title: M37W 4 rep1

status: Public on Feb 19 2023

city: Ithaca

first: yuan

last: jiang

address: 306 Tower Rd

institute: cornell university

description: 11607_5751_115999_H7HC7BGXF_maize_4lines_F02_M37W_4_2_ACCGTG

data_processing:
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.
Raw reads were cleaned up with bbduk (sourceforge.net/projects/bbmap/) to trim the adapter, poly-A and poly-G according to the instruction of 3′ RNA libraries preparation kit. The purified reads were mapped to Zea mays B73 reference genome V4 (http://plants.ensembl.org/index.html) with STAR
The Differentially Expressed Genes (DEGs) were identified in R program (https://www.r-project.org/) with EdgeR package
Genome_build: B73 reference genome V4 (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

organism: Zea mays

source_name: M37W 4 leaf

growth_protocol: photoperiod 14h/10h (day/night), light irradiance 250μmol·m-2·s-1 and humidity 50-70%.

extract_protocol:
RNA was harvested by using the Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified by RNA Clean and Concentrator-5 (Zymo Research, Tustin, CA, USA; catalog number R1014).
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.

treatment_protocol: 26℃ for control, 4℃ for chilling treatment

tag: line

value: 4 treatment

value: leaf


title: M37W 4 rep2

type: SRA

country: USA

description: 11607_5751_116007_H7HC7BGXF_maize_4lines_F03_M37W_4_3_CTCCAT

library_source: transcriptomic

molecule: total RNA

tag: treatment

tag: tissue


title: M37W ck rep1

description: 11607_5751_115998_H7HC7BGXF_maize_4lines_E02_M37W_ck_2_TGGCGA

source_name: M37W ck leaf


title: M37W ck rep2

description: 11607_5751_116006_H7HC7BGXF_maize_4lines_E03_M37W_ck_3_TAGGCT


title: S, biological1 [SEB_VEH]

status: Public on Feb 20 2023

type: RNA

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

description: Gene expression data from infiltrating monocytes into injured lungs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing:
affymetrix-algorithm-name = rma : dabg was used to label samples.
affymetrix-algorithm-version = 1.0 was used.
Expression Console software program-version = 1.3.0.187 was used to analyze microRNA.

label: biotin

organism: Mus musculus

source_name: Lung's infiltrating monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Forty eight hours post SEB exposure, infiltrating cells were isolated by using ficol gradient method. Single cell suspension of infiltrating cells in cold FACS, a PBS supplemented with 10% fetobovine serum (FBS), was added gently and crefully to the top of room temperature kept ficol before being centrifuged at 500xg, 30 minutes at room temperature with no-brakes. Then the middle layer of monocytes were transferred into new tubes and washed twice with cold FACS.

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

treatment_protocol: SEB was given intranasally at 5micrograms per mouse then followed by intraperitoneal injection within 120 minutes. Resveratrol was given at 100mg/kg twice. First dose fo resveratrol has been given 24 hours before SEB challenge and the second dose of resveratrol was given 90 minutes before intraperitoneal injection of SEB.

value: Lung

tag: genotype

tag: age

value: 8-week old

value: pretreated with vehicle


title: CML333 4 rep2

description: 11607_5751_116009_H7HC7BGXF_maize_4lines_H03_CML333_4_3_AATAGC

source_name: CML333 4 leaf


title: CML333 ck rep2

description: 11607_5751_116008_H7HC7BGXF_maize_4lines_G03_CML333_ck_3_GCATGG

source_name: CML333 ck leaf


title: B104 4 rep2

description: 11607_5751_116005_H7HC7BGXF_maize_4lines_D03_B104_4_3_ACAGAT

source_name: B104 4 leaf


title: B104 4 rep1

description: 11607_5751_115989_H7HC7BGXF_maize_4lines_D01_B104_4_1_GCTCGA


title: B104 ck rep2

description: 11607_5751_116004_H7HC7BGXF_maize_4lines_C03_B104_ck_3_AAGACA

source_name: B104 ck leaf


title: CML333 4 rep1

description: 11607_5751_115993_H7HC7BGXF_maize_4lines_H01_CML333_4_1_CGAAGG


title: B104 ck rep1

description: 11607_5751_115988_H7HC7BGXF_maize_4lines_C01_B104_ck_1_CAAGCA


title: CML333 ck rep1

description: 11607_5751_116000_H7HC7BGXF_maize_4lines_G02_CML333_ck_2_CAACAG


title: B73 ck rep2

description: 11607_5751_115994_H7HC7BGXF_maize_4lines_A02_B73_ck_2_AGATAG

source_name: B73 ck leaf


title: B73 ck rep1

description: 11607_5751_115986_H7HC7BGXF_maize_4lines_A01_B73_ck_1_TTTATG


title: MDA-LM2_72h_DMSO_3

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
align and count reads with salmon (v0.14.1) to annotated transcript ends (100nt)
compare alternative polyadenylation site usage with APAlog
Assembly: hg38
Supplementary files format and content: count table

organism: Homo sapiens

source_name: breast cancer cell line

growth_protocol: The cells (~1M cells per replicate) were grown in DMEM high glucose 10% FBS Pen Strep Amphotericin B, at 37C 5% CO2, until ~70% confluent and harvested.

extract_protocol:
RNA was extracted with Zymo QuickRNA Microprep kit with on-column DNase treatment.
3'-end sequencing: QuantSeq REV kit (Lexogen)

treatment_protocol: Where indicated, the cells were treated with 3 µM T4 in DMSO or an equivalent volume of DMSO (vehicle control) for 6h prior harvesting or media change for harvesting later.

tag: cell line

tag: metastatic capacity

value: highly metastatic to lungs

tag: rna

value: total

value: DMSO


title: MDA-LM2_72h_DMSO_2


title: MDA-LM2_72h_T4_1


title: MDA-LM2_72h_T4_3


title: B73 4 rep2

description: 11607_5751_116003_H7HC7BGXF_maize_4lines_B03_B73_4_3_TGACAC

source_name: B73 4 leaf


title: MDA-LM2_24h_T4_1


title: MDA-LM2_72h_DMSO_1


title: MDA-LM2_72h_T4_2


title: MDA-LM2_24h_DMSO_3


title: MDA-LM2_24h_DMSO_2


title: MDA-LM2_24h_DMSO_1


title: RS, biological1 [SEB_RES]

