk hindlimb unloaded MSC


title: T63: Colon tumor from patient 63

value: Colon cancer

value: FFPE tumor


title: K5 + Pacap 1h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 1h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Pacap (100 nM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 1h, replicate 4


title: B6-18mo-M-spleen-46_GT18-01794_GGCTAC_S63


title: 8wk hindlimb unloaded SSC

value: flow sorted SSCs

value: 8 weeks


title: B6-18mo-M-spleen-45_GT18-01793_TAGCTT_S50

value: male


title: B6-18mo-F-spleen-42_GT18-01792_GATCAG_S52

value: female


title: T66: Colon tumor from patient 66


title: T59: Colon tumor from patient 59


title: B6-18mo-F-spleen-41_GT18-01791_ACTTGA_S45


title: 8wk ambulatory MSC


title: B6-18mo-F-spleen-40_GT18-01790_CAGATC_S46


title: 8wk hindlimb unloaded MSC


title: Dnmt3a_KO_6M

city: Houston

first: Mira

last: Jeong

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome mm10 (GRCm38) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using Seurat package (https://satijalab.org/seurat/, version 2.3.4) for data analysis including quality control, normalization, dimensional reduction, clustering, and visualization. Cells with less than 15% of total expressed genes, and genes that were detected in less than 3% of total cells in each dataset were discarded forom all further analyses. In addition, cells with over 20% mitochondrial gene percentage were excluded for filtering of dead or poor-quality cells
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample condition.

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones and hematopoietic stem/progenitor cells were sorted using flow.
Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits v2 user guide.
10x Genomics  scRNA-sea

value: Male

tag: genotype

value: Dnmt3a knockout

value: BM

value: 6 months


title: T57: Colon tumor from patient 57


title: T58: Colon tumor from patient 58


title: K5 + Pacap 1h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 1h, replicate 3

value: Wistar

value: Cerebella

value: Cerebellar Granule Neurons (CGNs) primary culture

value: 8-day-old (P8)


title: K5+Pacap 30' rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 0.5h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Pacap (100 nM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, , 0.5h, replicate 4


title: K5 + Pacap 1h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 1h, replicate 1


title: T55: Colon tumor from patient 55


title: Dnmt3a_KO_2M_2

value: 2 months


title: K5 + Pacap 1h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, 1h, replicate 2


title: K5+Pacap 30' rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, , 0.5h, replicate 3


title: T65: Colon tumor from patient 65


title: Dnmt3a_KO_2M


title: T60: Colon tumor from patient 60


title: T61: Colon tumor from patient 61


title: T52: Colon tumor from patient 52


title: 8wk ambulatory SSC

value: limb bone marrow

value: AMB


title: T62: Colon tumor from patient 62

value: Colon cancer


title: B6-18mo-F-PBL-41_GT18-01785_CGATGT_S47

value: PBL


title: B6-18mo-M-PBL-47_GT18-01789_GCCAAT_S37


title: B6-18mo-F-PBL-42_GT18-01786_TTAGGC_S43


title: Dnmt3a_WT_6M

value: Wildtype


title: B6-18mo-M-PBL-46_GT18-01788_ACAGTG_S38


title: B6-18mo-F-PBL-40_GT18-01784_ATCACG_S35


title: T51: Colon tumor from patient 51

value: FFPE tumor


title: B6-18mo-M-PBL-45_GT18-01787_TGACCA_S41

value: male


title: Dnmt3a_WT_2M


title: T50: Colon tumor from patient 50


title: T49: Colon tumor from patient 49


title: T47: Colon tumor from patient 47


title: K5+Pacap 30' rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, , 0.5h, replicate 1


title: K5+Pacap 30' rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM, , 0.5h, replicate 2


title: T46: Colon tumor from patient 46

source_name: FFPE tumor


title: CTCF knockout biological replicate 2 ATAC-seq

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

institute: UCLA

data_processing:
Paired-end 42 bp reads measured on an Illumina NextSeq 500 were demultiplexed and mapped to the mm10 genome using BWA in mem mode with default parameters, allowing for 2 mismatches. Uniquely mapped reads from matched pairs were retained for further analysis, and PCR duplicates were removed before peak calling.
Peaks were called using MACS v2.1.0 at a cutoff of p-value 1e-7 on sorted .bam files from each sample, using the --nomodel parameter. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Individual replicate bigWigs were provided from ActiveMotif.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: Isolated cardiac myocytes

extract_protocol:
DNA from whole heart tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as described in Buenrostro et al. (PMID: 24097267)
Libraries were prepared according to Illumina's instructions (Nextera Library Prep Kit). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

treatment_protocol: DNA was isolated from mouse hearts 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.

value: CTCF knockout


title: K5 3h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 3h switch from 25 mM (K25) to 5 mM KCl (K5)

source_name: CGNs_medium aspirated_K5 + 0% FCS, 3h, replicate 4


title: CTCF knockout biological replicate 1 ATAC-seq


title: B6-18mo-M-naive-45_GT18-01805_GAGTGG_S51

value: naive


title: B6-18mo-M-naive-46_GT18-01806_ACTGAT_S60


title: K5 1h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 1h switch from 25 mM (K25) to 5 mM KCl (K5)

source_name: CGNs_medium aspirated_K5 + 0% FCS, 1h, replicate 4


title: K5 3h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS, 3h, replicate 3


title: K5 3h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS, 3h, replicate 2


title: K5 1h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS, 1h, replicate 1


title: K5 3h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS, 3h, replicate 1


title: T45: Colon tumor from patient 45


title: K5 1h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS, 1h, replicate 3


title: T42: Colon tumor from patient 42


title: K5 1h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS, 1h, replicate 2


title: K5 30' rep3

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 0.5h switch from 25 mM (K25) to 5 mM KCl (K5)

source_name: CGNs_medium aspirated_K5 + 0% FCS, 0.5h, replicate 3


title: B6-18mo-M-naive-47_GT18-01807_ATTCCT_S49


title: B6-18mo-F-naive-40_GT18-01802_GTGGCC_S53

value: female


title: B6-18mo-M-memory-47_GT18-01801_GTGAAA_S61

value: memory


title: K5 30' rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS, 0.5h, replicate 2


title: T40: Colon tumor from patient 40


title: T39: Colon tumor from patient 39


title: B6-18mo-M-memory-46_GT18-01800_GTCCGC_S55


title: K5 30' rep4

source_name: CGNs_medium aspirated_K5 + 0% FCS, 0.5h, replicate 4


title: TAC 3 days biological replicate 3 ATAC-seq

value: TAC

tag: time

value: 3 days


title: B6-18mo-F-naive-42_GT18-01804_CGTACG_S54


title: TAC 3 weeks biological replicate 3 ATAC-seq

value: 3 weeks


title: TAC 3 days biological replicate 2 ATAC-seq


title: B6-18mo-M-memory-45_GT18-01799_CCGTCC_S59


title: T36: Colon tumor from patient 36


title: T34: Colon tumor from patient 34


title: T33: Colon tumor from patient 33


title: Control biological replicate 2 ATAC-seq

value: Control


title: K25 3h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) at 3h following incubation with a serum-free medium supplemented with 25 mm KCl (K25).

source_name: CGNs_medium aspirated_K25 + 0% FCS, 3h, replicate 4

value: Wistar

value: Cerebella

value: Cerebellar Granule Neurons (CGNs) primary culture

value: 8-day-old (P8)


title: Control biological replicate 3 ATAC-seq


title: B6-18mo-F-memory-42_GT18-01798_ATGTCA_S62


title: TAC 3 weeks biological replicate 1 ATAC-seq


title: TAC 3 weeks biological replicate 2 ATAC-seq


title: K25 3h rep3

source_name: CGNs_medium aspirated_K25 + 0% FCS, 3h, replicate 3


title: TAC 3 days biological replicate 1 ATAC-seq


title: K5 30' rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS, 0.5h, replicate 1


title: T31: Colon tumor from patient 31

value: Colon cancer


title: Control biological replicate 1 ATAC-seq


title: B6-18mo-F-memory-41_GT18-01797_AGTTCC_S57


title: B6-12mo-M-spleen-219_GT17-14911_GCCAAT_S20

value: spleen


title: T28: Colon tumor from patient 28


title: B6-18mo-F-memory-40_GT18-01796_AGTCAA_S56


title: T27: Colon tumor from patient 27


title: K25 3h rep2

source_name: CGNs_medium aspirated_K25 + 0% FCS, 3h, replicate 2


title: K25 1h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) at 1h following incubation with a serum-free medium supplemented with 25 mm KCl (K25).

