title: brain_7d_sham_rep2

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

description: Gene expression after 7d in the brain of sham mice

hyb_protocol: The cyanine 3-labeled cRNA was hybridized to the lncRNA microarray slide by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: The microarray was scanned using Agilent DNA Microarray Scanner (Agilent p/n G2565BA) after washing.

data_processing: The lncRNA+mRNA raw data was extracted through Agilent Feature Extraction Software and summarized, and normalized using the GeneSpring GX v12.1 software.

source_name: brain, 7d, sham, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). The labeled cRNAs were purified by RNeasy Mini Kit. The quantity and quality of RNA were valued by a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). The OD 260/280 ratio between 1.8 and 2.1 are acceptable.

growth_protocol: Mice were housed in a well-ventilated room (five rats in one cage) at a constant room temperature (25 ± 1℃) and controlled humidity (50 ± 10%), with a 12 h light/dark cycle. All procedures involving the use and care of animals were performed in accordance with the guidelines of Central South University for the care and use of animals and were approved by the Medical Ethics Committee of Central South University (Animal ethical number: 2020sydw0929).

extract_protocol: RNA samples isolated using the TRIZOL method. The protocol includes cryopulverization of tissue using the biopulverizer, Homogenization using the Mini-Bead-Beater-16, lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent, phase separation, RNA Precipitation, RNA wash and redissolving the RNA.

treatment_protocol: Mice were randomly assigned to two groups: sham and ICH.The mice were sacrificed under 0.3% pentobarbital sodium (60 mg/kg, intraperitoneally) on the 7th day, and transcardially perfused with saline. Brains were harvested and the ipsilateral basal ganglia were isolated immediately.

value: ipsilateral striatum of brain

value: male

value: sham

tag: molecule type

value: lncRNA+mRNA


title: brain_7d_sham_rep3

status: Public on May 17 2023

type: RNA

country: China

molecule: total RNA

organism: Mus musculus

source_name: brain, 7d, sham, rep3

tag: tissue

tag: Sex

tag: treatment


title: RAW_infected_wt_rep2

city: Sevilla

first: Francisco

last: Ramos-Morales

state: Sevilla

address: Avda Reina Mercedes, 6

department: Genética

country: Spain

institute: Universidad de Sevilla

description: Gene expression data from RAW264.7 cells infected with wt Salmonella strain 14028

hyb_protocol: Labelled cDNA was hybridized to Clariom S Assay, MOUSE arrays  (Affymetrix) following the manufacturer’s instructions

scan_protocol: The arrays were scanned in a 3000 7G Scanner from Affymetrix

data_processing: Data processing was carried out with GeneChip Command Console 2.0 (Affymetrix) to generate .CEL and .CHP assays. Normalization was performed using the SST (signal space transformation)-RMA (robust multiple-array average) method. The Transcriptome Analysis Console (TAC) was used for data analysis.

label: biotin

source_name: RAW264.7 cells infected with wild-type Salmonella, biological rep2

label_protocol: Biotinylated single-stranded cDNA was prepared from 100 ng per sample of total intact RNA extracted from 6 independent samples (3 from RAW264.7 cells infected with wild-type Salmonella and 3 from RAW264.7 cells infected with srfJ mutant of Salmonella).

growth_protocol: RAW264.7 cells (ECAC no. 91062702) were cultured in DMEM supplemented with 10% foetal calf serum. 2 mM L-glutamine, 100 U/ml penicillin and 100 microg/ml streptomycin were included in the culture media. Cells were maintained in a 5% CO2 humidified atmosphere at 37ºC

extract_protocol: Total RNA from RAW264.7 cells was isolated using 1 ml of TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. An additional purification step was carried out with the RNeasy Min Elute Cleanup Kit (Qiagen).

treatment_protocol: RAW264.7 cells were plated in 24-well plates at 1.5 x 10E5 cells per well and incubated for 24 h at 37ºC with 5% CO2. Bacteria were grown in LB medium for 24 h at 37ºC with shaking and added at a multiplicity of infection of 250. The cell culture was washed twice with phosphate-buffered saline (PBS) 1 h postinfection, overlaid with DMEM containing 100 ug/ml gentamicin, and incubated for another hour. The culture was then washed twice with PBS, covered with DMEM with gentamicin (16 ug/ml), and incubated for 6 h.

tag: cell line

tag: bacteria

value: S. enterica serovar Typhimurium 14028


title: brain_7d_ICH_rep5

description: Gene expression after 7d in the brain of ICH mice

source_name: brain, 7d, ICH, rep5

value: ICH


title: brain_7d_ICH_rep4

source_name: brain, 7d, ICH, rep4


title: RAW_infected_srfJ_rep1

description: Gene expression data from RAW264.7 cells infected with srfJ mutant of Salmonella

source_name: RAW264.7 cells infected with srfJ mutant Salmonella, biological rep1

value: S. enterica serovar Typhimurium srfJ null mutant


title: RAW_infected_wt_rep1

source_name: RAW264.7 cells infected with wild-type Salmonella, biological rep1


title: brain_7d_sham_rep5

source_name: brain, 7d, sham, rep5


title: BTIC129_B1_ControlshRNA

type: SRA

city: Regensburg

first: Julia

last: Lorenz

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

country: Germany

institute: Regensburg university hospital

library_source: transcriptomic

data_processing:
fastq files were aligned to version 87 of Homo_sapiens reference genome GRCh38 using the HiSat2 aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm (v2.0.1).
Batch effects were removed with Combat_Seq of the SVA package using a negative binomial regression model
Expression data was normalized using the normalization function of DeSeq2 package or RPKM values
Differentially expressed genes (³1.0-fold and £5% false discovery rate) were identified by negative binomial generalized linear models statistics using the DeSeq2 package
Assembly: version 87 of Homo_sapiens reference genome GRCh38
Supplementary files format and content: tab-delimited text files include adjusted counts for each cell line (BITC13/BITC129)

organism: Homo sapiens

source_name: glioblastoma-derived brain tumor initiating cell (BTICs)

growth_protocol: 4 x 10^5 TSPO proficient or deficient BTICs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 24 hours.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Illumina Stranded mRNA Prep kit (Illumina) and processed as per manufacturer’s instructions.

treatment_protocol: BTICs were left untreated

tag: background strain

value: GB WHO IV, female, 63y at diagnosis

tag: genotype

value: control sh

value: untreated


title: RAW_infected_wt_rep3

source_name: RAW264.7 cells infected with wild-type Salmonella, biological rep3


title: SKD00401R-P19

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

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.

tag: cell type

value: DoubleNegative

value: Aorta

tag: strain

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

tag: age

value: 3 months


title: brain_7d_ICH_rep2

source_name: brain, 7d, ICH, rep2


title: brain_7d_ICH_rep1

source_name: brain, 7d, ICH, rep1


title: BTIC129_A1_ControlshRNA


title: brain_7d_sham_rep4

source_name: brain, 7d, sham, rep4


title: SKD00401R-P20


title: brain_7d_ICH_rep3

source_name: brain, 7d, ICH, rep3


title: SKD00401R-P18


title: brain_7d_sham_rep1

source_name: brain, 7d, sham, rep1


title: BTIC13_C1_TSPOshRNA

value: GB WHO IV, male, 42y at diagnosis

value: TSPO sh


title: BTIC13_B1_TSPOshRNA


title: BTIC13_A1_TSPOshRNA


title: SKD00401R-P15


title: BTIC13_C1_ControlshRNA


title: BTIC13_B1_ControlshRNA


title: SKD00401R-P14


title: SKD00401R-P13


title: BTIC13_A1_ControlshRNA


title: SKD00401R-P12


title: SKD00401R-P09


title: SKD00401R-P17


title: SKD00401R-P11


title: S2-Zld_aIgG_IP_rep1

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

country: USA

institute: University of Wisconsin Madison

library_source: genomic

data_processing:
Bowtie2 version 2.4.4 was used to align ChIP-seq reads to the Drosophila melanogaster genome (version dm6) with the following non-default parameters: -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Aligned reads were filtered to include only reads with a mapping quality score > 30. Reads mapping to unplaced scaffolds or the mitochondrial genome were discarded.
. Peak calling was performed using MACS2 version 2.2 with parameters -g dm --call-summits. Only peaks that were detected in all replicates were considered in downstream analysis.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigwig file: contains z-score normalized read depth for each sample. Reads from two biological replicates were combined prior to generation of bigWig.
Supplementary files format and content: narrowPeak files: contain MACS2 peaks for ChIP samples.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured at 27°C in Schneider's medium supplemented with 10% fetal bovine serum  and antibiotic/antimycotic.

extract_protocol:
For each ChIP experiment, ~50 million cells were crosslinked by adding methanol-free formaldehyde directly to the cell culture medium to a final concentration of 0.8%. Cells were rotated on a nutator for 7 minutes at room temperature (RT) before quenching of crosslinking by adding glycine to 125 mM. Crosslinked cells were pelleted by centrifugation at 600 × g for 3 minutes. Cells were washed twice with 1X PBS. Cells were lysed by resuspending in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X 100) with protease inhibitors (Pierce) and incubating on ice for 10 minutes. The resulting chromatin was pelleted for 5 minutes at 1500 × g and resuspended in RIPA buffer. Chromatin was sonicated in a Covaris S220 Ultrasonicator (5 cycles of 120 seconds with 60 second delay, 170 peak power, 10% duty factor, 200 cycles/burst). Sonicated chromatin was centrifuged for 10 minutes at 10,000 × g to pellet insoluble material. 5% of the supernatant was set aside as input, and the remainder was incubated at 4°C overnight with antibodies (6 µL anti-Zld, 8 µL anti-Grh, 10 µg anti-Twi, 7.5 µL anti-HA). 20 µL protein A beads (Dynabeads Protein A, ThermoFisher Scientific) blocked with BSA were added and samples were incubated at 4°C for 4 hours. Beads were separated on a magnet and washed 3× with low salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton-X 100, 150 mM NaCl), 2× high salt wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton-X 100, 300 mM NaC), 2× LiCl wash buffer (0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate), and 1× with TE buffer with NaCl (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). Beads were resuspended in elution buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) and incubated at 65°C for 10 minutes. The IP and input samples were treated with 4.5 µL RNAse A for 30 minutes. 5 µL Proteinase K was added and samples were incubated overnight at 65°C to reverse crosslinking. DNA was isolated by phenol:chloroform extraction, precipitated with EtOH, and resuspended in 20 µL H2O.
Preparation of sequencing libraries was performed using NEBNext Ultra II kit (NEB) with 7 PCR cycles for library amplification. Sequencing was performed on the Illumina Hi-Seq4000 using 50bp single-end reads, or on the Illumina NovaSeq 6000 using 150bp paired-end reads.