value: pretreated with resveratrol


title: MDA-LM2_06h_T4_3


title: MDA-LM2_06h_T4_1


title: MDA-gHNRNPC_Nuc_3

value: poorly metastatic

value: nuclear

tag: genotype/variation

value: HNRNPC knockdown


title: MDA-gHNRNPC_Nuc_2


title: B73 4 rep1

description: 11607_5751_115987_H7HC7BGXF_maize_4lines_B01_B73_4_1_AACGCC


title: MDA-LM2_06h_DMSO_2


title: MDA-LM2_06h_DMSO_1


title: MDA-gCTRL_Nuc_3

value: control


title: MDA-gHNRNPC_Nuc_1


title: MDA-LM2_06h_T4_2


title: MDA-LM2_24h_T4_3


title: MDA-gCTRL_Nuc_2


title: MDA-LM2_Nuc_3


title: MDA-LM2_Nuc_2


title: MDA-gCTRL_Nuc_1


title: MDA-LM2_24h_T4_2


title: MDA-LM2_Nuc_1


title: MDA-Par_Nuc_2


title: MDA-Par_Nuc_3


title: MDA-gHNRNPC_Cyto_3

value: cytoplasmic


title: MDA-Par_Nuc_1


title: MDA-gHNRNPC_Cyto_2


title: MDA-gCTRL_Cyto_3


title: MDA-gHNRNPC_Cyto_1


title: MDA-LM2_Cyto_2


title: MDA-gCTRL_Cyto_1


title: Input in OSKM expressing, Dox ON G1297

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

library_source: genomic

data_processing:
The sequencing quality was checked using fastqc.
Low quality bases and adapter sequences were trimmed using trimGalore (0.6.6).
The trimmed reads were mapped to mm9 using bowtie2 (2.4.2) with --very-sensitive, --non-deterministic, --no-mixed and --no-discordant options.
Reads which had mapq < 20, mapped to blacklisted regions or were duplicates were removed using samtools and picard.
bigWig files were generated using deeptools.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: G1297 cell line

growth_protocol: Cells were cultured in 10% FBS and 0.2 µg/ml Doxycycline in DMEM.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies; anti-V5 (Abcam, rabbit polyclonal, ab15828) and anti-OCT4 (CST, rabbit polyclonal, #2750).
Libraries were prepared using ThruPLEX DNA-Seq Kit (TaKaRa) according to the manufacturer's instruction.

treatment_protocol: Cells were infected with retrovial vectors encoding V5-tagged OCT4, SOX2, KLF4 and MYC, or with those encoding V5-tagged MYOD1. The cell culture media was replaced either with media with or without Dox four days after the infection. Three days after that, the cells were subjected to ChIP.

tag: antibody

value: input

value: OSKM expressing, Dox ON


title: MDA-LM2_06h_DMSO_3


title: V5 ChIP in OSKM expressing, Dox ON G1297


title: MDA-Par_Cyto_3


title: OCT4 ChIP in OSKM expressing, Dox ON G1297


title: MDA-LM2_Cyto_3


title: MDA-Par_Cyto_2


title: V5 ChIP in MYOD1 expressing, Dox ON G1297

value: MYOD1 expressing, Dox ON


title: OCT4 ChIP in OSKM expressing, Dox OFF G1297

value: OSKM expressing, Dox OFF


title: V5 ChIP in OSKM expressing, Dox OFF G1297


title: MDA-sgHNRNPC_rep3 (RNA-seq)

data_processing:
adapter trimming (AAGATCGGAAGAGCACACGTCT) with cutadapt (v2.3)
split reads by adapter barcode with fastx_barcode_splitter
extract UMIs, 2N from the 5' end, 5N from the 3' end, with umi_tools extract
align to contaminant rRNA reference with bowtie2 (v2.3.5)
align to mRNA reference with bowtie2 (v2.3.5)
convert sam files to bam files with samtools
Sort and index bam files with samtools
deduplicate reads with umi_tools dedup
calculate translation efficiencies using Ribolog
Assembly: hg38

growth_protocol: The cells (~10M cells per replicate) were grown in DMEM high glucose 10% FBS Pen Strep Amphotericin B, at 37C 5% CO2, until ~70% confluent and harvested.

extract_protocol:
The lysates for Ribo-seq were prepared in lysis buffer (20 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 0.15% v/v Igepal CA-630 and 25 U/mL Turbo DNase) and used for ribosome protected footprint isolation. The RNA for RNA-seq was isolated from the lysates with Zymo QuickRNA Miniprep kit.
Ribo-seq: as described in McGlincy and Ingolia, 2017. RNA-seq: SMARTer Pico Input Mammalian RNA-seq kit v2 (Takara)


title: MDA-Par_Cyto_1


title: MDA-sgCTRL_rep3 (RNA-seq)


title: MDA-sgHNRNPC_rep2 (RNA-seq)


title: MDA-sgCTRL_rep2 (RNA-seq)


title: RNAseq G1297 MYOD1 EWS/ATF1 ON 1

data_processing:
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-1.18 (Martin, 2011). The trimmed reads were mapped to the mouse reference genome (mm10) using STAR v2.6.0c with GENCODE vM25 (Frankish et al., 2019). The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 (Anders et al., 2015).
Genome_build: mm10

source_name: G1297 clear cell sarcoma cell line

growth_protocol: HCC827 cells were grown in DMEM (Nacalai Tesque) supplemented with 10% of FBS (Biosera) and penicillin-streptomycin (PS) (Nacalai Tesque). G1297 cells were cultured in ESC media supplemented with human recombinant LIF (Wako), 2-Mercaptoethanol (Invitrogen) and 50 µg/ml L-ascorbic acid (Sigma) after the transduction of the reprogramming factors.

extract_protocol:
RNA was extracted by using the NucleoSpin RNA Plus (Takara Bio).
RNA was quantified on a NanoDrop 2000c and Qubit. RNA (200 ng) was prepared for library construction. High-quality RNA (RNA Integrity Number value ≥8, as determined by Bioanalyzer) was used for library preparation. RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were sequenced on a NextSeq500 (Illumina) as 86 bp single reads.