source_name: CGNs_medium aspirated_K25 + 0% FCS, 1h, replicate 4


title: B6-12mo-M-spleen-217_GT17-14909_TGACCA_S25


title: K25 3h rep1

source_name: CGNs_medium aspirated_K25 + 0% FCS, 3h, replicate 1


title: T25: Colon tumor from patient 25

source_name: FFPE tumor


title: T24: Colon tumor from patient 24


title: B6-12mo-F-spleen-206_GT17-14907_CGATGT_S29


title: B6-12mo-F-spleen-205_GT17-14906_ATCACG_S30


title: T20: Colon tumor from patient 20


title: BIOCHIP_CPM_POSTIVE_HLCs_rep9

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA.
Demultiplexing, filtering, mapping and molecule assembly were performed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al., BMC Bioinformatics, 2014. doi: 10.1186/1471-2105-15-144).
Conversion from single pairs in BAM format to single pairs in BED12 format was done with https://github.com/Population-Transcriptomics/pairedBamToBed12
Assembly of single pairs in BED12 format to single molecules in BED12 format was done with https://github.com/mmendez12/umicount
CAGE peaks were called and gene expression tables generated using the CAGEr package (Haberle et al., Nucleic Acids Research, 2015. doi: 10.1093/nar/gkv054).
Genome_build: hg38
Supplementary_files_format_and_content: BED12 files, one RNA molecule per line; the score indicates how many read pairs were used to assemble the molecule.

source_name: induced Pluripotent Stem Cells (iPSC)

growth_protocol: Human iPSCs were cultured in biochips according to the protocol described by Danoy et al., Biotechnol Bioeng., 2021 (doi: 10.1002/bit.27667) applying or not a carboxypeptidase M positive (CPM+) cells selection step before cell inoculation.

extract_protocol:
Total RNA was harvested using Trizol reagent. 250ng of total RNA from each sample were used for the construction of the sequencing libraries.
NanoCAGE sequencing libraries were prepared according to the protocol described by Poulain et al., Methods in Molecular Biology, 2017 (doi: 10.1007/978-1-4939-6716-2_4).

tag: cell culture type

value: Biochip

tag: cell differentation stage

value: Hepato-Like Cells (HLC)

tag: cell selection method

value: Carboxypeptidase M positive (CPM+) cells sorting

tag: nanocage template-switching oligo barcode sequence

value: CACTGA

tag: nanocage template-switching oligo barcode number


title: RNAseq 5TGM1 bortezomib resistant replicate-3

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

description:
5TGM1.BR.rep3
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.

data_processing:
Reads were mapped against the mouse (mm10) or human (hg19) reference genome using the STAR spliced alignment algorithm version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.tsv: Tab-delimited file of gene expression.

source_name: Cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice

growth_protocol: All cell lines grown in IMDM media with 20% fetal bovine serum + penicillin-streptomycin + L-glutamine + sodium pyruvate + HEPES. 5TGM1.BR cells cultured in 20nM bortezomib, with media changed twice weekly. 8226.BR cells cultured in 10nM bortezomib, with media changed twice weekly. 8226.CR cells cultured in 10nM carfilzomib, with media changed twice weekly.

extract_protocol:
RNA was extracted from 1x10^7 cells using the Qiagen RNeasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cell lines were removed from drug five days before RNA extraction.

tag: cell line

value: Murine myeloma cell line

tag: drug resistance

value: Bortezomib


title: Ovol1_null_Untreated

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 2.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across all the libraries.
Genome_build: mm10

molecule: polyA RNA

source_name: Mouse back skin

growth_protocol: All mouse lines were maintained and bred following the procedures that conform with and have been approved by the UC Irvine Institutional Animal Care and Use Committee (IACUC).

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

treatment_protocol: Mice at 7~8 weeks of age received one dose of 62.5 mg 5% IMQ cream (Perrigo) on shaved backs.

tag: strain

value: untreated

tag: cell barcode suffix for aggr file


title: BIOCHIP_CPM_POSTIVE_HLCs_rep8

value: CACGAT


title: T19: Colon tumor from patient 19

value: FFPE tumor


title: Control_IMQ

value: IMQ


title: K25 1h rep1

source_name: CGNs_medium aspirated_K25 + 0% FCS, 1h, replicate 1

tag: age


title: K25 1h rep2

source_name: CGNs_medium aspirated_K25 + 0% FCS, 1h, replicate 2

tag: tissue


title: K25 30' rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) at 0.5h following incubation with a serum-free medium supplemented with 25 mm KCl (K25).

source_name: CGNs_medium aspirated_K25 + 0% FCS, 0.5h, replicate 4

tag: cell type


title: RNAseq 5TGM1 bortezomib resistant replicate-2

description:
5TGM1.BR.rep2
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: T17: Colon tumor from patient 17

tag: disease state


title: RNAseq 5TGM1 bortezomib resistant replicate-1

description:
5TGM1.BR.rep1
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice and then cultured in bortezomib until resistant.
Experiment performed on cell lines less than 1 month from resuscitation.


title: K25 30' rep1

source_name: CGNs_medium aspirated_K25 + 0% FCS, 0.5h, replicate 1


title: K25 30' rep3

source_name: CGNs_medium aspirated_K25 + 0% FCS, 0.5h, replicate 3


title: K25 30' rep2

source_name: CGNs_medium aspirated_K25 + 0% FCS, 0.5h, replicate 2


title: Control_Untreated

tag: treatment


title: T38: Colon tumor from patient 38


title: K25 1h rep3

source_name: CGNs_medium aspirated_K25 + 0% FCS, 1h, replicate 3


title: BIOCHIP_CPM_POSTIVE_HLCs_rep6

value: ACAGAT


title: RNAseq 5TGM1 wild type drug naïve replicate-3

description:
5TGM1.wt.rep3
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice.
Experiment performed on cell lines less than 1 month from resuscitation.

value: Naive


title: Ovol1_null_IMQ


title: T21: Colon tumor from patient 21


title: BIOCHIP_CPM_POSTIVE_HLCs_rep5

value: TATAGC


title: RNAseq 5TGM1 wild type drug naïve replicate-2

description:
5TGM1.wt.rep2
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice.
Experiment performed on cell lines less than 1 month from resuscitation.


title: T15: Colon tumor from patient 15


title: Hepatocyte Double KO rep2

city: La Jolla

first: Kaisa

last: Hanley

state: California

address: 9500 Gilman Drive MC 0864

institute: University of California San Diego

data_processing:
Raw data quality control were performed using fastqc
Sequenced reads were mapped to mm9 using star
Fragments Per Kilobase Million(FPKM) were calculated using cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: csv files with FPKM values for each sample and significant test results between two samples

source_name: liver

extract_protocol:
RNA was extracted from samples of whole liver using RNeasy Microarray Tissue Mini Kit (73304, Qiagen) or from isolated hepatocytes using RNeasy Plus Micro Kit (74034)
Libraries were prepared using Illumina TruSeq v2 kit according to manufacturer’s instructions

value: isolated hepatocyte


title: BIOCHIP_CPM_POSTIVE_HLCs_rep7

value: ATCGTG


title: T13: Colon tumor from patient 13

value: Colon cancer


title: Hepatocyte Double KO rep1


title: db-db-5

city: Beijing

first: huimin

last: liu

state: Beijing

address: 38 Xueyuan Rd , Haidian District

department: Peking University Health Science Center

country: China

institute: Peking University

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.
When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value).
Genome_build: MmiRBase v21

source_name: male leptin receptor-deficient db/db mice

growth_protocol: The submandibular glands of mice are preserved at -80 degrees Celsius.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:1) 3'-adaptor ligation;2) 5'-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.

value: 16-week-old male

value: submandibular gland


title: BIOCHIP_CPM_POSTIVE_HLCs_rep3

value: Biochip

value: Hepato-Like Cells (HLC)

value: GAGCGT


title: BIOCHIP_CPM_POSTIVE_HLCs_rep2

value: Carboxypeptidase M positive (CPM+) cells sorting

value: CTGAGC


title: T12: Colon tumor from patient 12


title: CTCF knockout biological replicate 3 ATAC-seq

source_name: Isolated cardiac myocytes

value: CTCF knockout


title: Hepatocyte Shp2 KO rep3


title: T11: Colon tumor from patient 11


title: B6-12mo-M-spleen-218_GT17-14910_ACAGTG_S18

tag: Sex

value: male

value: spleen


title: BIOCHIP_CPM_POSTIVE_HLCs_rep1

value: CACTCT


title: T16: Colon tumor from patient 16

value: FFPE tumor


title: T10: Colon tumor from patient 10


title: db-db-3


title: db-db-4


title: Hepatocyte Shp2 KO rep1

tag: genotype


title: T09: Colon tumor from patient 09


title: db-db-1


title: Hepatocyte Double KO rep3


title: BIOCHIP_NON_SORTED_HLCs_rep4

value: GTATGA


title: T18: Colon tumor from patient 18


title: Hepatocyte IkkB KO rep3

value: Alb-Cre+;IkkBf/f


title: RNAseq 5TGM1 wild type drug naïve replicate-1

description:
5TGM1.wt.rep1
Murine myeloma cell line arising from serial passage of spontaneous plasma cell myeloma developed in C57Bl/KaLwRij mice.
Experiment performed on cell lines less than 1 month from resuscitation.

