title: T cells_KPC-SubQ_Control-1

source_name: T cells_KPC-SubQ_Control-1


title: LQ001_3T3-L1

status: Public on Sep 19 2022

type: SRA

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

country: USA

institute: Columbia University

description: Chromium 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: GRCm38
Supplementary files format and content: Expression matrix of each sample.
Supplementary files format and content: For each sample, "features.tsv.gz" corresponded to gene names. "barcodes.tsv.gz" corresponded to cell barcodes. "matrix.mtx.gz" was the expression counts in sparce matrix.

molecule: total RNA

organism: Mus musculus

growth_protocol: 3T3-L1 cells were cultured in high glucose DMEM supplemented with 10% calf serum (CS, Gemini Bio-Products 100-506), and 1× Pen Strep (Thermo Fisher). Cells were differentiated in the standard adipogenic cocktail after reaching confluence for 2 days. The cocktail contains DMEM, 10% FBS (heat-inactivated, Corning 35-011-CV), 1 μM dexamethasone (DEX), 10 μg/mL insulin and 0.5 mM 3-isobutyl-1-methylxanthine (IBMX). After induction for two days, cells were maintained in a complete medium containing 2.5 μg/mL insulin until fully differentiated.

extract_protocol:
Cells were gently dissociated into single cells with trypsin enzymatic digestion.
Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: P-G3 polymers (10 μg/mL) were added to the medium since the induction of differentiation Day 0, and cells were harvested at indicated times for analyses.

tag: cell line

tag: cell type

value: fibroblasts

tag: time

tag: adipogenic differentiation_treatment

value: Untreated

tag: polymer treatment


title: FXRC22-23

city: Chicago

first: Xiaoying

last: Liu

state: IL

address: 240 E Huron St., McGaw M-319

institute: Northwestern University

library_source: transcriptomic

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Liver

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: DKO

tag: strain

tag: tissue

value: liver


title: FXRC24-26


title: OR3350_rep1

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road, #163

department: Waksman Institute

institute: Rutgers University

library_source: genomic

data_processing:
ChIP-seq processing pipeline standard for modERN/ModENCODE
The Illumina sequencing data were aligned to the reference genome using the Burrows–Wheeler Aligner (BWA).
ChIP-seq processing pipeline standard for modERN/ModENCODE
ChIP-seq processing pipeline standard for modERN/ModENCODE
Peaks above an irreproducibility discovery rate (IDR) of 0.1% were used to generate final peak sets
Genome_build: WS245/WBcel235
Supplementary_files_format_and_content: .wig files and IDR Thresholded Peak files

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Developmental synchronization was achieved by bleaching and L1 arrest.  Arrested L1s were plated on NGM plates seeded with OP50 bacteria and grown at 20C until L4s.

extract_protocol:
L4 stage animals were harvested, and samples were cross-linked with 2% formaldehyde for 30 min at room temperature and then quenched with 1 M Tris pH 7.5.  The pelleted nematodes were subsequently flash frozen in liquid nitrogen and stored at -80oC.  Pellets were thawed on ice and 750 ml of FA buffer containing protease inhibitors (Roche Cat#11697498001 Complete Protease Inhibitor Cocktail Tablet, 125 l 100 mM PMSF, and 25 l 1 M DTT per 25 ml FA buffer) was added, and samples were then transferred to a 2 ml KONTES dounce (Kimble Chase, Vineland, NJ).  Samples were dounced on ice 15 times with the small “A” pestle for two cycles with a 1 min hold between each cycle.  Samples were then dounced 15 times with the large “B” pestle for four rounds with a 1 min hold between each cycle.  Samples were then sonicated to shear chromatin into 200–800 bp DNA fragments.  For each sample, 4 mg of protein lysate was immunoprecipitated using anti-GFP antibodies (gifts of Tony Hyman and Kevin White).  GammaBind G Sepharose beads (GE Healthcare Life Sciences) were pre-washed and blocked in binding buffer and 0.1 mg/ml BSA.  Samples were pre-cleared by adding 100 l of 50/50 bead/buffer solution at 4oC, followed by centrifugation.  Samples of each replicate were removed and pooled to serve as total chromatin input. To each replicate, 15 g of antibody was added overnight at 4oC, followed by another overnight of incubation with the bead mix.  Immunoprecipitates (IPs) were washed four times with cold lysis buffer and twice with cold TE.  Pellets were resuspended in elution buffer and incubated at 65oC for 10 min. Samples were centrifuged and supernatants transferred to a fresh tube.  Pellets were resuspended in 29% TE and 0.67% SDS and immediately centrifuged.  Elution supernatants were combined and incubated at 65oC with mild shaking overnight.  Chromatin input samples were incubated at 60oC with mild shaking overnight following the addition of Proteinase K and SDS to final concentrations of 0.1 mg/ml and 0.01%, respectively.  The next day, inputs were incubated at 70oC for 20 min.  Proteinase K was added to each IP and incubated at 50oC for 2 hr.  RNaseA was added to the chromatin input to a concentration of 0.017 mg/ml and incubated at 37oC for 2 hr.  DNA was purified with MinElute columns (QIAGEN, Valencia, CA), eluting in 13 l (elution buffer provided with MinElute kit).  An additional 48 l EB was added to input samples after purification.  Samples were stored at -20oC.
The enriched DNA fragments and input control (genomic DNA from the same sample) for two biological replicates were used for library preparation and sequencing.  Samples were libraried and multiplexed using the Ovation Ultralow DR Multiplex Systems 1–8 and 9–16 (NuGEN Technologies, San Carlos, CA) following the manufacturer’s protocol, except that QIAGEN MinElute PCR purification kits were used to isolate the DNA.  Briefly, 1 ul of input DNA and 10 ul of IP DNA was used to prepare sequencing libraries using NuGEN Ultralow library kits.  Samples were prepared according to the manufacturer’s protocol.  Sequencing was performed on the Illumina HiSequation 2000/2500/4000

tag: developmental stage

tag: temperature

tag: chip antibody

value: Anti-GFP (gift from Tony Hyman and Kevin White)


title: FXRC21-27

value: SKO


title: FXRC15-16


title: OR3349_rep2

source_name: odIS131[hif-1::gfp); hif-1(ia4)

value: odIS131[hif-1::gfp); hif-1(ia4)


title: DSC-ip-4

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: dorsal spinal cord ip 4

data_processing:
Library strategy: Ribo-seq
Aligned to mouse genome (mm10) using STAR spliced read aligner
Count the reads with htseq-count
Normalization and differential expression analysis using Bioconductor packages
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with normalized values for each sample

source_name: dorsal spinal cord

extract_protocol:
Tissues of 12 CNS regions other than the striatum were collected from 4 animals of 2 months old Aldh1l1-CreERT2 x RiboTag mice (2 males and 2 females) and individually homogenized. RNA was extracted from 10-20% of cleared lysate as input containing RNA from all cell types using RNA extraction kit (Qiagen). The remaining lysate was incubated with mouse anti-HA antibody  for 4 hr at 4 °C followed by addition of magnetic beads  and overnight incubation at 4 °C. RNA was extracted from the immunoprecipitation (IP) samples containing astrocyte-enriched RNA using RNA extraction kit.
TruSeq Stranded RNA (100 ng) + RiboZero Gold
Astrocyte-specific bulk RNA-seq

value: dorsal spinal cord

tag: age

value: 2 months

tag: condition

value: ip

tag: region

value: DSC

tag: rip antibody

value: anti-HA

value: Aldh1l1-Cre/ERT2 x Ribotag


title: FXRC20


title: DSC-ip-3

description: dorsal spinal cord ip 3


title: FXRC17


title: OR3350_input

value: input


title: DSC-input-2

description: dorsal spinal cord input 2


title: OR3349_input


title: DSC-ip-2

description: dorsal spinal cord ip 2


title: LQ002_D3_UT

description: Chromium 10x Genomics

value: Immature adipocytes, adipocytes

value: Yes


title: DSC-input-3

description: dorsal spinal cord input 3


title: DSC-input-1

description: dorsal spinal cord input 1


title: DSC-ip-1

description: dorsal spinal cord ip 1


title: DSC-input-4

description: dorsal spinal cord input 4


title: OR3349_rep1


title: KC-88-T

city: Goyang-si

first: Sodam

last: Won

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea

country: South Korea

institute: national cancer center

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Raw read count and normalized values were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e for each sample.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Raw read count and Normalized values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Kidney tissue was flash frozen on dry ice and RNA was harvested using Trizol reagent. The TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: RCC

value: Kidney


title: OR3350_rep2


title: KC-88-N

value: normal


title: VSC-ip-3

description: ventral spinal cord ip 3

source_name: ventral spinal cord

value: ventral spinal cord

value: VSC


title: VSC-ip-1

description: ventral spinal cord ip 1


title: VSC-input-4

description: ventral spinal cord input 4


title: VSC-ip-2

description: ventral spinal cord ip 2


title: KC-110-T


title: KC-110-N


title: VSC-input-2

description: ventral spinal cord input 2


title: KC-109-T


title: VSC-input-1

description: ventral spinal cord input 1


title: KC-109-N


title: HB-ip-4

description: hindbrain ip 4

source_name: hindbrain

value: hindbrain

value: HB


title: HB-ip-3

description: hindbrain ip 3


title: HB-ip-2

description: hindbrain ip 2


title: VSC-ip-4

description: ventral spinal cord ip 4


title: Dpse_ChIP_polII-CTD_rep2

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description: chromatin from Drosophila pseudoobscura ovaries fixed by formaldehyde

data_processing:
genome_build: Nanopore genome assemby by Miller, G3, 2018, (PMID: 30087105)
R1 reads were trimmed of the adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting.  The trimmed reads were then mapped against the genome using bowtie 1.2.3, allowing up to three mismatches.  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of reads that are uniquely mapping to the genome

organism: Drosophila pseudoobscura

source_name: ovaries

growth_protocol: Flies were kept at standard conditions at room temperature.

extract_protocol:
Ovaries were dissected from 3 -7 days old female flies.   Ovaries were fixed with PBS containing 2% para-formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using BioRuptor (ten cycles of 30sec/30sec ON/OFF).
IP and 5% of input DNA were End-repaired (NEB) and ligated to the NEBNext adapter for Illumina (NEB, E7337A). The libraries were amplified by the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers.  Post amplification libraries were size selected at 200-500bp in length in a low-melt Agarose gel.