treatment_protocol: Transcription factor expression was induced by adding CuSO4 to the cell culture media. For all induction experiments, cells were plated at 1×10^6 cells per mL. Experiments were performed with cells harvested 48 hours after induction.

value: uninduced

tag: antibody

value: IgG


title: SKD00401R-P16


title: metafemale, rep2

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

data_processing:
Basecalls performed using CASAVA.
Trimmomatic was used to filter the raw data.
Reads were mapped to the genome by HISAT2.
Transcripts were assembled and quantitated using StringTie.
Assembly: Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa
Supplementary files format and content: Matrix table of normalized data

source_name: third-instar larvae

growth_protocol: All the stocks are incubated at 25 degree

extract_protocol:
The sequencing library was constructed by removing ribosomal RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: third-instar larvae

tag: sample type

value: metafemale

value: XXX

value: female


title: metafemale, rep3


title: SKD00401R-P06


title: SKD00401R-P07


title: Control male (meta female control), rep2

value: XY

value: male


title: Control male (meta female control), rep3


title: SKD00401R-P05


title: S2-Grh_aIgG_IP_rep1


title: metafemale, rep1


title: SKD00401R-P08


title: Control male (meta female control), rep1


title: Control female (meta female control), rep3

value: XX


title: SKD00401R-P03


title: SKD00401R-P04


title: Control female (meta female control), rep2


title: SKD00401R-P02


title: Control female (meta female control), rep1


title: SKD00401R-P01


title: SKD00401R-O24


title: SKD00401R-P10


title: SKD00401R-O23


title: sample_9

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
We aligned the reads to the bovine genome (Bos_taurus.ARS-UCD1.2.104) using Hisat2 (v 2.2.1). Next, we used Samtools (v 1.10) to retain the reads with one match to the genome, followed by the removal of duplicates using bammarkduplicates from biobambam2 (v 2.0.95). We used featurecounts (v 2.0.1)  to count reads according to the ensemble annotation (Bos_taurus.ARS-UCD1.2.104).
Assembly: Bos_taurus.ARS-UCD1.2.104
Supplementary files format and content: unfiltered count reads

organism: Bos taurus

source_name: caruncular

extract_protocol:
Samples were ground with a mortar and pestle, then mixed with Trizol reagent. Next we  proceeded with a standard guanidinium thiocyanate-phenol-chloroform extractionfollowing the manufacturer’s protocol.
Sequencing libraries were prepared at the Genomics Technology Core at the University of Missouri using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA).