value: Murine myeloma cell line

value: Naive


title: BIOCHIP_CPM_POSTIVE_HLCs_rep4

value: GCTGCA


title: BIOCHIP_NON_SORTED_HLCs_rep3

value: GCTCTC


title: db-m-4

source_name: WT

value: 16-week-old male

value: submandibular gland


title: T08: Colon tumor from patient 08

value: Colon cancer


title: Hepatocyte IkkB KO rep2

value: isolated hepatocyte


title: db-m-3


title: Hepatocyte Shp2 KO rep2


title: BIOCHIP_NON_SORTED_HLCs_rep2

value: Biochip

value: Hepato-Like Cells (HLC)

value: GAGATA


title: T07: Colon tumor from patient 07


title: db-m-2


title: db-m-1


title: T06: Colon tumor from patient 06


title: T05: Colon tumor from patient 05


title: Hepatocyte WT rep2

value: Wild type


title: T04: Colon tumor from patient 04


title: Hepatocyte WT rep3


title: pooled RNA from 1089, 1092, 1094, 1097 [OSA8]

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
quantify miRNA read counts with sRNAnalyzer
Genome_build: small RNA Databases provided on sRNAnalyzer website (http://srnanalyzer.systemsbiology.net/)
Supplementary_files_format_and_content: The processed.fa files contain reads went through adapter trimming, low-quality filtering and identical read counting and collapsing. These processed files were generated by sRNAnalyzer.

extract_protocol:
Fresh venous blood 20 ml was collected from each participant on awakening, and immediately transferred to a tube containing 3.2% sodium citrate (1:10 dilution). PBMCs were isolated by Ficoll-Hypaque gradient centrifugation (HISTOPAQUE®-119, Sigma-Aldrich, Inc.,USA), and then stored in RNAlater (Ambion Inc., USA) at -80°C until RNA isolation. A miRNeasy Mini Kit column-based system (Qiagen, Valencia, CA, USA) was used for isolation of total RNA, and treated with DNase according to the manufacture protocol. RNA samples were run on a RNA 6000 Nano Gel System (Agilent Technologies Inc., CA, USA) using an Agilent 2100 Bioanalyzer (Agilent) to determine the quality of RNA. Only samples with A260/A280 ratios of 1.9 to 2.1 and RNA Integrity Number >= 8 were used for further analysis.
The pooled RNA libraries were subject to NGS assay to determine miRNA expression profile. Illumina MiSeq platform was adopted for the profiling job. The RNA libraries were first prepared in accordance with TruSeq Small RNA Sample Preparation protocol (Illumina) followed by sequencing with MiSeq platform.

tag: subject status

value: mixed from 4 OSA patients

value: PBMC


title: pooled RNA from 1099, 1100, 1012, and 1031 [OSA9]


title: Thymic DC TBI.d4_rep2

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

data_processing:
Combined sequincing runs from different flow cells. Filtered using Illumina's base call quality threshold
Align to mm10 using STAR v2.5.2a (2-pass mapping)
Generate counts for each gene using Subread featureCounts v1.6.0
Reads were transformed into counts per million (CPM) using edgeR, then normalised by the method of trimmed mean of M-values (TMM) (Robinson and Oshlack 2010) using a scaling factor for the library sizes.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Thymic dendritic cells

extract_protocol:
Mouse thymi were harvested, enzymatically digested (DNase and Collagenase II), and pooled. RNA was harvested from FACS purified DCs (CD45+ MHC11+ CD11c+) using Qiagen RNeasy Micro Kit and quanitifed using Aligent Tapestation.
RNA libraries were prepared for sequencing using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and standard Illumina protocols

treatment_protocol: Mice underwent total body irradiation (TBI) 4 days before harvest for TBI.d7 thymi.

value: Dendritic cells

value: Thymus

value: 6-8 weeks

value: 4 days post TBI


title: Liver Double KO rep3

value: whole liver


title: T03: Colon tumor from patient 03

value: FFPE tumor


title: pooled RNA from 840 and 842 [OSA2]

value: mixed from 2 OSA patients


title: Liver Double KO rep2


title: Thymic DC untreated_rep2

value: untreated


title: pooled RNA from 815 and 836 [OSA1]


title: T01: Colon tumor from patient 01


title: T02: Colon tumor from patient 02


title: Liver Double KO rep1


title: B60_control RNA_senescence

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

description:
Test Group 3
flushed from huNSG femur

data_processing: Gene expression analysis was performed using Qiagen PCR Array Data Analysis Software and normalized to five housekeeping genes provided within the array (http://pcrdataanalysis.sabiosciences.com/ pcr/arrayanalysis.php). Hierarchical clustering and heat map generation were performed with Heatmapper software (http://www.heatmapper.ca/), as described (Babicki et al., 2016).

label: SYBR green

source_name: control RNA

label_protocol: RNA was reverse-transcribed with the RT2 First Strand Kit (Qiagen). 20 ng of cDNA was used for qPCR with the array kit, and was run on the 7300 Real Time PCR System (Life Technologies) with the cycling profile (40 cycles): 94°C for 15 secs and 60°C for 45 secs.

growth_protocol: Mobilized peripheral blood was collected from aged donors and were cultured for in RPMI 1640 supplemented with 10% FCS, 2 mM glutamine and 0.5 µM β-mercaptoethanol (β-ME) (R10 media).

extract_protocol: RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen, Germantown, MD).  Quality and concentration of RNA were determined with the Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific).

treatment_protocol: Cells were transfected with the listed microRNA(s) and subsequently used to humanize female NSG mice. Cells were recovered from the mice 14-15 weeks following humanization by flushing the femurs, and murine cells depleted using a mouse cell depletion kit.

value: Bone Marrow Mononuclear Cells

tag: human cell source


title: BIOCHIP_NON_SORTED_HLCs_rep1

tag: cell culture type

tag: cell differentation stage

value: CGATGA


title: Thymic DC untreated_rep1


title: pooled RNA from 1086, 1096, OH-DS-14, OH-DS-18 [0D]

source_name: PBMC_healthy donors

value: mixed from 4 healthy donors


title: Liver Shp2 KO rep3


title: B46_control RNA_senescence

description:
Test Group 3
flushed from huNSG femur

value: Mobilized peripheral blood was collected from aged donors


title: L1KO3

city: PHILADELPHIA

first: David

middle: Lynn

last: Wiest

state: PA

address: 333 COTTMAN AVENUE, REIMANN BUILDING, LAB  R364

department: Nuclear Dynamics and Cancer Program

institute: FOX CHASE CANCER CENTER

data_processing:
Data was aligned to Ensembl GRCm38 reference genome using Tophat2.
htseq-count was used to quantify abundances, using gene_name as GTF attribute
Counts from 6 samples were combined into count matrix file
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: MS Excel 2007+ with two header rows - Matrix table with raw gene counts for every gene and every sample

source_name: CD4-CD8-CD44-CD25+ DN3 (Cre+Rpl22l1f/f)

growth_protocol: Samples were processed immediately upon explant. No culture occurred.

extract_protocol: Samples were lysed in Trizol folowing which total RNA was isolated and processed as previously described (Miyazaki et al., 2017).

value: mix of C57BL/6 and 129

value: adult thymus

value: 6-8wks of age

value: L1 KO

value: primary thymocyte - DN3


title: pooled RNA from H09-69 and C81 [0A]

value: mixed from 2 healthy donors

value: PBMC


title: Hepatocyte WT rep1

value: Wild type

value: isolated hepatocyte


title: L1KO2


title: Liver Shp2 KO rep2

value: whole liver


title: B55_miR-combo_senescence

description:
Test Group 2
flushed from huNSG femur

source_name: miR-combo


title: Liver Shp2 KO rep1


title: L1KO1


title: B41_miR-combo_senescence

description:
Test Group 2
flushed from huNSG femur


title: Thymic DC TBI.d4_rep3

value: Dendritic cells

value: Thymus

value: 6-8 weeks

value: 4 days post TBI


title: Colon tumor from patient T09

description: Sequenced using MiSeq platform to profile mutations in tumor samples

data_processing:
Library strategy: Targeted Next-Generation DNA Sequencing
The Illumina MiSeq Reporter software (MSR, v2.6, Illumina) was used for initial base-calling and for generating FASTQ files.
Raw sequencing reads were trimmed for adaptor sequence, and masked of low-quality sequences using the MiSeq Reporter software (MSR, v2.6, Illumina). Alignment to human reference genome GRCh37/hg19 was executed with BWA-MEM aligner algorithm on MiSeq Reporter.
Variant calling was executed using two algorithms: MuTect2 (v2.2) from the GATK platform (Broad Institute, Cambridge, MA, USA) and the Illumina Somatic Variant Caller (integrated in the MiSeq Reporter, v2.6).
Variants on VCF files were annotated with SnpEff (v4.3) plus dbNSFP (v2.9.3) for downstream functional analysis.
Low quality calls were discarded to minimize false positive events: mapping quality below 30,TLOD <9 and read depth below 15x. Synonymous and germline variants were removed, along with polymorphisms having a worldwide population frequency above 1%, as reported in databases ExAC and 1000 Genomes Project.
Genome_build: Homo sapiens GRCh37/hg19
Supplementary_files_format_and_content: VCFs are tab-delimited text files including all detected DNA variants (rows) by sequencing in every sample. For each variant/row, functional information was subsequently annotated in column “INFO” using SnpEff (v4.3) plus dbNSFP (v2.9.3) databases.