tag: treatment 1

value: MYOD1 induced

tag: treatment 2

value: Dox (EWS/ATF1) ON


title: RNAseq G1297 MYOD1 EWS/ATF1 ON 3


title: MDA-LM2_rep3 (RNA-seq)


title: MDA-sgCTRL_rep1 (RNA-seq)


title: RNAseq G1297 MYOD1 EWS/ATF1 OFF 2

value: Dox (EWS/ATF1) OFF


title: RNAseq G1297 MYOD1 EWS/ATF1 ON 2


title: MDA-sgHNRNPC_rep1 (RNA-seq)


title: V5 ChIP in MYOD1 expressing, Dox OFF G1297

value: MYOD1 expressing, Dox OFF


title: RNAseq G1297 MYOD1 EWS/ATF1 OFF 3


title: MDA-LM2_Cyto_1

value: highly metastatic to lungs


title: MDA-LM2_rep2 (RNA-seq)


title: MDA-Par_rep1 (RNA-seq)


title: RNAseq G1297 OSKM EWS/ATF1 ON 3

value: OSKM induced


title: RNAseq G1297 OSKM EWS/ATF1 OFF 2


title: RNAseq G1297 OSKM EWS/ATF1 ON 2


title: MDA-sgHNRNPC_rep1 (Ribo-seq)

data_processing:
adapter trimming (AAGATCGGAAGAGCACACGTCT) with cutadapt (v2.3)
split reads by adapter barcode with fastx_barcode_splitter
extract UMIs, 2N from the 5' end, 5N from the 3' end, with umi_tools extract
align to contaminant rRNA reference with bowtie2 (v2.3.5)
align to mRNA reference with bowtie2 (v2.3.5)
convert sam files to bam files with samtools
Sort and index bam files with samtools
deduplicate reads with umi_tools dedup
calculate translation efficiencies using Ribolog
Assembly: hg38
Library strategy: Ribo-seq


title: MDA-sgHNRNPC_rep3 (Ribo-seq)


title: MDA-Par_rep3 (RNA-seq)


title: RNAseq G1297 GFP EWS/ATF1 ON 3

value: GFP induced


title: MDA-LM2_rep1 (RNA-seq)


title: RNAseq G1297 MYOD1 EWS/ATF1 OFF 1


title: MDA-Par_rep2 (RNA-seq)


title: RNAseq G1297 OSKM EWS/ATF1 ON 1


title: RNAseq G1297 GFP EWS/ATF1 ON 2


title: MDA-sgCTRL_rep2 (Ribo-seq)


title: MDA-sgCTRL_rep1 (Ribo-seq)


title: RNAseq G1297 GFP EWS/ATF1 ON 1

data_processing:
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-1.18 (Martin, 2011). The trimmed reads were mapped to the mouse reference genome (mm10) using STAR v2.6.0c with GENCODE vM25 (Frankish et al., 2019). The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 (Anders et al., 2015)
Genome_build: mm10


title: RNAseq G1297 GFP EWS/ATF1 OFF 3


title: MDA-LM2_rep3 (Ribo-seq)


title: MDA-LM2_rep2 (Ribo-seq)


title: MDA-gCTRL_Cyto_2


title: control_2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Pvalue <= 0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample.

source_name: HeLa cell

growth_protocol: The human HeLa cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). ZFP36 overexpression plasmid transfection of HeLa cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was isolated from A549 cells with Trizol. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase. Purified RNA was transcribed for cDNA by oligo dT primer. And then the insert fragment was synthesized by PCR amplification. A linearized vector digested by EcoRI and XhoI (NEB) and PCR insert were added to a PCR microtube for ligation with ClonExpress® II One Step Cloning Kit (Vazyme).
The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: Primer pairs used for Hot Fusion were designed with CE Design V1.04. Each of the primer comprises a fragment of gene specific sequence and a 17–30 bp sequence of the pIRES-hrGFP-1a vector. The pIRES-hrGFP-1a vector was digested by EcoRI and XhoI (NEB) at 37℃ for 2h~3h. Then enzyme-digested vector was run on 1.0% agarose gel and purified by Qiagen column kit. Plasmids were introduced into Escherichia coli strain by chemical transformation. Cells were plated onto LB agar plates containing 1µL/ml ampicillin, and incubated overnight at 37℃. Colonies were screened by colony PCR (28 cycles) with universal primers (located on the backbone vector).

value: HeLa cell

value: control plasmid


title: MDA-LM2_rep1 (Ribo-seq)


title: control_1st


title: RNAseq G1297 OSKM EWS/ATF1 OFF 1


title: RNAseq G1297 OSKM EWS/ATF1 OFF 3


title: MDA-sgHNRNPC_rep2 (Ribo-seq)

value: poorly metastatic


title: MDA-Par_rep3 (Ribo-seq)


title: MDA-sgCTRL_rep3 (Ribo-seq)


title: Lateral wall macrophage young adult 4 [LW_Mp_Yo_4]

city: Charleston

first: Jeremy

last: Barth

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Fastq files were imported into the Partek Flow system
Alignment to Mouse mm10 was done with TopHat2
Aligned reads were quantified to annotation model (Partek E/M) using mm10 RefSeq transcripts with settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Normalized counts and comparative measures were obtained with DESeq2 configured to a) include low signal measures and b) perform FDR step-up multiple test correction
Assembly: mm10
Supplementary files format and content: tab-delimited text file of normalized counts and comparison measures

source_name: lateral wall macrophage

growth_protocol: CX3CR1 GFP/+ mice were bred and maintained in a low-noise environment at the MUSC Animal Research Facility.

extract_protocol:
Dissections were performed to isolate whole cochlea or cochlea substructures (auditory nerve or lateral wall). A tissue isolate from one mouse was treated as an independent sample. Samples were dissociated and sorted for GFP-positive cells (macrophages) and GFP-negative cells (nonmacrophages) by FACS using a procedure adapted from Panganiban et at., 2022. Total RNA was purified from each sample using the RNeasy Micro kit (Qiagen). Quality of each total RNA preparation was assessed by 4200 TapeStation, with low-quality samples excluded from further analysis.
RNA libraries were prepared using the SMARTer Ultra and Nextera XT library prep. Sequencing was performed on an Illumina HiSeq 2500 using Rapid Run mode, paired end read, 1X50 Cycles. Sequencing was done a second time for a subset of the samples.

value: heterozygous CX3CR1 GFP knock-in mice (CX3CR1 GFP/+)

tag: sorted cell

value: macrophage

tag: mouse age

value: young (1.5 month)


title: Hnrnpk_1st

value: hnRNPK overexpression


title: Lateral wall nonmacrophage young adult 16 [LW_No_Yo_16]

source_name: lateral wall nonmacrophage

value: nonmacrophage


title: MDA-PABPC4_rep2

data_processing:
Library strategy: CLIP-seq
collapse PCR duplicates
extract UMIs with umi_tools
quality trim (-q 15) and remove adapter with cutadapt
align to reference genome with BWA (0.7.17)
remove PCR duplicates, parse alignments, and call peaks using a valley-seeking algorithm (with multi-testing correction) with CTK
Genome_build: hg38

growth_protocol: The cells (~30M cells per replicate) were grown in DMEM high glucose 10% FBS Pen Strep Amphotericin B, at 37C 5% CO2, until ~70% confluent and harvested.