value: caruncular

tag: gestation day

tag: gestation id

value: artificial insemination


title: SKD00401R-O22

value: DoubleNegative


title: sample_761

source_name: chorion

value: chorion

value: embryo transfer


title: SKD00401R-O21

value: Aorta

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

value: 3 months


title: sample_760


title: SKD00401R-O20


title: SKD00401R-O19


title: SKD00401R-O18


title: sample_75

source_name: extra-embryonic tissue

value: extra-embryonic tissue


title: SKD00401R-O16


title: sample_749


title: SKD00401R-O15


title: sample_747


title: SKD00401R-O14


title: SKD00401R-O17


title: sample_76


title: sample_744


title: SKD00401R-O13


title: sample_755


title: sample_8

source_name: intercaruncular

value: intercaruncular


title: sample_735


title: sample_736


title: sample_743


title: sample_734


title: SKD00401R-O12


title: SKD00401R-O11


title: SKD00401R-O10


title: sample_732


title: SKD00401R-O09


title: sample_731


title: SKD00401R-O08


title: sample_724


title: SKD00402R-B04

value: Endothelial


title: SKD00401R-O07


title: sample_723


title: SKD00401R-O06


title: SKD00401R-O05


title: sample_722


title: sample_721


title: sample_720


title: sample_72


title: SKD00401R-O01


title: SKD00401R-O04


title: sample_71


title: SKD00401R-O02


title: SKD00401R-O03


title: sample_733


title: SKD00401R-N23


title: SKD00401R-N22


title: SKD00401R-N24


title: sample_706


title: sample_719


title: sample_705


title: sample_703


title: SKD00401R-N20


title: SKD00401R-N21


title: SKD00401R-N19


title: sample_702


title: sample_701


title: SKD00401R-N18


title: SKD00401R-N17


title: sample_700


title: sample_7


title: SKD00401R-N16


title: sample_699


title: sample_698


title: SKD00401R-N15


title: SKD00401R-N14


title: sample_695


title: SKD00401R-N13


title: SKD00401R-N12


title: SKD00401R-N11


title: SKD00401R-N10


title: sample_688


title: sample_697


title: SKD00401R-N08


title: sample_696


title: SKD00401R-N09


title: sample_693


title: sample_692


title: sample_704


title: sample_678


title: sample_687


title: SKD00401R-N06


title: SKD00401R-N07


title: SKD00401R-N04


title: sample_676


title: sample_675


title: sample_674


title: SKD00401R-N02


title: sample_673


title: sample_665


title: SKD00401R-M23


title: sample_664


title: SKD00401R-N05


title: sample_661


title: sample_662


title: sample_677


title: SKD00401R-M20


title: sample_663


title: SKD00401R-M21


title: sample_66


title: sample_653


title: SKD00401R-M17


title: SKD00401R-N03


title: SKD00401R-M18


title: sample_651


title: sample_652


title: sample_650


title: SKD00401R-N01


title: SKD00401R-M24


title: SKD00401R-M14


title: SKD00401R-M13


title: SKD00401R-M22


title: SKD00401R-M12


title: sample_666


title: sample_649


title: SKD00401R-M19


title: sample_62


title: sample_654


title: SKD00401R-M16


title: SKD00401R-M15


title: SKD00401R-M10


title: SKD00401R-M09


title: sample_59


title: SKD00401R-M08


title: sample_58


title: sample_6


title: SKD00401R-M07


title: sample_57


title: SKD00401R-M06


title: sample_56


title: sample_54


title: SKD00401R-M05


title: sample_504


title: SKD00401R-M04


title: SKD00401R-M02


title: SKD00401R-M03


title: sample_502


title: sample_55


title: SKD00401R-L23


title: SKD00401R-L24


title: SKD00401R-M11


title: sample_494


title: sample_5


title: sample_61


title: sample_493


title: SKD00401R-L22


title: sample_492


title: SKD00401R-L21


title: sample_491


title: sample_490


title: SKD00401R-L19


title: SKD00401R-L20


title: sample_481


title: SKD00401R-L18


title: SKD00401R-L17


title: SKD00401R-L16


title: sample_477


title: SKD00401R-L15


title: SKD00401R-M01


title: sample_479


title: SKD00401R-L14


title: sample_473


title: SKD00401R-L13


title: sample_460


title: sample_478


title: SKD00401R-L10


title: sample_472


title: SKD00401R-L11


title: SKD00401R-L09


title: sample_458


title: SKD00401R-L08


title: sample_454


title: SKD00401R-L07


title: sample_489


title: sample_448


title: SKD00401R-L06


title: SKD00401R-L04


title: sample_444


title: sample_480


title: SKD00401R-L05


title: SKD00401R-L03


title: SKD00401R-L12


title: sample_430


title: sample_429


title: SKD00401R-K24


title: SKD00401R-L01


title: SKD00401R-K23


title: sample_427


title: SKD00401R-K22


title: sample_426


title: SKD00401R-K21


title: SKD00401R-K19


title: sample_425


title: SKD00401R-K20


title: SKD00401R-K18


title: sample_453


title: sample_415


title: sample_416


title: sample_440


title: sample_417


title: SKD00401R-K17


title: sample_414


title: SKD00401R-K16


title: sample_447


title: sample_413


title: sample_412


title: SKD00401R-K14


title: SKD00401R-K15


title: sample_438


title: SKD00401R-L02


title: sample_428


title: sample_404


title: SKD00401R-K13


title: sample_403


title: SKD00401R-K12


title: sample_402


title: SKD00401R-K11


title: sample_401


title: sample_400


title: SKD00401R-K10


title: sample_399


title: sample_391


title: SKD00401R-K08


title: SKD00401R-K07


title: SKD00401R-K06


title: sample_390


title: sample_389


title: sample_388


title: SKD00401R-K04


title: SKD00401R-K05


title: SKD00401R-K03


title: SKD00401R-K02


title: SKD00401R-K01


title: sample_386


title: sample_374


title: sample_375


title: sample_376


title: sample_387


title: SKD00401R-J24


title: SKD00401R-J23


title: sample_373


title: SKD00401R-J22


title: sample_371


title: SKD00401R-J21


title: SKD00401R-J20


title: sample_372


title: sample_362


title: SKD00401R-J19


title: sample_363


title: SKD00401R-K09


title: SKD00401R-J18


title: sample_361


title: SKD00401R-J17


title: sample_360


title: SKD00401R-J15


title: sample_358


title: SKD00401R-J16


title: sample_359


title: SKD00401R-J14


title: sample_350


title: sample_349


title: SKD00401R-J11


title: SKD00401R-J09


title: SKD00401R-J12


title: SKD00401R-J08


title: sample_348


title: sample_346


title: sample_337


title: sample_347


title: SKD00401R-J13


title: SKD00401R-J07


title: sample_336


title: SKD00401R-J10


title: sample_335


title: SKD00401R-J05


title: sample_334


title: sample_345


title: sample_332


title: sample_333


title: SKD00401R-J03


title: SKD00401R-J06


title: sample_330


title: SKD00401R-J01


title: sample_328


title: SKD00401R-I24


title: sample_318


title: SKD00401R-I23


title: sample_317


title: SKD00401R-I22


title: sample_316


title: SKD00401R-I21


title: sample_315


title: SKD00401R-I20


title: SKD00401R-I18


title: sample_314


title: SKD00401R-I19


title: SKD00401R-J04


title: SKD00401R-I17


title: sample_304


title: SKD00401R-I15


title: sample_305


title: sample_31


title: SKD00401R-I16


title: sample_303


title: sample_302


title: SKD00401R-I14


title: SKD00401R-J02


title: SKD00401R-I13


title: sample_301


title: sample_300


title: sample_30


title: SKD00401R-I12


title: SKD00401R-I11


title: SKD00401R-I09


title: SKD00401R-I10


title: sample_294


title: sample_29


title: SKD00401R-I08


title: sample_313


title: sample_286


title: sample_285


title: SKD00401R-I06


title: sample_28


title: SKD00401R-I07


title: SKD00401R-I05


title: sample_275


title: SKD00401R-I04


title: SKD00401R-I01


title: SKD00401R-I02


title: SKD00401R-H24


title: SKD00401R-H22


title: SKD00401R-I03


title: SKD00401R-H23


title: sample_273


title: sample_274


title: sample_27


title: sample_270


title: sample_271


title: SKD00401R-H21


title: SKD00401R-H20


title: sample_249


title: sample_248


title: SKD00401R-H19


title: sample_26


title: sample_247


title: SKD00401R-H18


title: SKD00401R-H17


title: sample_245


title: sample_235


title: sample_246


title: sample_238


title: SKD00401R-H15


title: sample_244


title: SKD00401R-H10


title: sample_272


title: sample_214


title: sample_213


title: sample_212


title: SKD00401R-H14


title: SKD00401R-H13


title: sample_210


title: SKD00401R-H11


title: SKD00401R-H09


title: sample_209


title: SKD00401R-H08


title: SKD00401R-H07


title: sample_17


title: SKD00401R-H12


title: sample_162


title: SKD00401R-H05


title: sample_161


title: sample_211


title: SKD00401R-H04


title: sample_160


title: SKD00401R-H16


title: SKD00401R-H06


title: SKD00401R-H03


title: sample_16


title: SKD00401R-H01


title: SKD00401R-H02


title: sample_159


title: SKD00401R-G24


title: sample_158


title: SKD00401R-G23


title: sample_157


title: SKD00401R-G22


title: SKD00401R-G21


title: SKD00401R-G20


title: sample_153


title: SKD00401R-G16


title: SKD00401R-G17


title: SKD00401R-G15


title: SKD00401R-G18


title: sample_144


title: sample_143


title: sample_14


title: sample_125


title: sample_124


title: SKD00401R-G19


title: sample_15


title: SKD00401R-G13


title: sample_122


title: SKD00401R-G14


title: sample_13


title: sample_123


title: sample_121


title: sample_120


title: sample_112


title: SKD00401R-G12


title: SKD00401R-G11


title: SKD00401R-G09


title: SKD00401R-G08


title: sample_12


title: sample_152


title: SKD00401R-G07


title: sample_110


title: SKD00401R-G05


title: SKD00401R-G01


title: SKD00401R-G02


title: SKD00401R-F24


title: SKD00401R-G04


title: SKD00401R-G03


title: SKD00401R-F23


title: E14-paused, Mycn-gRNA3, rep3

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.
Raw counts were imported into R, and analyzed by cell number normalization using ERCCs with edgeR (v3.32.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts of all genes (including ERCCs) for all samples.
Supplementary files format and content: tab-delimited text file with expression levels (log2) for all samples with cell number normalization.

growth_protocol: ESCs expressing dCas_Alkbh5 cells were grown on gelatin in FBS/LIF

extract_protocol:
RNA was extracted from equal number of ESCs (2x10^5 cells), with RNeasy Micro Kit with on-column DNase I digestion (QIAGEN). RNA was spiked with synthetic RNAs from the External RNAs Control Consortium (ERCC) Spike-in Mix1 (Thermo Fisher), with 2µl of 1:100 ERCC dilution added to 10µl of RNA, equivalent to ~1-2µg RNA.
Library preparation was done using the NEBNext Ultra II Directional Library Prep Kit for Illumina with the mRNA Magnetic Isolation Module from 1µg RNA, per manufacturer’s instructions (NEB).

treatment_protocol: Cells were transfected with 1μg lenti-sgRNA-BSD (coding for guide RNAs) and selected with 8μg/mL blasticidin for 3 days. Cells were then paused with 200 nM INK128 as mTor inhibitor for 5 days.

value: embryonic stem cells


title: SKD00401R-F22


title: SKD00401R-G10


title: E14-paused, Mycn-gRNA2, rep4


title: E14-paused, Mycn-gRNA2, rep3


title: E14-paused, Mycn-gRNA2, rep2


title: SKD00401R-F20


title: sample_111


title: SKD00401R-F19


title: E14-paused, NT-gRNA, rep4

value: control (NT-gRNA)


title: sample_109


title: SKD00401R-G06


title: SKD00401R-F17


title: E14-paused, Mycn-gRNA2, rep1


title: SKD00401R-F18


title: sample_107


title: sample_108


title: E14-paused, Mycn-gRNA3, rep4


title: E14-paused, NT-gRNA, rep3


title: sample_10


title: E14-paused, Mycn-gRNA3, rep2


title: E14-paused, NT-gRNA, rep2


title: E14-paused, NT-gRNA, rep1


title: SKD00401R-F15


title: E14-paused, Mycn-gRNA3, rep1


title: B6.6mo_S34

city: Athens

first: Αnastasia

last: Filia

address: Soranou Efessiou 4

country: Greece

institute: BRFAA

data_processing:
Sequenced reads were trimmed at the 3' end for adaptor sequence and low-quality sequence (q<30), then mapped to mm10 whole genome using STAR v2.6 and quantified using HtSeq and Gencode v. M19 annotation file.
EdgeR package in R was used to calculate CPM abundance values.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include CPM values for each Sample

source_name: bulk hippocampus

extract_protocol:
RNA was extracted using NucleoSpin®RNA kit
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit

value: bulk hippocampus

value: female

value: post natal 6 month

tag: disease

value: healthy


title: SKD00401R-F14


title: SKD00401R-F12


title: SKD00401R-F21


title: B6.6mo_S33


title: SKD00401R-F13


title: SKD00401R-F11


title: B6.6mo_S32


title: SKD00401R-F10


title: B6.3mo_S40

value: post natal 3 month


title: B6.3mo_S39


title: SKD00401R-F08


title: B6.3mo_S38


title: SKD00401R-F09


title: B6.6mo_S31


title: SKD00401R-F07


title: SKD00401R-F05


title: SKD00401R-F16


title: SKD00401R-F04


title: F1.6mo_S14

value: lupus symptomatic nephritic disease


title: B6.3mo_S36


title: B6.6mo_S35


title: SKD00401R-F03


title: B6.3mo_S37


title: SKD00401R-F06


title: F1.6mo_S13


title: F1.6mo_S11


title: SKD00401R-E23


title: F1.6mo_S10


title: SKD00401R-E24


title: F1.3mo_S8

value: lupus pre-autoimmunity stage


title: SKD00401R-E22


title: F1.3mo_S9


title: F1.6mo_S12


title: SKD00401R-E21


title: SKD00401R-E19


title: F1.3mo_S7


title: SKD00401R-E20


title: SKD00401R-E17


title: SKD00401R-E18


title: Ctrl_Th17

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA sample preparation Kit (illumina) following manufacturer's protocols.

value: spleen

value: CD4 T cells

value: WT

value: Th17 differentiation


title: SKD00401R-F01

value: Aorta

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

value: 3 months


title: Ctrl_Th0

value: Th0 differentiation


title: SKD00401R-E15

value: Endothelial


title: CD4KO_Th17

value: IPMK Knockout


title: Paused, ChIP Mettl3 IP, rep2

data_processing:
Reads that passed quality control were trimmed of adaptors using Trim Galore! v0.4.0 and aligned to mm10 using bowtie2 v2.2.5131. Unmapped reads were then mapped to hg19. SAM files were converted to BAM files, sorted, and indexed with samtools v1.9. Bam files were deduplicated using MarkDuplicates (picard v2.18.14). Peaks were called with MACS2 (using IP samples and their input as controls) with the options --gsize 3.0e9 -q 0.05 --nomodel –broad, and annotated by intersecting center positions with RefSeq annotations. The most upstream and downstream annotated TSS and TES, respectively, were considered for each gene. Then, peak analysis was performed using DiffBind v3.0.15 with score=DBA_SCORE_TMM_READS_FULL_CPM. Cell number normalization was done with edgeR (v3.32.1), using the ratio of mm10/hg19 reads for normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with expression levels (log2) for Mettl3 peaks, with cell number normalization.

source_name: embryonic stem cells

growth_protocol: ES cells were grown on gelatin for 2 weeks in FBS/LIF media, under control or paused condition.

extract_protocol:
ESCs were spiked with 2% of human cells (HeLa), then cross-linked in 1% formaldehyde/PBS for 10min at room temperature. After quenching with 125mM glycine for 5min at room temperature, followed by 15min at 4°C, cells were washed in cold PBS and stored at −80°C. Cells were diluted at 5 million cells per 100μl in shearing buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH8.0, 5mM NaF, Halt™ Protease Inhibitor Cocktail (Thermo Fisher), 1mM PMSF), rotating at 4°C for 30min, then 100μl lysate was passed into a microTUBE AFA Fiber Snap-Cap (Covaris). Chromatin was sheared to 200–500 bp fragments on a Covaris E220 with settings PIP 175, Duty 10%, CPB 200, for 7 minutes. Supernantants were pooled by condition, and immunoprecipitation was performed overnight using 200μl of lysate (~chromatin from 10 million cells) and 5µg of antibody (Proteintech 15073-1-AP), following the iDeal ChIP-seq kit for Transcription Factors (Diagenode) protocol. Elution, de-crosslinking, and DNA purification were performed per manufacturer’s instructions.
Libraries were constructed from ~2ng DNA and prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Paused cells were treated with 200nM INK128 as mTor inhibitor for 2 weeks.