source_name: FFPE tumor

extract_protocol:
DNA was extracted from each formalin-fixed paraffin-embedded (FFPE) tumor samples using the QIAmp DNA FFPE kit (Qiagen, Hilden, Germany) and then quantified using Qubit fluorometer assay (Thermo Fisher Scientific, MA, USA)
Enriched libraries were prepared from 50 ng of DNA per tumor sample using the SMARTer ThruPLEX DNA-seq Library Preparation kit (TaKaRa, Japan) and a predesigned gene capture pool of IDT xGen Lockdown probes (IDT, Coralville, Iowa, USA). Paired-end sequencing runs were performed on a MiSeq platform (Illumina, San Diego, CA, USA) following a protocol with 2x130 bp reads.

tag: disease stage

value: Colon cancer stage II

value: FFPE tumor


title: Liver IkkB KO rep3

value: Alb-Cre+;IkkBf/f


title: Thymic DC TBI.d4_rep1


title: B6-12mo-F-spleen-207_GT17-14908_TTAGGC_S24

data_processing:
Libraries were pooled and sequenced 75 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 40 million reads per sample.
Single-end RNA-seq reads were aligned to the mouse genome (mm10) with Bowtie 2 and counts were generated with RSEM.
To normalize the raw counts count-per-million (cpm) function from edgeR package is used and the genes that are log(cpm)<1 and expressed less than 2 samples were excluded from rest of the analyses.
For differential analysis pipeline, however, raw counts are used with the default options of edgeR package, and via TMM normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Count Files for B6/NZO

extract_protocol:
Data is obtained from spleen and peripheral blood lymphocytes (PBLs) of C57BL/6J and NZO/HILtJ mouse strains, hereafter B6 and NZO, respectively, at ages 3, 12, and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq, remaining cells collected for other RNA preparations.
30 ng of total RNA, with the addition of 6 µl ERCC Spike-In Control Mix 1 (Ambion Thermo Fisher) diluted 1:10,000, was used for library construction. Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 assay on the TapeStation (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturer's instructions.

value: female

value: spleen


title: L1WT3

source_name: CD4-CD8-CD44-CD25+ DN3 (Cre-Rpl22l1f/f)

value: mix of C57BL/6 and 129

value: adult thymus

value: 6-8wks of age

value: WT


title: Liver IkkB KO rep2


title: B50_miR-619_senescence

description:
Test Group 1
flushed from huNSG femur

value: Bone Marrow Mononuclear Cells

value: Mobilized peripheral blood was collected from aged donors


title: L1WT2

value: primary thymocyte - DN3


title: pooled RNA from H09-73 and H09-40 [0B]

value: mixed from 2 healthy donors

value: PBMC


title: Colon tumor from patient T96


title: Colon tumor from patient T95


title: B31_miR-619_senescence

description:
Test Group 1
flushed from huNSG femur


title: Liver IkkB KO rep1

value: whole liver


title: Colon tumor from patient T94


title: Liver WT rep3

value: Wild type


title: L1WT1


title: E09_no RNA_senescence

description:
Control Group
flushed from huNSG femur

source_name: no RNA


title: D29_no RNA_senescence

description:
Control Group
flushed from huNSG femur


title: D15_no RNA_senescence

description:
Control Group
flushed from huNSG femur


title: Liver WT rep2


title: Colon tumor from patient T89


title: Mesenchymal Anti-Ly6G 3

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

description:
Mesenchymal_Normalised_Counts.txt.gz
M13

data_processing:
Adapter trim with cutadapt 1.5
Align with Star 2.2.2a
Merge lane level bam files with samtools 1.8
Assess expected counts per feature with RSEM 1.3.0
Normalise and call differentially expressed genes with DESeq2
Genome_build: GRCm38-r86
Supplementary_files_format_and_content: Normalised Expression levels Grouped by Epithelial or Mesenchymal type in a tab delimited text file

extract_protocol:
Lungs were minced manually and then digested for 30 min at 37 degrees in a HBSS digestion solution containing DNase I (Sigma-Aldrich) and Liberase TM and TH (Roche Diagnostics). Samples were then washed, passed through a 100 um filter and incubated with Red Blood Cell Lysis buffer (Miltenyi Biotec) for 3-5 min. After a wash with MACS buffer (0.5% BSA and 250 mM EDTA in PBS), samples were passed through a 40 um filter and a 20 um strainer-capped flow cytometry tube to generate a single cell suspension. Samples were stained with a CD45, CD31, Ter119 and an EpCAM antibody.  CD45-CD45-Ter119-EpCAM+ and D45-CD45-Ter119-EpCAM- cells were isolated via FACS.
Total RNA was isolated using the miRNeasy Micro Kit (Qiagen, cat# 217084), optimised for high quality RNA extraction from samples with low cell numbers, according to the manufacturer’s instructions. Library generation was performed using the KAPA RNA HyperPrep with RiboErase (Roche).

treatment_protocol: Balb/c female mice 8 weeks old were sham-irradiated, irradiated or irradiated plus treated with an anti-Ly6G neutrophil depletion antibody. Lungs were collected 7 days later

value: Lung

value: Irradiation + anti-Ly6G depletion antibody


title: Mesenchymal Anti-Ly6G 4

description:
Mesenchymal_Normalised_Counts.txt.gz
M14


title: Liver WT rep1


title: Mesenchymal Anti-Ly6G 2

description:
Mesenchymal_Normalised_Counts.txt.gz
M12


title: D01_no RNA_senescence

description:
Control Group
flushed from huNSG femur


title: Mesenchymal Anti-Ly6G 1

description:
Mesenchymal_Normalised_Counts.txt.gz
M11


title: Colon tumor from patient T88

value: Colon cancer stage II

value: FFPE tumor


title: Colon tumor from patient T86


title: Colon tumor from patient T84


title: Mesenchymal Irradiation 3

description:
Mesenchymal_Normalised_Counts.txt.gz
M9

value: Irradiation + IgG control antibody


title: Mesenchymal Irradiation 4

description:
Mesenchymal_Normalised_Counts.txt.gz
M10


title: Colon tumor from patient T80


title: Mesenchymal Irradiation 2

description:
Mesenchymal_Normalised_Counts.txt.gz
M8


title: Colon tumor from patient T77


title: US23-0-3

city: Ithaca

first: Juliana

last: Gonzalez-Tobon

address: 236 Tower Rd

institute: Cornell University

description: Small non-coding RNAs

data_processing:
Adapter sequences were removed and the raw reads were trimmed to eliminate low quality bases and to select for only those between 18 and 45 bp using cutadapt v. 1.12
Quality was assessed using fastqc v. 0.11.2
rRNA and tRNA sequences were removed by aligning the reads to databases of known rRNAs and tRNAs, using Bowtie v. 1.1.2
The remaining reads were  aligned to the P. infestans genome also using Bowtie
The resulting sam files were used to calculate read counts using Htseq v. 0.6.1p1
Genome_build: Phytophtora infestans T30-4 genome ASM14294v1
Supplementary_files_format_and_content: txt files contain read counts of each strain-treatment-rep using Htseq

organism: Phytophthora infestans

source_name: Mycelium

extract_protocol:
Total RNA was extracted from the mycelium grown under each of the two treatment conditions using the RNeasy Plant Mini Kit of Qiagen.
Small RNA libraries were created following the protocol of Vargas-Asencio et al., (2017) (https://doi.org/10.1016/j.virusres.2016.10.001).

