title: QKI7 sgMETTL1 input rep2

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RIP-seq reads were aligned to the GRCh38 genome assembly using STAR
peaks were called using exomePeak.
the RIP peaks were annotated using an ad hoc perl script.
Assembly: GRCh38
Supplementary files format and content: peak files were generated using exomePeak

growth_protocol: The HepG2-cas9 cells were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin and plasmocin prophylactic for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish

extract_protocol:
After cross-link with UV, the cells were collected by trypsinization, lysed in 1 ml M-PER buffer (78501, Thermo Fisher Scientific) with 100 U/ml RNase inhibitor and 1 × protease inhibitor on ice for 20 min, and sonicated in a Bioruptor Pico device (Diagenode) with 30s on/30s off for 10 cycles. Then the lysates were collected and subject to RIP with Flag antibody and Protein A/G Magnetic Beads. The RIP RNAs were recovered from the beads with RNA clean and concentrater kit. Both Input and RIP RNAs were used for sequencing.
ribozero RNA
KAPA Stranded mRNA-Seq Kit (Illumina Platforms) was utilized to construct library and sequencing was performed on an Illumina Nova Seq 6000.

tag: cell line

value: human liver cancer cell line

value: QKI7 overexpression

value: METTL1 KO

tag: rip antibody


title: 1338over, pH, replicate 2

status: Public on May 17 2023

type: SRA

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

library_source: transcriptomic

data_processing:
Sequenced reads were aligned to M. tuberculosis genome using bowtie2 v2.3.4.3 with parameters --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The processed data files represent these counts for each sample.
Assembly: AL123456.3
Supplementary files format and content: csv table, processed files contain raw counts - the numbers of overlapping reads for every annotated gene in each sample

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: bacterial culture

growth_protocol: M. tuberculosis H37Rv, pMV_E and 1338over M. tuberculosis strains were initially grown from frozen stocks for 10 days in Sauton medium containing (per liter): 0.5 g KH2PO4, 1.4 g MgSO4×7H2O, 4 g L-asparagine, 60 ml glycerol, 0.05 g ferric ammonium citrate, 2 g sodium citrate, 0.1 ml 1% ZnSO4, pH 7.0 (adjusted with 1M NaOH), and supplemented with ADC growth supplement, 0.05% Tween 80 and 50 µg/ml kanamycin (Sigma-Aldrich, St Louis, MO, USA) at 37°C with agitation (200 rpm). The starter cultures were inoculated into fresh medium (the same composition) and incubated until the logarithmic phase.

extract_protocol:
Bacterial cultures were rapidly cooled on ice, centrifuged, and total RNA was isolated by phenol-chloroform extraction after cell disruption with Bead Beater. After isolation, RNA was treated with Turbo DNase (Life Technologies, Carlsbad, CA, USA) to remove traces of genomic DNA, and purified with the RNeasy mini kit (Qiagen, Venlo, Netherlands).
RNA samples were depleted of 16S and 23S rRNA using Ribonuclease H (NEB) and custom oligonucleotides according to the protocol published by Huang et al. [10.1093/nar/gkz1169]. Sequencing libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturers’ protocol.

treatment_protocol: Bacterial cultures were grown up to the log phase (OD600 = 1), washed  up with PBS and diluted to OD600 = 0.2 (107 CFU/ml) by Sauton medium (pH 5.5) with ADC growth supplement and  0.05% Tween for low pH stress. For nitrosative or oxidative stress washed cultures were diluted to OD600 = 0.2 (107 CFU/ml) by  Sauton medium (pH 7) with ADC growth supplement and 0.05% Tween  with addition of DETA/NO donor (0.5 mM) or H2O2 (10 mM) respectively.  Bacteria were incubated in stress conditions at 37◦C with agitation (200 rpm) for 24 h, then harvested for total RNA isolation.

tag: cell type

value: bacterial culture

tag: strain

tag: phase

value: logarithmic

tag: vector

tag: treatment

value: pH


title: 1338over, pH, replicate 3


title: Figure3_SH10

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

country: USA

institute: NIAMS/NIH

description: chao_sle_noHB_RNA-seq_results.transcript.rpkm.xlsx

data_processing:
BCL to FastQ and demultiplex using Casava 1.8.2
Map to hg19 using Tophat 2.1.1
For whole blood samples, filter out Hemoglobin reads using bedtools intersectBed and a custom GTF
Calculate RPKM using Partek GS 6.6
Genome_build: hg19

organism: Homo sapiens

growth_protocol: Dermal Fibroblasts were cultured in complete CD10 media and passaged at least once every seven days

extract_protocol:
Dermal fibroblast: For sequencing preparation, total RNA was harvested from primary cells using the RNeasy Mini Kit (Qiagen) and cDNA was synthesized using the SuperScript III First-Strand Synthesis SuperMix for qRT-PCR (Invitrogen)
Whole blood: Paxgene tubes were used to collect RNA from patient and control whole blood. For RNA-Sequencing, first- and second-strand cDNA was synthesized using the TruSeq RNA Sample Preparation Kit (Illumina) and sequenced using the HiSeq 2000 (Illumina). FastQ files were generated using CASAVA 1.8.2 and mapped to hg19 using Tophat 2.1.0. Hemoglobin and intergenic reads were removed using bedtools intersectBed. RPKM values were calculated using Partek GS 6.6.  The RPKM values were transformed to Z-scores by subtracting the mean and dividing by the standard deviation of a set of healthy controls (n=15)
PBMC: Peripheral blood mononuclear cells (PBMC) were isolated from whole blood using Ficoll-Paque (Amersham Biosciences) gradient centrifugation
standard Illumina mRNA library construction

treatment_protocol: Dermal fibroblast cells were stimulated with TNF, LPS, Poly I:C or left unstimulated for 3 hours

value: Untreated

tag: run

value: Chao

tag: disease

value: Lupus

value: peripheral blood


title: QKI7 sgMETTL1 IP rep1

state: CA

tag: genotype

value: Flag


title: Figure3_C8

value: Control


title: SKD00501R-M03

city: Solna

first: Martin

last: Enge

address: Solnavägen 1

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Demultiplexed RNA reads were aligned using STAR 2.7.7a, duplicate reads removed using Picard 2.22.0 and read counts summarized using HTSeq 0.9.1. Cutoffs of 20000 counts and 500 features were used.
Assembly: GRCm38 with ERCC-spike ins and the reporter-gene EYFP

molecule: polyA RNA

organism: Mus musculus

source_name: Aorta

extract_protocol:
Aortae was perfused for 1 min with PBS at room temperature and then dissected. Lumen side was exposed and digested with 1 mg/mL collagenase I, 1 mg/mL dispase, and 150 μg/mL DNase-I for 30 min at 37 °C. The cell suspension was strained and then depleted of Cd45+ cells with Cd45 magnetic beads (protocol according to manufacturer). To purify endothelial cells, the suspension was stained with Cd45 and Cd31 antobodies, as well as a cell viability dye. FACS sorting was used to sort out Cd45-, Cd31+, viable endothelial cells, as well as some Cd45-, Cd31-, viable cells for control. Cells were sorted into 384 well plates with lysis buffer.
Library was constructed using smartseq2 protocol, as previously has been described. Briefly, primer annealing, followed by RT and cDNA amplification was followed by cleanup of PCR products. The cDNA was tagmented and final library anmplified using custom barcodes, then pooled and cleaned with SPRI beads. Libraries were then sequenced.

value: Endothelial

tag: tissue

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

tag: age

value: 3 months


title: 1338over, H2O2, replicate 3


title: 1338over, H2O2, replicate 2


title: QKI7 sgMETTL1 input rep1


title: QKI7 sgNS IP rep2

value: control


title: SKD00501R-M01


title: Figure3_C7


title: pMV_E, control, replicate 1

value: no treatment


title: SKD00501R-L16


title: QKI7 sgNS IP rep1

value: human liver cancer cell line

value: QKI7 overexpression


title: Figure3_C77


title: 1338over, DETA/NO, replicate 3

value: bacterial culture

value: DETA/NO


title: Figure3_C76


title: SKD00501R-L15


title: QKI7 sgNS input rep2


title: Figure3_C9


title: Figure3_C75


title: 1338over, pH, replicate 1

value: logarithmic

value: pH


title: SKD00501R-M02


title: 1338over, H2O2, replicate 1


title: 1338over, DETA/NO, replicate 2


title: Frankincense-treated [Y3]

city: Yangsan

first: Ki-Tae

last: Ha

address: Busandaehak-ro 49

country: South Korea

institute: Pusan National University

description:
Y3
mRNA-seq

data_processing:
Reads were mapped to the GRCh38 reference using STAR (Spliced Transcripts Alignment to a Reference, ver. 2.7.8a). Read counts for each gene were obtained by RSEM (ver.1.3.1).
Assembly: GRCh38
Supplementary files format and content: *.genes.results: Tab-delimited text files include TMM values for each Sample.

growth_protocol: 12Z cells were maintained in DMEM/F12 supplemented with 10% charcoal-stripped fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNAs were extracted using RNeasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA library prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: 12Z cells were treated with 70 ug/mL frankincense extract diluted in DMSO for 12 hrs. As control, DMSO was used.

value: Immortalized Human Endometriotic Cell

value: Wild type

value: Frankincense


title: 1338over, DETA/NO, replicate 1


title: SKD00501R-L13


title: Figure3_C74

value: Untreated

value: Chao

value: peripheral blood


title: SKD00501R-L12

value: Endothelial

value: Aorta


title: Figure3_C72

value: Control


title: Vehicle-treated [C3]

description:
C3
mRNA-seq

value: DMSO


title: 1338over, control, replicate 3

value: no treatment


title: Frankincense-treated [Y1]

description:
Y1
mRNA-seq


title: Frankincense-treated [Y2]

description:
Y2
mRNA-seq


title: SKD00501R-L10

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: SKD00501R-L11


title: 1338over, control, replicate 2

value: bacterial culture


title: PfDNMT KO, RING, rep1

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained.
Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2
Differentially expressed genes are determined by DESeq2  with Padj < 0.01 and absolute log2 fold change higher than 1.
The transcriptional profiles are normalized by TPM for multi-time points or condition comparisons.
Assembly: pf3D7_V3.0.fasta
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Plasmodium parasite

growth_protocol: 3D7 strains of P. falciparum were cultured in type O+ human RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 50mg/L hypoxanthine, 25 mM NaHCO3, 0.5% Albumax II and 40 mg/ml gentamicin sulfate. The culture was maintained at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2.