extract_protocol:
The lysates were preared in lysis buffer (1X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% IGEPAL CA-630) and used for IP
CLIP: irCLIP (Zarnegar et al., 2016), PAPERCLIP: SMARTer smRNAseq kit (Takara)

treatment_protocol: The cells were washed in ice cold 1X PBS and crosslinked at 400 mJ/cm2, 254 nm.

tag: ip antibody

value: PABPC4 (Proteintech 14960-1-AP)


title: Hnrnpk_2nd


title: MDA-Par_rep2 (Ribo-seq)


title: MDA-PABPC4_rep1


title: Cochlea nonmacrophage young adult 14 [CO_No_Yo_14]

source_name: cochlea nonmacrophage


title: Knockdown 3 treated Differentiation cell 3

city: Pathumwan

first: Medania

last: Purwaningrum

state: Bangkok

address: Henri Dunant

department: Pharmacology

country: Thailand

institute: Faculty of Veterinary Science

description: Differentiated + siRNA 3 + IL-6 cell line 3

data_processing:
For the normalization it uses the average of housekeeping gene:  18S
Target gene signals were normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports differentiated/control ratios.

label: SYBR Green

source_name: hPDLSCs line 3

label_protocol: The cDNA was obtained from RNA using ImProm-IITM Reverse Transcription System (Promega, USA). Targeted genes were amplified and detected by FastStart Essential DNA Green Master (Roche Diagnostics, USA) and CF96TM real-time PCR detection system (BioRad) with 40 cycles at 94℃ for 15 seconds and 60℃ for 60 seconds.

extract_protocol: The total cellular RNA was extracted using TRIzolTM reagent (Thermo Fisher Scientific) and Direct-zolTM RNA Miniprep kit (Zymo Research, USA)

value: OM + siWnt5A + IL-6


title: MDA-Par_rep1 (Ribo-seq)


title: RNAseq G1297 GFP EWS/ATF1 OFF 1


title: Knockdown 3 treated Differentiation cell 2

description: Differentiated + siRNA 3 + IL-6 cell line 2

source_name: hPDLSCs line 2


title: Knockdown 3 treated Differentiation cell 1

description: Differentiated + siRNA 3 + IL-6 cell line  1

source_name: hPDLSCs line 1


title: MDA-HNRNPC_rep2

value: HNRNPC (Santa Cruz sc-32308)


title: Cochlea nonmacrophage young adult 6 [CO_No_Yo_6]


title: Knockdown 2 treated Differentiation cell 4

description: Differentiated + siRNA 2 + IL-6 cell line 4

source_name: hPDLSCs line 4

value: OM + siWnt10B + IL-6


title: MDA-HNRNPC_rep1


title: Cochlea nonmacrophage young adult 5 [CO_No_Yo_5]


title: MDA-sgHNRNPC_rna_r2

description: RNA-seq for MDA-sgHNRNPC (rep2)

data_processing:
adapter trimming (AAGATCGGAAGAGCACACGTCT) with cutadapt (v2.3)
split reads by adapter barcode with fastx_barcode_splitter
extract UMIs, 2N from the 5' end, 5N from the 3' end, with umi_tools extract
align to contaminant rRNA reference with bowtie2 (v2.3.5)
align to mRNA reference with bowtie2 (v2.3.5)
convert sam files to bam files with samtools
Sort and index bam files with samtools
deduplicate reads with umi_tools dedup
calculate translation efficiencies using Ribolog
Genome_build: hg38

growth_protocol: The cells (~10M cells per replicate) were grown in DMEM high glucose 10% FBS Pen Strep Amphotericin B, at 37C 5% CO2, until ~70% confluent and harvested. The PDXs were implanted in female NSG mice and harvested ar tumor size of 1.0 cm

extract_protocol:
The lysates for Ribo-seq were prepared in lysis buffer (20 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% v/v Triton X-100 and 25 U/mL Turbo DNase) and used for ribosome protected footprint isolation. The RNA for RNA-seq was isolated from the lysates with Zymo QuickRNA Miniprep kit.
Ribo-seq: as described in McGlincy and Ingolia, 2017. RNA-seq: SMARTer Pico Input Mammalian RNA-seq kit v2 (Takara)


title: Knockdown 2 treated Differentiation cell 3

description: Differentiated + siRNA 2 + IL-6 cell line 3


title: Knockdown 2 treated Differentiation cell 2

description: Differentiated + siRNA 2 + IL-6 cell line 2


title: Knockdown 2 treated Differentiation cell 1

description: Differentiated + siRNA 2 + IL-6 cell line  1


title: Knockdown 1 treated Differentiation cell 4

description: Differentiated + siRNA 1 + IL-6 cell line 4

value: OM + siWnt2B + IL-6


title: Cochlea nonmacrophage young adult 2 [CO_No_Yo_2]


title: MDA-sgHNRNPC_rna_r1

description: RNA-seq for MDA-sgHNRNPC (rep1)


title: MDA-sgCTRL_rna_r2

description: RNA-seq for MDA-sgCTRL (rep2)


title: Knockdown 3 treated Differentiation cell 4

description: Differentiated + siRNA 3 + IL-6 cell line 4


title: Knockdown 1 treated Differentiation cell 3

description: Differentiated + siRNA 1 + IL-6 cell line 3


title: Knockdown 1 treated Differentiation cell 2

description: Differentiated + siRNA 1 + IL-6 cell line 2


title: MDA-sgCTRL_rna_r1

description: RNA-seq for MDA-sgCTRL (rep1)


title: Knockdown 1 treated Differentiation cell 1

description: Differentiated + siRNA 1 + IL-6 cell line  1


title: inhibitor 4 treated Differentiation cell 3

description: Differentiated + inhibitor 4 + IL-6 cell line  3

value: OM + DAPT + IL-6


title: Cochlea nonmacrophage old adult 11 [CO_No_Ol_11]

value: old (12-14 month)


title: Cochlea nonmacrophage old adult 18 [CO_No_Ol_18]


title: Cochlea nonmacrophage old adult 10 [CO_No_Ol_10]


title: MDA-LM2_rna_r1

description: RNA-seq for MDA-LM2 (rep1)

value: highly metastatic to lungs


title: inhibitor 4 treated Differentiation cell 1

description: Differentiated + inhibitor 4 + IL-6 cell line  1


title: inhibitor 3 treated Differentiation cell 4

description: Differentiated + inhibitor 3 + IL-6 cell line  4


title: inhibitor 4 treated Differentiation cell 2

description: Differentiated + inhibitor 4 + IL-6 cell line  2


title: Cochlea macrophage young adult 15 [CO_Mp_Yo_15]