value: 0 ug/ml of mefenoxam

tag: replicate


title: US23-100-1

description: Small non-coding RNAs

value: 100 ug/ml of mefenoxam


title: US23-100-3

description: Small non-coding RNAs


title: Mesenchymal Control4

description:
Mesenchymal_Normalised_Counts.txt.gz
M6

value: Sham-irradiation + IgG control antibody


title: US23-100-2

description: Small non-coding RNAs


title: US23-0-2

description: Small non-coding RNAs


title: Colon tumor from patient T76


title: Colon tumor from patient T92


title: Mesenchymal Irradiation 1

description:
Mesenchymal_Normalised_Counts.txt.gz
M7


title: US23-0-1

description: Small non-coding RNAs


title: Colon tumor from patient T66


title: Colon tumor from patient T71


title: Mesenchymal Control2

description:
Mesenchymal_Normalised_Counts.txt.gz
M4


title: Mesenchymal Control1

description:
Mesenchymal_Normalised_Counts.txt.gz
M3


title: Mesenchymal Control3

description:
Mesenchymal_Normalised_Counts.txt.gz
M5


title: US22-100-2

description: Small non-coding RNAs


title: US22-100-1

description: Small non-coding RNAs


title: Colon tumor from patient T83


title: Colon tumor from patient T55


title: US22-0-2

description: Small non-coding RNAs


title: Colon tumor from patient T52


title: Epithelial Anti-Ly6G 4

description:
Epithelial_Normalised_Counts.txt.gz
E14


title: RC1-100-3

description: Small non-coding RNAs


title: Epithelial Anti-Ly6G 1

description:
Epithelial_Normalised_Counts.txt.gz
E11


title: Epithelial Irradiation 4

description:
Epithelial_Normalised_Counts.txt.gz
E10


title: Colon tumor from patient T47


title: Colon tumor from patient T49


title: US22-0-1

description: Small non-coding RNAs


title: RC1-100-2

description: Small non-coding RNAs


title: Epithelial Anti-Ly6G 2

description:
Epithelial_Normalised_Counts.txt.gz
E12


title: Colon tumor from patient T46


title: Colon tumor from patient T42


title: RC1-100-1

description: Small non-coding RNAs


title: Epithelial Irradiation 2

description:
Epithelial_Normalised_Counts.txt.gz
E8


title: RC1-0-3

description: Small non-coding RNAs


title: Colon tumor from patient T63


title: Colon tumor from patient T40


title: US22-100-3

description: Small non-coding RNAs


title: Epithelial Irradiation 1

description:
Epithelial_Normalised_Counts.txt.gz
E7


title: RC1-0-1

description: Small non-coding RNAs


title: RC1-0-2

description: Small non-coding RNAs


title: Epithelial Control4

description:
Epithelial_Normalised_Counts.txt.gz
E6


title: Colon tumor from patient T39


title: Epithelial Anti-Ly6G 3

description:
Epithelial_Normalised_Counts.txt.gz
E13


title: Colon tumor from patient T38


title: Colon tumor from patient T51


title: Epithelial Control3

description:
Epithelial_Normalised_Counts.txt.gz
E5


title: Hepatocyte IkkB KO rep1

value: Alb-Cre+;IkkBf/f

value: isolated hepatocyte


title: Colon tumor from patient T33


title: Epithelial Control2

description:
Epithelial_Normalised_Counts.txt.gz
E4


title: empty vector rIIS Heat Shock Rep 2

city: New Delhi

first: Neeraj

last: Kumar

state: Delhi

address: Ansari Nagar

country: India

institute: All India Institute of Medical Sciences, New Delhi

data_processing:
Imaging, base calling and quality scoring were done as per standard manufacturer’s guidelines (Illumina Inc.).
The demultiplexing and conversion of BCL file format reads to FASTQ file format was done with the Illumina-supported CASAVA v1.8.2 software package.
Read counts were then aligned to the reference genome (WBcel 235) and their normalized abundance were calculated as Reads Per Kilobase Million (RPKM) using QIAGEN CLC Genomics Workbench v12.0.3.
Genes fold change was calculated among samples based on negative binomial Generalized Linear Model (GLM) which corrects for differences in library size between samples and the effects of cofounding factors.
Genes with absolute fold change of at least 1.5 and standard-p value below 0.05 were considered as differentially expressed.
Genome_build: WBcel 235
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were grown on nematode growth medium (NGM) supplemented with 100 µg/ml ampicillin and 2mM IPTG.

extract_protocol:
Worms grown on empty vector or transcription factors RNAi plates. RNA was harvested using Trizol reagent. The cDNA libraries were constructed with TruSeq RNA Library Prep Kit v2 (Illumina Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stains were kept on empty vector and transcription specific RNAi clones

tag: Stage

tag: temerature

value: 20 ˚C+33 ˚C for 2 hrs


title: Epithelial Control1

description:
Epithelial_Normalised_Counts.txt.gz
E3


title: US22-0-3

description: Small non-coding RNAs

tag: strain


title: Colon tumor from patient T27


title: VIP6_F

city: Melbourne

first: Thi

middle: Thanh Mai

last: Truong

state: VIC

address: Gate 12 Royal Parade, Parkville

department: BioSciences

institute: The University of Melbourne

description:
DESeq2_VIT_In_vivo_Placenta_vs._VIT_Control_Placenta.txt
DESeq2_VIT_In_vivo_Placenta_vs._VIT_AOX_Placenta.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of  raw FASTQ data files was assessed with FastQC
Trim Galore! was used to trim the 13 bp of Illumina standard adapters from the ends of reads.
Reads were aligned to the UCSC GRCm38.98/mm10 reference genome with RNA STAR
featureCounts was used to measure gene expression as counted reads
DESeq2 was used to identify differentially expressed genes (DEGs) and their fold changes from count data.
Genome_build: UCSC GRCm38.98/mm10
Supplementary_files_format_and_content: DESeq2 txt/tabular files contain Ensembl Gene IDs (ENSG), mean normalised counts, log2(fold change), standard error of the log2(fold change), Wald statistic, p-value, and p-value adjusted with the Benjamini-Hochberg procedure which controls false discovery rate (FDR), for each gene

source_name: Murine 14.5 Placenta

growth_protocol: Embryos were collected from superovulated female mice and cultured in G series media supplemented with or without antioxidants. Embryos were also collected from superovulated female mice and cultured in G series media then vitrified and thawed with or without antioxidants. Alternatively, in vivo derived embryos were flushed from uteri on day 4. D4 blastocysts were transferred to the uteri of pseudopregnant female mice and allowed to grow for a further 10 days. Fetuses and placentas were collect on E14.5 and tissues harvested for RNA extraction

extract_protocol:
Fetuses and accompanying placentae were removed from uterine horns, flash frozen on dry ice, and RNA was harvested using a Qiagen RNeasy Plus Mini Kit. RNA was analysed on the Illumina HiSeq 2500 system at the Australian Genome Research Facility (AGRF)  with 1 ug of total RNA as input for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos (and resultant fetal tissues designated treatment) were cultured in G series media supplemenented with a combination of antioxidants (alpha-lipoic acid, N-acetly-L-cysteine and L-carnitine) for the duration of the culture period. Control embryos were cultured in G series media containing no antioxidants. For vitrification groups embryos were collected from superovulated female mice and cultured in G series media then vitrified and thawed with or without antioxidants.

value: Placenta

value: C57BL/6 x CBA F1

tag: developmental stage

value: In vivo developed

value: Female


title: Colon tumor from patient T24

city: Barcelona

first: Sara

last: Lahoz

address: Carrer del Rosselló, 149

institute: Institut D'Investigacions Sanitàries August Pi i Sunyer


title: 50 days cortical organoid_HRP2_26 hours_n=3

city: Atlanta

first: Adriana

last: Harbuzariu

state: Georgia

address: 720 Westiview Dr SW, HG Room 354

department: MBI

institute: Morehouse School of Medicine

description: Organoids containing neurons, astrocytes, microglia were used

hyb_protocol: Hybridization was performed by creating first a Master Mix (by adding Hybridization buffer to the Reporter CodeSet tube). Then, each sample was added to the Master Mix, followed by Capture ProbeSet. The tubes were then placed immediately in the thermal cycler for at least 16 hours. After that, the samples were taken to nCounter Prep Station and scanend.

scan_protocol: After hybridization, the excess probes were removed, and the target-probe complexes were aligned on the imaging surface. The samples were then scanned with an automated fluorescent microscope and labeled barcodes were counted. Housekeeping genes were included in this format.

data_processing: The raw data was supplied by NanoString and showed here in a separate sheet that includes the control and housekeeping genes genes. To process the data, we used nCounter software.

label: biotin

source_name: brain cortical organoids 50 days culture

label_protocol: RNA was directly tagged with a capture probe and a reporter probe that are specific for Immunology gene pannel with more than 500 target genes, creating a unique target-probe complex.

growth_protocol: After iPSC dissociation using Accutase, cells were seeded in low attachment plates using ROCK inhibitor to form embryoid bodies (EB). After 6 days, EB were grow in induction medium and then expanded in Matrigel droplets at day 13. On day 17, the Matrigel matrix was mechanically removed and organoids were cultured in maturation medium until harvest at 50 days. All the materials used were purchased from Stem Cell Technologies.

extract_protocol: Cortical organoids grown for 50 days in culture and treated with HRP2+/- NRG1 were collected and RNA was extracted using PARIS kit (Thermo Fisher Scientific) as per manufacturer’s recommendations. The RNA concentration was determined by reading the absorption at 260/280 nm using a NanoDrop Spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Organoids were treated with 4.2 μg/ml HRP2 for 26 hours. In some experiments, after 8 hours of HRP2 treatment, NRG1 was added at 100ng/m for 18 hours.

value: brain cortical organoids

tag: age

value: 50 days of culture

value: HRP2 for 26 hours


title: 50 days cortical organoid_HRP2+NRG1_26 hours_n=3

tag: tissue

value: HRP2+NRG1 for 26 hours


title: Colon tumor from patient T21

value: Colon cancer stage II


title: VIP5_F


title: 50 days cortical organoid_Basal untreated_26 hours_n=3

value: untreated


title: Control (Replicate 2)

city: Boston

first: Ksenia

middle: S

last: Anufrieva

state: MA

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

data_processing:
Rna-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic (v. 0.35).
Trimmed RNAseq reads were quantified against Homo Sapiens GRCh38 genome annotation at the transcript level using Salmon (v. 1.4). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
For alternative splicing analysis trimmed RNAseq reads were mapped to Homo Sapiens GRCh38 genome annotation using STAR. The STAR software (v. 2.7.6) was used in a 2-pass mode, where the first pass was used to identify non-annotated junctions in the input data. The new genome index was generated using annotated junctions and the common set of novel junctions which were found during first pass mode. During the second pass we re-run all the samples with this new genome.
To compare splicing events between samples, we ran rMATS splicing tool using the following parameters recommended by the developers: -c 0.0001 and -novel SS1 (multi-align reads are ignored as a default). Minor splicing differences were filtered out by thresholds of FDR < 0.05 and IncLevelDifference value > 5%.
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data files format and content: tab-delimited tsv files include TPM values for every gene and every sample

source_name: GBM neurospheres

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. Glioblastoma neurospheres were cultivated in DMEM/F12 (Sigma) medium containing 2% MACS NeuroBrew-21 (Miltenyi Biotec) supplement (% vol.), 1% Penicillin-Streptomycin solution (ThermoFisher) (% vol.), 20 ng/ml basic fibroblast growth factor (bFGF (Sigma)), and 20 ng/ml epidermal growth factor (EGF (Sigma)). bFGF and EGF were added twice a week and the culture medium was changed every 5-10 days. Spheres were dissociated using StemPro Accutase (ThermoFisher).