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS. Total RNA was isolated from the purified parasites using Quick-RNA MiniPrep kit (Zymo Research). The RNA was treated with the ezDNaseTM Enzyme (Invitrogen) to remove contaminating genomic DNA. RNA pellets were dissolved in 50 µL RNase-free water, and the RNA integrity was checked using the Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. RNA was fragmented by heating at 94 °C for 8 min, and cDNA was synthesized using reverse transcriptase with random primers. Afterward, 3’ dTMP adapters were ligated to the 3’ dAMP library fragments. The quality of the barcoded libraries was validated using the Agilent Bioanalyzer. The DNA 1000 Reagents were used to quantify the library sizes and confirm the absence of primer dimers. Libraries were quantified using a KAPA Universal Library Quantification Kit (Roche), and library concentrations were adjusted for library size. Libraries were sequenced on an Illumina NextSeq 550 in the Rapid Run mode using 150 nt paired end read sequencing .

value: gene disruption (PfDNMT KO)

tag: Stage

value: Ring stage


title: SKD00501R-L14


title: Figure3_C71


title: 1338over, control, replicate 1

value: logarithmic


title: Vehicle-treated [C2]

description:
C2
mRNA-seq

value: Immortalized Human Endometriotic Cell


title: Figure3_C70


title: QKI7 sgNS input rep1

value: human liver cancer cell line

value: QKI7 overexpression

value: control


title: Vehicle-treated [C1]

description:
C1
mRNA-seq

value: Wild type


title: ya96flow480: HUVEC under flow 48 hr rep4

city: Chicago

first: Luisa

last: Iruela-Arispe

state: IL

address: 303 East Superior Street Simpson Querrey, 8-522

department: Cell and Developmental Biology

institute: Northwestern University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Each log10 FPKM gene expression profile was rescaled to zero-mean and unit-resolution for both the cord vs culture and flow vs static datasets. Data was adjusted for sample chip batch effects using an empirical Bayes framework with the ComBat function from the sva package; no covariates were included in the model and the algorithm was set to use non-parametric adjustments.
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited text file include log10-transformed FPKM values for each sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Primary umbilical vein endothelial cells were isolated as previously described 41, 55 from umbilical cords 2-4 hours after delivery at the University of California, Los Angeles (UCLA). All HUVECs were de-identified and under UCLA IRB (IRB #16-001694). Cells were grown in culture in MCDB 131 with antibiotics (VEC Technologies, Rensselaer, NY) and containing 10% fetal bovine serum (FBS, Omega Scientific, Tarzana, CA) Cells were subsequently grown to 90-100% confluence in 10-cm2 plates and harvested at specified passages.

extract_protocol:
Human umbilical cords were collected under Institutional Review Board (UCLA IRB#16-001694) at time of the delivery and processed 2-4 hours from time of birth. The umbilical vein was cannulated with a 18G animal feeding needle with a blunt tip in the direction of oxygenated blood flow from the placenta to the fetus. The umbilical vein was serially washed with 20 mL of phosphate-buffered saline (PBS) 2x. Subsequently, for ex-vivo samples 1mL of RLT from RNeasy Micro Kit (Qiagen, Germantown, MD), was flushed through closed circuit and re-aspirated with the distal end of the umbilical cord clamped and stored in -80-degrees C until all RNA was ready to be extraction. The length of time to obtained cells was approximately 30-60 minutes from cord clamping at delivery. For the in-vitro samples, after PBS wash, 8 mL of collagenase (210 IU, Worthington Biochemical, Lakewood, NJ) was flushed into the umbilical vein and it was incubated at 37-degrees C for 20-minutes. The flushed cells were subsequently collected and collagenase was inactivated with the addition of equivalent volume 10% feta bovine serum (FBS) with MCDB 131 media (VEC Technologies, Rensselaer, NY). The cells were pelleted, resuspended in media and plated. After cells became confluent they were passaged using 1x Trypsin (Corning, Manassas, VA) and cells were collected with RLT for RNA extraction in early passage (passage 2-3) or late passage (passage 7-8).  Subsequently all RNA was extracted concomitantly using RNeasy Micro Kit (Qiagen, Germantown, MD). Contamination with genomic DNA was eliminated with incubation of DNase I at room temperature. Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA) was used to assess RNA integrity and Qubit (Invitrogen, Carlsbad, CA) was used for RNA concentration and purity.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Orbital shear stress (130 rpm) was applied to confluent cell cultures by using an orbital shaker positioned inside the incubator as previously discussed 71. The shear stress within the cell culture well corresponds to arterial magnitudes (11.5 dynes/cm2) of shear stress. Control cells were identical passage endothelial cells that were exposed to static conditions (0 dyne/cm2).

tag: donorid

value: Human umbilical vein endothelial cell

tag: experimentalcondition


title: Figure3_C6

value: Untreated

value: Chao

value: peripheral blood


title: ya95flow480: HUVEC under flow 48 hr rep3


title: QKI7 sgMETTL1 IP rep2

value: METTL1 KO

value: Flag


title: SKD00501R-L08

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: Figure3_C73

value: Control


title: SKD00501R-L06

value: 3 months


title: Huh7 cells, sgcontrol, biol rep 2

city: chongqing

first: Pan

last: Mingang

address: No. 1, Medical College Road, Yuzhong District, Chongqing

country: China

institute: ChongQing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

value: hepatocellular carcinoma cells

value: WT


title: Huh7 cells, sgcontrol, biol rep 3


title: ya94flow480: HUVEC under flow 48 hr rep2


title: ya93flow480: HUVEC under flow 48 hr rep1


title: SKD00501R-L05


title: Figure3_C67


title: Huh7 cells, sgRAD51, biol rep 3

value: RAD51 knockdown


title: ya96flow240: HUVEC under flow 24 hr rep4


title: SKD00501R-L09


title: ya95flow240: HUVEC under flow 24 hr rep3


title: SKD00501R-L04


title: SKD00501R-L03


title: Huh7 cells, sgRAD51, biol rep 2


title: Figure3_C66


title: SKD00501R-L02


title: SKD00501R-L07


title: Huh7 cells, sgRAD51, biol rep 1


title: Figure3_C63


title: SKD00501R-L01


title: SKD00501R-K16


title: Figure3_C69


title: 52-C4BX

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using Tophat (v2.1.1)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE v25
Supplementary files format and content: csv file; raw counts

source_name: Tumor

extract_protocol:
Total RNA for Library Preparation and Sequencing analysis was purified from tumor tissue using the RNAeasy Plus Kit (QIAGEN) that included a genomic DNA elimination step.
Coding RNA transcripts were enriched using human exome panel hybridization (Twist Biosciences).  Size, concentration, and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v3, following the manufacurer’s protocol.
Sequencing of 8–10 pM of each library was done on the NovaSeq sequencer as 100bp paired-end read runs.

value: Tumor


title: 52-BLBX

value: BLBX


title: Huh7 cells, sgcontrol, biol rep 1


title: Figure3_C62


title: SKD00501R-K15


title: ya95flow080: HUVEC under flow 8 hr rep3


title: ya93flow240: HUVEC under flow 24 hr rep1


title: 49-BLBX


title: ya94flow080: HUVEC under flow 8 hr rep2


title: Figure3_C61


title: Figure3_C65


title: ya94flow240: HUVEC under flow 24 hr rep2


title: Figure3_C60


title: 48-primary

value: Primary


title: ya96flow005: HUVEC under flow 30 min rep4

value: Human umbilical vein endothelial cell


title: ya93flow080: HUVEC under flow 8 hr rep1


title: 48-BLBX


title: SKD00501R-K12


title: 48-C4BX


title: SKD00501R-K13


title: SKD00501R-K11


title: Figure3_C5

value: Untreated


title: 44-Primary


title: ya95flow005: HUVEC under flow 30 min rep3


title: Figure3_C57

value: Chao


title: SKD00501R-K10


title: ya94flow005: HUVEC under flow 30 min rep2


title: SKD00501R-K09


title: Figure3_C64

value: peripheral blood


title: ya96flow000: HUVEC under flow 0 min rep4


title: Figure3_C59


title: ya93flow005: HUVEC under flow 30 min rep1


title: Figure3_C58


title: SKD00501R-K14


title: 43-BLBX


title: 44-EOTBX

value: EOTBX


title: ya94flow000: HUVEC under flow 0 min rep2


title: Figure3_C56


title: 42-Primary


title: SKD00501R-K07


title: 42-C4BX


title: ya93flow000: HUVEC under flow 0 min rep1


title: Figure3_C55


title: Figure3_C53


title: SKD00501R-K06


title: 39-Primary


title: SKD00501R-K05


title: ya75l: HUVEC from late culture rep7

value: cultureLate


title: 39-C4BX


title: ya95flow000: HUVEC under flow 0 min rep3


title: ya74l: HUVEC from late culture rep6


title: Figure3_C52


title: 38-BLBX


title: SKD00501R-K08

value: Endothelial


title: 39-BLBX


title: SKD00501R-K04

value: Aorta


title: ya73l: HUVEC from late culture rep5


title: Figure3_C50


title: Figure3_C51


title: 37-BLBX


title: SKD00501R-K01

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: Figure3_C4

value: Control


title: ya72l: HUVEC from late culture rep4


title: Figure3_C54


title: ya70l: HUVEC from late culture rep3


title: 34-Primary


title: SKD00501R-K02

value: 3 months


title: Figure3_C48


title: Figure3_C68


title: Figure3_C47


title: 33-C4BX


title: ya65l: HUVEC from late culture rep1


title: SKD00501R-K03


title: ya75e: HUVEC from early culture rep7

value: cultureEarly


title: 32-BLBX


title: SKD00501R-J13


title: 33-BLBX


title: ya74e: HUVEC from early culture rep6


title: SKD00501R-J16


title: 35-C4BX


title: ya66l: HUVEC from late culture rep2


title: SKD00501R-J14


title: Figure3_C45


title: SKD00501R-J15


title: Figure3_C49


title: SKD00501R-J12


title: ya73e: HUVEC from early culture rep5


title: 30-BLBX


title: Figure3_C46


title: Figure3_C44


title: 30-Primary


title: 29-C4BX


title: SKD00501R-J10


title: SKD00501R-J09


title: Figure3_C43


title: SKD00501R-J11


title: 30-C4BX


title: ya70e: HUVEC from early culture rep3


title: SKD00501R-J08


title: ya72e: HUVEC from early culture rep4


title: Figure3_C40


title: 25-primary


title: SKD00501R-J06


title: Figure3_C42


title: Figure3_C41


title: ya65e: HUVEC from early culture rep1


title: ya75c: HUVEC from cord rep7

value: cord


title: 25-C4BX


title: SKD00501R-J07


title: Figure3_C3


title: 29-BLBX


title: Figure3_C39


title: ya66e: HUVEC from early culture rep2


title: ya73c: HUVEC from cord rep5


title: SKD00501R-J05


title: Figure3_C38


title: 25-BLBX


title: SKD00501R-J04


title: 24-C4BX


title: ya72c: HUVEC from cord rep4


title: ya74c: HUVEC from cord rep6


title: 24-BLBX


title: Figure3_C37


title: Figure3_C36


title: ya70c: HUVEC from cord rep3


title: SKD00501R-J02


title: ya66c: HUVEC from cord rep2


title: SKD00501R-J03


title: ya65c: HUVEC from cord rep1


title: Figure3_C34


title: Figure3_C35


title: SKD00501R-I16


title: SKD00501R-J01


title: 23-primary


title: 104766-001-042R

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

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.
Assembly: 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

growth_protocol: The study was approved by the governmental central committee on animal experiments (AVD5010020172064) and the animal welfare body of The Netherlands Organization for Applied Scientific Research (IVD TNO; TNO-452/TNO-459) and was in compliance with European Community specifications regarding the use of laboratory animals. APOE*3-Leiden transgenic mice were housed and bred at the AAALAC-accredited SPF animal facility at TNO (TNO Leiden). Female animals were used for this study since they develop NASH and liver fibrosis [15,16,35] concomitantly with atherosclerosis and respond well to statins.During the study, mice were group-housed in a temperature-controlled room (21 ± 369 2°C) on a 12h light-dark cycle at 50-60% humidity and had free access to heat-sterilized 370 tap water and food. Body weight, food intake (per cage) and clinical signs were monitored 371 regularly.