value: ovaries

tag: Sex

value: female

tag: stain

value: wild type

value: 2 - 7 days old

value: standard food

value: RNA Polymerase II CTD (gift from Hiroshi Kimura, PMID:25252976)


title: TG-11

description: cortex transgenic rep 11

data_processing:
Cell Ranger from 10x Genomics was used for alignment and quantification
Genome_build: mm10
Supplementary_files_format_and_content: There are 3 files for each sample: barcodes, features, and count matrix, in the forms of tab-separated values and market exchange format, respectively

source_name: cortex

extract_protocol:
scRNA-seq was performed to profile the whole cortex, hippocampus, and striatum of C57BL/6 mice at 8-10 weeks of age and or the frontal cortex of APP/PS1 mice at 10-11 months of age. The brain was immediately dissected out and was sectioned into 400 mm slices in ice-cold artificial cerebrospinal fluid (ACSF) oxygenated with 95% O2 and 5% CO2 and immediately transferred to an oxygenated recovery solution. The cortical, hippocampal, or striatal tissue was dissected out in ice-cold ACSF and cut into small pieces. The tissue was digested in ACSF containing 1 mg/ml pronase at 34 °C for 30 min. The digested tissue was dissociated in ice-cold oxygenated ACSF containing 1% fetal bovine serum. The dissociated cells were filtered through a 20 mm filter and washed with ice-cold ACSF. To remove myelin, the cell pellet was resuspended in PBS and processed with debris removal kit (Miltenyi Biotec). Isolated cells were diluted to 1000 cells/ml in 0.04% BSA/PBS and processed with 10X Genomics platform.  The library preparation and sequencing were performed following 10X Genomics Chromium protocols.
Single cell suspension from mouse brain tissues were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 and v3 (10X Genomics) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.
10X Genomics Chromium

value: cortex

value: 10-11 months


title: TG-10

description: cortex transgenic rep 10


title: KC-108-T


title: HB-ip-1

description: hindbrain ip 1

value: 2 months

value: ip

value: anti-HA

value: Aldh1l1-Cre/ERT2 x Ribotag


title: KC-107-N

value: normal

value: Kidney


title: TG-9

description: cortex transgenic rep 9


title: HB-input-3

description: hindbrain input 3

value: input


title: Dpse_ChIP_input_rep2


title: KC-108-N


title: KC-107-T

value: RCC


title: VSC-input-3

description: ventral spinal cord input 3

value: ventral spinal cord

value: VSC


title: TG-8

description: cortex transgenic rep 8


title: HB-input-2

description: hindbrain input 2

value: hindbrain

value: HB


title: Dpse_ChIP_input_rep1

value: ovaries

value: female

value: wild type

value: 2 - 7 days old


title: HB-input-4

description: hindbrain input 4


title: Dpse_ovary_polyA

description: polyA selected RNA from Drosophila pseudoobscura ovaries

data_processing:
genome_build:  Nanopore genome assemby by Miller, G3, 2018, (PMID: 30087105)
We used both R1 and R2 reads from the standard RNA-seq, and only the R1 reads from the Quantseq 3' mRNA-seq for the mapping and analyses.   Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting.  Trimmed reads were mapped against the genome using STAR 2.7.3a, allowing up to three mismatches.  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of reads that are uniquely mapping to the genome

extract_protocol:
Ovaries were dissected from 3 -7 days old female flies. Total RNA was extracted from ovaries using TRIZOL. Oligo-dT magnetic beads (NEB) was used to purify polyA+ RNA.  PolyA+ RNA was used to make standard RNA-seq libraries while the total RNA was used to make a Quant-seq mRNA 3' end sequencing library.
The RNA-seq library was made using NEB Ultra II Directional RNA library prep kit (NEB), while the mRNA 3' end-seq library was made using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen).  For both library constructions, we used the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers to amplify the libraries.

value: standard food


title: HB-input-1

description: hindbrain input 1

value: 2 months


title: KC-106-T


title: KC-106-N


title: TG-6

description: cortex transgenic rep 6

value: cortex

value: 10-11 months


title: TG-5

description: cortex transgenic rep 5


title: Dpse_ovary_unoxidised_sRNA

description: unoxidised small RNAs (18-40nt) from Drosophila pseudoobscura ovaries without 2S rRNA

data_processing:
genome_build:Nanopore genome assemby by Miller, G3, 2018, (PMID: 30087105)
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting.  The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses.  Trimmed reads were mapped with bowtie v1.2.3 to the respective genomic sequences (allowing up to one mismatch) or transposon reference sequences (allowing up to three mismatches).  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers
Supplementary files format and content: *.TE-mapping.txt: counts of piRNA (>22nt & <41nt) reads that mapped to the transposon reference sequences (allowing up to three mismatches, --all --best --strata option in bowtie), normalised to one million all genome mappers
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of piRNA reads (>22nt and <41nt) that are uniquely mapping to the genome

extract_protocol:
Either ovaries or embryos were collected for the RNA extraction.  Ovaries were dissected from 3 -7 days old female flies. Embryos were collected between zero to two hours after fertilisation. Embryos were further dechorionated by 20% bleach and further rinsed by water.  Total RNA was extracted from ovaries/embryos using TRIZOL.
For oxidised small RNA libraries: Small RNAs were first size-selected by 12% w/v UREA-PAGE, and oxidised using sodium periodate.  For non-oxidised small RNA libraries: 2S rRNA was first removed from the total RNA using a biotinylated DNA ligo 'TACAACCCTCAACCATATGTAGTCCAAGCA'. 2S-rRNA-depleted total RNA was then size-selected by 12% w/v UREA-PAGE to yield the pool of small RNA.  The oxidised or unoxidised small RNAs were further size-selected by PAGE before 3' and 5' adapters were ligated.  The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the library was amplified using KAPA LongRange DNA polymerase (Sigma) with TruSeq compatible primers.

tag: treatment

value: oxidised


title: MB-ip-4

description: midbrain ip 4

source_name: midbrain

value: midbrain

value: ip

value: MB

value: anti-HA

value: Aldh1l1-Cre/ERT2 x Ribotag


title: KC-105-T

value: RCC

value: Kidney


title: Dpse_embryo_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila pseudoobscura embryos

source_name: embryos

value: embryos

value: pooled male and female

value: 0 - 2 hr post-fertlisation

value: unoxidised


title: MB-ip-3

description: midbrain ip 3


title: KC-105-N

value: normal


title: MB-ip-2

description: midbrain ip 2


title: TG-2

description: cortex transgenic rep 2


title: Dpse_ovary_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila pseudoobscura ovaries

value: ovaries

value: female

value: wild type

value: 2 - 7 days old

value: standard food


title: TG-7

description: cortex transgenic rep 7

value: cortex

value: 10-11 months


title: siLARP1

city: Nagoya

first: Koichi

last: Ogami

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University

description: 5’capped 3’ polyA RNA

data_processing:
Base-callingg: Guppy 2.3.1
Quality check: MinIONQC 1.3.5
Alignment: minimap2 2.15 with parameters  -ax splice -uf -k 12 -c -L -N 5 —secondary=no
Poly(A) tail analysis: nanopolish 1.18.2. For SQK-RNA002 libraries, we used the script in the sqk-rna002 branch.
Read counts: FeatureCounts (Subread 1.6.2)
Genome_build: hg38
Supplementary_files_format_and_content: Counts_features.txt (raw counts for all features in all samples)

source_name: cultured HEK293T cells

growth_protocol: HEK293T cells were cultured in FBS-containing DMEM with or without 250nM Torin1

extract_protocol:
GST-eIF4Ek119A (100 μg) was immobilized on 50 μL of MagneGST Glutathione Particles (Promega) at 10 °C for 2 hr in 200 μL of 4E pull-down (4E-PD) buffer (10 mM Tris-HCl (pH 8.0), 100 mM KCl, 2 mM EDTA, 2.5 % glycerol, 1.3 % polyvinylalcohol (polymerization degree about 500), 0.005 % Triton X-100, 1mM DTT) and unbound protein was removed by washing three times with 200 μL of 4E-PD buffer. Prior to the cap-purification, total RNA was first subjected to LiCl-precipitation twice to remove abundant 5' capped small ncRNAs. The LiCl-precipitated RNA (30 μg) was heat-denatured at 65 °C for 10 min and mixed with GST-eIF4Ek119A-bound MagneGST particles in 200 μL of 4E-PD buffer supplemented with 25 μg yeast tRNA and 40 U recombinant RNase inhibitor (TaKaRa) for 2 hr at 25 °C. After washing three times with 500 μL of 4E-PD buffer, GST-eIF4Ek119A was eluted in 100 μL of elution buffer (100 mM Tris-HCl (pH 8.6), 1 mM EDTA, 0.005 % Triton X-100, 150 mM NaCl, 40 mM glutathione, 1 mM DTT, 5 U/mL Turbo3C protease) at r.t. for 10 min. The elution was repeated four times, and the eluate was combined and phenol-chloroform extracted followed by EtOH precipitation in the presence of glycogen (Roche). The precipitated RNA was dissolved in 10 μL of QW and further purified using 1.8 volume of Agencourt RNAClean XP (Beckman). After elution in 10 μL of QW, RNA concentration was determined using QuantiFluor RNA System (Promega).
Library preparation for nanopore sequencing was performed using the Oxford Nanopore’s direct RNA sequencing kit (SQK-RNA001 or SQK-RNA002) according to the manufacturer’s instruction except that we used 1μg of the cap-purified RNA and 0.5 μL of RNA calibration strand (RCS) for adapter ligation. To improve throughput, we performed reverse transcription using SuperScript III (Thermo Scientific) after the adapter ligation. All the procedures above were performed in DNA LoBind tubes (Eppendorf).
Nanopore direct RNA-sequencing

treatment_protocol: siRNAs were transfected using RNAi MAX for 42 hours, and then treated with DMSO or Torin1

tag: cell type

value: Transfected with:LARP1 siRNA

tag: agent

value: Treated with:DMSO


title: MB-input-4

description: midbrain input 4

value: midbrain

value: 2 months

value: input

value: MB

value: Aldh1l1-Cre/ERT2 x Ribotag


title: TG-4

description: cortex transgenic rep 4


title: Dpse_ChIP_polII-CTD_rep1

value: RNA Polymerase II CTD (gift from Hiroshi Kimura, PMID:25252976)