extract_protocol:
RNA was isolated by RNeasy mini kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with lentiviruses encoding RPL22L1a, RPL22L1b or an empty vector. On the day of transduction spheres were dissociated into single cells with StemPro Accutase (ThermoFisher) and incubated with viral supernatants for 24 hr in the presence of 8 μg/ml polybrene (EMD Millipore). Two days after infection, transduced cells were selected with 1 mg/ml puromycin (Sigma) for 3 days.

tag: patient

value: Brain

tag: disease

value: GBM

value: GBM neurospheres overexpressing empty vector (pCDH-EF1-MSC-IRES-Puro).


title: T3: FSS rep3

city: Shanghai

first: Yu

last: Jin

state: State...

address: 639 Zhizaoju Road

institute: Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2-2.1.0
Reads Counts were calculated using htseq-count , Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples
Supplementary_files_format_and_content: tab-delimited text files include counts values for all Samples

source_name: cartilage

growth_protocol: Chondrocytes were obtained from the articular cartilage of 3-week-old male C57BL/6J mice. Specifically, obtained cartilage was digested in 0.25% trypsin-EDTA in 37°C for 0.5 h. After being cut into approximately 1 mm3 small pieces, the cartilage was incubated with 0.2% collagenase II at 37 °C for 3 h. Finally, cell suspension was collected and cultured in DMEM/F12 (Gibco, USA) containing fetal bovine serum (Gibco, BRL) and 1% penicillin-streptomycin. Passage 1-3 from the primary cells were used for further experiments in this study.

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Chondrocytes were seeded onto the culture slips at a density of 2 × 105 cells and put into a parallel-plate flow system. The system is a six-chamber laminar flow device which includes a total of six 75 x 25 x 1 mm culture slips. After being exposed to 20 dyne/cm2 FSS treatment for 2 h, the cells were collected for further experiments.

value: cartilage

tag: cell type

value: primary chondrocytes

tag: treatment

value: high shear stress treatment


title: VIP4_F

tag: Sex


title: RPL22L1b  (Replicate 2)

value: GBM neurospheres overexpressing RPL22L1b


title: Colon tumor from patient T20

value: FFPE tumor


title: T2: FSS rep2


title: Colon tumor from patient T18


title: N3: NC rep3


title: VIP3_M

value: Placenta

value: C57BL/6 x CBA F1

value: Male


title: RPL22L1b  (Replicate 1)


title: Colon tumor from patient T15


title: RPL22L1a (Replicate 2)

value: GBM neurospheres overexpressing RPL22L1a


title: Colon tumor from patient T13


title: empty vector Control Rep 1

value: 20 ˚C


title: N2: NC rep2


title: N1: NC rep1


title: VIP1_M

value: In vivo developed


title: VIP2_M


title: Colon tumor from patient T111


title: RPL22L1a (Replicate 1)


title: Fc-Control

data_processing:
To increase read quality before mapping RIP-Seq data were trimmed using Trimmomatic (v. 0.35).
Trimmed RNA-Seq reads were mapped against Homo Sapiens GRCh38 genome annotation using STAR (v. 2.7.6) according to recommendations from the STAR manual 2.4.0.1 with the following parameters: the maximum number of mismatches for paired reads was 4% of the read length, the maximum number of multiple alignments allowed for a read was 10, non-canonical junctions were removed, the minimum number of allowed splice overhangs was 8 for unannotated junctions and 1 for annotated junctions, the minimum intron length was 20, the maximum intron length was 1,000,000, and the number of “spurious” junctions was reduced.
Transript expression signal was quantified using RSEM.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files format and content: tab-delimited tsv files include TPM values for every gene and every sample

extract_protocol:
RPl22L1a or RPL22L1b protein-RNA complexes were purified from glioma spheres stably expressing Fc-RPl22L1a or Fc-RPL22L1b correspondingly with Magna RIP RNA-Binding Protein Immunoprecipitation Kit (EMD Millipore) according to the manufacturer’s protocol.  Ribosomal RNA was removed using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with lentiviruses encoding Fc-tagged RPL22L1a, RPL22L1b or a control protein. On the day of transduction spheres were dissociated into single cells with StemPro Accutase (ThermoFisher) and incubated with viral supernatants for 24 hr in the presence of 8 μg/ml polybrene (EMD Millipore). Two days after infection, transduced cells were selected with 1 mg/ml puromycin (Sigma) for 3 days.

value: GBM neurospheres overexpressing Fc-tagged control protein


title: VIF6_F

description:
DESeq2_VIT_In_vivo_Liver_vs._VIT_Control_Liver.txt
DESeq2_VIT_In_vivo_Liver_vs._VIT_AOX_Liver.txt

source_name: Murine 14.5 Liver

value: Liver

value: Female


title: Fc-RPL22L1b

value: Brain

value: GBM neurospheres overexpressing Fc-tagged RPL22L1b


title: VIF5_F


title: Colon tumor from patient T110

value: Colon cancer stage II


title: Saccharomyces cerevisiae_rep1_input

first: Zonggui

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

data_processing:
Library strategy: f5C-seq
Adapter sequences were trimmed by using cutadapt
Clean reads were mapped to genome by using STAR
Sitecalling was performed by custom script
Genome_build: S288C
Supplementary_files_format_and_content: tab-delimited files include mutation count, background coverage and mutation ratio for each modified sites.

organism: Saccharomyces cerevisiae

source_name: cell line

growth_protocol: Saccharomyces cerevisiae cell line was used in this study for f5C analysis. Saccharomyces cerevisiae monoclonal cell was selected from a plate and grown in 4 mL YPD medium (1% yeast extract, 2% peptone and 2% glucose) overnight at 28 °C with 160 rpm.

extract_protocol:
Total RNA was isolated from cell lines with TRIzol reagent. For poly(A)+ RNA purification, mRNA was extracted by two successive rounds of poly(A)+ purification using Oligo d(T)25 Magnetic Beads (NEB).
The untreated and pyridine borane treated samples were performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® following its manufacturer's instruction in parallel for Illumina sequencing.

treatment_protocol: Fragmented mRNA was treated with 0.9 M pyridine borane in NaOAc buffer (0.6 M, pH 5.2) at 37 ℃ for 24 h as the experimental sample.

tag: cell line

value: Saccharomyces cerevisiae


title: Control (Replicate 1)

value: GBM

value: GBM neurospheres overexpressing empty vector (pCDH-EF1-MSC-IRES-Puro).


title: T1: FSS rep1

value: cartilage

value: primary chondrocytes

value: high shear stress treatment


title: VIF4_F

value: C57BL/6 x CBA F1


title: Colon tumor from patient T109

value: FFPE tumor


title: Colon tumor from patient T108


title: Fc-RPL22L1a

value: GBM neurospheres overexpressing Fc-tagged RPL22L1a


title: VIF3_M

value: Male


title: S100A7_3

first: Haiqing

last: Bai

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human Alveolus Chip

growth_protocol: Primary human lung alveolar epithelial cells (Cell Biologics, H-6053) was seeded on 0.1% gelatin-coated 12-well plate according to manufacturer’s instruction; Alveolar Chip culture method is descirbed in associated manuscript

extract_protocol:
For RNA extraction, chips were removed from pods. An empty 200 µL filtered tip was inserted to top channel outlet and washed with 100 µL DPBS (+/+) into the top channel inlet to wash the apical channel. After collecting top channel washes, a new empty 200 µL filtered tip was inserted to top channel outlet and 100 ul RNase easy lysis buffer (Qiagen, #74034) was used to lyse epithelial cells by quickly pressing and releasing the micropipette plunger 3 times. Lysates were collected in a clean labelled 1.5 ml tube and stored at -80˚C for RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina HiSeq with 150-bp pair-ended reads

treatment_protocol: Human Alveolus Chips were transfected with plasmid DNA using the TransIT-X2 reagent (Mirus Bio). 3 ug of plasmid DNA (pcDNA3-EGFP as control or pcDNA3-S100A7GFP) and 6 ul TransIT-X2 reagent were constituted in 300 ul OPT-MEM before added to 3 ml chip flow medium. Then 1.5 ml of the solution was added to apical and basal inlet reservoirs and flew at 60 ul/h for 24 hours. Then apical channel was empties to reestablish ALI; basal channel was changed to normal flow medium for additional 24 hours before qPCR analysis.