extract_protocol:
For next generation sequencing total RNA was isolated from snap-frozen liver tissue us-490 ing the RNA-Bee total-RNA isolation kit (Bio-Connect, Huissen, The Netherlands) and 491 was purified with NucleoSpin RNA Clean-up (Macherey-Nagel, Düren, Germany). RNA 492 concentrations were determined by Nanodrop 1000 (Isogen Life Science, De Meern, The 493 Netherlands) and RNA quality was evaluated with 2100 Bioanalyzer (Agilent Technolo-494 gies). Isolated RNA was used for generation of strand-specific mRNA-seq libraries for 495 next generation sequencing.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). Strand-specific cDNA libraries were generated from total-RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext 496 Ultra II Directional RNA Library Prep Kit (NEB #E7760S/L, New England Biolabs, Ips-497 wich, MA, USA) resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 v1.5 system (Illumina, New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-40 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: The number of animals per group was calculated a priori with a power analysis using GPower3.1, based on a minimal effect size of 50%, standard deviation of 50% and using a one-sided test with 95% confidence interval and power of 0.85. Female APOE*3-Leiden mice (8-14 weeks old) were fed a semi-synthetic Western type diet (WTD) containing among others 15% (w/w) cocoa butter, 40.5% (w/w) sucrose and 1% (w/w) cholesterol (Ssniff Spezialdiäten GmbH, Soest, Germany) for a run-in period of three weeks. Hereafter, at t=0, mice were matched for age, body weight and 4h-fasted plasma cholesterol and triglycerides into two groups of n=16 each. From baseline (t=0) onward, one of these two WTD-fed groups was provided 3.0 mg/kg/day atorvastatin (Lipitor pills, obtained from the Leiden University Medical Center pharmacy) as admixture to the diet. At t=5 weeks, the atorvastatin dose was increased to 4.5 mg/kg body weight/day to obtain a 30% decrease in total cholesterol levels, as is representative for a large group of patients in the mild-hyperlipidemic population. Atorvastatin was selected because of its broad dosing window and the absence of hepatotoxic effects within these dosages. At t=22 weeks, the WTD was supplemented with 0.05% (w/w) sodium cholate (Ssniff Spezialdiäten) to further raise plasma cholesterol levels. Mice continued on this diet for another ten weeks to further increase hepatic fibrosis and atherosclerosis development further. At t=32 weeks, animals were sacrificed by CO2 asphyxiation, terminal blood was collected through heart puncture, and livers, hearts and aortic roots were fixed in formalin or snapfrozen in liquid nitrogen. In addition to the two WTD-fed groups, a group of ten mice that were kept on a maintenance chow diet (Ssniff Spezialdiäten) was included as healthy reference.

value: liver

tag: treatmentperiod

tag: mousenr


title: 21-EOTBX-2

value: Tumor


title: 104766-001-041R


title: Figure3_C32


title: SKD00501R-I15


title: SKD00501R-I14


title: Figure3_C31


title: 21-EOTBX-1


title: SKD00501R-I13


title: 104766-001-040R


title: 21-C4BX


title: Figure3_C30


title: 104766-001-039R


title: SKD00501R-I12


title: 21-BLBX

value: BLBX


title: 104766-001-037R


title: SKD00501R-I11


title: 104766-001-038R


title: Figure3_C2


title: 23-BLBX


title: 20-C4BX


title: Figure3_C33


title: 20-BLBX


title: Figure3_C29


title: SKD00501R-I10


title: SKD00501R-I09


title: 104766-001-036R


title: 19-Primary

value: Primary


title: Figure3_C27


title: Figure3_C28


title: SKD00501R-I08


title: 104766-001-035R


title: 104766-001-034R


title: Figure3_C26


title: 104766-001-033R


title: 19-EOTBX


title: SKD00501R-I07


title: 17-Primary


title: SKD00501R-I06


title: 104766-001-032R


title: 17-BLBX


title: 23-C4BX


title: SKD00501R-I05


title: SKD00501R-I04


title: 16-Primary


title: Figure3_C23


title: Figure3_C25


title: 104766-001-030R


title: 104766-001-031R


title: Figure3_C22


title: 16-EOTBX


title: Figure3_C24


title: Figure3_C21


title: SKD00501R-I02


title: 15-C4BX


title: SKD00501R-I03


title: SKD00501R-I01


title: Figure3_C20


title: SKD00501R-H16


title: 104766-001-028R


title: 104766-001-026R


title: Figure3_C1


title: 14-BLBX


title: 104766-001-027R


title: 13-C4BX


title: 104766-001-025R


title: 13-BLBX


title: SKD00501R-H15


title: Figure3_C18


title: SKD00501R-H14


title: 104766-001-024R


title: 15-BLBX


title: 104766-001-023R


title: SKD00501R-H13


title: 12-C4BX


title: 11-primary


title: 104766-001-022R


title: Figure3_C17


title: 104766-001-029R


title: Figure3_C16


title: 104766-001-021R


title: SKD00501R-H12


title: Figure3_C14


title: SKD00501R-H10


title: Figure3_C19


title: 11-EOTBX-2


title: 104766-001-020R


title: 11-EOTBX-1


title: SKD00501R-H11


title: Figure3_C13


title: 11-C4BX


title: SKD00501R-H09


title: 104766-001-019R


title: Figure3_C12


title: Figure3_C11


title: 11-BLBX


title: SKD00501R-H08


title: 12-BLBX


title: 104766-001-018R


title: 104766-001-017R


title: Figure3_C15


title: SKD00501R-H07


title: SKD00501R-H06


title: Figure3_C10


title: 104766-001-016R


title: 10-primary


title: Figure3_160223_0420_NOMID19_peripheral_blood

value: NOMID


title: 104766-001-015R


title: 10-BLBX


title: SKD00501R-H05


title: SKD00501R-H04


title: Figure3_160223_0420_NOMID18_peripheral_blood

value: Untreated


title: 104766-001-014R


title: 5-Primary


title: SKD00501R-H03


title: Figure3_160223_0420_NOMID17_peripheral_blood


title: 104766-001-013R


title: Figure3_151217_0413_NOMID16_peripheral_blood


title: SKD00501R-H02


title: Figure3_151217_0413_NOMID15_peripheral_blood


title: 5-BLBX


title: SKD00501R-H01


title: 104766-001-011R


title: SKD00501R-G16


title: Figure3_151217_0413_NOMID14_peripheral_blood


title: 104766-001-010R


title: Figure3_151217_0413_NOMID13_peripheral_blood


title: 4-BLBX


title: 6-BLBX


title: SKD00501R-G15


title: 3-Primary


title: 2-primary


title: Figure3_151208_0406_NOMID12_peripheral_blood


title: 5-C4BX


title: Figure3_151208_0406_NOMID11_peripheral_blood


title: 104766-001-008R


title: SKD00501R-G14


title: Figure3_140225_140305_NOMID10_peripheral_blood


title: 104766-001-012R


title: Figure3_140225_140305_NOMID9_peripheral_blood


title: 2-BLBX


title: SKD00501R-G12


title: SKD00501R-G13


title: 104766-001-007R


title: 104766-001-006R


title: Figure3_140225_140305_NOMID8_peripheral_blood


title: 4-C4BX


title: 104766-001-009R


title: 2-C4BX


title: SKD00501R-G11


title: 104766-001-004R


title: Figure3_140225_140305_NOMID7_peripheral_blood


title: SKD00501R-G10


title: SKD00501R-G09


title: 104766-001-003R


title: Figure3_130220_0042_NOMID6_peripheral_blood


title: 1-C4BX


title: 1-BLBX


title: SKD00501R-G08


title: Figure3_130220_0042_NOMID5_peripheral_blood


title: HEKn MALAT1 LNA-GapmeR_rep3

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description: RNA extracted from transfected HEKn treated for three days with CaCl2

data_processing:
Demultiplexed and trimmed fastq's are generated from Illumina BaseSpace with FastqGeneration app
Alignment and raw counts are generated with nf-core/rnaseq v3.3 pipline. The pipiline are running with default parameters
Assembly: GRCh37
Supplementary files format and content: Matrix table with raw gene counts for every gene and each sample

source_name: keratinocytes

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) and purified from DNA contamination through a DNase I (Qiagen, IT) digestion step. Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.

value: skin; Neonatal Foreskin

value: Primary human keratinocytes

value: normal


title: 104766-001-001R


title: HEKn MALAT1 LNA-GapmeR_rep2


title: 1-EOTBX

value: EOTBX


title: SKD00501R-G07

value: Endothelial


title: 104766-001-005R


title: Figure3_130220_0042_NOMID4_peripheral_blood

value: peripheral blood


title: SKD00501R-G06

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: HEKn MALAT1 LNA-GapmeR_rep1


title: E14-Mettl3-KO paused, time 8h, rep2

city: Toronto

first: Evelyne

middle: Anne

last: Collignon

state: ON

address: 60 Murray Street, Box42,

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

data_processing:
Libraries were trimmed of adaptors and quality-checked using Trim Galore! v0.4.0, and then aligned to the mm10 transcriptome with ERCC sequences using TopHat2115 v2.0.13. Gene counts were obtained from the featureCounts function of subread (v1.5.0) with options: -t exon -g gene_id.
3UTR raw counts were imported into R and analyzed with edgeR (v3.32.1). Conversions counts were normalized to total counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts (total and T-to-C conversion) of all genes for all samples.
Supplementary files format and content: tab-delimited text file with expression levels (log2) for all samples with normalization; and half-lives of all transcripts in paused condition calculated for WT and KO ESCs separately.

growth_protocol: ES cells were grown on gelatin for 2 weeks in FBS/LIF media, under paused condition (200 nM INK128).

extract_protocol:
RNA was extracted from equal number of ESCs (5x10^5 cells),RNA extraction using phenol-chloroform extraction, as per manufacturer’s instructions. RNAs were treated with 10mM iodoacetamide and ethanol precipitated.
Library preparation was done with Quant-seq 3′-end mRNA library preparation (Lexogen) using 100ng RNA.