value: embryonic stem cells

value: paused

tag: chip antibody

value: Mettl3 (Proteintech, 15073-1-AP)


title: SKD00401R-E16


title: SKD00401R-F02


title: SKD00401R-E13


title: Paused, ChIP Mettl3 IP, rep1


title: CD4KO_Th0


title: SKD00401R-E12


title: SKD00401R-E14


title: FBS, ChIP Mettl3 IP, rep1

value: control (FBS)


title: SKD00401R-E10


title: SKD00401R-E11


title: FBS, ChIP input, rep1

value: none (input)


title: SKD00401R-E08


title: FBS, ChIP input, rep2


title: Paused, ChIP input, rep1


title: F1.3mo_S5

value: bulk hippocampus

value: female

value: post natal 3 month


title: SKD00401R-E06


title: E14-Mettl3-KO, paused, rep3


title: SKD00401R-E05


title: FBS, ChIP Mettl3 IP, rep2


title: SKD00401R-E03


title: E14-Mettl3-KO, paused, rep2


title: E14-WT, paused, rep2


title: SKD00401R-D24


title: SKD00401R-E02


title: E14-WT, FBS, rep3


title: SKD00401R-E01


title: E14-Mettl3-KO, FBS, rep2


title: SKD00401R-D23


title: Paused, ChIP input, rep2


title: SKD00401R-E04


title: SKD00401R-E09


title: E14-Mettl3-KO, paused, rep1


title: E14-WT, paused, rep1


title: E14-WT, FBS, rep2


title: SKD00401R-E07


title: SKD00401R-D22


title: E14-Mettl3-KO, FBS, rep1


title: SKD00401R-D20


title: SKD00401R-D19


title: SKD00401R-D18


title: E14-WT, paused, rep3


title: E14-WT, FBS, rep1


title: mouse 6

city: Heidelberg

first: Evi P.

last: Vlachou

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
Adapter (Nextera transposase sequence) and quality trimming (Phred score cutoff of 20, overlap of 3 bp) was performed with the TrimGalore version: 0.6.4_dev (Cutadapt version: 1.18) (Krueger, 2015), keeping the sequencing reads with a length of at least 36 bps.
Genome reference-based alignment was performed using the slice-aware STAR alignment tool with the default parameters with Release M25 (GENCODE-GRCm38.p6) of the mouse genome. The reference genome was indexed with a bp overhang of 100-1.
The generated bam files were sorted using Samtools based on the chromosome coordinates. Unmapped reads, PCR duplicates, and reads with an alignment p.score <20 were removed by filtering the sorted bam files.
The count matrices with only the exonic sequences were generated using the summarizeOverlaps function of the GenomicAlignments package (1.30 version - (Lawrence et al., 2013)). Gene annotation was performed with the makeTxDbFromGFF function of the GenomicFeatures package (1.46.1), the AnnotationDbi 1.52.0 and the org.Mm.eg.db 3.12.0 package.
Assembly: mm10
Supplementary files format and content: Column-separated values files

extract_protocol:
Spleens were collected  in cold RPMI buffer (usually 10 ml),  and with the use of a 2 ml syringe plunger, spleens were mashed through a 40 µm Nylon cell strainer which is put in a small Petri dish. Cells are spun down (1400 rpm, 7 min, 4 °C) and resuspend in 10% FCS/DMSO to freeze the cells at -80°C. Normally 200 µl of a 10 ml spleen suspension are used for one FACS staining or around 600.000 cells.
Single-cell RNA sequencing was performed following the SMART-seq 2.5 library preparation protocol as described in Picelli et al. (Picelli et al., 2014), and modified by the DKFZ scOpenLab in Bioquant, Heidelberg. Plate preparation was assisted by the BRAVO Agilent and Mosquito LV liquid handling platforms. Quality control was performed on the TapeStation provided by Agilent Technology, using a D5000 Tape.  Single cell library preparation was performed using the Nextera XT DNA SMP Prep Kit (96 SMP). DNA was cleaned-up using a magnetic size selection. The samples were finally quantified and assessed on a D1000 TapeStation.
Smartseq2.5 scRNA-seq, 75 bps, Single-end

value: B cells

value: spleen

value: 24-26 weeks


title: E14-Mettl3-KO, FBS, rep3


title: mouse 1


title: SKD00401R-D17

value: Aorta


title: SKD00401R-D16

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


title: SKD00401R-D15

value: 3 months


title: SKD00401R-D14


title: SKD00401R-D11


title: SKD00401R-D13


title: SKD00401R-D21


title: SKD00401R-D09


title: SKD00401R-D12


title: SKD00401R-D10


title: SKD00401R-D07


title: SKD00401R-D08


title: SKD00401R-D04


title: SKD00401R-D06


title: SKD00401R-D05


title: SKD00401R-D02


title: SKD00401R-D03


title: SKD00401R-D01


title: Human CRC cells treated with 0.01% DMSO replicate 1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols.

scan_protocol: GeneChips were scanned using Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated for 4 days before RNA extraction.

tag: tissue/cell type

value: colorectal adenocarcinoma

tag: gender

value: Female

value: DMSO


title: SKD00401R-C24

value: Endothelial

tag: tissue


title: Human CRC cells treated with 1 uM HMBA replicate 2

label_protocol: In accordance with manufacturer's protocols.

tag: treatment

value: HMBA


title: Human Embryonic stem cells treated with 0.001% DMSO replicate 2

tag: cell line

value: embryonic cell line


title: SKD00401R-C23


title: Human CRC cells treated with 1 uM HMBA replicate 1


title: Human CRC cells treated with 0.01% DMSO replicate 2


title: Human Embryonic stem cells treated with 10 uM HMBA replicate 1


title: Human Leukemic cells treated with 0.1 uM ABT-263 replicate 1

value: acute promyelocytic leukemia


title: Human Embryonic stem cells treated with 0.001% DMSO replicate 1


title: SKD00401R-C22


title: Human Leukemic cells treated with 0.01% DMSO replicate 2


title: Human Leukemic cells treated with 0.01% DMSO replicate 1


title: Human Leukemic cells treated with 0.1 uM ABT-263 replicate 2


title: Human GBM cells treated with 10 nM AZD-8330 replicate 2

value: Glioblastoma

value: Male


title: SKD00401R-C21


title: SKD00401R-C20


title: Human Embryonic stem cells treated with 10 uM HMBA replicate 2


title: Human GBM cells treated with 0.01% DMSO replicate 1


title: Human GBM cells treated with 0.01% DMSO replicate 2


title: SKD00401R-C19


title: SKD00401R-C18


title: Human GBM cells treated with 10 nM AZD-8330 replicate 1


title: HCC70 cells, ursolic acid, 5µM, 48 hrs

city: Sacramento

first: Hongye

last: Zou

state: CA

address: 4645 2nd Ave, Research III

institute: UC Davis

data_processing:
The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow. Briefly, sequence reads were aligned to the reference human genome assembly (hg38) with BWA and Bowtie software.
Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: breast

growth_protocol: C4-2B and HCC70 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated from cells using TRIzol Reagent (Invitrogen). 1 µg of total RNA was used for the construction of sequencing libraries.
Libraries from 1 μg of total RNA were prepared by using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions

value: breast

value: cancer cells

value: WT

value: ursolic acid, 5uM

tag: time

value: 48 hrs


title: HCC70 cells, vehicle, 48 hrs

value: vehicle


title: HCC70 cells, ursolic acid, 10µM, 48 hrs

value: ursolic acid, 10uM


title: HCC70 cells, ursolic acid, 10µM, 24 hrs

value: 24 hrs


title: SKD00401R-C16

value: Aorta

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

value: 3 months


title: Human Embryonic stem cells treated with ABT-263 0.1 uM replicate 2

value: Female


title: Human Embryonic stem cells treated with AZD-8330 0.1uM replicate 2


title: SKD00401R-C17

value: Endothelial


title: HCC70 cells, ursolic acid, 5µM, 24 hrs


title: Human Embryonic stem cells treated with 0.01% DMSO replicate 1

value: embryonic cell line

value: DMSO


title: Human Embryonic stem cells treated with ABT-263 0.1 uM replicate 1


title: Human Embryonic stem cells treated with AZD-8330 0.1uM replicate 1


title: SKD00401R-C13


title: SKD00401R-C14


title: SKD00401R-C12


title: SKD00401R-C15


title: C4-2B cells, digoxin, 100nM, 48 hrs

source_name: prostate

value: prostate

value: digoxin, 100nM


title: C4-2B cells, vehicle (Digoxin), 48 hrs


title: HCC70 cells, vehicle, 24 hrs

value: breast


title: C4-2B cells, ursolic acid, 10µM, 48 hrs

value: cancer cells


title: SKD00401R-C10


title: SKD00401R-C11


title: SKD00401R-C09


title: SKD00401R-C08


title: C4-2B cells, vehicle (UA), 48 hrs

value: WT


title: C4-2B cells, vehicle (Digoxin), 24 hrs


title: SKD00401R-C07


title: C4-2B cells, digoxin, 100nM, 24 hrs


title: C4-2B cells, ursolic acid, 10µM, 24 hrs


title: SKD00401R-C06


title: C4-2B cells, vehicle (UA), 24 hrs


title: SKD00401R-C05


title: SKD00401R-C04


title: SKD00401R-C03


title: SKD00401R-C02


title: FigureS3B_180821_P7_Unstim_PBMC_rep1

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: 180821_0160_rna-seq_results.gene.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