value: primary alveolar epithelial cells

tag: time points

value: day 16

tag: % mechanical strain

tag: infection

value: No


title: Saccharomyces cerevisiae_rep2_experiment

value: pyridine borane for 24h


title: Saccharomyces cerevisiae_rep1_experiment


title: Colon tumor from patient T105

tag: disease stage


title: VIF2_M

value: Liver

value: In vivo developed


title: S100A7_2


title: Colon tumor from patient T104

value: Colon cancer stage II


title: VIF1_M


title: S100A7_1


title: Colon tumor from patient T103


title: VTP6_F

description:
DESeq2_VIT_In_vivo_Placenta_vs._VIT_AOX_Placenta.txt
DESeq2_VIT_Control_Placenta_vs._VIT_AOX_Placenta.txt

value: Placenta

value: Vitrification treated

value: Female


title: pooled RNA from 1067, 1084, 1041 and OH-DS-17 [OSA7]

tag: subject status

value: mixed from 4 OSA patients

value: PBMC


title: control_3


title: VTP5_F


title: Saccharomyces cerevisiae_rep2_input

value: Saccharomyces cerevisiae


title: Colon tumor from patient T101


title: Colon tumor from patient T100


title: VTP3_M

value: C57BL/6 x CBA F1


title: AlloHSC-iNKT (PBSC) replicate 3 [ATO_PBSC_4]

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced with 50bp single end reads on an Illumina HiSeq3000.
The reads were mapped with STAR 2.5.3a to the human genome (hg38).
The counts for each gene were obtained using --quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample

source_name: AlloHSC-iNKT (PBSC)

growth_protocol: All samples were isolated from human healthy donor peripheral nlood monunuclear cells provided by UCLA Virology Core

extract_protocol:
All samples were stored in RNA later stabilization solution and subsequently total RNA was extracted using RNA mini Kit (7326830, BioRad). cDNA was synthesized by using iScript cDNA Synthesis Kit (1708890, BioRad) and qPCR performed.
For RNA-sequencing, libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using Illumina TruSeq Stranded Total RNA Sample Prep kit and sequenced with 50bp single end reads on an Illumina HiSeq3000.

treatment_protocol: All samples were sorted using MACS microbeads or FACS flow sorting performed by UCLA FACS Core

value: human T cells

tag: cell subtype

value: AlloHSC-iNKT (PBSC)


title: control_1


title: VTP2_M

value: Male


title: AlloHSC-iNKT (PBSC) replicate 2 [ATO_PBSC_3]


title: Endo_H3N2_rep_3

treatment_protocol: Human Alveolus Chips were transfected with plasmid DNA using the TransIT-X2 reagent (Mirus Bio). 3 ug of plasmid DNA and 6 ul TransIT-X2 reagent were constituted in 300 ul OPT-MEM before added to 3 ml chip flow medium. Then 1.5 ml of the solution was added to apical and basal inlet reservoirs and flew at 60 ul/h for 24 hours. Then apical channel was empties to reestablish ALI; basal channel was changed to normal flow medium for additional 24 hours before qPCR analysis.

value: primary microvascuular endothelial cells


title: AlloHSC-iNKT (PBSC) replicate 1 [ATO_PBSC_1]


title: VTP1_M


title: AlloHSC-iNKT (CB) replicate 3 [ATO_CB_3]

source_name: AlloHSC-iNKT (CB)

value: AlloHSC-iNKT (CB)


title: VTF6_F

description:
DESeq2_VIT_In_vivo_Liver_vs._VIT_AOX_Liver.txt
DESeq2_VIT_Control_Liver_vs._VIT_AOX_Liver.txt


title: AlloHSC-iNKT (CB) replicate 2 [ATO_CB_2]


title: Endo_control_rep_2

value: day 16

value: No


title: Colon tumor from patient T102

treatment_protocol: All patients were first-line treated with surgery, and none of them received adjuvant chemotherapy.

value: FFPE tumor


title: Epi_H3N2_rep_3

value: primary alveolar epithelial cells


title: VTF4_F

value: Liver


title: Endo_control_rep_1


title: VTF2_M


title: VTF3_M


title: VTP4_F

value: Placenta


title: VTF1_M

value: Vitrification treated


title: Epi_H3N2_rep_2


title: Endo_H3N2_rep_2


title: RLN (17-15)

first: Virginia

last: Amador

email: VAMADOR@clinic.cat, PBALSAS@clinic.cat

state: Barcelona

address: Roselló 149-153

institute: IDIBAPS

hyb_protocol: Hybridization master mix was prepared and split into the 12 tubes containing the samples to analyze. Samples were then incubated in a PCR machine, for 16hours at 67ºC.

scan_protocol: cartridges were scanned and counted using the Nanostring scanner at its higher resolution (555 FOVs).

data_processing: Normalitzation with nSolver Analysis Software 4.0. Standard normalization uses a combination of Positive Control Normalization, which uses synthetic positive control targets, and CodeSet Content Normalization, which uses housekeeping genes, to apply a sample-specific correction factor to all the target probes within that sample lane.

source_name: Non-neoplastic Reactive Lymph  Node (RLN)

label_protocol: Samples were labeled with Nanostring Reporter Probes.

extract_protocol: Nucleic acids were extracted from 10-µm sections of FFPE biopsies from lymph nodes using the QIAGEN AllPrep DNA/RNA FFPE kit (QIAGEN, Hilden, Germany) after deparaffinization according to the manufacturer´s instructions.

tag: sox11 status

value: Lymph node

tag: tumoral content


title: Endo_H3N2_rep_1


title: Epi_H3N2_rep_1


title: RLN (R3244)


title: RLN (R3245)


title: VCP6_F

description:
DESeq2_VIT_In_vivo_Placenta_vs._VIT_Control_Placenta.txt
DESeq2_VIT_Control_Placenta_vs._VIT_AOX_Placenta.txt
DESeq2_In_Vitro_Control_Placenta_ vs._ VIT_Control_Placenta.txt

tag: strain

tag: developmental stage

value: Vitrification control

value: Female


title: Epithelial Irradiation 3

description:
Epithelial_Normalised_Counts.txt.gz
E9

tag: tissue

value: Lung

value: Irradiation + IgG control antibody


title: VTF5_F

value: C57BL/6 x CBA F1


title: Epi_control_rep_2


title: Epi_control_rep_1


title: VCP2_M


title: Kelly_380-1

city: Darlinghurst

first: Niantao

last: Deng

state: NSW

address: 384 Victoria Street

department: Cancer Theme

institute: Garvan Institute of Medical Research

data_processing:
Star alignment
RSEW raw counts
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: Kelly cell line

growth_protocol: 6x10^5 Kelly cells were seeded in 6 well plates. Kelly media: Roswell Park Memorial Institute (RPMI) medium (Gibco) supplemented with 10% Fetal Bovine Serum (FBS) (Hyclone)

extract_protocol:
RNA was extracted using the Qiagen miRNeasy mini kit (Qiagen). RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies) and integrity verified using an Agilent Bioanalyser 2100 with the 6000 Nano Assay (Agilent Technologies).
Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina) with 1 μg of input RNA.

treatment_protocol: Cells were reverse transfected with 25 nM microRNA mimics (Dharmacon) with Dharmafect 1 Transfection reagent. The following day the media was changed. 48 hour after transfection cell pellets were harvested for RNA extraction.

value: Kelly

value: neuroblastoma

tag: miRNA mimic


title: MCL_LN_SOX11- (82574)

source_name: Primary Mantle Cell Lymphoma (MCL)

value: Pretreated patient


title: MCL_LN_SOX11- (17-03)


title: Kelly_1283-2


title: VCP4_F


title: AlloHSC-iNKT (CB) replicate 1 [ATO_CB_1]

value: human T cells

value: AlloHSC-iNKT (CB)


title: Epi_control_rep_3

value: day 16

value: No


title: VCP5_F


title: RLN (R3243)


title: RLN (17-10)


title: control_2

value: primary alveolar epithelial cells


title: RLN (17-34)


title: Kelly_99b-2


title: ovary, metastasis from lobular breast cancer, region 1

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

country: Germany

institute: Medical School Hannover

description: internal ID D45

hyb_protocol: EZ-96 DNA Methylation-Lightning Kit and according to Infinium HD AssayMethylation Protocol

scan_protocol: According to Infinium HD AssayMethylation Protocol

data_processing:
R packages: MethylAid (version 1.12.0), ChAMP (version 2.9.10)
the non_normalized.txt contains unmethylated and methylated signal intensities

label: QuDye dsDNA

label_protocol: Qubit dsDNA HS assay kit (Life Technologies, Carlsbad, U.S.A.)