treatment_protocol: Cells were pre-incubated with 100μM S4U, protected from light and with media exchange every 3h, for a total of 12h. Then, the medium was changed back to standard (no S4U), and cells were collected at different times (0h, 1h, 3h, 8h).

value: embryonic stem cells

tag: cell line

value: paused

tag: time


title: E14-Mettl3-KO paused, time 8h, rep1

tag: cell type


title: HEKn NEAT1 LNA-GapmeR_rep3


title: Figure3_130220_0042_NOMID2_peripheral_blood


title: E14-WT paused, time 8h, rep2

value: WT


title: SKD00501R-G04

tag: strain

value: 3 months


title: SKD00501R-G05


title: E14-WT paused, time 8h, rep1


title: Figure3_121024_SN923_0165_BD161WACXX_NOMID1_peripheral_blood


title: SKD00501R-G03


title: HEKn NEAT1 LNA-GapmeR_rep2


title: Figure3_150415_0359_UI9_peripheral_blood

value: Undifferentiated Interferonopathy


title: 104766-001-002R

value: liver


title: HEKn Non Targeting LNA-GapmeR_rep3


title: Figure3_150108_0325_UI8_peripheral_blood


title: E14-Mettl3-KO paused, time 3h, rep2


title: SKD00501R-G01


title: HEKn Non Targeting LNA-GapmeR_rep2


title: Figure3_130220_0042_NOMID3_peripheral_blood


title: Figure3_150108_0325_UI7_peripheral_blood


title: E14-WT paused, time 3h, rep1


title: Figure3_150108_0325_UI6_peripheral_blood


title: HEKn Non Targeting LNA-GapmeR_rep1


title: SKD00501R-F15


title: E14-Mettl3-KO paused, time 1h, rep2


title: SKD00501R-F16


title: Figure3_140708_140725_combined_UI5_peripheral_blood


title: E14-Mettl3-KO paused, time 1h, rep1


title: SKD00501R-G02


title: Figure3_140708_140725_combined_UI4_peripheral_blood


title: E14-WT paused, time 1h, rep2


title: HEKn NEAT1 LNA-GapmeR_rep1


title: Figure3_140708_140725_combined_UI3_peripheral_blood


title: SKD00501R-F13


title: SKD00501R-F11


title: E14-Mettl3-KO paused, time 0, rep2


title: E14-Mettl3-KO paused, time 3h, rep1


title: SKD00501R-F12


title: HEK293FT-PIE-SRSF3

first: Xiangbin

last: Ruan

address: 6054 S. DREXEL AVE.

institute: University of Chicago

data_processing:
RNA base variants calling was performed by JACUSA2_v2.0.0
raw Fastq files were aligned and mapped to hg38 or mm10 reference with STAR
known SNPs in dbSNP version 138 (hg38) or version 137 (mm10) or SNVs with low read depth (less than 5-read depth) were filtered out
Gene-level counts were calculated by Rsubread
Assembly: hg38/mm10
Supplementary files format and content: text files include RNA editing information for each group/sample
Supplementary files format and content: text files include gene-level count values for each sample

source_name: HEK293FT cultured cells

growth_protocol: HEK293FT cells (purchased from ATCC) were cultured at 37 ℃ in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from transfected cells with Direct-zol RNA microprep kit according to manufacturer’s instructions (ZYMO)
TruSeq Stranded mRNA Library Prep kit (Illumina) was used for preparing sequencing libraries

treatment_protocol: Cells transfected in suspension with lipofectamine 2000 and changed to fresh medium 6 hours after transfection,

value: transfected with pR220_PIE-SRSF3 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-YTHDC1

value: transfected with pR249_PIE-YTHDC1 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-STAU2

value: transfected with pR223_PIE-STAU2 vector with Lipofectamine 2000 for 24h


title: Figure3_140708_140725_combined_UI2_peripheral_blood

value: Untreated


title: HEK293FT-PIE-TARDBP

description: PIE-TARDBP

value: transfected with pR258_PIE-TARDBP vector with Lipofectamine 2000 for 24h


title: E14-Mettl3-KO paused, time 0, rep1


title: Figure3_130716_SN7001365_0063_AC1FYFACXX_UI1_peripheral_blood


title: SKD00501R-F10


title: Figure3_151217_0413_HC18_peripheral_blood

value: HC


title: HEK293FT-PIE-SRSF2

value: transfected with pR219_PIE-SRSF2 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-YTHDC2

value: transfected with pR250_PIE-YTHDC2 vector with Lipofectamine 2000 for 24h


title: E14-WT paused, time 0, rep1


title: SKD00501R-F09

value: Endothelial


title: Figure3_141120_0310_HC17_peripheral_blood

value: peripheral blood


title: HEK293FT-PIE-SRSF1

value: transfected with pR218_PIE-SRSF1 vector with Lipofectamine 2000 for 24h


title: SKD00501R-F14

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: SKD00501R-F08


title: HEK293FT-PIE-QKI7

value: transfected with pR205_PIE-QKI7 vector with Lipofectamine 2000 for 24h


title: E14-WT paused, time 1h, rep1

value: embryonic stem cells

value: WT

value: paused


title: Figure3_131118_SN923_0215_AD2BFTACXX_SAVI_1_HC16_peripheral_blood


title: SKD00501R-F07

value: 3 months


title: WT BAT HSF1 ChIPseq after 40min cold stress rep2.1

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

library_source: genomic

data_processing:
Reads were trimmed to remove low-quality bases and adapter sequences using TrimGalore v0.6.0 (https://github.com/FelixKrueger/TrimGalore) with default settings. Trimmed reads were aligned to the GRCm38.p6 reference genome from GENCODE vM24 using bwa mem v0.7.17 (Li, 2013), marking duplicates using SAMBLASTER v0.1.24 (Faust & Hall, 2014). Alignments were filtered using SAMtools view v1.9 (Li et al., 2009) with the parameters ‘-q 30 -F 2828’ and ‘-f 2’.
For peak calling, alignments were additionally filtered using SAMtools view with the parameter ‘-F 1024’ to remove duplicate reads. Peaks were called using ‘callpeak’ in MACS2 v2.2.7.1 (Zhang et al., 2008) using the parameters, “-f BAMPE -g ‘mm’ -q 0.05 --keep-dup ‘all’” and specifying the corresponding input samples using the “-c” parameter.
Bigwig files were generated using the bamCoverage tool in deepTools v3.4.3 (Ramírez et al., 2016) using the parameters, “--binSize 10 --extendReads --normalizeUsing ‘CPM’ --samFlagExclude 1024 --samFlagInclude 64” and “--blackListFileName” to specify the ENCODE blacklist v2.
Assembly: mm10
Supplementary files format and content: Bigwig files containing CPMs.
Supplementary files format and content: narrowPeak files containing peaks called by MACS2.

molecule: genomic DNA

source_name: BAT

extract_protocol:
BAT was fixed with 0.8% formaldehyde for 12min (H3K27Ac ChIP) or with 2mM DSG for 25min followed by 0.8% formaldehyde for 12min (other ChIPs). Sonication was done with Diagenode Bioruptor UCD-200, 5" on and 5" off for 3x3min.
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core form 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to uniquely barcoded dual indexes (IDT, Coralville, IA USA).

value: BAT

tag: chip antibody

value: Cell Signaling Tech 4356

value: 40min cold stress


title: SKD00501R-F06


title: HEK293FT-PIE-NOVA1

value: transfected with pR221_PIE-NOVA1 vector with Lipofectamine 2000 for 24h


title: Figure3_131118_SN923_0215_AD2BFTACXX_SAVI_1_HC15_peripheral_blood

value: Untreated

value: HC


title: SKD00501R-F05


title: Figure3_121003_and_121016_Combined_HC14_peripheral_blood


title: TXNIP KO BAT HSF1 ChIPseq input after 40min cold stress

value: TXNIP KO


title: Figure3_120810_Yins_run_HC13_peripheral_blood

value: Relative


title: SKD00501R-F04

value: Endothelial


title: HEK293FT-PIE-LIN28B

value: transfected with pR212_PIE-LIN28B vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-QKI6

value: transfected with pR204_PIE-QKI6 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-LIN28A

value: transfected with pR211_PIE-LIN28A vector with Lipofectamine 2000 for 24h


title: SKD00501R-F03

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: HEK293FT-PIE-KHDRBS3

value: transfected with pR253_PIE-KHDRBS3 vector with Lipofectamine 2000 for 24h


title: TXNIP KO BAT HSF1 ChIPseq after 40min cold stress rep1


title: WT RT input for BAT HSF1 ChIPseq 2

value: WT


title: WT RT input for BAT HSF1 ChIPseq

value: RT


title: TXNIP KO BAT HSF1 ChIPseq after 40min cold stress rep2

value: BAT


title: WT BAT HSF1 ChIP at RT rep2

value: Cell Signaling Tech 4356


title: Figure3_120810_Yins_run_HC11_peripheral_blood

value: peripheral blood


title: SKD00501R-F01

value: 3 months


title: SKD00501R-F02


title: Figure3_120810_Yins_run_HC12_peripheral_blood

value: Untreated


title: WT BAT HSF1 ChIPseq after 40min cold stress rep1.1

value: 40min cold stress


title: WT BAT HSF1 ChIP at RT rep1


title: SKD00501R-E16


title: Figure3_120810_Yins_run_HC8_peripheral_blood

value: HC


title: WT BAT HSF1 ChIPseq input after 4 hour cold stress

value: 4h cold stress


title: Figure3_120810_Yins_run_HC9_peripheral_blood

value: Relative-HC


title: Figure3_120810_Yins_run_HC7_peripheral_blood


title: HEK293FT-PIE-IGF2BP1

value: transfected with pR213_PIE-IGF2BP1 vector with Lipofectamine 2000 for 24h


title: SKD00501R-E14

value: Endothelial


title: HEK293FT-PIE-IGF2BP2

value: transfected with pR248_PIE-IGF2BP2 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-KHDRBS2

value: transfected with pR252_PIE-KHDRBS2 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-FUBP1

value: transfected with pR254_PIE-FUBP1 vector with Lipofectamine 2000 for 24h


title: WT BAT HSF1 ChIPseq after 4 hour cold stress rep1


title: SKD00501R-E13

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: Figure3_120810_Yins_run_HC5_peripheral_blood