title: siLARP1_Torin1

description: 5’capped 3’ polyA RNA

value: Treated with:250nM Torin1


title: KC-101-T

value: RCC

value: Kidney


title: KC-104-N

value: normal


title: KC-99-T


title: TG-1

description: cortex transgenic rep 1


title: MB-ip-1

description: midbrain ip 1

value: ip

value: anti-HA


title: WT-10

description: cortex wild type rep 10

value: APP/PS1dE9-wild type control


title: WT-11

description: cortex wild type rep 11

value: cortex


title: MB-input-3

description: midbrain input 3


title: KC-99-N


title: MB-input-2

description: midbrain input 2


title: KC-104-T


title: Alox15 KO, replicate2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for downstream analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file include counts for each sample

source_name: granulocytes

extract_protocol:
RNA was extracted using RNeasy mini Kit (Qiagen, cat. no. 74106) and digested with DNase I (Qiagen, cat. no. 79254)
The libraries were prepared using a Lexogen Quantseq kit

value: granulocytes

tag: alox15 status

value: knockout

tag: group

value: untreated

tag: replicate


title: CB-ip-4

description: cerebellum ip 4

source_name: cerebellum

tag: tissue

value: cerebellum

value: CB

tag: genotype


title: Alox15 KO, replicate3


title: MB-input-1

description: midbrain input 1

value: midbrain

value: 2 months

value: input


title: KC-98-N


title: WT-9

description: cortex wild type rep 9

value: 10-11 months


title: Alox15 KO, replicate1


title: Alox15 WT, replicate4

value: wild type


title: CB-ip-3

description: cerebellum ip 3

value: Aldh1l1-Cre/ERT2 x Ribotag


title: KC-97-T

value: RCC

value: Kidney


title: KC-97-N

value: normal


title: WT-5

description: cortex wild type rep 5


title: siCtrl_Torin1

description: 5’capped 3’ polyA RNA

value: Transfected with:control siRNA

value: Treated with:250nM Torin1


title: CB-ip-1

description: cerebellum ip 1

value: ip

value: anti-HA


title: Alox15 WT, replicate2

value: granulocytes


title: KC-96-T


title: CB-input-4

description: cerebellum input 4


title: WT-6

description: cortex wild type rep 6

value: cortex

value: APP/PS1dE9-wild type control


title: Alox15 WT, replicate3

value: untreated


title: WT-4

description: cortex wild type rep 4


title: Alox15 WT, replicate1


title: KC-98-T


title: KC-96-N


title: CB-input-3

description: cerebellum input 3

value: cerebellum

value: CB


title: WT-7

description: cortex wild type rep 7


title: WT-8

description: cortex wild type rep 8


title: siCtrl

description: 5’capped 3’ polyA RNA

value: Treated with:DMSO


title: CB-ip-2

description: cerebellum ip 2

value: 2 months


title: CB-input-2

description: cerebellum input 2

value: input


title: KC-102-T


title: KC-102-N


title: Blood_P2_memB_IGM

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

country: Netherlands

institute: LUMC

data_processing:
454 sequences were demultiplexed based on their multiplex identifier sequence and 40 nucleotides trimmed from both sides to remove the primer sequence using the ARGalaxy demultiplex tool. Illumina FASTQ files were paired (PEAR), demultiplexed, trimmed with cutadapt  and converted into FASTA files. FASTA files from both 454 and Illumina data were analyzed using IMGT/High-V-Quest (Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol. 2012;882:569-604)
Assembly: GRCh38
Supplementary files format and content: IMGT-HighVQuest output Summary file:
Library strategy: Amplicon-seq

source_name: Blood

extract_protocol:
RNA was isolated using RNeasy Plus Kits (Qiagen) and transcribed into cDNA using random hexamer primers and Superscript III® (both Invitrogen).
Amplicon-seq: IGH transcripts of the SLO samples were amplified from 5µl cDNA per reaction in a multiplex PCR using the forward VH1-6 FR1 (BIOMED-2) primers and the CgCH1, the IGHA or the IGHM reverse primer (sequence available upon request). These PCR products were purified and sequenced using Roche 454 sequencing as previously described
Amplicon-seq: IGH transcripts of the PBMC samples were amplified using the forward VH1-6 FR1 (BIOMED-2) primers and costum IGHG, IGHA and IGHM reverse primers (sequence available upon request). PCR products were purified and sequenced using 2x300 Illumina sequencing (Illumina).

treatment_protocol:
Secondairy Lymphoid Organ samples of 3 CVID patients (P1-3) and 3 healthy donors (HAD, HDB, HDC) were flow sorted into 5 B-cell subsets: naïve, centroblasts (CB), centrocytes (CC), memory B-cells (Mem B) and plasmablasts (PB)
Peripheral blood mononuclear cell samples of 2 CVID patients (P1,2) and 3 healthy donors (HDL, HDM, HDR) were flow sorted into 4 B-cell subsets: naïve, natural effector B-cells (NE),  memory B-cells (Mem B) and plasmablasts (PB)

value: Blood

value: memory B cells

tag: primers

value: IGM


title: Blood_P2_naive_IGM

value: naive B cells


title: CB-input-1

description: cerebellum input 1

value: Aldh1l1-Cre/ERT2 x Ribotag


title: WT-1

description: cortex wild type rep 1

value: 10-11 months


title: KC-100-T

value: RCC

value: Kidney


title: HY-ip-4

description: hypothalamus ip 4

source_name: hypothalamus

value: hypothalamus

value: ip

value: HY

value: anti-HA


title: Blood_P2_memB_IGHGA

value: IGG and IGA


title: Blood_P2_PB_IGM

value: plasmablasts


title: KC-100-N

value: normal


title: HIP-6

description: hippocampus rep 6

source_name: hippocampus

value: hippocampus

value: 2 months

tag: strain

value: control


title: HY-ip-3

description: hypothalamus ip 3

tag: age


title: HIP-4

description: hippocampus rep 4


title: HY-ip-2

description: hypothalamus ip 2

tag: condition


title: KC-95-T


title: Blood_P2_NE_IGM

value: Blood

value: natural effector B-cells


title: HIP-5

description: hippocampus rep 5


title: Blood_P1_naive_IGM

value: naive B cells

value: IGM


title: HIP-2

description: hippocampus rep 2


title: HY-ip-1

description: hypothalamus ip 1

tag: region

value: Aldh1l1-Cre/ERT2 x Ribotag


title: Blood_P1_memB_IGM

value: memory B cells


title: STR-5

description: striatum rep 5

source_name: striatum

value: striatum


title: KC-94-T

value: RCC

value: Kidney


title: HIP-1

description: hippocampus rep 1


title: HY-input-3

description: hypothalamus input 3

value: hypothalamus

value: input

value: HY

tag: rip antibody


title: KC-94-N

tag: disease state


title: STR-4

description: striatum rep 4


title: HY-input-4

description: hypothalamus input 4


title: KC-93-T


title: Blood_P1_memB_IGHGA

value: IGG and IGA


title: Blood_P1_PB_IGM

value: plasmablasts


title: HY-input-2

description: hypothalamus input 2


title: CTX-6

description: cortex rep 6

value: cortex


title: KC-95-N

value: normal


title: KC-93-N


title: KC-92-T


title: HY-input-1

description: hypothalamus input 1

value: 2 months


title: Blood_P1_NE_IGM

value: Blood


title: Blood_P1_PB_IGHGA


title: CTX-4

description: cortex rep 4

value: control


title: KC-92-N


title: Blood_HDR_naive_IGM

value: naive B cells


title: TH-ip-4

description: thalamus ip 4

source_name: thalamus

value: thalamus

value: ip

value: TH

value: anti-HA


title: TH-ip-3

description: thalamus ip 3

value: Aldh1l1-Cre/ERT2 x Ribotag


title: KC-91-T

value: RCC

value: Kidney


title: CTX-3

description: cortex rep 3


title: Blood_HDR_memB_IGM

value: memory B cells

value: IGM


title: CTX-2

description: cortex rep 2


title: KC-91-N


title: TH-ip-2

description: thalamus ip 2


title: TH-ip-1

description: thalamus ip 1


title: Blood_HDR_memB_IGHGA

value: IGG and IGA


title: Blood_HDR_PB_IGHGA

value: plasmablasts


title: Blood_HDR_PB_IGM


title: CTX-0

description: cortex rep 0

value: cortex


title: TH-input-4

description: thalamus input 4

value: input


title: KC-90-T


title: KC-90-N

value: normal


title: CTX-5

description: cortex rep 5

value: 2 months


title: 104267-001-042

first: Florine

last: Seidel

address: Zernikedreef 9

institute: TNO Innovation for Life

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Mus_musculus.GRCm38.gencode.vM19
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver, sinister lobe (snap frozen)

growth_protocol: All animal experiments were conducted in accordance with the European Union regulations on animal research and approved by an independent Animal Welfare Body (IVD TNO; approval number TNO-451). Male Ldlr-/-.Leiden mice were bred at TNO Metabolic Health Research, Leiden, the Netherlands and group-housed in a specific-pathogen-free animal facility (temperature ~21˚C, relative humidity 50-60%) on a 12-hour light/dark cycle. The animals received food and water ad libitum. At t=0, 17-18 week-old mice were matched into 3 experimental groups based on body weight, blood glucose, plasma cholesterol and plasma triglyceride levels. Group sizes were based on power calculations for detection of a difference in the main end-point hepatic inflammation (at α=0.05 and power = 0.8), on top of this 2 animals per group were added to compensate for potential drop-outs during the study. Accordingly, a healthy reference group (Chow, n=8) remained on a standardized chow diet (Sniff R/M diet V1530, Uden, the Netherlands). A HFD control group (HFD+vehicle, n=17) and a treatment group (HFD+BB5.1, n=17) were fed a well-established obesity-inducing (36) energy-dense HFD (45 kcal % fat with 39 kcal% fat from lard and 6 kcal% fat from soybean oil, 20 kcal% protein and 35 kcal% carbohydrates, D12451, Research Diets, New Brunswick, NJ, USA).