source_name: cochlea macrophage


title: MDA-Par_rna_r2

description: RNA-seq for MDA-Par (rep2)


title: Cochlea nonmacrophage old adult 19 [CO_No_Ol_19]


title: MDA-Par_rna_r1

description: RNA-seq for MDA-Par (rep1)


title: inhibitor 3 treated Differentiation cell 3

description: Differentiated + inhibitor 3 + IL-6 cell line  3


title: inhibitor 2 treated Differentiation cell 4

description: Differentiated + inhibitor 2 + IL-6 cell line  4


title: inhibitor 3 treated Differentiation cell 1

description: Differentiated + inhibitor 3 + IL-6 cell line  1


title: inhibitor 2 treated Differentiation cell 1

description: Differentiated + inhibitor 2 + IL-6 cell line  1


title: inhibitor 2 treated Differentiation cell 3

description: Differentiated + inhibitor 2 + IL-6 cell line  3


title: Cochlea macrophage young adult 9 [CO_Mp_Yo_9]


title: inhibitor 4 treated Differentiation cell 4

description: Differentiated + inhibitor 4 + IL-6 cell line  4


title: Cochlea macrophage old adult 17 [CO_Mp_Ol_17]


title: MDA-LM2_rna_r2

description: RNA-seq for MDA-LM2 (rep2)


title: MDA-sgHNRNPC_rpf_r1

description: Ribo-seq for MDA-sgHNRNPC (rep1)

data_processing:
Library strategy: Ribo-seq
adapter trimming (AAGATCGGAAGAGCACACGTCT) with cutadapt (v2.3)
split reads by adapter barcode with fastx_barcode_splitter
extract UMIs, 2N from the 5' end, 5N from the 3' end, with umi_tools extract
align to contaminant rRNA reference with bowtie2 (v2.3.5)
align to mRNA reference with bowtie2 (v2.3.5)
convert sam files to bam files with samtools
Sort and index bam files with samtools
deduplicate reads with umi_tools dedup
calculate translation efficiencies using Ribolog
Genome_build: hg38


title: inhibitor 2 treated Differentiation cell 2

description: Differentiated + inhibitor 2 + IL-6 cell line  2


title: Cochlea macrophage old adult 7 [CO_Mp_Ol_7]


title: MDA-sgCTRL_rpf_r2

description: Ribo-seq for MDA-sgCTRL (rep2)


title: inhibitor 1 treated Differentiation cell 3

description: Differentiated + inhibitor 1 + IL-6 cell line  3

value: OM + Dkk1 + IL-6


title: inhibitor 1 treated Differentiation cell 2

description: Differentiated + inhibitor 1 + IL-6 cell line  2


title: inhibitor 1 treated Differentiation cell 4

description: Differentiated + inhibitor 1 + IL-6 cell line  4


title: inhibitor 3 treated Differentiation cell 2

description: Differentiated + inhibitor 3 + IL-6 cell line  2


title: Cochlea macrophage old adult 12 [CO_Mp_Ol_12]


title: MDA-sgCTRL_rpf_r1

description: Ribo-seq for MDA-sgCTRL (rep1)


title: Cochlea unsorted young adult 13 [CO_DNS_Yo_13]

source_name: cochlea dissociated cells

value: unsorted


title: Cochlea macrophage old adult 1 [CO_Mp_Ol_1]


title: inhibitor 1 treated Differentiation cell 1

description: Differentiated + inhibitor 1 + IL-6 cell line  1


title: MDA-LM2_rpf_r2

description: Ribo-seq for MDA-LM2 (rep2)


title: Treated Differentiation cell 1

description: Differentiated + IL-6 cell line  1

value: OM + IL-6


title: Treated Differentiation cell 2

description: Differentiated + IL-6 cell line 2


title: Auditory nerve nonmacrophage young adult 8 [AN_No_Yo_8]

source_name: auditory nerve nonmacrophage


title: Treated Differentiation cell 4

description: Differentiated + IL-6 cell line 4


title: Treated Differentiation cell 3

description: Differentiated + IL-6 cell line 3


title: MDA-LM2_rpf_r1

description: Ribo-seq for MDA-LM2 (rep1)


title: Auditory nerve macrophage young adult 3 [AN_Mp_Yo_3]

source_name: auditory nerve macrophage


title: Untreated Differentiation cell 4

description: Differentiated cell line 4

value: OM


title: Untreated Differentiation cell 3

description: Differentiated cell line 3


title: MDA-sgHNRNPC_rpf_r2

description: Ribo-seq for MDA-sgHNRNPC (rep2)

value: poorly metastatic


title: MDA-Par_rpf_r2

description: Ribo-seq for MDA-Par (rep2)


title: RNAseq MP-CCS-SY siMTOR 3

description:
STAR.TPM.tsv
MP_siMTOR_3

data_processing:
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-1.18 (Martin, 2011). The trimmed reads were mapped to the mouse reference genome (mm10) or the human reference genome (hg38) using STAR v2.6.0c with GENCODE vM25 or v36 (Frankish et al., 2019). The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: STAR.TPM.tsv

source_name: CCS cancer cell line

growth_protocol: The cell lines were grown in DMEM (Nacalai Tesque) supplemented with 10% of FBS (Biosera) and penicillin-streptomycin (PS) (Nacalai Tesque).

extract_protocol:
RNA was extracted by using the RNeasy Plus Mini Kit (QIAGEN) or NucleoSpin RNA Plus (Takara Bio).
RNA was quantified on a NanoDrop 2000c and Qubit. RNA (200 ng) was prepared for library construction. High-quality RNA (RNA Integrity Number value ≥8, as determined by Bioanalyzer) was used for library preparation. RNA-seq libraries were generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB). The number of PCR cycles was minimized to avoid skewing the representation of the libraries. RNA-seq libraries were sequenced on a NextSeq500 (Illumina) as 86 bp single reads.