title: WT BAT HSF1 ChIPseq input after 40min cold stress

value: WT


title: SKD00501R-E12


title: HEK293FT-PIE-CELF4

value: transfected with pR237_PIE-CELF4 vector with Lipofectamine 2000 for 24h


title: Figure2_140617_P1_s08_TNF

description: 140429_140521_140617_RNA-Seq_results.transcript.reads.xlsx

source_name: Patient IIU040

value: TNF

value: NDAS

value: Dermal Fibroblast


title: Figure3_120810_Yins_run_HC10_peripheral_blood

value: Untreated

value: Relative

value: peripheral blood


title: HEK293FT-PIE-CELF2

value: transfected with pR235_PIE-CELF2 vector with Lipofectamine 2000 for 24h


title: HEK293FT-PIE-KHDRBS1

value: transfected with pR251_PIE-KHDRBS1 vector with Lipofectamine 2000 for 24h


title: WT BAT HSF1 ChIPseq after 40min cold stress rep2

value: BAT

value: Cell Signaling Tech 4356

value: 40min cold stress


title: SKD00501R-E11

value: Endothelial

value: 3 months


title: Figure2_140617_P1_s07_unstimulated

value: unstimulated


title: HEK293FT-PIE-CELF1

value: transfected with pR234_PIE-CELF1 vector with Lipofectamine 2000 for 24h


title: SKD00501R-E10

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: HEK293FT-PUM2-AD

value: transfected with pR288_mCherry-PUM2 vector with Lipofectamine 2000 for 24h


title: SKD00501R-E15


title: Figure2_140617_Healthy_control_IIU043_s06_LPS

source_name: Healthy control IIU043

value: LPS

value: HC


title: WT BAT HSF1 ChIPseq after 4 hour cold stress rep2

value: WT

value: 4h cold stress


title: WT BAT HSF1 ChIPseq after 40min cold stress rep1


title: SB28-WT

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Single-cell gene expression was obtained using kits from 10x Genomics (Single Cell 3' v3). Libraries were sequenced on the Illumina NovaSeq platform at 28bp by 90bp setting to obtain at least 60,000 reads per cell. Read processing, read alignment, cell-barcode demultiplexing, and gene-specific UMI counting was performed with CellRanger (v3.0.2)(Zheng et al., 2017) using the mouse references mm10(ensemble version r97, MH029771.1-sfGFP and GQ357182.1-eGFP CDS sequences were downloaded from Genbank and added to the references, see DOI:https://doi.org/10.6084/m9.figshare.21094390 for details).
Distinct samples were processed independently and reviewed for quality that each sample achieved > 7000 cells, > 3000 expressed genes, 94.1% reads in cells. Both samples were then aggregated by CellRanger for downstream analyses. Seurat (version 4.0.6)(Stuart et al., 2019) were then used for analysis based on filtered feature barcode matrices. Briefly, cells with < 200 expressed genes or genes expressed in < 3 cells were filtered out from analysis. SCTransform (Seurat function) were used to normalize the data using top 3000 variable genes and regressing out the effect of mitochondrial expression percentage and cell cycle scores(Tirosh et al., 2016).
We then performed Principal Component Analysis (PCA) on the scaled genes and selecting the top 10 PCs for following analysis because the standard deviation plateaued after top 10 PCs in ElbowPlot (Seurat function). tSNE and UMAP have been ran and clusters have been identified using default parameters from Seurat. (Details command lines used, QC files, UMAP/tSNE projection and clustering meta data could be found at DOI:https://doi.org/10.6084/m9.figshare.21094390).
barcode suffix "-1" to "-2" were SB28-KO and SB28-WT
Assembly: mm10
Supplementary files format and content: filtered 10x h5 file

source_name: tumor tissue inoculated SB28 tumors

extract_protocol:
Single cell suspensions were obtained using Tumor Dissociation Kit (Miltenyi™, 130-096-730) and the gentleMACS Octo Dissociator (Miltenyi™) per manufacture instruction.
Single cell suspensions were processed in the University of Texas Genomic Sequencing and Analysis Facility. Cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).

tag: inoculated site

value: Brain


title: SB28-KO


title: SKD00501R-E08


title: Figure2_140617_Healthy_control_IIU043_s05_TNF

tag: treatment

value: TNF

value: Dermal Fibroblast


title: Figure2_140617_Healthy_control_IIU043_s04_unstimulated

tag: run


title: Figure3_120810_Yins_run_HC6_peripheral_blood

value: Untreated

tag: disease

value: Relative

value: peripheral blood


title: HEK293FT-AP-PUM2

value: transfected with pR287_AP-PUM2 vector with Lipofectamine 2000 for 24h


title: SKD00501R-E09

value: Endothelial

tag: genotype

value: 3 months


title: SKD00501R-E07

tag: tissue


title: HEK293FT-mCherry-AD

description: Nontargeting/mCherry-AD control

value: transfected with pR283_mCherry-AD vector with Lipofectamine 2000 for 24h


title: Figure2_140617_P1_s03_LPS

value: NDAS


title: RNA-PP2AcWT-2

data_processing:
Paired-end 150-cycle sequencing was performed on Illumina NovaSeq sequencers, per the manufacturer’s directions (Illumina).
Reads were first trimmed for adapters using fastp (v0.20.0)(Chen et al., 2018),  then alignment to the mouse genome mm10(Gencode GRCm38) by STAR (version 2.7.1a, parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1")(Dobin et al., 2013) and counted by HTSeq(v0.11.2)(Anders et al.) based on GENCODE mouse gene annotation (vM22) (Harrow et al., 2012).
STAR results were chosen for following analysis since they got more reads counts that all samples achieved 90M reads counts. After normalization by trimmed mean of M-values normalization (edgeR v3.34.0) (Robinson and Oshlack, 2010), Voom (limma v3.48.3) (Law et al.) was used to identify differential expressed genes. Pathway enrichment analysis were then performed at Enrichr server (Kuleshov et al., 2016) on significant differential expressed genes.
Assembly: mm10
Supplementary files format and content: tsv file of gene-based counts using HTSeq

extract_protocol:
Total RNA was isolated using the PureLink™ RNA Mini Kit (Invitrogen, 12183025).
RNA sequencing was performed by the University of Texas Genomic Sequencing and Analysis Facility. Poly(A) enrichment was performed.

value: Wild Type


title: SKD00501R-E06

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

tag: age


title: RNA-PP2AcWT-1


title: HEK293FT-AP-mCherry-AD

description: Nontargeting/AP-mCherry-AD control

value: transfected with pR281_AP-mCherry-AD vector with Lipofectamine 2000 for 24h


title: RNA-PP2AcWT-3


title: Figure2_140617_P1_s02_TNF


title: SKD00501R-E05


title: HEK293FT-AP-dCas13b-AD

description: Nontargeting/AP-dCas13b-AD control

value: transfected with pR004_AP-dCas13b-AD vector with Lipofectamine 2000 for 24h


title: Figure2_140617_P1_s01_unstimulated

value: unstimulated


title: RNA-PP2AcKO-3

value: PP2A KO


title: Figure2_140521_P1_s08_TNF

value: TNF


title: HEK293FT-AP-AD

description: Nontargeting/AP-AD control

value: transfected with pR203_AP-AD vector with Lipofectamine 2000 for 24h


title: SKD00501R-E03


title: HEK293FT-PIE-YTHDF2, 48h, rep2

description:
PIE-YTHDF2
YTHDF2vsAPAD.DP5.wo.snp

value: transfected with pR005_PIE-YTHDF2 vector with Lipofectamine 2000 for 48h


title: RNA-PP2AcKO-2


title: Figure2_140521_P1_s07_unstimulated

value: Dermal Fibroblast


title: RNA-PP2AcKO-1


title: SKD00501R-E02


title: HEK293FT-PIE-YTHDF2, 48h, rep1

description:
PIE-YTHDF2
YTHDF2vsAPAD.DP5.wo.snp


title: Figure2_140521_Healthy_control_IIU043_s06_LPS

value: LPS

value: HC


title: HEK293FT-PIE-YTHDF1, 48h, rep2

description:
PIE-YTHDF1
YTHDF1vsAPAD.DP5.wo.snp

value: transfected with pR016_PIE-YTHDF1 vector with Lipofectamine 2000 for 48h


title: SKD00501R-E01

value: Endothelial

value: 3 months


title: Figure2_140521_Healthy_control_IIU043_s05_TNF


title: HEK293FT-AP-mCherry

description: Nontargeting/AP-mCherry control

value: transfected with pR282_AP-mCherry vector with Lipofectamine 2000 for 24h


title: L-733,060 3

city: Guangzhou

first: Peipei

address: Duobao road 63

institute: The Third Affiliated Hospital, Guangzhou Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly:  mm10
Supplementary files format and content:  tab-delimited text files include TPM/counts for each Sample

source_name: corneal limbus

extract_protocol:
Total RNA was isolated from tissues using the Magzol Reagent (Magen, China)according to the manufacturer's protocol.
RNA libraries were prepared for sequencing according to instructions of  NEBNext® Ultra RNA Library Prep Kit for Illumina after the mRNA was enriched by oligo dT using NEB Next® Poly(A) mRNA Magnetic Isolation Module.

treatment_protocol: After anesthesia, mice were subconjunctivally injected NK1 receptor antagonist L-733,060 on day0 and day3. The control mice were treated with sterile water. After a week, corneal limbus were collected for RNA-seq.

value: corneal limbus

value: WT

value: subconjunctival injection of NK1 receptor antagonist L-733,060


title: HEK293FT-PIE-YTHDF1, 48h, rep1

description:
PIE-YTHDF1
YTHDF1vsAPAD.DP5.wo.snp


title: SKD00501R-D16

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: L-733,060 2


title: SKD00501R-D15


title: HEK293FT-APAD, 48h, rep4

description: Nontargeting/APAD control

value: transfected with pR008_APAD vector with Lipofectamine 2000 for 48h


title: Figure2_140521_P1_s03_LPS

value: NDAS


title: L-733,060 1


title: SKD00501R-D14


title: HEK293FT-APAD, 48h, rep3

description: Nontargeting/APAD control


title: Figure2_140521_P1_s02_TNF

value: TNF


title: SKD00501R-E04


title: CTRL 2

value: subconjunctival injection of sterile water


title: SKD00501R-D13


title: HEK293FT-PIETadA*-PUM2, 24h, rep2

description:
PIETadA*-PUM2
PUM2.vs.APTA.DP5.wo.snp

value: transfected with pR180_PIETadA*-PUM2 vector with Lipofectamine 2000 for 24h


title: Figure2_140521_P1_s01_unstimulated

value: unstimulated

value: Dermal Fibroblast


title: CTRL 1

source_name: corneal limbus

value: corneal limbus


title: SKD00501R-D12


title: SKD00501R-D11


title: HEK293FT-PIETadA*-PUM2, 24h, rep1

description:
PIETadA*-PUM2
PUM2.vs.APTA.DP5.wo.snp


title: HEK293FT-AP-TadA*, 24h, rep2

description: AP-TadA*

value: transfected with pR177_AP-TadA* vector with Lipofectamine 2000 for 24h


title: HEK293FT-AP-TadA*, 24h, rep1

description: AP-TadA*


title: Figure2_140521_Healthy_control_IIU043_s04_unstimulated

value: HC


title: Hashtag CarT-Vax+aIFNG_Day14_1

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

state: MA

address: 500 Main St

department: Koch Institute

institute: MIT

description: Seq-Well

data_processing:
Raw read processing of scRNA-seq reads was performed as previously described13. Briefly, reads were aligned to the mm10 reference genome and collapsed by cell barcode and unique molecular identifier (UMI).
Paired TCR sequencing and read alignment was performed as previously described. Briefly, reads were aggregated by cell barcode and UMI, and UMI with under 5 reads were discarded. ClusterSets.py was used to divide sequences for each UMI into sets of similar sequences. Only sets of sequences that comprised greater than 90% of the sequences obtained for that UMI were considered further. Consensus sequences for each UMI were determined using the BuildConsensus.py function. Consensus sequences were then mapped against TCRV and TCRJ IMGT references sequences with IgBlast.
Cell hashing data was aligned to HTO barcodes using CITE-seq-Count v1.4.2 (https://zenodo.org/badge/latestdoi/99617772).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