extract_protocol:
Mice were sacrificed by isoflurane inhalation (4%) and heart puncture, and non-fasted terminal blood was collected. After that, mice were perfused with PBS for 10 min (1 ml/min) and the livers and hearts (including aortic root) were isolated. For the blood samplings and sacrifice, the order of the cages was randomized . In addition, all mice were individually numbered in a way that people conducting the experiment as well as the analyses were only aware of the mouse number and blinded to the corresponding experimental group. Ribonucleic acid (RNA) was extracted from 25-40 mg snap-frozen liver (sinister lobe, Chow n=6, HFD+vehicle n=12, HFD+BB5.1 n=12) as previously described (43). RNA integrity and concentration were examined for each sample using the RNA 6000 Nano LabChip kit and a bioanalyzer 2100 (both Agilent Technologies, Amstelveen, the Netherlands).
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7420S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: Each animal cage contained 2 to 6 animals from the same experimental group. To provide equal housing conditions for each group and avoid bias, cages from different groups were randomized (using a Random Integer generator) over the shelves in the animal room. Chow and HFD+vehicle animals received 200-μl intraperitoneal injections of a neutral vehicle (sterile phosphate-buffered saline (PBS)) while HFD+BB5.1 received 200-μl intraperitoneal injections of an established anti- C5 antibody (BB5.1, 5 mg/ml in PBS, 1 mg/mouse, (30)). Mice were treated with a vehicle or the anti-C5 antibody twice a week from week 20 until the end of the study (week 31). For administrating the treatments, the animals were injected per group to minimize the risk of a dosing error, but the order of the cages was rotated equally between all timepoints. Every week individual body weight was measured and food intake was monitored per cage to calculate the average food intake per mouse per day. Blood (200 μl) was collected via the tail vein at weeks 20, 22, 26 and 31 weeks after a 5-hour fast.

tag: treatmentperiod

tag: mousenr

value: B


title: Blood_HDR_NE_IGM

value: Blood

value: natural effector B-cells


title: CTX-1

description: cortex rep 1

value: control


title: TH-input-3

description: thalamus input 3

value: thalamus

value: TH


title: Blood_HDM_naive_IGM

value: naive B cells


title: TH-input-2

description: thalamus input 2

value: Aldh1l1-Cre/ERT2 x Ribotag


title: 104267-001-041


title: HIP-0

description: hippocampus rep 0

value: hippocampus


title: U251 cells, ST101, biological replicate 3

city: Harrison

first: Lila

last: Ghamsari

address: 500 Mamaroneck Ave, Suite 320

institute: Sapience Therapeutics

data_processing:
Original image data files from Illumina sequencer were transformed into sequenced reads by CASAVA base recognition
Raw data were stored in FASTQ (fq) files
Low quality reads containing adaptors, uncertain nucleotides and Q scores of over 50% bases below 5 were filtered out.
High quality raw reads were aligned to the human genome (GRCh38) using STAR aligner (RRID:SCR_004463)
The number of mapped read-pairs were counted based on the GENCODE v36 annotation (GENCODE, 286  RRID:SCR_014966)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include read counts and FPKM values for each Sample

growth_protocol: A549, MCF7 and U251 cells were maintained in F-12K, EMEM+ 1% Non Essential Amino Acids,  EMEM+ 2mM Glutamine + 1% Non Essential Amino Acids + 1mM Sodium Pyruvate, respectively, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell pellets were resuspended in RNAlater (Thermo Fisher Scientific, USA) and total RNA was extracted using Qiagen RNeasy Protect Mini Kit (Qiagen Inc. USA) according to manufacturer’s  instructions and treated with Qiagen RNase-free DNase to remove genomic DNA.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols

treatment_protocol: Cells were treated with either 10µM ST101 or vehicle for 24 hours

tag: cell line

value: Glioblastoma

value: WT

tag: treatment


title: U251 cells, ST101, biological replicate 2

tag: cell type


title: 104267-001-039


title: Blood_HDM_memB_IGM

value: memory B cells

value: IGM


title: U251 cells, ST101, biological replicate 1


title: 104267-001-038


title: 104267-001-037


title: 104267-001-035


title: U251 cells, vehicle, biological replicate 2

value: Vehicle


title: HIP-ip-3

description: hippocampus ip 3

value: ip

value: HIP

value: anti-HA


title: Blood_HDM_memB_IGHGA

value: IGG and IGA


title: Blood_HDM_PB_IGM

value: Blood

value: plasmablasts


title: U251 cells, vehicle, biological replicate 1


title: U251 cells, vehicle, biological replicate 3


title: HIP-ip-4

description: hippocampus ip 4

value: 2 months


title: 104267-001-033

value: B


title: HIP-ip-1

description: hippocampus ip 1


title: HIP-ip-2

description: hippocampus ip 2


title: Blood_HDM_PB_IGHGA


title: Blood_HDM_NE_IGM

value: natural effector B-cells


title: TH-input-1

description: thalamus input 1

value: thalamus

value: input

value: TH


title: HIP-input-4

description: hippocampus input 4

value: hippocampus

value: Aldh1l1-Cre/ERT2 x Ribotag


title: 104267-001-031


title: Blood_HDL_naive_IGM

value: naive B cells


title: MCF7 cells, ST101, biological replicate 2

value: Breast adenocarcinoma

value: WT


title: HIP-input-3

description: hippocampus input 3


title: 104267-001-030


title: Blood_HDL_memB_IGM

value: memory B cells

value: IGM


title: HIP-input-2

description: hippocampus input 2

value: HIP


title: MCF7 cells, ST101, biological replicate 1


title: MCF7 cells, vehicle, biological replicate 3

value: Vehicle


title: 104267-001-029


title: Blood_HDL_memB_IGHGA

value: Blood

value: IGG and IGA


title: MCF7 cells, ST101, biological replicate 3


title: 104267-001-028


title: 104267-001-027


title: Blood_HDL_PB_IGM

value: plasmablasts


title: MCF7 cells, vehicle, biological replicate 1


title: 104267-001-025

value: H


title: MCF7 cells, vehicle, biological replicate 2


title: VCX-ip-2

description: visual cortex ip 2

source_name: visual cortex

value: visual cortex

value: 2 months

value: ip

value: VCX

value: anti-HA


title: Blood_HDL_NE_IGM

value: natural effector B-cells


title: VCX-ip-4

description: visual cortex ip 4

value: Aldh1l1-Cre/ERT2 x Ribotag


title: A549 cells, ST101, biological replicate 3

value: Lung carcinoma


title: Whole ovarian tissue [72h lgl-KD+NICD-OE single-cell RNA-Seq dataset 2]

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for base-calling
Single-ended fastq files for the whole-tissue RNA-Seq samples were aligned to Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using STAR (v2.7) aligner. featureCounts (Subread package) was run on individual bam files for the generation of count-matrix.
Genome index for single-cell analysis was built using the Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using 10X genomics cellranger (version 3.0.1) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for single-cell RNA-Seq datasets.
Genome_build: dm6
Supplementary_files_format_and_content: csv files contain raw counts for each whole-genome RNA Seq sample.
Supplementary_files_format_and_content: Loom file generated after velocyto processing of the 3 files (barcodes.tsv, features.tsv and matrix.mtx) obtained from the standard cellranger pipeline for each single-cell RNA-Seq dataset. All these files are readable in R and were processed using the Seurat pipeline which resulted in the individual rds files for each dataset.

organism: Drosophila melanogaster

source_name: Whole ovarian tissue

growth_protocol: 100 adult ovaries from 50 female Drosophila melanogaster flies maintained at 25°C, with access to males and yeast supplements for 3 days

extract_protocol:
For bulk-RNA sequencing: Whole ovaries were extracted from 40 females in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS. The anterior part of the ovaries were carefully removed before stage 10 egg chambers. Samples were transferred to a steril Eppendorf tube and media was aspirated. Samples were flash frozen using liquid nitrogen and stored until day of the library preparation in -80°C. Total RNA was extracted using Trizol. For single-cell RNA sequencing: Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Bulk sequencing libraries were made using the Ultra II Directional RNA library prep kit for Illumina using the protocol for NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490). Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the Illumina Hi-Seq 2500 (bulk RNA-Seq) and Illumina NovaSeq 6000 (single-cell RNA-Seq) instrument flow cell for a 100-cycle sequencing run.

treatment_protocol: Flies were transferred to 29°C incubator for 1 (24h), 3 (72h) and 4 (96h) days depending on the dataset, and were subsequently dissected.

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-Upd, UAS-Dcr2

value: 3 day in 29°C


title: 104267-001-022


title: A549 cells, ST101, biological replicate 2

value: WT


title: A549 cells, ST101, biological replicate 1


title: Whole ovarian tissue [72h lgl-KD+NICD-OE single-cell RNA-Seq dataset 1]

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-NICD, UAS-Dcr2


title: 104267-001-023


title: HIP-input-1

description: hippocampus input 1

value: hippocampus

value: input

value: HIP


title: A549 cells, vehicle, biological replicate 3

value: Vehicle


title: Whole ovarian tissue [72h lgl-KD single-cell RNA-Seq dataset]


title: 104267-001-018

value: H


title: Whole ovarian tissue [w1118 single-cell RNA-Seq dataset]

value: no treatment


title: VCX-input-4

description: visual cortex input 4

value: visual cortex

value: 2 months

value: VCX


title: 104267-001-019


title: VCX-input-3

description: visual cortex input 3

value: Aldh1l1-Cre/ERT2 x Ribotag


title: VCX-ip-3

description: visual cortex ip 3

value: ip

value: anti-HA


title: Blood_HDL_PB_IGHGA

value: Blood

value: plasmablasts

value: IGG and IGA


title: VCX-ip-1

description: visual cortex ip 1


title: 400 pSer2 Pol II ChIP_input

city: Tianjin

first: Meijuan

last: Geng

address: No.22 Qixiangtai Road

country: China

institute: Tianjin Medical Universuty

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
ChIP-Seq data were mapped to reference genome by bowtie2.
ChIP-Seq peaks were generated using peak finding algorithm MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated by MACS2.

growth_protocol: CAL-62 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
CAL-62 cells were fixed with 1% formaldehyde for 10 minutes at room temperature (RT). Cross-linking was stopped with 150 mM glycine. Cells were harvested and sonicated to obtain chromatin fragments (100–500 bp) with SONICS Vibra-cellTM.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

treatment_protocol: CAL-62 cells were treated with either DMSO or THZ531 for 6 h.