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: PBMC


title: FigureS3B_180821_IIU030_Unstim_PBMC_rep2


title: FigureS3B_180821_P7_Unstim_PBMC_rep2


title: FigureS3B_180821_HC4_Unstim_PBMC_rep2

value: HC


title: SKD00401R-C01

tag: genotype


title: SKD00401R-B24

tag: cell type


title: FigureS3B_180821_HC4_Unstim_PBMC_rep1


title: FigureS3B_180821_HC3_Unstim_PBMC


title: SKD00401R-B22

tag: strain


title: LN26

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: metastatic 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

value: FP

tag: collection method

value: Surgery


title: SKD00401R-B21

source_name: Aorta

value: Aorta

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

tag: age


title: FigureS3B_180821_HC2_Unstim_PBMC


title: Human Embryonic stem cells treated with 0.01% DMSO replicate 2

value: Female


title: FigureS3B_180821_IIU030_Unstim_PBMC_rep1


title: perirenal adipose tissue, buffalo-5

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

description: PRAT 5

data_processing:
Raw data were filtered with Fastp (v0.20.1) to remove reads with low quality or adapter.
Clean data were mapped to a river buffalo genome with HISAT2 (v2.2.1).
Mapped reads were assembled by StringTie (v2.1.4) to obtain transcripts.
The assembled transcripts were annotated by Gffcompare (v0.11.2).
Expression of transcript was analyzed by StringTie (v2.1.4) and presented as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: The river buffalo genome was assembled by our team (not published) and can be provided from corresponding authors by e-mail.
Supplementary files format and content: Excel file (.xlsx) include FPKM values for all samples

organism: Bubalus bubalis

source_name: adipose tissue

growth_protocol: Buffaloes were weaned at 3 months of age, started to fatten at 15 months of age, and slaughtered at 20 months of age.

extract_protocol:
Total RNA was isolated using RNeasy Lipid Tissue Mini Kit (QIAGEN, GER) according to the manual instruction.
Approximately 2 μg of total RNA per sample was used for library construction according to the protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

value: adipose tissue

tag: breed

value: Nili-Ravi

tag: Sex

value: female

value: 20 month

tag: development stage

value: fatten


title: LVT-Ctrl-20

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

data_processing: Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

source_name: left ventricle tissue-Ctrl-20

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Wistar

value: left ventricle tissue

value: male

value: 8-10 week


title: SKD00401R-B20

value: Endothelial

value: 3 months


title: perirenal adipose tissue, buffalo-4

description: PRAT 4


title: LVT-Ctrl-17

source_name: left ventricle tissue-Ctrl-17


title: LVT-LPS-6

source_name: left ventricle tissue-LPS-6


title: perirenal adipose tissue, buffalo-3

description: PRAT 3

value: Murrah

value: 21 month


title: FigureS3B_180821_HC1_Unstim_PBMC_rep1

value: Untreated

tag: disease

value: HC

value: PBMC


title: LVT-Ctrl-16

source_name: left ventricle tissue-Ctrl-16


title: LVT-Ctrl-15

source_name: left ventricle tissue-Ctrl-15


title: SKD00401R-B19

value: Aorta

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


title: LVT-LPS-5

source_name: left ventricle tissue-LPS-5


title: LVT-Ctrl-18

source_name: left ventricle tissue-Ctrl-18


title: LVT-LPS-7

source_name: left ventricle tissue-LPS-7


title: LVT-LPS-1

source_name: left ventricle tissue-LPS-1


title: perirenal adipose tissue, buffalo-2

description: PRAT 2

value: adipose tissue


title: perirenal adipose tissue, buffalo-1

description: PRAT 1

value: 19 month


title: SKD00401R-B18


title: FigureS3B_180821_D5P3_Unstim_PBMC_rep2

value: NDAS


title: LVT-LPS-3

source_name: left ventricle tissue-LPS-3


title: pericardial adipose tissue, buffalo-6

description: PCAT 6

value: Nili-Ravi

value: female

value: fatten


title: SKD00401R-B23


title: perirenal adipose tissue, buffalo-6

description: PRAT 6


title: FigureS3B_180821_D5P3_Unstim_PBMC_rep1


title: pericardial adipose tissue, buffalo-5

description: PCAT 5

value: 20 month


title: FigureS3B_180821_HC1_Unstim_PBMC_rep2


title: SKD00401R-B17


title: pericardial adipose tissue, buffalo-4

description: PCAT 4


title: pericardial adipose tissue, buffalo-3

description: PCAT 3

value: male


title: SKD00401R-B16

value: Endothelial


title: pericardial adipose tissue, buffalo-2

description: PCAT 2


title: pericardial adipose tissue, buffalo-1

description: PCAT 1


title: SKD00401R-B15

value: 3 months


title: omental adipose tissue, buffalo-6

description: OAT 6


title: SKD00401R-B13


title: omental adipose tissue, buffalo-3

description: OAT 3

value: Murrah


title: FigureS3B_180821_P4_Unstim_PBMC_rep1


title: SKD00401R-B14


title: omental adipose tissue, buffalo-4

description: OAT 4


title: FigureS3B_180821_P4_Unstim_PBMC_rep2


title: omental adipose tissue, buffalo-1

description: OAT 1


title: SKD00401R-B12


title: omental adipose tissue, buffalo-5

description: OAT 5


title: inguinal adipose tissue, buffalo-6

description: IAT 6

value: 21 month


title: omental adipose tissue, buffalo-2

description: OAT 2


title: Figure3_SL9

description: chao_sle_noHB_RNA-seq_results.transcript.rpkm.xlsx

value: Untreated

value: Chao

value: Lupus

value: peripheral blood


title: inguinal adipose tissue, buffalo-5

description: IAT 5


title: SKD00401R-B11

value: Aorta

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


title: FigureS3B_180821_D5P1_Unstim_PBMC_rep1

value: PBMC


title: FigureS3B_180821_D5P1_Unstim_PBMC_rep2

value: NDAS


title: Figure3_SL7


title: SKD00401R-B10


title: inguinal adipose tissue, buffalo-2

description: IAT 2

value: adipose tissue


title: inguinal adipose tissue, buffalo-3

description: IAT 3


title: SKD00401R-B09


title: inguinal adipose tissue, buffalo-1

description: IAT 1

value: 19 month


title: inguinal adipose tissue, buffalo-4

description: IAT 4

value: Nili-Ravi

value: female

value: fatten


title: Figure3_SL75


title: Figure3_SL76


title: SKD00401R-B08

value: Endothelial


title: sternum subcutaneous adipose tissue, buffalo-4

description: SSAT 4

value: 20 month


title: sternum subcutaneous adipose tissue, buffalo-5

description: SSAT 5


title: sternum subcutaneous adipose tissue, buffalo-3

description: SSAT 3

value: Murrah

value: male


title: sternum subcutaneous adipose tissue, buffalo-2

description: SSAT 2


title: sternum subcutaneous adipose tissue, buffalo-1

description: SSAT 1


title: sternum subcutaneous adipose tissue, buffalo-6

description: SSAT 6

value: 21 month


title: SKD00401R-B07

value: 3 months


title: Figure3_SL74

value: Untreated

value: Chao

value: Lupus


title: SKD00401R-B06

value: Aorta

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


title: Figure3_SL72

value: peripheral blood


title: back subcutaneous adipose tissue, buffalo-4

description: BSAT 4

value: adipose tissue


title: back subcutaneous adipose tissue, buffalo-6

description: BSAT 6


title: SKD00401R-B05


title: Figure3_SL73


title: Figure3_SL71


title: SKD00401R-B04


title: Figure3_SL70


title: SKD00401R-B03


title: Figure3_SL8


title: SKD00401R-B02


title: Figure3_SL6


title: Tuft-2

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequencing data was trimmed using Trimmomatic (version 0.36) and aligned to the mm10 genome using STAR (version 2.7.3a)
Reads were assigned to genes using HTSeq (intersection non-empty, version 0.12.4)
Assembly: mm10
Supplementary files format and content: Gene counts: NonTuftVsTuft_unadj.counts.gz

source_name: Thymus

extract_protocol:
RNA was extracted using the QIagen RNAeasy kit.
RNA was processed using the SMARTer Ultra Low Input RNA Kit for Sequencing method.

value: Thymus

value: UEA+ MHCIIlo CD80- Sca1- CD63- CD117+ CD66a+


title: back subcutaneous adipose tissue, buffalo-1

description: BSAT 1

value: 19 month


title: back subcutaneous adipose tissue, buffalo-2

description: BSAT 2

value: fatten


title: SKD00401R-B01

value: Endothelial


title: Non-Tuft-3

value: UEA+ MHCIIlo CD80- Sca1- CD63- CD117- CD66a-


title: back subcutaneous adipose tissue, buffalo-5

description: BSAT 5

value: Nili-Ravi

value: female

value: 20 month


title: Tuft-1


title: Non-Tuft-2


title: Figure3_SL68


title: Non-Tuft-1


title: SKD00401R-A24

value: 3 months


title: WT_AS_2

city: Kanazawa City

first: Tsuyoshi

last: Hattori

state: Ishikawa

address: 13-1 Takara-Machi

department: Department of Neuroanatomy

institute: Kanazawa University

data_processing:
Base-calling were performed using Illumina HiSeq Control Software 2.2.38
Demultiplexing and trimming adapters from sequenced reads were performed by  bcl2fastq 2.17
Reads were aligned to genome assembly MusPutFur1 and GRCm38 using STAR 2.7.0f
Fragments Per Kilobase of exon per Million mapped reads (FPKM) ware calculated using cufflinks 2.2.1
Assembly: MusPutFur1, GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for every gene

source_name: brain

growth_protocol: Astrocyte cultures were prepared from the cerebral cortices of P1 to P3 neonatal mice. Cerebral cortices were digested at 37 °C in Hanks' Balanced Salt Solution with 2 mg/mL Dispase II. Cells were plated on poly-D-lysine-coated T75 flasks and cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum. After 14 days of cultivation, the culture flasks were shaken at 200 rpm for 12 hs and the supernatant was discarded. The astrocytes were detached using 0.05% trypsin-EDTA and plated at 1 × 105 cells/cm2 density. After 5 days of cultivation, cells were harvested.

extract_protocol:
RNA was extracted using RNA Basic Kit (FastGene #FG-8025).
Libraries were prepared using TruSeq Stranded mRNA Sample Preparation Kit (20020594, Illumina, Inc.), with polyA selection for ribosomal RNA depletion.

value: brain

value: primary astrocytes

value: WT


title: CD38_KO_AS2

value: CD38 KO


title: SKD00401R-A23

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.