extract_protocol:
Endogenous CD45.2+ CD4 and CD8 T cells were sorted collectively into 1x RPMI +10%FBS, 2-5x104 total T cells were obtained for each group. Cells were pelleted at 1000xg for 5min, resuspended in 1xRPMI at 20,000 cells per 200μl and then processed for scRNA-seq using the Seq-Well platform with second strand chemistry, as previously described11. Whole transcriptome libraries were barcoded and amplified using the Nextera XT kit (Illumina) and were sequenced on a Novaseq 6000 (Illumina). Hashtag oligo libraries were amplified as described previously12 and were sequenced on a Nextseq 550.
Seq-Well

value: Tumor

value: T cell

value: CAR T-Vax + aIFNg

value: Day 14


title: Hashtag CarT-Vax+aIFNG_Day14_2

description: Seq-Well


title: Figure2_140429_Healthy_control_IIU043_s06_TNF


title: Figure2_140429_Healthy_control_IIU043_s08_PolyIC


title: Hashtag CarT-Vax_Day14_2

description: Seq-Well

value: CAR T-Vax


title: Figure2_140429_Healthy_control_IIU043_s07_LPS

value: LPS


title: SKD00501R-D09

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: SKD00501R-D10


title: LN49

city: Fukuoka

first: Shoichi

last: Nakamura

country: Japan

institute: Kyushu University

description: ELN.integrated.rds

data_processing:
The sequence data were quantified and mapped to human reference genome (GRCh38) using the Cell Ranger toolkit by 10x Genomics.
The matrix data were imported using the Seurat R package (version 3.6.3).
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: normal lymph node

extract_protocol: Esophagus were resected, and a part of resected tissue was made into sigle cells. RNA was extracted and barcorded using Chromium Single Cell 3' Reagent Kits v3.1 (PN- 1000121).

value: esophagus

tag: nact

tag: collection method

value: Surgery


title: CTRL 3

value: corneal limbus

value: WT

value: subconjunctival injection of sterile water


title: Figure2_140429_Healthy_control_IIU043_s05_unstimulated

data_processing:
BCL to FastQ and demultiplex using Casava 1.8.2
Map to hg19 using Tophat 2.1.1
For whole blood samples, filter out Hemoglobin reads using bedtools intersectBed and a custom GTF
Calculate RPKM using Partek GS 6.6
Genome_build: hg19

extract_protocol:
Dermal fibroblast: For sequencing preparation, total RNA was harvested from primary cells using the RNeasy Mini Kit (Qiagen) and cDNA was synthesized using the SuperScript III First-Strand Synthesis SuperMix for qRT-PCR (Invitrogen)
Whole blood: Paxgene tubes were used to collect RNA from patient and control whole blood. For RNA-Sequencing, first- and second-strand cDNA was synthesized using the TruSeq RNA Sample Preparation Kit (Illumina) and sequenced using the HiSeq 2000 (Illumina). FastQ files were generated using CASAVA 1.8.2 and mapped to hg19 using Tophat 2.1.0. Hemoglobin and intergenic reads were removed using bedtools intersectBed. RPKM values were calculated using Partek GS 6.6.  The RPKM values were transformed to Z-scores by subtracting the mean and dividing by the standard deviation of a set of healthy controls (n=15)
PBMC: Peripheral blood mononuclear cells (PBMC) were isolated from whole blood using Ficoll-Paque (Amersham Biosciences) gradient centrifugation
standard Illumina mRNA library construction

value: unstimulated

value: Dermal Fibroblast


title: Figure2_140429_P1_s04_PolyIC

value: NDAS


title: SKD00501R-D07

data_processing:
Demultiplexed RNA reads were aligned using STAR 2.7.7a, duplicate reads removed using Picard 2.22.0 and read counts summarized using HTSeq 0.9.1. Cutoffs of 20000 counts and 500 features were used.
Assembly: GRCm38 with ERCC-spike ins and the reporter-gene EYFP

extract_protocol:
Aortae was perfused for 1 min with PBS at room temperature and then dissected. Lumen side was exposed and digested with 1 mg/mL collagenase I, 1 mg/mL dispase, and 150 μg/mL DNase-I for 30 min at 37 °C. The cell suspension was strained and then depleted of Cd45+ cells with Cd45 magnetic beads (protocol according to manufacturer). To purify endothelial cells, the suspension was stained with Cd45 and Cd31 antobodies, as well as a cell viability dye. FACS sorting was used to sort out Cd45-, Cd31+, viable endothelial cells, as well as some Cd45-, Cd31-, viable cells for control. Cells were sorted into 384 well plates with lysis buffer.
Library was constructed using smartseq2 protocol, as previously has been described. Briefly, primer annealing, followed by RT and cDNA amplification was followed by cleanup of PCR products. The cDNA was tagmented and final library anmplified using custom barcodes, then pooled and cleaned with SPRI beads. Libraries were then sequenced.


title: SKD00501R-D08


title: LN45

description: ELN.integrated.rds


title: LN12

description: ELN.integrated.rds

value: FP


title: Figure2_140429_P1_s03_LPS


title: Hashtag CarT-Vax_Day14_1

description: Seq-Well

value: Tumor

value: T cell


title: LN09

description: ELN.integrated.rds


title: SKD00501R-D06


title: Hashtag CarT_Day14_4

description: Seq-Well

value: CAR T only

value: Day 14


title: Hashtag CarT_Day14_3

description: Seq-Well


title: Hashtag CarT_Day14_2

description: Seq-Well


title: Figure2_140429_P1_s02_TNF

value: TNF


title: SKD00501R-D05

value: Endothelial

value: Aorta


title: LN07

description: ELN.integrated.rds


title: Figure2_140429_P1_s01_unstimulated


title: ESN08

source_name: normal tissue


title: SKD00501R-D03

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: Hashtag CarT-Vax_Day7_2

description: Seq-Well

value: CAR T-Vax

value: Day 7


title: QKI7 RIP rep2

city: Monrovia

first: Jianjun

last: Chen

institute: Beckman Research Institute of City of Hope

description:
ribozero RNA
QKI7-bound transcripts  RIP-seq IP (HepG2)
qki7.2.ip

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
reads were aligned to the GRCh38 genome assembly using STAR
the TPM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: Hepatocellular carcinoma

growth_protocol: The HepG2 cells with forced expression of QKI5, QKI6 and QKI7 were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin and plasmocin prophylactic for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish

extract_protocol:
After cross-link with UV, the cells were collected by trypsinization, lysed in 1 ml M-PER buffer (78501, Thermo Fisher Scientific) with 100 U/ml RNase inhibitor and 1 × protease inhibitor on ice for 20 min, and sonicated in a Bioruptor Pico device (Diagenode) with 30s on/30s off for 10 cycles. Then the lysates were collected and subject to RIP with Flag antibody and Protein A/G Magnetic Beads. The RIP RNAs were recovered from the beads with RNA clean and concentrater kit. Both Input and RIP RNAs were used for sequencing.
KAPA Stranded mRNA-Seq Kit (Illumina Platforms) was utilized to construct library and sequencing was performed on an Illumina Nova Seq 6000.

treatment_protocol: Without special treatment

tag: cell linr

tag: rip antibody

value: Flag (Cat#:F3165, Sigma-Aldrich)


title: Hashtag CarT-Vax_Day7_1

description: Seq-Well


title: SKD00501R-D04


title: Hashtag CarT_Day7_3

description: Seq-Well


title: QKI7 RIP rep1

description:
ribozero RNA
QKI7-bound transcripts  RIP-seq IP (HepG2)
qki7.1.ip


title: SKD00501R-D02


title: QKI6 RIP rep2

description:
ribozero RNA
QKI6-bound transcripts  RIP-seq IP (HepG2)
qki6.2.ip


title: SKD00501R-D01


title: Hashtag CarT_Day7_2

description: Seq-Well


title: Zack_SB_Lane_3

first: Eldad

last: Zacksenhaus

state: Ontario

address: 101 College Street

institute: University Health Network

data_processing:
Samples were demultiplexed using fastx_barcode_splitter with parameters ' --bol --mismatches 2' . Sample barcodes and genotypes found in the "Sample_information.csv" file.
Read 1 Adaptors were trimmed with cutadapt (v1.8) using parameters ‘-m 5 --no-indels --discard-untrimmed -g R1_5prime=^NNNNNNNNTGTATGTAAACTTCCGACTTCAACTG’
Only the reads starting with a TA were kept for downstream steps
R1 reads were then paired with their respective paired reads (R2)
alignment with novoalign (v3.05.01) using parameters ‘-r ALL 1 -R 0 -c 8 -o SAM’ on paired reads
insertion location and orientation was parsed from sam files and annotated
Assembly: mm9
Supplementary files format and content: Final processed files contain insertion locations. Each insertion is annotated (where possible) and has a corresponding read count. All insertions are found in the Primary_metastatic_combined_insertions.txt file.

source_name: Primary mammary tumor

extract_protocol:
DNA was purified by DNeasy Blood and Tissue Kit, Qiagen, Cat # 69506
DNA was sheared and then ligated with adaptors. SB insertion junctions were selected amplfied using nested PCR and sent for sequencing.
Shear-SPLINK

value: Primary mammary tumor

value: MMTV-Cre:Rbf/f:T2/Onc3a:R26lsl_SB11 and MMTV-Cre:Rbf/f:T2/Onc3b:R26lsl_SB11 female mice

value: No treatment


title: Hashtag CarT_Day7_1

description: Seq-Well


title: Zack_SB_Lane_5

source_name: Lung metastasis

value: Lung metastasis


title: QKI5 RIP rep2

description:
ribozero RNA
QKI5-bound transcripts  RIP-seq IP (HepG2)
qki5.2.ip


title: Zack_SB_Lane_4


title: Zack_SB_Lane_6


title: SKD00501R-C14

first: Martin

institute: Karolinska Institutet

source_name: Aorta


title: QKI6 RIP rep1

description:
ribozero RNA
QKI6-bound transcripts  RIP-seq IP (HepG2)
qki6.1.ip


title: Zack_SB_Lane_2


title: No364 liver CD44-/-

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4
Reads were aligned to the mouse reference genome sequence (ENSEMBL Mus musculus GRCm38.84) using HISAT2 (hisat2-2.0.2-beta).
Read counts were determined by read summarization with feature Counts (subread-2.0.0).
Assembly: GRCm38.74
Supplementary files format and content: 20230320_g3_g5_rawcounts.csv: read counts per gene per sample

extract_protocol:
Total RNA was isolated from cell lines using RNeasy mini kit (Qiagen) as per manufacturer’s instructions.
Library preparation was done using Illumina’s TruSeq stranded mRNA kit following the manufacturer’s description.