value: representative anaplastic thyroid carcinoma cell line

value: treated with 400 nM THZ531 for 6h

tag: chip antibody

value: none (input)


title: 104267-001-015


title: 104267-001-017


title: VCX-input-2

description: visual cortex input 2

value: input


title: VCX-input-1

description: visual cortex input 1


title: 400 pSer2 Pol II ChIP

value: pSer2 Pol II (Cell Signaling Technology, Cat. No.13499)


title: 100 pSer2 Pol II ChIP_input

value: treated with 100 nM THZ531 for 6h


title: SCX-ip-3

description: sensory cortex ip 3

source_name: sensory cortex

value: sensory cortex

value: SCX


title: 104267-001-014

value: H


title: A549 cells, vehicle, biological replicate 2

value: Lung carcinoma

value: WT

value: Vehicle


title: 104267-001-013


title: 100 pSer2 Pol II ChIP


title: SCX-ip-2

description: sensory cortex ip 2

value: 2 months

value: ip

value: Aldh1l1-Cre/ERT2 x Ribotag


title: 104267-001-010


title: DMSO pSer2 Pol II ChIP_input

value: treated with DMSO for 6h


title: A549 cells, vehicle, biological replicate 1


title: SCX-input-4

description: sensory cortex input 4


title: 104267-001-009


title: SCX-ip-1

description: sensory cortex ip 1

value: anti-HA


title: 104267-001-008

value: C


title: DMSO pSer2 Pol II ChIP

value: representative anaplastic thyroid carcinoma cell line


title: Arcuate nucleus-median eminence cells, Irx5KO pooled

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

country: Canada

institute: The Hospital for Sick Children

data_processing:
Base-calling performed with Illumina's bcl2fastq follwed by Picard FastqToSam. Read1 contains cellular and molecular barcodes (20 bp), Read2 contains cDNA sequence (50 bp).
Read2 was aligned with STAR v2.6.0b and tagged with its respective cellular and molecular barcode.
Aligned exonic reads were tagged with the name of the respective gene.
Digital gene expression (DGE) matrix was extracted from the aligned library, with a row for each gene and a column for each cell. The "knee" of the cummulative distribution plot of reads was used to estimate the number of cells being sequenced.
Cells from sample 1-2 were merged into a single DGE matrix for analysis using Seurat v3, where cells expressing less than 200 genes and genes expressed in less than 3 cells were filtered out.
Dead/dying cells (determined by mitochonrial gene percentage >10%) and cell doublets (gene expressed > 4500) were removed.
Gene measurements in each cell were normalized by the total expression, multiplied by 10,000 and log-transformed.
Following identification of highly-variable genes and data scaling, the dimensionality of the dataset was heuristically dertermined by ElbowPlot (a ranking principle components based on the percentage of variance explained by each one).
Cell were clustered using the graph-based clustering approach applied in Seurat, followed by vizualization through t-SNE or UMAP plots.
Merged_DGE.txt in supplementary file contains cells and genes extracted from final Seurat object.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include DGE matrices for each sample, with a row for each gene and a column for each cell. Cell number was determined by plotting the cumulative distribution plot of reads.

source_name: Arcuate nucleus-median eminence

extract_protocol:
Micro-dissected arcuate nucleus and median eminence were dissociated to single-cell suspensions. Live cells were sorted and processed through Drop-seq with flow rates of 3000 μL/hr (cells and beads) and 13,000 μL/hr (oil) were used, and beads were resuspended at 167,000 per mL. Droplets were broken with perfluorooctanol in SSC to release beads.
The beads were washed and resuspended in a reverse transcriptase mix, followed by a treatment with exonuclease I to remove unextended primers. The beads were then counted and PCR amplified. The amplified cDNA was fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina) using custom primers that enabled the specific amplification of only the 3' ends (described in Macosko et al. Cell 2015).

value: Microdissected Arcuate nucleus and median eminence of the hypothalamus

value: 7-8 weeks

tag: number of mice pooled


title: e11_18_f_wt_8_br

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: WT control animal

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GRCM38.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

extract_protocol:
Mice tissue sections were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skeletal muscle

value: Rps9 WT / Rps9 WT

value: 18 months

tag: Sex

value: Female


title: SCX-input-3

description: sensory cortex input 3

tag: tissue

value: sensory cortex

value: input

value: SCX


title: 104267-001-004


title: e11_18_f_wt_43_br

description: WT control animal

tag: genotype


title: SCX-input-2

description: sensory cortex input 2


title: SCX-ip-4

description: sensory cortex ip 4


title: Arcuate nucleus-median eminence cells, WT pooled

value: Wildtype


title: e11_18_f_wt_32_br

description: WT control animal


title: MCX-ip-4

description: motor cortex ip 4

source_name: motor cortex

value: motor cortex

value: 2 months

value: MCX


title: MCX-ip-3

description: motor cortex ip 3

value: ip

value: Aldh1l1-Cre/ERT2 x Ribotag


title: 104267-001-003

value: C


title: e11_18_f_wt_24_br

description: WT control animal


title: MCX-ip-2

description: motor cortex ip 2

value: anti-HA


title: 6hs9-B28-D

city: Chapel Hill

first: Jimena

last: Giudice

state: NC

address: 6340B MBRB, Campus Box 7545

department: Cell Biology and Physiology

institute: UNC - Chapel Hill

data_processing:
Sequenced reads were mapped to the mm10 genome with STAR
Alternative splicing was determined using MISO
Gene counts were generated using Salmon
Differential gene expression was determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix output from DESeq2

molecule: nuclear RNA

source_name: C2C12 myoblast cells

extract_protocol:
RNA was extracted immediately after stretching using Qiagen kits
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: myoblasts/myotubes

value: myotubes

tag: stretch/no stretch

value: stretch

tag: time


title: 6hs10-B28-D


title: 104267-001-005


title: e11_18_f_wt_19_br

description: WT control animal

tag: strain

value: Skeletal muscle

tag: age


title: MCX-ip-1

description: motor cortex ip 1

tag: condition

tag: region

tag: rip antibody


title: SCX-input-1

description: sensory cortex input 1


title: MCX-input-3

description: motor cortex input 3


title: e11_18_f_wt_16_br

description: WT control animal

value: Rps9 WT / Rps9 WT


title: 6hs8-B25-D


title: 6hs7-B25-D


title: e11_18_f_wt_30_br

description: WT control animal

value: 18 months


title: 6hno9-B28-D

value: no stretch


title: MCX-input-4

description: motor cortex input 4


title: e11_18_f_wt_11_br

description: WT control animal

value: Female


title: 6hno8-B25-D


title: 6hno10-B28-D


title: OB-ip-4

description: olfactory bulb ip 4

source_name: olfactory bulb

value: olfactory bulb

value: OB


title: MCX-input-2

description: motor cortex input 2

value: input


title: MCX-input-1

description: motor cortex input 1

value: motor cortex


title: 6hno7-B25-D


title: OB-ip-3

description: olfactory bulb ip 3

value: 2 months


title: OB-ip-2

description: olfactory bulb ip 2


title: WI-38, etoposide treated, scRNA-seq

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: 10x Genomics

data_processing:
Cell Ranger software version 6.0.0 was used for demultiplexing, barcoded processing, sequence alignment, and for generating matrix files
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Etoposide-treated WI38 cells were trypsinized, washed and resuspended in PBS, and subjected to single-cell GEM (Gel Bead-Emulsion) generation with Chromium Controller (10x Genomics)
scRNA-seq library was performed according to the manufacter’s instructions (10x Genomics Chromium Next Gem Single Cell 3' Regent Kits v3 protocol, 10x Genomics). In brief, single cell suspension was loaded into a Chromium Next GEM Chip G (10x Genomics), and GEMs were generated using the Chromium Single Cell Controller (10x Genomics). We used 11 and 13 cycles for cDNA amplification and Sample Index PCR (Single Index Kit T Set A, 10x Genomics), respectively

value: fibroblasts

value: etoposide


title: 3hs10-B28-D


title: OB-ip-1

description: olfactory bulb ip 1

data_processing:
Library strategy: Ribo-seq
Aligned to mouse genome (mm10) using STAR spliced read aligner
Count the reads with htseq-count
Normalization and differential expression analysis using Bioconductor packages
Genome_build: mm10
Supplementary_files_format_and_content: xlsx file with normalized values for each sample

extract_protocol:
Tissues of 12 CNS regions other than the striatum were collected from 4 animals of 2 months old Aldh1l1-CreERT2 x RiboTag mice (2 males and 2 females) and individually homogenized. RNA was extracted from 10-20% of cleared lysate as input containing RNA from all cell types using RNA extraction kit (Qiagen). The remaining lysate was incubated with mouse anti-HA antibody  for 4 hr at 4 °C followed by addition of magnetic beads  and overnight incubation at 4 °C. RNA was extracted from the immunoprecipitation (IP) samples containing astrocyte-enriched RNA using RNA extraction kit.
TruSeq Stranded RNA (100 ng) + RiboZero Gold
Astrocyte-specific bulk RNA-seq

value: ip

value: Aldh1l1-Cre/ERT2 x Ribotag


title: 3hs9-B28-D


title: OB-input-4

description: olfactory bulb input 4


title: 3hs8-B25-D


title: OB-input-3

description: olfactory bulb input 3


title: 3hs7-B25-D


title: 3hno10-B28-D


title: OB-input-2

description: olfactory bulb input 2


title: OB-input-1

description: olfactory bulb input 1


title: 3hno9-B28-D


title: 104267-001-002

tag: treatmentperiod

tag: mousenr

value: C


title: 104267-001-001


title: e11_18_f_mut_44_br

description: Rps9 D95N mutant experimental animal

value: Rps9 D95N / Rps9 WT heterozygous


title: e11_18_f_mut_50_br

description: Rps9 D95N mutant experimental animal


title: e11_18_f_mut_28_br

description: Rps9 D95N mutant experimental animal


title: e11_18_f_mut_42_br

description: Rps9 D95N mutant experimental animal


title: siBDNF_Sen_2

description:
siBDNF-transfected WI-38 cells were cultured for 8 days in 50 µM etoposide-containing media.
mRNA

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_geneCOUNT.txt: Tab-delimited text files containing counts.

growth_protocol: Human WI-38 (Coriell Institute) cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), Penn/Strep (Gibco), Sodium Pyruvate (Gibco), and non-essential amino acids (Gibco) in a 5% CO2 incubator. Cells were maintained at low population doubling levels (PDL), between PDL15 and PDL25. Etoposide was added to the media as indicated every three days; control conditions included equivalent concentrations of vehicle (DMSO).

extract_protocol:
RNA was extracted with RLT buffer (Qiagen) and purified using the QIAcube system (Qiagen) through the RNeasy plus method. The quality and quantity of RNA were checked using Agilent RNA 6000 nano kit on the Agilent Bioanalyzer.
125ng of high quality of RNA was used for sequencing library prep using Illumina TruSeq Stranded mRNA Library prep kit according to manufacturer’s protocol (Illumina, San Diego, CA). The quality and quantity of sequencing libraries were checked using Agilent DNA 1000 Screen Tape on the Agilent Tapestation.