value: Aorta

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


title: CD38_KO_AS1


title: WT_AS_1


title: Figure3_SL66

value: Untreated

value: Chao

value: Lupus

value: peripheral blood


title: back subcutaneous adipose tissue, buffalo-3

description: BSAT 3

value: adipose tissue

value: Murrah

value: male

value: 21 month

value: fatten


title: 2aOKO_O4_04

city: Singapore

first: Vetrivel

last: Sengottuvel

address: 8 College Road

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke NUS Medical School

data_processing:
Partek Flow (Version 10)
RNA-seq reads were mapped against mm39 using STAR 2.7.8a aligner, raw counts were obtained by feature counts and normalization done using median ratio (DESeq2 only) transform on all samples.
Differential gene expression analysis was performed on normalized values and a gene is considered significantly differentially expressed when p-value <0.05 and fold change ≥ 1.25.
Assembly: mm39
Supplementary files format and content: Excel sheet include normalized values for each sample.

source_name: Brain

extract_protocol:
Single cell suspension from mouse brain tissue was prepared using Papain based Neural Tissue Dissociation Kit from Miltenyi Biotech. OPC and O4 cells were isolated using CD140a+ and O4+ microbeads respectively from Miltenyi Biotech. Total RNA was extracted using Qiagen microprep column kit and 900ng of total RNA per sample was used for RNA library preparation.
RNA libraries were prepared using standard Illumina protocols for sequencing.

value: Brain


title: SKD00401R-A22

first: Martin

last: Enge

institute: Karolinska Institutet

value: Endothelial

value: 3 months


title: Figure3_SL65


title: Tuft-3

value: Thymus

value: UEA+ MHCIIlo CD80- Sca1- CD63- CD117+ CD66a+


title: 2aOKO_O4_03


title: Figure3_SL69


title: SKD00401R-A21


title: Figure3_SL64


title: 2aOKO_O4_02


title: 2aOKO_O4_01


title: SKD00401R-A20


title: SKD00401R-A19


title: Figure3_SL67


title: Figure3_SL63


title: 2aOKO_OPC_04

value: OPC


title: 2afl/fl_O4_02


title: 2aOKO_OPC_03


title: 2afl/fl_O4_01


title: 2aOKO_OPC_02


title: Figure3_SL61


title: Figure3_SL62


title: SKD00401R-A18

value: Aorta


title: Figure3_SL60


title: 2afl/fl_OPC_03


title: SKD00401R-A17

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


title: 2afl/fl_OPC_02


title: Figure3_SL5

value: Untreated


title: 2afl/fl_OPC_01


title: 2afl/fl_O4_03


title: SKD00401R-A15


title: NDCR_2

city: Hong  Kong

first: Yueqin

last: ZHU

state: China

address: Sassoon Road

institute: Hong Kong University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v0.21.0)
Trimmed sequence reads were mapped to GRCh38/rn6  using STAR(v2.7.7a)
Read count extraction and normalization were performed using RSEM(v1.3.3)
Assembly: GRCh38/rn6
Supplementary files format and content: tab-delimited text files include read count for each sample

source_name: liver grafts,normal,rat transplant model

extract_protocol:
Total RNA was extracted from liver grafts using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver graft

value: normal


title: SKD00401R-A14

city: Solna

address: Solnavägen 1


title: Figure3_SL59

value: Chao

value: Lupus

value: peripheral blood


title: NDCR_1


title: FDCR_3

source_name: liver grafts,steatotic,rat transplant model

value: steatotic


title: Figure3_SL58


title: FDCR_2


title: SKD00401R-A13

source_name: Aorta


title: SKD00401R-A12


title: FDCR_1


title: SW480 cells, CR36#2 36 hrs

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt(default parameter)
Trimmed sequence reads were mapped to GRCh38 using Hisat2(v2.0.1) with default parameter
Read count extraction and normalization were performed using HTSeq(v0.6.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: SW480 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA-seq library construction and analysis was carried out by Genewiz using Illumina PolyA selection

treatment_protocol: SW480 cells werecultured in the full medium (FM) or cystine-restriction medium (CR)

value: colon cancer cell

value: WT

value: cystine-restriction medium for 36 hrs

value: Hour 36


title: SW480 cells, CR36#3 36 hrs


title: 2aOKO_OPC_01

value: Brain


title: SW480 cells, CR36#1 36 hrs


title: SW480 cells, CR0#3 0 hrs

value: cystine-restriction medium for 0 hrs

value: Hour 0


title: Figure3_SL56


title: SW480 cells, CR0#2 0 hrs


title: SKD00401R-A16

value: Endothelial

value: 3 months


title: SKD00401R-A10

value: Aorta

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


title: Figure3_SL53

value: Untreated


title: Figure3_SL54


title: SKD00401R-A09


title: SKD00401R-A08


title: SW480 cells, CR0#1 0 hrs


title: NDCR_3

value: Liver graft

value: normal


title: Figure3_SL52

value: Chao

value: Lupus


title: SKD00401R-A07


title: Figure3_SL57

value: peripheral blood


title: Figure3_SL51


title: SKD00401R-A06


title: SKD00401R-A11


title: SKD00401R-A05


title: Figure3_SL55


title: SKD00401R-A04


title: HS-276+TGF-_N6_FS

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Primary fibroblast
6857-SB-8

data_processing:
Trimmed using cutadapt 2.3
Aligned and quantified using RSEM-STAR (RSEM 1.3.3 STAR 2.7.8a)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text of raw counts

source_name: Foreskin fibroblast

growth_protocol: Foreskin fibroblast 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 isolated from treated and untreated fibroblasts using quick-RNATM MiniPrep Kit from (Zymo research).
RNA libraries for RNA-seq were prepared using Ilumina paltform via poly A enrichment method following manufacturer's protocols.

treatment_protocol: Foreskin fibroblasts were serum-starved for 24 h (0.1% bovine serum albumin) and HS-276 was added to the cultures 24 h after TGF-β1 stimulation

value: Foreskin fibroblast


title: Figure3_SL49


title: HS-276+TGF-_N8_FS

description:
Primary fibroblast
6857-SB-9


title: Control_N5_FS

description:
Primary fibroblast
6857-SB-1

value: Control


title: TGF-Beta_N6_FS

description:
Primary fibroblast
6857-SB-5

value: TGF-Beta


title: Control_N6_FS

description:
Primary fibroblast
6857-SB-2


title: TGF-Beta_N8_FS

description:
Primary fibroblast
6857-SB-6


title: TGF-Beta_N5_FS

description:
Primary fibroblast
6857-SB-4


title: HS-276+TGF-_N5_FS

description:
Primary fibroblast
6857-SB-7


title: SKD00401R-A03


title: Figure3_SL48


title: Figure3_SL47


title: SKD00401R-A01


title: HEK293FT-PIE-PUM2_24h_1cell_rep3

city: Chicago

first: Xiangbin

last: Ruan

state: IL

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 reference with STAR
known SNPs in dbSNP version 138 (hg38) or SNVs with low read depth (less than 5-read depth) were filtered out
Gene-level counts were calculated by Rsubread
Assembly: hg38
Supplementary files format and content: text files include RNA editing information for each group

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 lysis buffer (water containing Rnase inhibitor on dry ice)
Smart-Seq2

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

value: HEK293FT cell line

value: transfected with pR023_PIE-PUM2 vector with Lipofectamine 2000 for 24h, and FACS sorted


title: HEK293FT-PIE-PUM2_24h_1cell_rep1


title: HEK293FT-APAD_24h_10cell_rep2

description: Nontargeting/APAD control

value: transfected with pR008_APAD vector with Lipofectamine 2000 for 24h, and FACS sorted


title: Figure3_SL46


title: SKD00501R-P16

value: DoubleNegative


title: Figure3_SL50


title: HEK293FT-APAD_24h_10cell_rep1

description: Nontargeting/APAD control


title: HEK293FT-APAD_24h_1cell_rep3

description: Nontargeting/APAD control


title: Control_N8_FS

description:
Primary fibroblast
6857-SB-3


title: Figure3_SL4


title: Figure3_SL45


title: HEK293FT-APAD_24h_1cell_rep2

description: Nontargeting/APAD control


title: SKD00501R-P15


title: SKD00401R-A02

value: Endothelial


title: HEK293FT-PIE-PUM2_24h_10cell_rep2


title: HEK293FT-PIE-PUM2_24h_1cell_rep2


title: RNAseq, p53KO, etopoisde-treated conditioned media, Replicate B

city: Worcester

first: Michael

middle: J

last: Lee

state: MA

address: 368 Plantation Street

institute: UMass Chan Medical School

description:
Column 12
p53KO_Etopoisde_CM_B
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

data_processing:
Sequences were aligned and counted using the DolphinNext RNA-seq Pipeline
Genes with less than 20 counts were trimmed
DESeq2 was used to calculate L2FC and adjusted p-value
Assembly: hg19
Supplementary files format and content: comma-delimited file for counts and comma-delimited file for DESeq2 output

source_name: U-2 OS

growth_protocol: U-2 OS osteosarcoma cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine in a humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA extracted using Qiagen RNeasy Mini Kit
Total RNA libraries were prepared and sequenced by BGI Genomics

treatment_protocol: Treatment with media conditioned by U2OS p53KO cells treated with etoposide (31.6uM)

value: U-2 OS

value: Osteosarcoma

value: p53 WT

value: Conditioned media from etoposide-treated U2OS p53 KO

value: 8 hours


title: RNAseq, p53KO, etopoisde-treated conditioned media, Replicate A

description:
Column 11
p53KO_Etopoisde_CM_A
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv


title: Figure3_SL44

value: Untreated


title: Figure3_SL43

value: Chao


title: SKD00501R-P13

value: Aorta

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

value: 3 months


title: HEK293FT-PIE-PUM2_24h_10cell_rep1


title: Figure3_SL42

value: Lupus

value: peripheral blood


title: SKD00501R-P11


title: RNAseq, p53KO, DMSO-treated conditioned media, Replicate A

description:
Column 7
p53KO_DMSO_CM_A
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

treatment_protocol: Treatment with media conditioned by untreated U2OS p53KO cells

value: Conditioned media from untreated U2OS p53 KO


title: RNAseq, p53KO, DMSO-treated conditioned media, Replicate B

description:
Column 8
p53KO_DMSO_CM_B
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv


title: Figure3_SL41


title: RNAseq, WT, etoposide-treated conditioned media, Replicate B

description:
Column 10
WT_Etopoisde_CM_B
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

treatment_protocol: Treatment with media conditioned by U2OS cells treated with etoposide (31.6uM)

value: Conditioned media from etoposide-treated U2OS


title: Figure3_SL40


title: SKD00501R-P10


title: Figure3_SL3


title: SKD00501R-P09


title: RNAseq, WT, etoposide-treated conditioned media, Replicate A

description:
Column 9
WT_Etopoisde_CM_A
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv


title: HEK293FT-APAD_24h_1cell_rep1

description: Nontargeting/APAD control

value: HEK293FT cell line

value: transfected with pR008_APAD vector with Lipofectamine 2000 for 24h, and FACS sorted


title: neuroblastoma_TRAP1_OE_2

city: HYderabad

first: Sreedhar

middle: Subbarao

last: Amere

state: Telangana

address: Habsiguda

country: India

institute: CSIR-CCMB

data_processing:
Illumina adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded. The processed reads were then mapped to the human genome GRCh38 using hisat2 with default parameters. Uniquely aligned reads were counted using featureCounts of Subread package. There were 60683 genes in the gtf file, downloaded from ensembl, for which we had count information. Genes with total read count 10 across all the samples were removed resulting in 22290 genes for further analysis. Differential gene expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 1 were considered differentially expressed. For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Assembly: human genome GRCh38

extract_protocol:
Total RNA was isolated from cells using Trizol (#15596-018, Invitrogen).
RNA library was genrated using TruSeq RNA Library Prep Kit v2 - Illumina following manufacturer's protocol.