value: MP-CCS-SY

tag: cell type

value: clear cell sarcoma cell

value: siMTOR treated


title: MDA-Par_rpf_r1

description: Ribo-seq for MDA-Par (rep1)

source_name: breast cancer cell line


title: Control Undifferentiation Cell 4

description: Control cell line 4

value: Control


title: RNAseq MP-CCS-SY siMTOR 2

description:
STAR.TPM.tsv
MP_siMTOR_2


title: MDA-sgHNRNPC-sgPABPC4_rep1

data_processing:
collapse PCR duplicates
extract UMIs with umi_tools
align and count reads with salmon (v0.14.1)
compare alternative polyadenylation site usage with APAlog
Genome_build: hg38

extract_protocol:
RNA was extracted with Zymo QuickRNA Microprep kit with on-column DNase treatment.
3'-end sequencing: QuantSeq REV kits (Lexogen)

tag: sample type

value: HNRNPC and PABPC4 double knockdown


title: RNAseq MP-CCS-SY siMTOR 1

description:
STAR.TPM.tsv
MP_siMTOR_1


title: Control Undifferentiation Cell 3

description: Control cell line 3


title: MDA-sgHNRNPC-sgPABPC4_rep2


title: EAE Spinal cord, S85, DHT, female, rep1

city: Le Kremlin-Bicêtre

first: Elisabeth

last: TRAIFFORT

address: 80 Rue du Général Leclerc

country: France

institute: Inserm

data_processing:
Quality of raw data was evaluated with FastQC. Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.6.3) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file
Library orientation, library composition and coverage along transcripts were checked with Picard tools
The edgeR R-package was used to perform both data normalization and differential expression analyses
Assembly: mm10
Supplementary files format and content: excel_genes were considered regulated when p-value < 0.05 and Fold change > 1.2

source_name: Spinal cord

extract_protocol:
Total RNA was isolated from the spinal cords with the Trizol Reagent protocol (ThermoFisher) and RNeasy Mini Kit (Qiagen) according to instructions of the provider
The RNA-Seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) and sequenced with the Novaseq 6000 platform (ILLUMINA, 32*106 100bp pair-end reads per sample).

treatment_protocol: Dihydrotestosterone (DHT) or the corresponding vehicle were administered at neurological disabilities onset

value: Spinal cord

tag: Sex

value: female

value: DHT


title: Control Undifferentiation Cell 1

description: Control cell line 1

tag: treatment


title: Control Undifferentiation Cell 2

description: Control cell line 2


title: EAE Spinal cord, S83, DHT, female, rep1

tag: tissue


title: MDA-sgCTRL-sgPABPC4_rep2

value: PABPC4 knockdown + non-targeting control


title: EAE Spinal cord, S81, Vehicle, female, rep1

value: Vehicle


title: EAE Spinal cord, S82, Vehicle, female, rep1


title: EAE Spinal cord, S80, Vehicle, female, rep1


title: RNAseq MP-CCS-SY siEWS/ATF1 1

description:
STAR.TPM.tsv
MP_siEA_1

value: siEWS/ATF1 treated


title: MDA-sgCTRL-sgPABPC4_rep1


title: MDA-sgHNRNPC-sgCTRL_rep2

value: HNRNPC knockdown + non-targeting control


title: Untreated Differentiation cell 1

description: Differentiated cell line 1


title: Untreated Differentiation cell 2

description: Differentiated cell line 2


title: EAE Spinal cord, S79, Vehicle, female, rep1


title: EAE Spinal cord, S84, DHT, female, rep1


title: RNAseq MP-CCS-SY siControl 3

description:
STAR.TPM.tsv
MP_siControl_3

value: siControl treated


title: pre-anthesis IAA9-silenced ovaries

city: Verona

first: Nicola

last: Vitulo

state: Select State

address: Strada le Grazie, 15

country: Italy

institute: University of Verona

description: Column name I1_IAA9sil

data_processing:
Libraries were constructed by ligating 3' and 5' adapters to the 3' and 5' ends of small RNAs, respectively; after cDNA synthesis, double_x0002_stranded cDNA libraries were generated by PCR enrichment.
After purification and size selection, libraries with insertions between 18 and 40 bp were sequenced with the NovaSeq 6000 platform.
The length distribution was analyzed to determine the composition of the three small RNA samples.
Assembly: Small RNA reads were mapped to the S. lycopersicum reference genome using Bowtie v1-3-0 with 0 mismatches, to analyze their expression level and distribution.

organism: Solanum lycopersicum

source_name: ovaries

growth_protocol: Tomato (Solanum lycopersicum) cv UC82 plants were  grown in the glasshouse with a 12 h light/dark cycle (22-28 °C day, 17-18 °C night). Flower buds from a population of 8-10 plants were collected for subsequent treatments.

extract_protocol:
Total RNA extraction was performed using the “NucleoSpin RNA Plant” kit (Macherey-Nagel). 3 µg of total RNA was used for the construction of sequencing libraries.
Preparation and sequencing of small RNA libraries were performed by Novogene (United Kingdom)

treatment_protocol: Flower pedicels were  injected with dsRNA-LDHs (5 µg:1 mg; 1:200 mass ratio per ovary) or LDHs alone (control, mock-treated). After 6 h, flower buds were emasculated and either bagged to avoid pollination and left on plants for 5 days. After 5 days, ovaries were collected and, after verifying target gene silencing, used for small RNA-Seq library preparation.

value: ovaries

tag: genotype

value: unpollinated detached ovaries treated with exogenous dsRNA against IAA9


title: pre-anthesis WT ovaries

description: Column name L1_control

value: unpollinated detached  mock-treated ovaries


title: pre-anthesis AGL6-silenced ovaries

description: Column name A1_AGL6sil

value: unpollinated detached ovaries treated with exogenous dsRNA against AGL6


title: EAE Spinal cord, S18, DHT, male, rep1

value: male


title: MDA-sgHNRNPC-sgCTRL_rep1


title: RNAseq MP-CCS-SY siEWS/ATF1 3

description:
STAR.TPM.tsv
MP_siEA_3

value: MP-CCS-SY

value: clear cell sarcoma cell


title: RNAseq MP-CCS-SY siControl 2

description:
STAR.TPM.tsv
MP_siControl_2


title: EAE Spinal cord, S16, DHT, male, rep1


title: MDA-sgCTRL-sgCTRL_rep2

value: Double non-targeting control


title: RNAseq MP-CCS-SY siControl 1

description:
STAR.TPM.tsv
MP_siControl_1


title: EAE Spinal cord, S15, DHT, male, rep1


title: OPCs, siSCR

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

data_processing:
RNA from siSCR or siHsc70 rat OPCs were subjected to 50-bp single-end sequencing with a BGISEQ-500 sequencer
At least 20 million clean reads of sequencing depth were obtained for each sample
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, read_count values for each Sample

organism: Rattus norvegicus

source_name: Forebrain tissue

growth_protocol: Rat OPCs were isolated from cortices of pups at P2-P4.  Mixed cortical cells were obtained by sequential immunopanning with antibodies against GalC and anti-A2B5 antibody-coated plates. Isolated OPCs were grown in OPC growth medium (OGM) (DMEM/F-12, Gibco, Thermo Fisher Scientific) with the addition of 2% B-27 (Gibco, Thermo Fisher Scientific); 1% N2 (Gibco, Thermo Fisher Scientific); 20 ng/mL PDGF-AA (Peprotech, 100-13A); 10 ng/mL CNTF (Peprotech, 450-13); 20 ng/mL bFGF (Sino Biological, 10014-HNAE); 5 uM forskolin (Sigma, F6886); 10 ng/mL biotin (Sigma, B4639); 5 ug/mL insulin (Sigma, I-6634); trace elements B (Corning, 16615008); sodium pyruvate (Thermo Fisher Scientific, 11360-070); penicillin-streptomycin (Thermo Fisher Scientific, 15140-122); and 1 ng/mL NT3 (Peprotech, 450-03). OPCs were differentiated using OPC differentiation medium (ODM). This medium differed from the OGM, in that T3 (60 nM) was added, and PDGF-AA, bFGF, and NT3 were removed.