treatment_protocol: Cells were transfected with RNAiMAX (Invitrogen) following the manufacturer’s instructions. Briefly, cells at 50% confluency were transfected with ON-TARGETplus SMARTPool (Dharmacon) non-targeting siCtrl (Catalog ID: D-001810-10-05), siNTrk2 (Catalog ID: L-003160-00-0005), or siBDNF (Catalog ID: L-017626-00-0005) siRNAs at a final concentration of 25 nM.

tag: cell line

tag: treatment

value: siBDNF

value: Etoposide-induced senescence (8 days)


title: e11_18_f_mut_4_br

description: Rps9 D95N mutant experimental animal

value: Skeletal muscle


title: e11_18_f_mut_41_br

description: Rps9 D95N mutant experimental animal

value: 18 months


title: siBDNF_Sen_3

tag: cell type


title: 3hno7-B25-D

value: myotubes

value: no stretch


title: 1hs9-B28-D

value: stretch


title: Deug_ovary_QuantSeq

description: 3' ends of mRNAs from Drosophila eugracilis ovaries

data_processing:
genome_build:  ASM1815383v1/GCF_018153835.1
We used both R1 and R2 reads from the standard RNA-seq, and only the R1 reads from the Quantseq 3' mRNA-seq for the mapping and analyses.   Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting.  Trimmed reads were mapped against the genome using STAR 2.7.3a, allowing up to three mismatches.  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of reads that are uniquely mapping to the genome

organism: Drosophila eugracilis

source_name: ovaries

value: ovaries

value: female

value: wild type

value: 2 - 7 days old

value: standard food


title: 3hno8-B25-D


title: Deug_ovary_polyA

description: polyA selected RNA from Drosophila eugracilis ovaries


title: 1hs8-B25-D


title: 1hs7-B25-D


title: 1hs4-B17-D


title: 1hno10-B28-D


title: Deug_embryo_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila eugracilis embryos

data_processing:
genome_build:ASM1815383v1/GCF_018153835.1
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting.  The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses.  Trimmed reads were mapped with bowtie v1.2.3 to the respective genomic sequences (allowing up to one mismatch) or transposon reference sequences (allowing up to three mismatches).  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers
Supplementary files format and content: *.TE-mapping.txt: counts of piRNA (>22nt & <41nt) reads that mapped to the transposon reference sequences (allowing up to three mismatches, --all --best --strata option in bowtie), normalised to one million all genome mappers
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of piRNA reads (>22nt and <41nt) that are uniquely mapping to the genome

source_name: embryos

value: embryos

value: pooled male and female

value: 0 - 2 hr post-fertlisation

value: unoxidised


title: Deug_Piwi-IP_oxidised_sRNA

description: Piwi-bound small RNAs (18-40nt) from Drosophila eugracilis embryos, oxidised

value: oxidised


title: Deug_Aub-IP_oxidised_sRNA

description: Aubergine-bound small RNAs (18-40nt) from Drosophila eugracilis embryos, oxidised


title: Deug_ovary_unoxidised_sRNA

description: unoxidised small RNAs (18-40nt) from Drosophila eugracilis ovaries without 2S rRNA


title: Dmoj_embryo_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila mojavensis embryos

data_processing:
genome_build:ASM1815372v1/GCF_018153725.1
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting.  The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses.  Trimmed reads were mapped with bowtie v1.2.3 to the respective genomic sequences (allowing up to one mismatch) or transposon reference sequences (allowing up to three mismatches).  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers
Supplementary files format and content: *.TE-mapping.txt: counts of piRNA (>22nt & <41nt) reads that mapped to the transposon reference sequences (allowing up to three mismatches, --all --best --strata option in bowtie), normalised to one million all genome mappers
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of piRNA reads (>22nt and <41nt) that are uniquely mapping to the genome

organism: Drosophila mojavensis


title: Dmoj_ovary_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila mojavensis ovaries


title: e11_18_f_mut_21_br

description: Rps9 D95N mutant experimental animal

value: Rps9 D95N / Rps9 WT heterozygous

value: Female


title: siCtrl_Sen_3

description:
siCtrl-transfected WI-38 cells were cultured for 8 days in 50 µM etoposide-containing media.
mRNA

value: fibroblasts

value: siCtrl

value: Etoposide-induced senescence (8 days)


title: siBDNF_Sen_1

value: siBDNF


title: siCtrl_Prolif_1

description:
siCtrl-transfected WI-38 cells were cultured for 8 days in DMSO-containing media.
mRNA

value: Proliferating


title: siNTRK2_Sen_2

description:
siNTRK2-transfected WI-38 cells were cultured for 8 days in 50 µM etoposide-containing media.
mRNA


title: siNTRK2_Sen_3


title: siCtrl_Sen_2


title: siCtrl_Prolif_2


title: siCtrl_Sen_1


title: siCtrl_Prolif_3


title: 1hno9-B28-D

value: myotubes

value: no stretch


title: 1hno8-B25-D


title: siNTRK2_Sen_1


title: 1hno7-B25-D


title: Deug_ovary_oxidised_sRNA_rep1

description: oxidised small RNAs (18-40nt) from Drosophila eugracilis ovaries

value: ovaries

value: female

value: wild type


title: CP-5

city: Beijing

first: Wan

last: Chang

state: China

address: Panjiayuan

department: State Key Laboratory of Molecular Oncology, National Cancer Center

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Text file for counts and RPKM values of each gene

source_name: KYSE150 cells

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCC

value: ESCC cell line KYSE150

value: control


title: 6hs10-B31-UD

value: myoblasts

value: stretch


title: CP-4


title: 6hno10-B31-UD


title: 6hs9-B31-UD


title: 6hno9-B31-UD


title: 6hs8-B27-UD


title: Deug_ovary_oxidised_sRNA_rep2

value: 2 - 7 days old

value: oxidised

value: standard food


title: 6hs7-B27-UD


title: NB64

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

country: Germany

institute: University Children’s Hospital of Cologne

data_processing:
Software used for basecalling are HCS1.4.8+RTA1.12.4.2, HCS1.4.8+RTA1.12.4.2 and HCS1.5+RTA1.13.48.
Sequenced reads were masked for low-complexity or low-quality sequence (entropy < 15), then mapped to the genome, the RefSeq and AceView 2011 gene models, the mitochondrial genes, the rRNA and RNA genes, the spike-in sequence, and finally the imaginary genome as a mapping specificity control. For each read repair, alignment on all targets, genes or genome, are scored, and only the best scores are kept.
The Magic expression index for the gene is measured as the log base 2 of the number of bases aligned in the gene, divided by the number of terabases aligned in known genes and by the length of the gene, with several corrections. Genes that are not significantly expressed, i.e., with less than 4 reads above the experimental noise level, acquire an N/A flag.
TERRA expression was computed by first mapping the paired-end reads to the hg19 reference with STAR, and using TelomereHunter with default parameters to count reads containing the four most common TVRs TTAGGG, TGAGGG, TCAGGG and TTGGGG.
Assembly: human genome (NCBI 37)
Supplementary files format and content: tab-delimited text file includes Magic expression index values for each sample
Supplementary files format and content: tab-delimited text file includes TERRA expression values for each sample

source_name: neuroblastoma

extract_protocol:
Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further. 30-60mg of snap-frozen neuroblastoma specimen was cryo-sectioned and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.
Library construction was performed according to the standard TruSeqTM protocol.

treatment_protocol:
NB04
All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery.

value: neuroblastoma

tag: tmm group

value: TEL[+]

tag: mycn status

value: amplified

tag: age at_diagnosis_(months)

tag: inss stage

value: male

tag: event-free survival_(years)

tag: event (relapse_or_progression)_(yes/no)

value: no

tag: overall survival_(years)

tag: death (yes/no)

tag: treatment intensity

value: high-risk treatment


title: NB66

tag: tissue

value: ALT[+]

value: non-amplified

tag: Sex


title: NB65

value: female


title: NB63


title: NB55

value: yes


title: CP-2

value: ESCC

value: ESCC cell line KYSE150

tag: genotype


title: NB67


title: CP-3

value: control


title: NB54

value: ambiguous


title: 6hno8-B27-UD

tag: myoblasts/myotubes

value: myoblasts

tag: stretch/no stretch

value: no stretch

tag: time


title: CP-1

tag: cell line


title: 6hno7-B27-UD


title: NB48


title: NB49


title: CC-4


title: CC-5


title: 3hs10-B31-UD

value: stretch


title: CC-3


title: NB53

value: neuroblastoma


title: 3hs8-B27-UD


title: 3hs9-B31-UD


title: CC-2


title: 3hs7-B27-UD


title: CC-1


title: NB43


title: NB46


title: NB45


title: 3hno10-B31-UD


title: B2PS-5

value: overexpressed OTUB2


title: B2PS-4


title: 3hno9-B31-UD


title: NB41

value: TEL[+]


title: NB38

value: TMM[-]


title: 3hno8-B27-UD


title: B2PS-3


title: NB27

value: male


title: 3hno7-B27-UD


title: B2PS-2


title: NB24

value: high-risk treatment


title: 1hs10-B31-UD


title: B2PS-1


title: NB23

value: no

value: no chemotherapy


title: RSK2 knockout cell_100ng/ml EGF 5 hour_ biological rep3

type: RNA

city: Honolulu

first: Won Seok

last: Yang

state: HI

address: University of Hawaii Cancer Center, 701 Ilalo st, Lab 454

institute: University of Hawaii Cancer Center

description: Gene expression data from EGF stimulation for 5 hours

hyb_protocol: In a rotating chamber, 2.3 μg DNA were hybridized to the Clariom S Human Array for 16 h at 45 °C. Washed and stainned on an Affymetrix Fluidics Station FS450.

scan_protocol: Hybridized arrays were scanned on the Affymetrix GeneChip Array Scanner 3000-7G.

data_processing: Generated CEL files were normalized using the SST-RMA-GENE-FULL algorithm in the Transcriptome Analysis Console (TAC) 4.0 software. Genes with fold change greater than 2 and (False Discovery Rate) FDR adjusted p-value less than 0.05 were considered differentially expressed. CEL files normalization using the SST-RMA-GENE-FULL algorithm and differential expression analysis [one-way analysis of variance (ANOVA)] were carried out using the Transcriptome Analysis Console (TAC) 4.0 software. Genes with fold change greater than 2 and (False Discovery Rate) FDR adjusted p-value less than 0.05 were considered differentially expressed.