value: osteosarcoma

value: C57BL/6 x 129/Sv x FVB


title: SKD00501R-C13

last: Enge


title: Zack_SB_Lane_1


title: TCRsequencing

description: TCR sequencing

value: Tumor

value: T cell


title: SKD00501R-C15


title: QKI5 RIP rep1

description:
ribozero RNA
QKI5-bound transcripts  RIP-seq IP (HepG2)
qki5.1.ip


title: QKI7 input rep2

description:
ribozero RNA
QKI7-bound transcripts  RIP-seq input (HepG2)
qki7.2.in


title: SKD00501R-C16


title: Hashtag CarT_Day14_1

description: Seq-Well

value: CAR T only

value: Day 14


title: CarT-Vax+aIFNG_Day14_1

description: Seq-Well

value: CAR T-Vax + aIFNg


title: QKI6 input rep2

description:
ribozero RNA
QKI6-bound transcripts  RIP-seq input (HepG2)
qki6.2.in


title: SKD00501R-C12

value: Endothelial

value: Aorta


title: No279 liver CD44-/-


title: No280 liver CD44-/-


title: CarT-Vax+aIFNG_Day14_2

description: Seq-Well


title: CarT-Vax_Day14_2

description: Seq-Well


title: No368 liver CD44+/+


title: SKD00501R-C10

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: QKI6 input rep1

description:
ribozero RNA
QKI6-bound transcripts  RIP-seq input (HepG2)
qki6.1.in


title: No345 liver CD44+/+


title: CarT_Day14_4

description: Seq-Well


title: QKI5 input rep2

description:
ribozero RNA
QKI5-bound transcripts  RIP-seq input (HepG2)
qki5.2.in


title: CarT_Day14_3

description: Seq-Well


title: QKI5 input rep1

description:
ribozero RNA
QKI5-bound transcripts  RIP-seq input (HepG2)
qki5.1.in


title: SKD00501R-C07


title: SKD00501R-C09


title: mES_RAD21_mAC_1C4_IAA_EdUHU

city: Beijing

first: Jinchun

address: No. 5, Yiheyuan street

institute: Peking University

data_processing:
The "RepFind" pipeline was applied as described in  Liu et al., 2021.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bamCoverage
Library strategy: NAIL-seq

source_name: cultured cell

growth_protocol: The V6.5 mouse ES cells were cultured with 2i media containing 15% FBS, 1uM PD0325901 (SelleckChem, S1036), 3uM CHIR99021 (SelleckChem, S1263), 1000 U/mL mouse LIF (Millipore, ESG1107), and other supplements as described (Liu et al., 2021b).

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of EdU.
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.
NAIL-seq (Liu et al., 2021)

treatment_protocol: Cells were incubated with 1.25 mM thymidine (Sigma, T9250) as well as 1 mg/mL dox for 14 hours, followed by dox and 50 ng/mL nocodazole (Sigma, M1404) for 7 hours to synchronize into M phase. After synchronization, mES cells were released into a fresh medium with 4 mM HU for 3.5 hours. 500 mM IAA was added 1 hour before release.

value: mES V6.5


title: SKD00501R-C08

city: Solna

address: Solnavägen 1


title: No244 liver CD44+/+


title: QKI7 input rep1

description:
ribozero RNA
QKI7-bound transcripts  RIP-seq input (HepG2)
qki7.1.in


title: AD2_Mox

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix, cell annotations and UMAP embeddings

source_name: Retinal organoids

growth_protocol: adaped protocol based on Kuwahara et al., 2015

extract_protocol:
Retinal organoids (week 22) were dissociated to single cells using the Neurosphere Dissociation kit (P) (Miltenyi Biotech) according to the manufacturer’s protocol
Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)

treatment_protocol: drug exposure for 24 hours

value: Retinal organoids

value: Mox


title: mES_RAD21_mAC_1C4_NT_EdUHU

value: Cells were incubated with 1.25 mM thymidine (Sigma, T9250) as well as 1 mg/mL dox for 14 hours, followed by dox and 50 ng/mL nocodazole (Sigma, M1404) for 7 hours to synchronize into M phase. After synchronization, mES cells were released into a fresh medium with 4 mM HU for 3.5 hours.


title: CarT_Day14_2

description: Seq-Well

source_name: Tumor


title: SKD00501R-C11


title: AD2_LPS

value: LPS


title: CarT-Vax_Day14_1

description: Seq-Well

value: CAR T-Vax


title: SKD00501R-C06


title: SKD00501R-C05


title: CarT-Vax_Day7_2

description: Seq-Well

value: Day 7


title: CarT_Day14_1

description: Seq-Well


title: HU094_mES_RT_WT_IAA_G2_repeat2

description: We applied NAIL-seq to identify the replication timing in WT and RAD21-depleted mES cells.

data_processing:
Library strategy: NAIL-seq
The "RepFind" pipeline was applied as described in  Liu et al., 2021.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: mES

extract_protocol:
Genomic DNA was isolated, tagged with biotin by click-iT reaction, subjected to the sequential isolation of EdU.
After on-beads ligation, purified DNA was tagged with Illumina sequencing primers and sequenced on Hi-seq, 2×150 bp.

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the G2 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.

value: WT


title: HU094_mES_RT_WT_IAA_S3_repeat2

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S3 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.


title: HU094_mES_RT_WT_IAA_S2_repeat2

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S2 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.


title: HU094_mES_RT_WT_IAA_S4_repeat2

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S4 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.


title: CarT-Vax_Day7_1

description: Seq-Well

value: Tumor


title: AD2_iMG_LPS


title: SKD00501R-C03


title: AD2_iMG_Mox


title: CarT_Day7_3

description: Seq-Well

value: T cell


title: CarT_Day7_2

description: Seq-Well

value: CAR T only


title: SKD00501R-C02


title: HU094_mES_RT_WT_IAA_S1_repeat2

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the S1 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.


title: AD2_iMG

value: iMG


title: AD2_iMG_Chloro


title: AD2_Chloro

value: Chloro


title: AD2


title: HU094_mES_RT_WT_IAA_G2_repeat1


title: SKD00501R-B16

value: Endothelial


title: CarT_Day7_1

description: Seq-Well


title: SKD00501R-B15

value: Aorta


title: HU094_mES_RT_WT_IAA_G1_repeat2

treatment_protocol:
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 3 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the G1 fraction with Hoechest
The cells were treated by 1ug/ml dox for 24 hours, then treated by IAA for 6 hours, labeled by 20 uM EdU for 15 minutes, 10ug/ml Hoechest was added 15 min prior to IAA, then the cells were washed by PBS for once, then sorting the indicated fraction with Hoechest.


title: SKD00501R-C04

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: HU094_mES_RT_WT_IAA_S4_repeat1


title: 5-FU treated Tespa1-/- LSKs, rep2

first: Yukai

last: Lu

address: gaotanyan

institute: Army Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the GRCm38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 10 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 3.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Bone marrow

value: hematopoietic stem cells

value: stem cells

value: Tespa1 mutant

value: Isolation of hematopoietic stem cells from 5-FU treated (Day 9) Tespa1 knock out mouse bone marrow


title: 5-FU treated Tespa1-/- LSKs, rep3


title: HU094_mES_RT_WT_IAA_S3_repeat1


title: cocultured endothelial plus smooth muscle cells replicate 2

city: Los Angeles

first: Feiyang

last: Ma

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

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to the mouse reference genome (refdata-cellranger-hg38-1.2.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
30 minutes following SQ injection of 400 i.u of heparin 3 C57BL/6J male mice were sacrificed and perfused with 10mL of Versene. Following perfusion, adventitial fat was removed from each vessel and the vessels were isolated and minced into small pieces. Following harvest, the vessel pieces were placed in 1mL digestion buffer containing DNASE I, 1M HEPES, Liberase and HBSS and incubated at 37C till the vessels were digested into a single cell suspension. The suspension was neutralized with DMEM + 10%FBS and ran through a 40uM filter and then centrifuged for 5 min at 10,000 x g. Following centrifugation, the cell pellet was resuspended and assessed for viability prior to library preparation using trypan blue staining with the TC20 cell counter (BioRad). Single-cell suspension of cells in 0.4% BSA-PBS were added to each channel on the 10x chip. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification.
Single-cell RNAseq libraries were prepared by using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics).


title: 5-FU treated Wild type LSKs, rep3

value: Wild type

value: Isolation of hematopoietic stem cells from 5-FU treated (Day 9) littermate  Wild type mouse bone marrow


title: SKD00501R-B13

value: 3 months


title: 5-FU treated Wild type LSKs, rep2


title: cultured smooth muscle cells replicate 2

source_name: cultured smooth muscle cells

value: cultured smooth muscle cells


title: HU094_mES_RT_WT_IAA_S2_repeat1

value: WT


title: cultured smooth muscle cells replicate 1


title: HU094_mES_RT_WT_IAA_S1_repeat1


title: SKD00501R-B11


title: SKD00501R-C01


title: Tespa1-/- LSKs, rep3

value: Isolation of hematopoietic stem cells from Tespa1 knock out mouse bone marrow


title: 5-FU treated Wild type LSKs, rep1


title: cultured endothelial cells replicate 2

source_name: cultured endothelial cells

value: cultured endothelial cells


title: HU094_mES_RT_WT_IAA_G1_repeat1


title: SKD00501R-B10


title: cultured endothelial cells replicate 1


title: HU094_mES_RT_RAD21_1C4_IAA_G2


title: SKD00501R-B09


title: HU094_mES_RT_RAD21_1C4_IAA_S4


title: Tespa1-/- LSKs, rep1


title: cocultured endothelial plus smooth muscle cells replicate 1


title: 5-FU treated Tespa1-/- LSKs, rep1


title: cord endothelial cell replicate 1

source_name: cord endothelial cell

value: cord endothelial cell


title: SKD00501R-B08


title: LN229_BLM_KO_cell line treated rep 3

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
mapping by STAR
MarkDuplicates
Counts features by Featurecounts
Assembly: hg38
Supplementary files format and content: tab separated text file with features assigned to genes

source_name: LN229_BLM_KO_cell line treated

extract_protocol: polyA+ KAPA Library kit

value: brain

value: BLM knock out

tag: sample type

value: LN229_BLM_KO_cell line

tag: transfection

value: CRISPR/Cas9 BLM KO

value: temozolomide and olaparib treatment


title: SKD00501R-B07

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: HU094_mES_RT_RAD21_1C4_IAA_S3


title: SKD00501R-B12


title: Wild type LSKs, rep3

city: chongqing

value: Bone marrow

tag: cell line

value: hematopoietic stem cells

value: stem cells

value: Isolation of hematopoietic stem cells from littermate Wild type mouse bone marrow


title: HU094_mES_RT_RAD21_1C4_IAA_S2


title: SKD00501R-B06

tag: cell type

value: 3 months


title: LN229_BLM_KO_cell line treated rep 2


title: HU094_mES_RT_RAD21_1C4_IAA_S1

tag: strain


title: SKD00501R-B05


title: Wild type LSKs, rep1

value: Wild type


title: Tespa1-/- LSKs, rep2

value: Tespa1 mutant

value: Isolation of hematopoietic stem cells from Tespa1 knock out mouse bone marrow


title: LN229_BLM_KO_cell line treated rep 1


title: LN229_BLM_KO_cell line untreated rep 2

source_name: LN229_BLM_KO_cell line untreated

value: untreated


title: Irradiated Tespa1-/- LSKs, rep3

value: Isolation of hematopoietic stem cells from irradiated Tespa1 knock out mouse bone marrow


title: Irradiated Tespa1-/- LSKs, rep2


title: LN229_BLM_KO_cell line untreated rep 1

value: brain

value: BLM knock out


title: Wild type LSKs, rep2


title: PHGN_Treated_BiologicalRepC [PHGN-TrC]