value: Brain

value: neuroblastoma

value: TRAP-1 overexpression


title: neuroblastoma_TRAP1_KD_3

value: TRAP-1 knockdown


title: neuroblastoma_TRAP1_KD_2


title: neuroblastoma_TRAP1_OE_3


title: neuroblastoma_TRAP1_KD_1


title: RNAseq, WT, DMSO-treated conditioned media, Replicate B

description:
Column 6
WT_DMSO_CM_B
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

treatment_protocol: Treatment with media conditioned by untreated U2OS cells

value: U-2 OS

value: Osteosarcoma

value: p53 WT

value: Conditioned media from untreated U2OS


title: neuroblastoma_WT_3

value: WT


title: SKD00501R-P14

value: DoubleNegative

value: Aorta

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


title: SKD00501R-P08

value: 3 months


title: SKD00501R-P12


title: Figure3_SL38

value: Untreated

value: Chao

value: Lupus

value: peripheral blood


title: neuroblastoma_WT_2

value: Brain


title: SKD00501R-P07


title: neuroblastoma_TRAP1_OE_1

value: neuroblastoma


title: SKD00501R-P06


title: RNAseq, WT, DMSO-treated conditioned media, Replicate A

description:
Column 5
WT_DMSO_CM_A
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

value: 8 hours


title: RNAseq, WT, T0, Replicate B

description:
Column 4
WT_T0_B
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

treatment_protocol: Untreated sample collected at the assay start point

value: 0 hours


title: Figure3_SL36


title: neuroblastoma_WT_1


title: Figure3_SL35


title: HaCaT cells, pLVX-puro, Control, Rep3

city: Greenwood

first: Maryam

last: Nasiri Aghdam

state: South Carolina

address: 132 Edinborough Circle

department: Genetics and Biochemistry

institute: Clemson University

data_processing:
Data quality was verified by the FastQC v.0.11.9 tool on the Galaxy platform.
Reads were mapped to the hg38v38 human genome using STAR v.2.7.9a. Mapped reads were filtered based on the mapping quality utilizing the Qualimap v.2.2.1. tool
DESeq2 v.1.36.0 (20) input files for differential expression calculation between our ex-perimental groups. After data pre-processing, the normalized counts from DESeq2 v.1.36.0 (20) input files for differential expression calculation between our ex-perimental groups. After data pre-processing, the normalized counts from DESeq2 v.1.36.0 was used for differential expression and the GSEA v. 4.3.2 desktop application was used for gene set enrichment analysis
For accurate reconstruction of all expressed isoforms of each gene and to estimate the relative abundance of those isoforms, the StringTie v2.2.0 was utilized.
IsoformSwitchAnalyzeR was used for detecting and visualizing the mechanisms of alternative splicing and individual isoform switch events
Assembly: hg38v38 and Homo_sapiens.GRCh38.102.gtf
Supplementary files format and content: GTF files used for IsoformSwitchAnalyzeR

source_name: HaCaT cells

growth_protocol: Cell lines were grown in Invitrogen's GIBCO™ DMEM (Dulbecco's Modified Eagle Medium) medium with L-glutamine (584 mg/L), sodium pyruvate (110 mg/L), and D-glucose (4.5 g/L). The medium was supplemented with penicillin (100U/mL), streptomycin (100μg/mL), and 10% fetal bovine serum. The cultures were maintained at a confluence of 70-80%; upon reaching this level, the cells were detached with 0.25% trypsin (EDTA 380mg/L) and counted to make the necessary dilutions for the experiments.

extract_protocol:
Total RNA was obtained from 5 x 106 cells of each cell line using the PureLinkTM RNA Mini Kit extraction system (Ambion).
Sequencing of total mRNA has been performed on the Illumina Nova-Seq 6000 platform with a 150 bp paired-end method

treatment_protocol: RT-qPCR confirmed the expression of E5, E6, and E7 through specific primers.

value: HaCaT cells

value: Immortalized keratinocytes

value: pLVX-puro


title: RNAseq, WT, T0, Replicate A

description:
Column 3
WT_T0_A
RNAseq_ConditionedMedia_counts.csv
RNAseq_DESeq2_p53KOmedia_v_p53WTmedia.csv

value: U-2 OS

value: Osteosarcoma

value: p53 WT


title: PfDNMT KO, Schi, rep3

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: Schizont stage

value: no treatment


title: SKD00501R-P04

value: DoubleNegative

value: Aorta

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

value: 3 months


title: PfDNMT KO, Schi, rep2


title: Figure3_SL34

value: Untreated

value: Chao

value: Lupus

value: peripheral blood


title: Figure3_SL39


title: PfDNMT KO, Schi, rep1


title: SKD00501R-P03


title: SKD00501R-P02


title: Overexpression, Schi, rep3

value: Overexpression


title: SKD00501R-P01


title: HaCaT cells, pLVX-puro, Control, Rep2

value: HaCaT cells

value: Immortalized keratinocytes


title: Figure3_SL33


title: HaCaT cells, pLVX-84E7, Rep3

value: 84E7 oncogene


title: SKD00501R-O16


title: Figure3_SL32


title: HaCaT cells, pLVX-puro, Control, Rep1

value: pLVX-puro


title: Figure3_SL37


title: SKD00501R-P05


title: Figure3_SL31


title: Figure3_SL30


title: HaCaT cells, pLVX-84E7, Rep1


title: HaCaT cells, pLVX-84E7, Rep2


title: Overexpression, Schi, rep1


title: Overexpression, Schi, rep2


title: Figure3_SL2


title: Complementation, Schi, rep3

value: Complementation


title: HaCaT cells, pLVX-84E6, Rep3

value: 84E6 oncogene


title: SKD00501R-O14


title: Complementation, Schi, rep2

value: Schizont stage


title: HaCaT cells, pLVX-84E6, Rep2


title: HaCaT cells, pLVX-84E6, Rep1


title: SKD00501R-O13


title: Figure3_SL28


title: Figure3_SL27


title: Figure3_SL29


title: HaCaT cells, pLVX-84E5, Rep3

value: 84E5 oncogene


title: Complementation, Schi, rep1

value: no treatment


title: SKD00501R-O10

value: DoubleNegative

value: Aorta


title: SKD00501R-O11

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

value: 3 months


title: SKD00501R-O12


title: 3D7 WT, Schi, rep2

value: wildtype


title: 3D7 WT, Schi, rep3


title: 3D7 WT, Schi, rep1


title: HaCaT cells, pLVX-16E7, Rep3

value: 16E7 oncogene


title: SKD00501R-O15


title: PfDNMT KO, Troph, rep3

value: gene disruption (PfDNMT KO)

value: Trophzoite stage


title: SKD00501R-O09


title: SKD00501R-O08


title: HaCaT cells, pLVX-84E5, Rep1

value: HaCaT cells


title: HaCaT cells, pLVX-84E5, Rep2

value: Immortalized keratinocytes


title: Figure3_SL25

value: Untreated

value: Chao

value: Lupus

value: peripheral blood


title: Figure3_SL23


title: PfDNMT KO, Troph, rep2


title: HaCaT cells, pLVX-16E7, Rep2


title: SKD00501R-O07


title: Figure3_SL26


title: HaCaT cells, pLVX-16E7, Rep1


title: Figure3_SL22


title: PfDNMT KO, Troph, rep1


title: SKD00501R-O06


title: Figure3_SL21


title: HaCaT cells, pLVX-16E6, Rep3

value: 16E6 oncogene


title: Overexpression, Troph, rep3

value: Overexpression


title: HaCaT cells, pLVX-16E6, Rep2


title: SKD00501R-O05


title: SKD00501R-O04


title: Figure3_SL20


title: Figure3_SL1


title: Overexpression, Troph, rep2

value: no treatment


title: Overexpression, Troph, rep1


title: Complementation, Troph, rep3

value: Complementation


title: Figure3_SL19


title: HaCaT cells, pLVX-16E5, Rep3

value: 16E5 oncogene


title: SKD00501R-O03

value: DoubleNegative

value: Aorta

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


title: HaCaT cells, pLVX-16E6, Rep1


title: Figure3_SL24


title: SKD00501R-O01

value: 3 months


title: Figure3_SL18


title: HaCaT cells, pLVX-16E5, Rep1


title: SKD00501R-O02


title: HaCaT cells, pLVX-16E5, Rep2


title: Complementation, Troph, rep2


title: Figure3_SL17


title: Complementation, Troph, rep1


title: SKD00501R-N16

value: Endothelial


title: Figure3_SL16


title: 3D7 WT, Troph, rep3

value: wildtype

value: Trophzoite stage


title: HEKn_NEAT1 ANTISENSE

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

description: Genomic DNA extracted from NEAT1-antisense RNA pulldown in HEKn treated for six days with CaCl2

data_processing:
Demultiplexed and trimmed fastq's are generated from Illumina BaseSpace with FastqGeneration app
Alignment and processed data files are generated with nf-core/chipseq v1.2.2 pipline. The pipiline are running with default parameters
Assembly: hg19
Supplementary files format and content: peak file, bigWig
Library strategy: ChIRP-seq

source_name: keratinocytes

extract_protocol:
Lysates were clarified from sonicated nuclei. Biotinylated DNA probes were hybridized to target lncRNA and isolate bound chromatin using magnetic streptavidin beads. Quantity of the eluited genomic DNA by NanoDrop Spectrophotometer (NanoDrop Technologies, DE).
Libraries were prepared according to Illumina's instructions accompanying the Accel-NGS 2S Plus DNA Library Kit (Swift biosci#21024).