label: Biotin

source_name: U251 RSK2 CRISPR deleted cells treated with EGF for 5 hours

label_protocol: Biotinylated cRNA were prepared as described in the Thermo Fisher Scientific GeneChip Whole Transcript (WT) Expression manual from 100ng total RNA.

growth_protocol: 37 degree in 5% CO2 incubator

extract_protocol: Total RNA were extracted using DNA/RNA AllPrep Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 100ng/ml EGF was treated for 5 hours in starved overnight cells in 6 well dishes.

value: U251 Glioblastoma derived cell line

value: RSK2 CRISPR deleted

tag: treatment

value: 100ng/ml EGF


title: RSK2 knockout cell_100ng/ml EGF 5 hour_ biological rep2


title: RSK1 knockout cell_100ng/ml EGF 5 hour_ biological rep3

source_name: U251 RSK1 CRISPR deleted cells treated with EGF for 5 hours

value: RSK1 CRISPR deleted


title: 1hs9-B231-UD


title: Control cell_100ng/ml EGF 5 hours_biological rep2

source_name: U251 Control cells treated with EGF for 5 hours

value: Non target control


title: RSK1 knockout cell_100ng/ml EGF 5 hour_ biological rep2


title: NB21

tag: tmm group

value: non-amplified


title: 1hs8-B27-UD

value: myoblasts


title: Control cell_100ng/ml EGF 5 hours_biological rep3


title: NB16

tag: mycn status

value: amplified

value: female

value: yes


title: B2-5

value: ESCC

value: ESCC cell line KYSE150

value: overexpressed OTUB2


title: B2-4


title: 1hs7-B27-UD

value: stretch


title: B2-3


title: 1hno10-B31-UD

value: no stretch


title: NB11

value: neuroblastoma

value: TEL[+]

tag: age at_diagnosis_(months)

value: no

value: high-risk treatment


title: B2-2


title: NB08

tag: inss stage

value: male


title: 1hno9-B31-UD


title: B2-1


title: 9 WT biofilm + macrophages + G-MDSCs

city: Omaha

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

department: Pathology & Microbiology

institute: University of Nebraska Medical Center

data_processing:
Data were processed utilizing STAR as the aligner and RSEM as the tool for annotation and quantification of gene levels.
Assembly: Staphylococcus aureus subsp. aureus USA300 FPR3757
Supplementary files format and content: Excel files give normalized expression abundance in TPM and FPKM values for all the available genes.

organism: Staphylococcus aureus

source_name: USA 300 LAC

growth_protocol: S. aureus biofilms were grown in static conditions at 37 degrees Celsius on human plasma-coated 12-well plated in biofilm medium (RPMI + 10%FBS + 1% L-glutamine + 1% HEPES) with daily medium replinishment.

extract_protocol:
RNA was isolated using beat-beating and TRIzol Reagent (Invitrogen) according to manufacturer's instructions.
RNA sequencing libraries were prepared beginning with 250 ng of total RNA using a ScriptSeq Complete Kit (Bacterial) – Low Input protocol (Cat. No. SCL6B, Epicentre Technologies, Madison, WI). The protocol was performed as recommended by the manufacturer with the following modification at step 3.B.1. In order to remove both eukaryotic and prokaryotic ribosomal RNA from the total preparation, instead of using 2 ul of kit provided bacterial rRNA removal solution, 1 ul of RiboZero human / mouse / rat removal solution was mixed with 1 ul of the bacterial rRNA removal solution. In addition to the above, AMPure bead purification of rRNA-depleted sample was used in step 3.D.2 of the protocol.

treatment_protocol: 4-day-old biofilm was co-cultured with medium alone, mouse in vitro-derived G-MDSCs, and/or mouse in vitro-derived macrophages for 2 hours.

tag: strain

value: USA 300 LAC

value: murine in vitro bone maarow-derived macrophages and G-MDSCs


title: 7 WT biofilm + G-MDSCs

value: murine in vitro bone maarow-derived G-MDSCs


title: 8 WT biofilm + G-MDSCs


title: 10 WT biofilm + macrophages + G-MDSCs


title: RSK1 knockout cell_ 0.1% DMSO_ biological rep3

description: Gene expression data from starved overnigh in 0.1% FBS media

value: U251 Glioblastoma derived cell line

value: RSK1 CRISPR deleted

value: 0.1% DMSO


title: RSK2 knockout cell_ 0.1% DMSO_ biological rep3

source_name: U251 RSK2 CRISPR deleted cells starved overnigh in 0.1% FBS media

value: RSK2 CRISPR deleted


title: 1hno8-B27-UD

value: myoblasts


title: 6 WT biofilm + G-MDSCs


title: CAL-62_400 nM THZ531 rep2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
Differentially expressed genes were identified using DESeq2 algorithms.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total RNA was collected using TRIzol reagent following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CAL-62 cells were treated in duplicate with either DMSO or THZ531 for 6 h.

tag: cell type

value: representative anaplastic thyroid carcinoma cell line

value: 400 nM THZ531 for 6h


title: 1hno7-B27-UD


title: CAL-62_400 nM THZ531 rep1


title: 5 WT biofilm + macrophages

value: murine in vitro bone marrow-derived macrophages


title: Postal

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: meningioma

extract_protocol:
Fresh meningiomas were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3. RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacturer’s instructions (Single Cell 3' v3, 10x Genomics).

value: meningioma


title: Frontal

description: 10x Genomics


title: Input

city: Chongqing

first: dapeng

last: ju

address: 1 Yixueyuan Road, Yuzhong District

institute: Department of Anesthesiology The Second Affiliated Hospital,,Chongqing Medical University ,

data_processing:
ChIP-seq reads were aligned to the GRCm38 genome assembly using bowtie2 version 2.4.1 with parameters -p 10
peaks were called using MACS2 version 2.1.4 with parameters callpeak -f BAM -B -g mm
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by  MACS2 version 2.1.4, bedtools v2.29.2

source_name: mouse forebrain

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 9 am to 9 pm), and ad libitum access to water and a standard chow diet.

extract_protocol:
Forebrains from four mice each group were mixed and homogenized in PBS containing 2mM EGS (ethylene glycol bis (succinimidyl succinate) and incubated for 20 min at room temperature. Formaldehyde was added to brain homogenates at 1% concentration and incubated for 8 min at room temperature to cross-link chromatin factors and DNA. The cross-linking reaction was stopped by adding glycine to a final concentration of 125 mM and incubated for 5 min at room temperature. Nuclei were pelleted through a sucrose gradient by centrifugation with an SW55Ti rotor (Beckman) at 37,000 rpm for 40 min at 4°C. The isolated nuclei were then subjected to chromatin preparation with Qsonica Q800R3 (at 70% amplitude, 15 s on / 45 s off) for a total of 10 min sonication. Approximately 30 µg sheared chromatin from ABC-CREB or ABC-HDAC4CA mouse forebrains and 4 µg anti-HA antibody (ab9110, Abcam) were applied to a 240 µl reaction system with freshly supplemented protease inhibitor cocktail. Immunoprecipitation was performed strictly according to the ChIP-IT High Sensitivity Kit instructions (53040, Active Motif). Considerable amount anti-HA affinity beads (Smart-lifesciences, SA068001) with sheared chromatin from ABC-mCherry mouse forebrains was seted as IgG ChIP control. Eluted DNA was analyzed with high-throughput sequencing.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Four weeks before forebrain collection, adult mice were injected with mCherry, HDAC4CA, or CREB expressing  AAV virus.

tag: chip-grade antibody

tag: developmental stage

value: adult

value: forebrain

value: AAV virus expressing mCherry-3HA


title: Otub2 KO-4

source_name: Epithelial cells

value: Tongue-derived Epithelial cells

value: otub2-knockout systemically


title: 4 WT biofilm + macrophages

value: USA 300 LAC


title: CAL-62_100 nM THZ531 rep2

value: 100 nM THZ531 for 6h


title: CREB ChIP

value: AAV virus expressing CREB-3HA


title: Otub2 KO-3


title: CAL-62_100 nM THZ531 rep1


title: 3 WT biofilm + macrophages


title: Control-2

value: Wildtype


title: 2 WT biofilm

value: medium only


title: CAL-62_DMSO rep2

value: DMSO for 6h


title: IgG ChIP

value: Smart-lifesciences (Cat #SA068001); Lot# A20102302


title: Control-1


title: 1 WT biofilm


title: HDAC4CA ChIP

value: AAV virus expressing HDAC4CA-3HA


title: CAL-62_DMSO rep1

value: representative anaplastic thyroid carcinoma cell line


title: Heat stress soybean pod replicate 3

status: Public on Sep 18 2022

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

institute: The Division of Plant Sciences and Technology

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to G_max V2.1 whole genome using Hisat2 V2.2.1.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 20110.
Assembly: Glycine_max_v2.1.51
Supplementary files format and content: replicatewise_fpkm.txt: Matrix table of FPKM values for all samples.
Supplementary files format and content: replicatewise_readcounts.txt: Matrix table of Raw counts values for all samples.

organism: Glycine max

source_name: Pods

growth_protocol: Soybean (Glycine max, cv Magellan) seeds were inoculated with Bradyrhizobium japonicum inoculum and germinated in Promix BX for a week in a growth chamber under short day growth condition (12-h light/12-h dark), at 28/24 ℃ day/night temperature and 500 μmol photons m-2 s-1. The temperature of the chambers was ramped from 24 to 28 °C between 6.00-8.00 AM and decreased to 24 °C from 16.00-20.00 PM. Seedlings were transplanted into pots containing 1 kg mixture of Promix BX and perlite mixed in ratio of 10:1 and soaked in 1 l of water-fertilizer mix (Zack’s classic blossom booster 10-30-20) . Plants were then grown under 28/24 ℃ day/night temperatures and 1000 μmol photons m-2 s-1 light intensity (12-h light/12-h dark photoperiod) for the next 16-18 days (until start of first open flower, R1 developmental stage) while irrigating twice a week with Zack’s classic blossom booster 10-30-20 fertilizer.