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

data_processing:
Base calling was performed using the RTA v2 software built into the Illumina NextSeq 500 instrument.
Demultiplexing and FASTQ file generation was performed with Illumina’s Basespace informatics platform
Data analysis was performed using the Qiagen CLC Genomics Workbench (CLCGxWB) version 11 software. Sequencing reads were mapped to the H. sapiens reference genome (GRCh38 assembly, Ensemble Release 89),  using default parameters with a strand-specific alignment protocol. The mapping results generated values for Fragments Per Kilobase of exon per Million reads mapped (FPKM) for each gene. The “Differential Expression for RNA-Seq” tool in CLCGxWB software was used, using default parameters, to identify differentially expressed genes between chemical-treated and solvent-treated samples.
Assembly: H. sapiens reference genome (GRCh38 assembly, Ensemble Release 89)
Supplementary files format and content: Excel file showing FPKM values for each Sample.

extract_protocol:
Qiagen RNeasy Mini kit was used for total RNA extraction. An on-column RNase-free DNase I treatment was included. RNA quality was assessed on the Agilent 2100 Bioanalyzer.
Sequencing libraries were generated with 3 µg of RNA using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. The libraries were assessed for size and purity using the Agilent 2100 Bioanalyzer, and quantitated by qPCR using a KAPA Biosystems Library Quantitation kit. Libraries were normalized, pooled, and diluted to a loading concentration of 1.8 pM, loaded on an Illumina High-Output Flow Cell, and sequenced on the Illumina NextSeq 500 instrument.

treatment_protocol: T98G cells were treated with solvent (DMSO), DEOX (10 mM), PHEN (100 uM), GNET (8 uM), DEOX (10 mM) + PHEN (100 uM), or GNET (8 uM) + PHEN  (100 uM) for 2 hours. After treatment, cells were washed twice with PBS buffer and used for RNA isolation. In all experiments, each treatment consisted of 3 biological replicates, and RNA from each replicate was used to generate sequencing libraries.

value: PHGN

tag: time

value: 2 h


title: Irradiated Tespa1-/- LSKs, rep1


title: PHGN_Treated_BiologicalRepB [PHGN-TrB]


title: LN18_BLM_KO_cell line treated rep 3

source_name: LN18_BLM_KO_cell line treated

value: LN18_BLM_KO_cell line

value: CRISPR/Cas9 BLM KO

value: temozolomide and olaparib treatment


title: Irradiated Wild type LSKs, rep3

value: Bone marrow

value: Isolation of hematopoietic stem cells from irradiated littermate Wild type mouse bone marrow


title: PHGN_Treated_BiologicalRepA [PHGN-TrA]


title: LN18_BLM_KO_cell line untreated rep 3

source_name: LN18_BLM_KO_cell line untreated


title: LN229_BLM_KO_cell line untreated rep 3

value: LN229_BLM_KO_cell line


title: SKD00501R-B01

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP


title: PHDE_Treated_BiologicalRepC [PHDE-TrC]

value: PHDE


title: SKD00501R-B02

value: 3 months


title: SKD00501R-A16


title: Irradiated Wild type LSKs, rep2

value: hematopoietic stem cells

value: stem cells

value: Wild type


title: PHDE_Treated_BiologicalRepB [PHDE-TrB]


title: Irradiated Wild type LSKs, rep1


title: SKD00501R-A15


title: LN18_BLM_KO_cell line untreated rep 2

value: brain

value: BLM knock out

value: untreated


title: PHDE_Treated_BiologicalRepA [PHDE-TrA]

value: 2 h


title: SKD00501R-B04


title: HU094_mES_RT_RAD21_1C4_IAA_G1


title: SKD00501R-B03


title: SKD00501R-A14


title: IUE-PIE-PUM2-CD133plus

city: Chicago

data_processing:
RNA base variants calling was performed by JACUSA2_v2.0.0
raw Fastq files were aligned and mapped to hg38 or mm10 reference with STAR
known SNPs in dbSNP version 138 (hg38) or version 137 (mm10) or SNVs with low read depth (less than 5-read depth) were filtered out
Gene-level counts were calculated by Rsubread
Assembly: hg38/mm10
Supplementary files format and content: text files include RNA editing information for each group/sample
Supplementary files format and content: text files include gene-level count values for each sample

source_name: Embryo mouse neocortex tissue

extract_protocol:
Total RNA was extracted from transfected cells with Direct-zol RNA microprep kit according to manufacturer’s instructions (ZYMO)
TruSeq Stranded mRNA Library Prep kit (Illumina) was used for preparing sequencing libraries

value: Embryo mouse neocortex tissue

value: IUE with pR023_PIE-PUM2 vector for 48h


title: IUE-PIE-PUM2-CD24plus


title: LN18_BLM_KO_cell line treated rep 1

value: LN18_BLM_KO_cell line

value: CRISPR/Cas9 BLM KO

value: temozolomide and olaparib treatment


title: LN18_BLM_KO_cell line untreated rep 1

value: wild type


title: IUE-APAD-CD133plus

description: Nontargeting/APAD control

value: IUE with pR008_APAD vector for 48h


title: PHEN_Treated_BiologicalRepB [PHEN-TrB]

value: PHEN


title: LN229 glioma cell line untreated rep 3

source_name: LN229 glioma cell line untreated

value: LN229 glioma cell line


title: IUE-APAD-CD24plus

description: Nontargeting/APAD control


title: SKD00501R-A12

value: Endothelial

value: Aorta

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: LN18_BLM_KO_cell line treated rep 2

value: brain


title: IUE-pCIG-CD133plus

description: Mock control

value: IUE with pCAGIG vector for 48h


title: SKD00501R-A11


title: PHEN_Treated_BiologicalRepA [PHEN-TrA]


title: GNET_Treated_BiologicalRepC [GNET-TrC]

value: GNET


title: SKD00501R-A10


title: LN229 glioma cell line untreated rep 1

value: untreated


title: LN229 glioma cell line untreated rep 2


title: GNET_Treated_BiologicalRepB [GNET-TrB]

value: 2 h


title: SKD00501R-A09


title: LN18 glioma cell line untreated rep 3

source_name: LN18 glioma cell line untreated

value: LN18 glioma cell line


title: GNET_Treated_BiologicalRepA [GNET-TrA]


title: PHEN_Treated_BiologicalRepC [PHEN-TrC]


title: SKD00501R-A08


title: DEOX_Treated_BiologicalRepC [DEOX-TrC]

value: DEOX


title: 4h_wt_4_10698

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description: 4 hour optogenetic stimulation, AgRP-IRES-Cre wt/wt ROSA26 ChR2 fl/wt mice

data_processing:
The pool was sequenced for 37.5 million reads using an Illumina NovaSeq6000 instrument and a PE100 sequencing protocol.
Data was processed using the nf-core/rnaseq v3.0 pipeline
Alignment to reference genome was done using STAR vSTAR_2.6.1d
Gene abundance estimation was done using Salmon 1.4.0
Differential gene expression analysis of IP samples was carried out using DESeq2 1.30.0
Genome_build: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary_files_format_and_content: Excel speadsheets containing raw salmon counts per sample as well as fold change and significance level for each annotated gene.

growth_protocol: Mice were housed in individually ventilated cages (IVCs) within a controlled environment at 22°C – 24°C and a 12-hr light/12-hr dark cycle. Animals received ad libitum access standard rodent chow (ssniff V1554, 59494 Soest, Germany) and water unless otherwise indicated in an experiment.

extract_protocol:
Both cohort of mice were sacrificed at ZT7.5 and liver samples were extracted and snapped frozen in liquid nitrogen. Total murine liver RNA was isolated using the mirVana Isolation Kit (Ambion) in accordance to the manufacturer’s instructions. Murine liver RNA concentration was measured by Nanodrop ND-100 (Peqlab Biotechnology, France), and diluted to a final concentration of 200 – 250 ng/mL. RNA integrity number (RIN) was analyzed with the Agilent RNA 6000 Nano Kit (5067-1511, Agilent Technologies) and the Agilent 2100 Bioanalyzer. All samples displayed a RIN of >8.
RNA libraries were prepared with 1 µg of total RNA using the Illumina® TruSeq® mRNA stranded sample preparation Kit. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperatures. The RNA fragments underwent reverse transcription using random primers. This is followed by second-strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of the library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

treatment_protocol: Mice were stimulated with blue laser (473 nm) light, consisting of pulse trains (10 ms pulses of 20 Hz; 3 s on, 1 s off) at ZT3.5 (4 h stimulation) and ZT5.5 (2 h stimulation) in the absence of food.

value: Liver

tag: diet

value: Random Fed

value: 4 hours

value: wtwt; fl/wt


title: LN18 glioma cell line untreated rep 2

value: wild type

tag: treatment


title: SKD00501R-A13


title: 4h_wt_5_11035

source_name: 4 hour optogenetic stimulation, AgRP-IRES-Cre wt/wt ROSA26 ChR2 fl/wt mice


title: DEOX_Treated_BiologicalRepB [DEOX-TrB]


title: SKD00501R-A06

source_name: Aorta


title: DEOX_Treated_BiologicalRepA [DEOX-TrA]


title: 4h_wt_3_10771


title: 4h_wt_2_10559


title: IUE-pCIG-CD24plus

first: Xiangbin

institute: University of Chicago

description: Mock control

value: Embryo mouse neocortex tissue


title: DMSO_Control_BiologicalRepB [PGD-UnB]

value: DMSO


title: 4h_wt_1_10536


title: SKD00501R-A04

value: Endothelial

value: Aorta


title: SKD00501R-A03

value: Amotl2flow/flow / Cdh5-RREert /ROSA26-EYFP

value: 3 months


title: DMSO_Control_BiologicalRepC [PGD-UnC]


title: SKD00501R-A05