extract_protocol:
Total RNA fraction was extracted using Eastep®Super Total RNA Extraction Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Approximately 2.0×10^6 OPCs were resuspended in 100 mL Basic Nucleofector Kit for Primary Mammalian Glial Cells (Lonza, O-017). Additionally,  10 uL of 20 mM siRNA ( siHsc70: TCATGACTGTCCTCATCAA) was added to the solution. The solution was then placed in a cuvette provided in the Nucleofector Kit and electroporated using a Lonza Nucleofector 2b device (LONZA) according to the manufacturer's protocol and program O-017. Next, cells were resuspended in medium and incubated for 30 min at 37°C, 5% CO2, before changing to new media to remove dead cells.

value: Forebrain tissue

value: Oligodendrocyte

value: wild type

value: electroporate siSCR into OPCs


title: RNAseq MP-CCS-SY siEWS/ATF1 2

description:
STAR.TPM.tsv
MP_siEA_2


title: RNAseq G1297 GFP EWS/ATF1 OFF 2

source_name: G1297 clear cell sarcoma cell line

value: GFP induced

value: Dox (EWS/ATF1) OFF


title: RNAseq HCC827 Gefitinib OSKM ON 3

data_processing:
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt-1.18 (Martin, 2011). The trimmed reads were mapped to the human reference genome (hg38) using STAR v2.6.0c with GENCODE v36 (Frankish et al., 2019). The uniquely mapped reads were summarized at the gene level using HTSeq-count v0.11.2 (Anders et al., 2015).
Genome_build: hg38

source_name: HCC827 lung cacner cell line

value: Dox (OSKM) ON

value: Gefitinib treated


title: EAE Spinal cord, S3, Vehicle, male, rep1

value: Spinal cord

value: Vehicle


title: EAE Spinal cord, S8, Vehicle, male, rep1


title: MDA-sgHNRNPC_rep2

extract_protocol:
RNA was extracted with Zymo QuickRNA Microprep kit with on-column DNase treatment.
3'-end sequencing: QuantSeq FWD and REV kits (Lexogen)

value: HNRNPC knockdown


title: EAE Spinal cord, S2, Vehicle, male, rep1


title: MDA-sgCTRL_rep2

value: Non-targeting control


title: Liver, AAV8-AGXT, 319

city: Shreveport

first: Oren

last: Rom

state: LA

address: Biomedical Research Institute Rm F4-27 1501 Kings Hwy

institute: LSU Health Shreveport

data_processing:
Primary analysis, including base calling and quality scoring, was performed onboard the Illumina NovaSeq 6000 (NovaSeq Control Software v1.8.0; RTA v3): Samples were de-multiplexed, the adapter sequences were removed (the first 9 cycles of sequencing were trimmed), and FASTQ files were generated
The quality of the raw FASTQ files was checked through FastQC v0.11.8. Trimmomatic v.0.35 was used to trim the low-quality reads with the parameters: SLIDINGWINDOW:4:20 MINLEN:25. The resulted high-quality reads were then mapped to the mouse reference genome (GRCm38.90) using HISAT2 v.2.1.0.13. Gene level quantification was performed using HTSeq-counts v0.6.0 based on the GRCm38.90 genome annotations.
Assembly: mouse reference genome (GRCm38.90)
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: Liver

extract_protocol:
Livers were harvested at endpoint (week 24). Total RNA from mouse liver samples was extracted using QIAGEN’s RNeasy kit. Samples were quantitated with a Qubit RNA assay (ThermoFisher Scientific) and RNA quality was determined with the Agilent TapeStation RNA assay (Agilent Technologies).
Libraries were prepared with the Stranded mRNA Prep, Ligation Kit (Illumina). One ug of RNA was processed for each sample: mRNA was purified and fragmented. cDNA was synthesized, and 3’ ends were adenylated. Anchor sequences were ligated to each sample and limited-cycle PCR was performed to amplify and index the libraries.
The average library size was determined using an Agilent TapeStation D1000 assay (Agilent Technologies) and libraries were quantitated with qPCR (Bio-rad CFX96 Touch Real-Time PCR, NEB Library Quant Kit for Illumina).  Libraries were normalized to 0.5 nM and pooled.  The library pool was denatured and diluted to approximately 100 pM.  A 1% library of 2.5 pM PhiX was spiked in as an internal control.

treatment_protocol: C57BL/6J mice were injected with AAV8-TBG-GFP or AAV8-TBG-AGXT and fed a high-fat, high-cholesterol, high-fructose diet for 24 weeks

value: Liver

value: Wild-type

tag: diet

value: NASH diet


title: EAE Spinal cord_S1, Vehicle, male, rep1

value: male


title: MDA-sgHNRNPC_rep1

tag: cell line


title: Liver, AAV8-AGXT, 316


title: Liver, AAV8-AGXT, 308


title: Liver, AAV8-AGXT, 309


title: RNAseq HCC827 DMSO OSKM ON 3

value: DMSO treated


title: RNAseq HCC827 Gefitinib OSKM ON 1


title: Liver, AAV8-GFP, 315


title: RNAseq HCC827 DMSO OSKM ON 1


title: OPCs, siHsc70

value: Forebrain tissue

value: electroporate siHsc70 into OPCs


title: MDA-LM2_rep2

value: highly metastatic to lungs


title: RNAseq HCC827 Gefitinib OSKM OFF 3

value: Dox (OSKM) OFF


title: MDA-sgCTRL_rep1


title: MDA-LM2_rep1


title: PT_7, tumor_ST

city: ShangHai

first: Ke-Da

last: Yu

address: No.270, Dongan Road

institute: ShangHai Cancer Center

description:
10X Visium
ST_barcodes.tsv.gz
ST_features.gz
ST_matrix.mtx.gz
ST_D_tissue_image.png