value: skin; Neonatal Foreskin

value: Primary human keratinocytes

value: normal


title: HEKn_LacZ INPUT

description: Genomic DNA extracted from LacZ RNA pulldown in HEKn treated for six days with CaCl2


title: SKD00501R-N15


title: Figure3_SL15

first: Stephen

last: Brooks

institute: NIAMS/NIH

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: Untreated

value: Chao

value: Lupus


title: 3D7 WT, Troph, rep2


title: glutamatergic neurons, G3BP2-KD rep3

city: Basel

first: Marco

last: Terrigno

address: Grenzacherstrasse 124

department: Neuroscience

country: Switzerland

institute: F. Hoffmann-La Roche AG

data_processing:
NovaSeq Control Software 1.7.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (0.32)
Basecalling was performed using Real-Time Analysis (RTA) v3.4.4 and fastq generated with bcl2fastq2.20 v2.20.0.422
Mapping of the reads was performed with STAR (v2.5.1b), followed by estimation of transcripts abundance using RSEM (RNA-Seq by Expectation Maximization v1.3.0) and differential gene expression analysis performed with DESeq2 (v1.28.1 )
Assembly: GRCh38
Supplementary files format and content: pairwise analysis of siRNA-treated and NT-treated Glutaneurons
Supplementary files format and content: tab-delimited text files include normalized gene counts

source_name: iCell Glutaneurons

extract_protocol:
RNA isolation was performed using RNeasy Mini Kit  (Qiagen) following manufacture’s instruction.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Gold rRNA Removal Kit

value: iCell Glutaneurons

value: neurons

value: wt

value: G3BP2 siRNA, (Horizon, Cat. E-015329-00)


title: SKD00501R-N14


title: 3D7 WT, Troph, rep1

value: no treatment


title: glutamatergic neurons, G3BP2-KD rep2


title: SKD00501R-N12

value: Aorta


title: glutamatergic neurons, G3BP2-KD rep1


title: Figure3_SL12

city: Bethesda

address: 50 SOUTH DR, RM 1140

value: peripheral blood


title: glutamatergic neurons, NT, rep3

value: Non-targeting siRNA (Horizon, Cat. D-001910-10)


title: PfDNMT KO, RING, rep2

value: gene disruption (PfDNMT KO)

value: Ring stage


title: PfDNMT KO, RING, rep3


title: SKD00501R-N10

value: Endothelial

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

value: 3 months


title: Figure3_SL11


title: Overexpression, RING, rep3

value: Overexpression


title: glutamatergic neurons, NT, rep2


title: glutamatergic neurons, NT, rep1


title: SKD00501R-N11


title: SKD00501R-N08


title: SKD00501R-N09


title: Figure3_SH9

value: Untreated


title: Expanded-NK-JDH rep2

city: Busan

first: Yoo-Soo

last: Park

address: Jwadong-gil 40

institute: Dongnam Institute of Radiological & Medical Sciences

data_processing:
A sequencing library using the SureSelectXT RNA Direct Reagent Kit (Agilent Technologies) and sequenced it using the Illumina Novaseq6000.
Library protocol : SureSelectXT RNA Direct For Preparation of Strand-Specific Sequencing for the Illumina Platform Version A0
After mapping the preprocessed reads to the reference genome using the HISAT2 program, aligned reads were generated.
After conducting a transcript assembly using the StringTie program, DEG analysis was performed using edgeR.
Assembly: GRCh38_NCBI_109
Supplementary files format and content: tab-delimited text files include Read count, FPKM and TPM values for each Sample

source_name: lymphocytes

growth_protocol: The culture medium was used Lymphocyte Growth Medium-3 (LGM-3, Lonza, MD, USA) containing 500 IU/ml of recombinant human IL-2 (PROLEUKIN) and 5% (v/v) human serum (Biowest, MO, USA). NK cell expansion was performed under GMP conditions for 21 days.

extract_protocol:
RNA was extracted from the cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using SureSelectXT RNA Direct Reagent Kit following manufacturer's protocols.

treatment_protocol: Highly purified NK cells were seeded in 5 µg/ml anti-human CD16 mAb-coated 24-well culture plates. Additionally, autologous PBMCs were irradiated with 25 Gy γ-radiation after stimulation for more than 30 minutes using an 0.5 μg/ml of anti-Human CD3 antibody, 1000 U/ml of recombinant human IFN-γ and 1000 U/ml of recombinant human IL-2. Stimulated autologous PBMCs were co-cultured with purified NK cells as feeder cells.

value: lymphocytes

value: expansion with feeder cells


title: Figure3_SH8

value: Chao

value: Lupus


title: Overexpression, RING, rep1


title: Overexpression, RING, rep2


title: SKD00501R-N07


title: Figure3_SL14


title: Expanded-NK-PYS rep1


title: SKD00501R-N13


title: SKD00501R-N06


title: Figure3_SH7


title: Complementation, RING, rep3

value: Complementation


title: Complementation, RING, rep2


title: Figure3_SL10


title: Figure3_SH6


title: SKD00501R-N05


title: Figure3_SH5


title: 3D7 WT, RING, rep3

value: wildtype


title: SKD00501R-N03


title: Figure3_SH4


title: Figure3_SH3


title: Nl CD45pos USC16.17.18 GEX

city: Los Angeles

first: Melissa

middle: G

last: Lechner

address: 10833 Le Conte Ave, CHS 57-154

department: Div of Endocrinology, Diabetes, and Metabolism

institute: UCLA Geffen School of Medicine

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #11

data_processing:
The reads are first mapped to GRCh38 (human) reference using cellranger software from 10x Genomics
Filtered output matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used for downstream analysis with Seurat
Cells with a mitochondiral gene percentage greater than or equal to 30 were removed
The raw counts and metadata from the Seurat object after IntegrateData and ScaleData step across samples are provided as processed data file
Subsequent clustering are descibed in the full manuscript
Assembly: GRCh38
Supplementary files format and content: irae_ht_integrated_counts.csv

source_name: Human thyroid FNAB, controls with no thyroid disease

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
Chromium Single Cell GEM, Library & Gel Bead Kit

treatment_protocol: Thyroid fine needle aspiration specimens from patients with immune checkpoint inhibitor thyroiditis, Hashimoto's thyroditis, or no thyroid disease, as defined in the manuscript

tag: disease state

value: control

tag: cell number


title: Nl CD45pos USC16.17.18 VDJ

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #12


title: Figure3_SL13

tag: treatment


title: HT CD45pos USC006 VDJ

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #10

source_name: Human thyroid FNAB, HT

value: Hashimoto's thyroiditis


title: Complementation, RING, rep1

value: no treatment


title: Resting-NK-PYS rep1

value: freshly isolated


title: SKD00501R-N02

tag: tissue

value: Aorta


title: SKD00501R-N01


title: 3D7 WT, RING, rep1

value: Ring stage


title: HT CD45pos USC006 GEX

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #9


title: SKD00501R-N04

value: Endothelial


title: Figure3_SH2

description: chao_sle_noHB_RNA-seq_results.transcript.rpkm.xlsx

value: peripheral blood


title: SKD00501R-M16

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

value: 3 months


title: Figure3_SH22

value: Untreated


title: Resting-NK-JDH rep2

value: lymphocytes


title: Figure3_SH21


title: pMV_E, pH, replicate 3

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

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

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.

value: bacterial culture

tag: phase

value: logarithmic

tag: vector

value: pH


title: HT CD45pos USC005 GEX

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #7


title: SKD00501R-M15

tag: genotype


title: pMV_E, pH, replicate 2

tag: cell type


title: ICI CD45pos IR8 VDJ

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #6

source_name: Human thyroid FNAB, IrAE

value: inhibitor-associated thyroiditis


title: Figure3_SH20

tag: run

value: Chao

value: Lupus


title: SKD00501R-M14

tag: strain


title: pMV_E, pH, replicate 1


title: Figure3_SH1


title: 3D7 WT, RING, rep2

value: wildtype


title: ICI CD45pos IR8 GEX

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #5


title: SKD00501R-M13


title: SKD00501R-M12


title: SKD00501R-M11


title: HT CD45pos USC005 VDJ

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #8

value: Hashimoto's thyroiditis


title: ICI CD45 h9 VDJ

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #4


title: HT CD45pos h7

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #3


title: HT CD45pos h6


title: SKD00501R-M10


title: SKD00501R-M09


title: Figure3_SH17


title: Figure3_SH15


title: Figure3_SH16


title: Figure3_SH18


title: Figure3_SH19


title: ICI CD45pos h4


title: HT CD45pos h5


title: SKD00501R-M07


title: SKD00501R-M08


title: Figure3_SH14


title: pMV_E, H2O2, replicate 1


title: pMV_E, DETA/NO, replicate 2

value: DETA/NO


title: pMV_E, H2O2, replicate 2


title: pMV_E, DETA/NO, replicate 1


title: pMV_E, H2O2, replicate 3


title: pMV_E, control, replicate 3

value: no treatment


title: Figure3_SH13


title: ICI CD45pos h3


title: SKD00501R-M06

value: Aorta


title: pMV_E, DETA/NO, replicate 3


title: ICI CD45 h9 GEX


title: SKD00501R-M05

value: Endothelial


title: Figure3_SH12

value: peripheral blood


title: pMV_E, control, replicate 2


title: SKD00501R-M04

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


title: Figure3_SH11