extract_protocol:
Soybean pods were collected from plants and immediately frozen in liquid nitrogen. About 10-15 pods were pooled together from 8-10 different plants for each biological repeat and total RNA was isolated using Qiagen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: At R1, plants were randomly divided into control (CT), and 3 stress categories as water-deficit (WD), heat stress (HS), and combination of water-deficit and heat stress (WD+HS) in four different BDR16 growth chambers placed side-by-side in the same room. The relative humidity of chambers was maintained at about 50-60% in all chambers. The plants under WD and WD+HS treatments were irrigated with only 30% of the water available for, while plants in the CT and HS treatments were irrigated with 100% of the water available for transpiration. For HS and WD+HS treatments, temperature of chambers was maintained to 38 °C Day and 28 °C night temperature by ramping the temperature between 6.00-8.00 AM and decreasing it down to 28 °C between 16.00-20.00 PM.

value: Pods

tag: cultivar

value: Magellan

value: Heat stress


title: Combined water deficit and heat stress pod replicate 3

tag: tissue

value: Water deficit and heat stress


title: Water deficit soybean pod replicate 3

value: Water deficit


title: Heat stress soybean pod replicate 2


title: Heat stress soybean pod replicate 1


title: Combined water deficit and heat stress pod replicate 1


title: Combined water deficit and heat stress pod replicate 2


title: Water deficit soybean pod replicate 2


title: Water deficit soybean pod replicate 1


title: Control soybean pod replicate 3

value: No treatment


title: Control soybean pod replicate 2


title: Control soybean pod replicate 1


title: rMANF, biological replicate 3

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence (using cutadapt) low-quality sequences removed (using fastp).
Trimmed sequence reads were mapped to mm10 transcriptome using STAR2 v2.6.0b and salmon v0.14.1.
Raw counts were collected using htseq v0.11.0 and TPM calculated using gencode reported gene lengths.
Assembly: mm10
Supplementary files format and content: log2TPM.IgG.MANF.txt: Tab-delimited text file includes log2 converted TPM values for each Sample.

source_name: heart

growth_protocol: To establish murine melanoma cancer model B16F10, 0.8 × 10^5 cells were subcutaneously implanted into the right flank of female C57BL/6 mice.

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: When the mean tumor volume reached approximately 60 mm3, animals were randomized into treatment groups (n = 8/group) for vehicle (PBS) or recombinant MANF treatment (2 μg/kg, Intraperitoneal injection, everyday) treatment.

value: heart

tag: Sex

value: female

value: wild type

value: recombinant MANF


title: WT_heart_15w_biological rep1

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

hyb_protocol: Hybridization of cRNA was performed according to standard Affymetrix guidelines and the cRNA was stained with streptavidin phycoerythrin.

scan_protocol: The arrays were scanned using a GeneArray Scanner at exciation wavelength 488nm.

data_processing: Microarray probe intensities were RMA normalized using Transcriptome Analysis Console (TAC) software (version 3.0) and differential gene expression was subsequently performed using Expression Console software (version 1.4.1)

label: biotin

source_name: Heart, 15 weeks old

label_protocol: Total RNA is reverse transcribed into cDNA and in vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

extract_protocol: Total RNA was extracted from frozen mouse heart tissue powder using an RNeasy Fibrous Tissue Kit (Qiagen).

tag: gender

value: male

value: FVB

tag: genotype

value: WT


title: ErbB2 KI_heart_15w_biological rep1

value: ErbB2 KI


title: ErbB2 KI_heart_15w_biological rep3


title: ErbB2 KI_heart_15w_biological rep2


title: rMANF, biological replicate 2


title: rMANF, biological replicate 1


title: KI:KO_heart_15w_biological rep1

value: KIKO


title: WT_heart_15w_biological rep2


title: ERR⍺ KO_heart_15w_biological rep3

value: ERRa KO


title: ERR⍺ KO_heart_15w_biological rep2


title: KI:KO_heart_15w_biological rep3


title: vehicle, biological replicate 2

value: vehicle


title: vehicle, biological replicate 3


title: vehicle, biological replicate 1


title: Control cell_0.1% DMSO_biological rep3

source_name: U251 Control cells starved overnigh in 0.1% FBS media

value: U251 Glioblastoma derived cell line

value: Non target control

value: 0.1% DMSO


title: KI:KO_heart_15w_biological rep2


title: VWF 16h biol rep 4

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
paired reads of 150 bp length were mapped against GRCm38 (mm10) using STAR with the following options: --outFilterType BySJout  --outFilterMultimapNmax 20  --outFilterMismatchNmax 2  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --alignSJstitchMismatchNmax 5  -1   5   5    --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimSegmentReadGapMax 3  --chimOutJunctionFormat 1   --quantMode GeneCounts  --twopassMode Basic
quantification was carried out during STAR mapping through the option --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: readcount.txt

source_name: Bone marrow derived macrophages

growth_protocol: BMDM were seeded in 12 well plates, 1 million cells per well, and incubated overnight in RPMI GlutMax supplemented with 10% FBS, penicillin (100 IU/ml), streptomycin (100ug/ml) and recombinant murine (M-CSF, 25μg/ml).

extract_protocol:
RNA was extracted with the RNeasy Kit (QIAGEN)
Samples frozen at -80℃ before shipping on dry ice to Novogene who performed RNA sequencing analysis.

treatment_protocol: Cells were washed with PBS and replenished with fresh media containing 1 mM CaCl2, then incubated with pd-VWF (10μg/ml) or LPS (100ng/ml) for 3.5 hours (T1) or 16 hours (T2) respectively.

value: Bone marrow derived macrophages

value: incubation with VWF

value: 16 hours


title: ERR⍺ KO_heart_15w_biological rep1

value: heart


title: VWF 16h biol rep 3


title: RSK2 knockout cell_ 0.1% DMSO_ biological rep2

value: RSK2 CRISPR deleted


title: RSK1 knockout cell_ 0.1% DMSO_ biological rep2

value: RSK1 CRISPR deleted


title: WT_heart_15w_biological rep3


title: VWF 16h biol rep 5


title: SLP HDAC4CA ZT0.5 HY replicate 3

first: Rui

last: Zhou

address: NIBS

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped with STAR (version 2.6.1a) to the GRCm38 mouse reference genome with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: mouse hypothalamus

extract_protocol:
Total RNA was isolated from the brain tissues using RNAprep Pure Tissue Kit (TIANGEN).
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L, NEB).

treatment_protocol: Mice were retro-obital injected with AAV viruses 3 weeks before dissection.

tag: overexpression

tag: zt time


title: SLP HDAC4CA ZT0.5 HY replicate 4


title: VWF 16h biol rep 2

tag: time


title: RSK2 knockout cell_100ng/ml EGF 5 hour_ biological rep1

tag: cell line

tag: treatment

value: 100ng/ml EGF


title: Control cell_100ng/ml EGF 5 hours_biological rep1


title: Control cell_0.1% DMSO_biological rep2


title: RSK2 knockout cell_ 0.1% DMSO_ biological rep1


title: SLP HDAC4CA ZT0.5 HY replicate 2


title: RSK1 knockout cell_100ng/ml EGF 5 hour_ biological rep1


title: RSK1 knockout cell_ 0.1% DMSO_ biological rep1


title: Control cell_0.1% DMSO_biological rep1


title: Osteogenic medium_donor 1

city: Aachen

first: Claudia

last: Goettsch

address: Pauwelsstr. 30

institute: RWTH Aachen

description: Gene expression data from OM-calcified human coronary artery smooth muscle cells at day 7.

hyb_protocol: Affymetrix GeneChip Hybridization, Wash & Stain Kit , according to the manufacturer's protocol;

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 controlled by GeneChip Command Console (AGCC) version 4.0 to produce CEL intensity files.

data_processing: The raw data were analyzed by using the Transcriptome Analysis Console software (TAC4.0, ThermoFisher Scientific, USA) with default parameters for gene level expression analysis based on the annotation Hg38 clariom_D_Human.r1.na36.hg38.a1.transcript.csv. SST-RMA was applied for normalization and summarization.

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: Human coronary artery smooth muscle cells from three independent donors were cultured in the presence of control media (DMEM, 10% FBS, 1% penicillin-streptomycin).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Calcification was induced for 7 days with osteogenic medium (OM) consisting of control media supplemented with 10 nM dexamethasone, 10 mM β-glycerol phosphate and 100 µM l-ascorbate phosphate.

tag: treament

value: Osteogenic medium


title: Control osteogenic medium_donor 2

description: Gene expression data from non-calcified human coronary artery smooth muscle cells at day 7.

source_name: Human coronary artery smooth muscle cells

value: Control


title: Osteogenic medium_donor 2

source_name: Human coronary aortic smooth muscle cells


title: SLP HDAC4CA ZT0.5 HY replicate 1


title: Control calcium-phosphate medium_donor 1

description: Gene expression data from non-calcified human coronary artery smooth muscle cells at day 3.

growth_protocol: Human coronary artery smooth muscle cells from three independent donors were cultured in control media (DMEM, 10% FBS, 1% penicillin-streptomycin).

treatment_protocol: Calcification was induced for 3 days with CaP consisting of control medium supplemented with 1.8 mM CaCl2 and 0.9 mM Na2HPO4/NaH2PO4 to reach a final concentration of 3 mM calcium and 2 mM phosphate.


title: VWF 3.5h biol rep 4

value: 3.5 hours


title: SLP HDAC4CA ZT0.5 TH replicate 3

source_name: mouse thalamus


title: Control osteogenic medium_donor 3


title: Calcium-phosphate medium_donor 1

description: Gene expression data from CaP-calcified human coronary artery smooth muscle cells at day 3.

value: Calcium phosphate medium


title: Osteogenic medium_donor 3


title: SLP HDAC4CA ZT0.5 TH replicate 4


title: Calcium-phosphate medium_donor 2


title: Control calcium-phosphate medium_donor 2


title: VWF 3.5h biol rep 5


title: VWF 16h biol rep 1


title: SLP HDAC4CA ZT0.5 TH replicate 2


title: VWF 3.5h biol rep 3


title: Control osteogenic medium_donor 1


title: Calcium-phosphate medium_donor 3


title: VWF 3.5h biol rep 1


title: LPS 16h biol rep 4

value: incubation with LPS


title: Control calcium-phosphate medium_donor 3


title: LPS 16h biol rep 3


title: LPS 16h biol rep 2


title: LPS 16h biol rep 1


title: SLP HDAC4CA ZT0.5 CTX replicate 4

source_name: mouse cortex


title: VWF 3.5h biol rep 2


title: SLP eGFP ZT0.5 HY replicate 4

value: eGFP


title: SLP HDAC4CA ZT0.5 CTX replicate 1


title: SLP eGFP ZT0.5 HY replicate 3


title: SLP HDAC4CA ZT0.5 CTX replicate 2