extract_protocol: Maxwell RSC DNA FFPE Kit (Promega, Madison, U.S.A.) on a Maxwell RSC instrument (Promega)

tag: gender

value: female

value: ovary

tag: region type

value: lobular


title: VCP3_M

value: Placenta

tag: treatment

value: Male


title: VCP1_M

value: Vitrification control

tag: Sex


title: MCL_LN_SOX11- (17-02)

value: Lymph node


title: ovary, metastasis from lobular breast cancer, region 6

description: internal ID D1257

value: glandular


title: VCF3_M

description:
DESeq2_VIT_In_vivo_Liver_vs._VIT_Control_Liver.txt
DESeq2_VIT_Control_Liver_vs._VIT_AOX_Liver.txt
DESeq2_In_Vitro_Control_Liver_vs._VIT_Control_Liver.txt

value: Liver

value: C57BL/6 x CBA F1


title: Kelly_1003-1

tag: cell line

value: Kelly

tag: cell type

value: neuroblastoma


title: Activated gamma delta T cells replicate 8 [Activate_gd_8]

source_name: Activated gamma delta T cells

value: human T cells

value: Activated gamma delta T cells


title: ovary, metastasis from lobular breast cancer, region 4

description: internal ID D1255


title: Activated gamma delta T cells replicate 9 [Activate_gd_9]


title: VCF6_F

value: Female


title: Kelly_1283-3


title: MCL_LN_SOX11+ (R3156)

value: Pretreated patient


title: Kelly_1915-3


title: ovary, metastasis from lobular breast cancer, region 5

description: internal ID D1256


title: VCF2_M


title: Activated gamma delta T cells replicate 7 [Activate_gd_7]


title: ovary, metastasis from lobular breast cancer, region 3

description: internal ID D1254


title: MCL_LN_SOX11+ (R3166)


title: VCF5_F


title: VCF4_F


title: Activated gamma delta T cells replicate 6 [Activate_gd_6]


title: VCF1_M


title: Endo_control_rep_3

value: primary microvascuular endothelial cells

tag: time points

value: day 16

tag: % mechanical strain

value: No


title: Kelly_Sc-2

value: Scrambled control


title: MCL_LN_SOX11+ (R3159)


title: Activated gamma delta T cells replicate 5 [Activate_gd_5]


title: Kelly_485-5


title: Activated gamma delta T cells replicate 4 [Activate_gd_4]


title: Kelly_485-1


title: MCL_LN_SOX11+ (R3134)


title: Kelly_485-2


title: AIP4_F

description:
DESeq2_In_vivo_Placenta_vs._Control_Placenta.txt
DESeq2_In_vivo_Placenta_vs._AOX_Placenta.txt

value: Placenta

value: In vivo developed


title: AIP5_F


title: Kelly_99b-7


title: MCL_LN_SOX11+ (R3153)


title: Kelly_380-3


title: MCL_LN_SOX11+ (R3161)


title: MCL_LN_SOX11+ (R3149)


title: MCL_LN_SOX11+ (R3148)


title: AIP3_M

value: Male


title: MCL_LN_SOX11+ (R3139)

value: Lymph node


title: AIP2_M


title: Kelly_380-2


title: Kelly_Sc-4


title: MCL_LN_SOX11+ (10-33)


title: AIP1_M


title: AIP6_F


title: B60_controlRNA

description: Test Group 3

data_processing: Gene expression analysis was performed using Qiagen PCR Array Data Analysis Software and normalized to five housekeeping genes provided within the array (http://pcrdataanalysis.sabiosciences.com/ pcr/arrayanalysis.php). Hierarchical clustering and heat map generation were performed with Heatmapper software (http://www.heatmapper.ca/), as described (Babicki et al., 2016).

source_name: flushed from huNSG femur

extract_protocol: RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen, Germantown, MD).  Quality and concentration of RNA were determined with the Nanodrop ND-1000 spectrophotometer (ThermoFisher Scientific).

value: Bone Marrow Mononuclear Cells

tag: human cell source

value: Mobilized peripheral blood was collected from aged donors


title: Kelly_1915-2


title: B46_controlRNA

description: Test Group 3


title: Kelly_1003-4


title: AIF5_F

description:
DESeq2_In_vivo_Liver_vs._Control_Liver.txt
DESeq2_In_vivo_Liver_vs._AOX_Liver.txt

value: Liver

value: C57BL/6 x CBA F1


title: B55_miR-combo

description: Test Group 2


title: Kelly_1283-4

value: Kelly

value: neuroblastoma


title: B41_miR-combo

description: Test Group 2


title: Kelly_Sc-5


title: SCI_MP_48h_duplicate2

city: Taipei

first: Yuan-Chii

last: Lee

address: 250, Wuxing Street

department: Graduate Institute of Biomedical Informatics

institute: Taipei Medical University

description: Gene Expression data

hyb_protocol: According to the Affymetrix manufactor's manual.

data_processing: The data are normalized using RMA in GeneSpring GX 10.

source_name: spinal cord  with injury, MP, 48h

growth_protocol: Long Evans female rats (8 or 9 week-old) were purchased from National Laboratory Animal Center, Taipei, Taiwan. All animals were housed in a 12-h light/dark cycle and had free access to water and food all the time. For animal care and surgical procedures, we followed the National Institutes of Health Guide for the Care and Use of Laboratory Animals (NIH Publications No. 80-23, revised 1978) and all surgical protocols were approved by the Animal Care and Use Committee of Taipei Medical University.

extract_protocol: Following different time after MP, EPO or control medication, SCI animals were anesthetized with a mixture of Zoletil 50 and Rompun described earlier and the 5-mm lesion spinal cord was removed, frozen immediately in liquid nitrogen and stored in liquid nitrogen prior to RNA extraction. Total RNA was extracted by the Trizol method and the integrity of RNA was examined by Agilent Bioanalyzer (Agilent Technologies, Inc. Headquarters, Palo Alto, CA, USA) before oligo microarray analysis started.

treatment_protocol: In MP experiment, animals were randomly assigned into four groups: spinal cord injury with 70% ethanol (SCI + EtOH), spinal cord injury with MP (30 mg/kg) (SCI + MP), Sham + EtOH and Sham + MP. In EPO experiment, animals were randomly assigned into four groups: spinal cord injury with H2O (SCI + H2O), spinal cord injury with EPO (5000 U/kg) (SCI + EPO), Sham + H2O and Sham + EPO. Animals were sacrificed at 2, 4, 6, 8, 12, 24 and 48 hours after medication. Additional animals including Sham + EtOH, SCI + EtOH, Sham + H2O, and SCI + H2O were sacrificed immediately after control medication. For all surgeries, animals were anesthetized by a mixture of Zoletil 50 (25 mg/kg) and Rompun (xylazine, 10 mg/Kg) via intraperitoneal injections.

tag: injury

value: SCI

tag: medication

value: MP

tag: time


title: Kelly_485-3


title: SCI_MP_24h_duplicate2

description: Gene Expression data

scan_protocol: According to the Affymetrix manufactor's manual.

source_name: spinal cord  with injury, MP, 24h


title: SCI_MP_12h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, MP, 12h

label_protocol: According to the Affymetrix manufactor's manual.


title: B50_miR-619

first: Pranela

address: 185 South Orange Avenue

description: Test Group 1


title: SCI_MP_48h_duplicate1

description: Gene Expression data


title: B31_miR-619

description: Test Group 1


title: SCI_MP_12h_duplicate1

description: Gene Expression data


title: Kelly_99b-4


title: SCI_MP_24h_duplicate1

description: Gene Expression data


title: SCI_MP_8h_duplicate1

description: Gene Expression data

source_name: spinal cord  with injury, MP, 8h


title: AIF1_M


title: AIF2_M


title: ATP6_F

description:
DESeq2_In_vivo_Placenta_vs._AOX_Placenta.txt
DESeq2_Control_Placenta_vs._AOX_Placenta.txt

source_name: Murine 14.5 Placenta

value: In vitro treated

value: Female


title: Kelly_99b-3


title: AIF6_F


title: E09_noRNA

description: Control Group


title: SCI_MP_6h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, MP, 6h


title: SCI_MP_6h_duplicate1

description: Gene Expression data


title: SCI_MP_8h_duplicate2

description: Gene Expression data


title: AIF4_F


title: SCI_MP_4h_duplicate2

description: Gene Expression data

source_name: spinal cord  with injury, MP, 4h


title: SCI_MP_4h_duplicate1

description: Gene Expression data


title: Kelly_380-4


title: D29_noRNA

description: Control Group


title: D15_noRNA

description: Control Group


title: Kelly_1915-4_2


title: SCI_MP_2h_duplicate1

description: Gene Expression data

source_name: spinal cord  with injury, MP, 2h


title: ATP4_F


title: ATP5_F


title: SCI_MP_2h_duplicate2

description: Gene Expression data


title: Kelly_1915-1_2


title: D01_noRNA

description: Control Group


title: ATP3_M


title: Kelly_1283-1


title: ATP2_M


title: H. burtonii YPD + 1M sorbitol 1hr #2

city: Seoul

first: Dong Wook

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Hyphopichia burtonii whole genome using Tophat
FPKM calculation using cufflinks.
Genome_build: Hyphopichia burtonii (NCBI ASM385679v1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Hyphopichia burtonii

source_name: H. burtonii YPD + 1M sorbitol 1hr

growth_protocol: precultured wildtype H. burtonii was inoculated in YPD and supplemented YPD broth at OD600 = 0.6 and culture 1 hour

extract_protocol:
After culture, OD 5 of samples were harvested and total RNA were extracted RNA preparation method following DOI: 10.1016/j.ab.2019.113408 paper
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA-Seq Library Prep Kit standard protocols.

tag: isolation source

value: Nuruk

tag: genotype/variation

value: WT

value: YPD + 1M sorbitol 1hr


title: Kelly_1003-3