library_source: transcriptomic single cell

data_processing:
Raw sequencing data for each single- cell sample were converted to matrices of expression using cellranger (version 3.1.0, 10x Genomics). Raw sequencing data for each spatial transcriptome sample were converted to matrices of expression using Space Ranger (version 1.2.0, 10X Genomics).
integrate single cell RNA-seq and spatial transcriptomes with MIA.
different gene analysis with Seurat (version 3.1.1)
Assembly: GRCh38 human reference genome
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: human breast cancer

extract_protocol:
Cells suspension from primary tumor and paired lymph node metastasis samples were loaded into the 10X Chromium Controller using the Chromium 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1. Fresh frozen primary tumor samples slide gene expression were detected by 10X Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x chromium single cell 3' Reagent Kits v3.1 protocols or 10x Visium spatial protocols and standard Illumina protocols

value: human breast cancer

value: female

tag: site

value: Primary tumor

tag: donor

tag: pathological type

value: Invasive ductal carcinoma


title: MDA-sgCTRL-sgCTRL_rep1

value: Double non-targeting control


title: MDA-Par_rep2

value: poorly metastatic


title: Liver, AAV8-GFP, 311


title: PT_6, tumor_ST

description:
10X Visium
ST_barcodes.tsv.gz
ST_features.gz
ST_matrix.mtx.gz
ST_C_tissue_image.png


title: RNAseq HCC827 Gefitinib OSKM OFF 1

value: Gefitinib treated


title: PT_3, tumor_ST

description:
10X Visium
ST_barcodes.tsv.gz
ST_features.gz
ST_matrix.mtx.gz
ST_B_tissue_image.png


title: PT_2, tumor_ST

description:
10X Visium
ST_barcodes.tsv.gz
ST_features.gz
ST_matrix.mtx.gz
ST_A_tissue_image.png


title: Liver, AAV8-GFP, 303


title: RNAseq HCC827 DMSO OSKM OFF 3


title: MDA-Par_rep1


title: RNAseq HCC827 DMSO OSKM OFF 1


title: Sagittal plane of mouse embryo of E12.5

city: Shanghai

first: Ji

last: Qi

address: E401, Life Science Building, Jiangwan Campus, Fudan University, 2005 Songhu Rd.

department: School of Life Sciences

institute: Fudan University

description: Sagittal section

data_processing:
Sequenced reads were trimmed by SpaceRanger of 10X Genomics (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome)
Unique molecular identifiers (UMIs) for each spot were counted to remove PCR duplicates.
Genome_build: mm10
Supplementary_files_format_and_content: Tables with raw gene counts for each gene and each spot

molecule: polyA RNA

source_name: Embryo

extract_protocol:
Dissections were performed and embryos of E9.5-E12.5 were immediately frozen in liquid nitrogen-cooled isopentane and were embedded in pre-cooled OCT. Tissue preparation and optimization were performed on 10X Visium platform, including tissue sectioning, H&E staining, tissue permeabilization, fluorescent cDNA synthesis and imaging, according to the manufacturer’s protocol.
cDNAs of samples were sequenced on Illumina novaseq platform and were subjected to 150 cycles of paired-end (2 × 150 bp) sequencing

tag: strain

value: Embryo


title: PT_7, lymph_node_sc

description:
10x Genomics
sc_barcodes.tsv.gz
sc_features.tsv.gz
sc_matrix.mtx.gz

value: Lymph node metastasis


title: Sagittal plane of mouse embryo of E11.5

description: Sagittal section


title: PT_6, lymph_node_sc


title: Sagittal plane of mouse embryo of E10.5

description: Sagittal section


title: PT_3, lymph_node_sc


title: Sagittal plane of mouse embryo of E9.5

description: Sagittal section


title: 95Cc.del_rep1

city: Wuhan City

first: Liang

middle: an

last: min

state: Hubei Province

address: 299 Bayi Road

department: College of Life Sciences

institute: Wuhan University

description:
strand specific
total RNA (remove rRNA)

data_processing:
FsatQC v0.11.5 and cutadapt v1.15 used for base calling
Raw reads from RNA-seq were quality filtered and trimmed by Trimmomatic(v0.39)
Histat (v2.1.0) used for mapping to the Drosophila genome
Assembly: dm6

organism: Drosophila melanogaster

source_name: Larva L3

extract_protocol: Total RNA from the 3rd instar larvae of the WT and the five U1-gene deletion strains were isolated by TRIzol (Invitrogen) and treated with RNase-free DNase I (Takara). Construction of cDNA libraries and sequencing were performed using Illumina HiseqXten-PE150 by Novogene

treatment_protocol: The wild type (WT) Drosophila melanogaster used in this study is a w1118 isogenic strain and five five U1-gene deletion strains were constructed using CRISPR/Cas9-mediated knock-in system

value: BDSC 5905

tag: Stage

value: Larva L3

tag: region

value: whole individual


title: Normal

city: HsinChu

first: Chih-Hung

last: Chou

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

data_processing:
Reads of small RNA-seq were trimmed 3’adapter and quality pre-processed using cutadapt v1.9.1 and FASTX-Toolkit v0.0.13.2, respectively.
The reads with Phred quality score ≥ 20 and longer than 18 nucleotides were retained.
The UCSC reference genome and miRBase v21 were employed for annotation of reads that could be mapped to genome.
Genome_build: hg38
Supplementary_files_format_and_content: RPM sample matrix file

source_name: plasma

extract_protocol:
Blood was centrifuged at 3000 rpm for 10 min to separate plasma and stored at −80°C. For small RNA sequencing, total RNA was extracted from 3 ml of pooled plasma using a combined version of phenol–chloroform extraction followed by column purification.
Library was constructed by TruSeq Small RNA Preparation Kits (Illumina Inc, CA,  USA) according to the manufacturer’s instructions.

tag: diagnosis

value: Healthy control


title: 95Cc.del_rep3

description:
strand specific
total RNA (remove rRNA)


title: Ictal

value: Ictal phase


title: 95Cb.del_rep3

description:
strand specific
total RNA (remove rRNA)


title: PT_2, lymph_node_sc


title: 95Cb.del_rep2

description:
strand specific
total RNA (remove rRNA)


title: PT_7, tumor_sc


title: PT_6, tumor_sc


title: E_7

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422, Illumina), allowing no mismatches in the index read. Primary read mapping and UMI analysis were conducted via the GeneGlobe Data Analysis Center (Qiagen).
Genome_build: GRCm38
Supplementary_files_format_and_content: raw read counts are provided in a csv ifle

source_name: fecal exosomes

growth_protocol: Four-week old IL-10 KO mice (Stock No. 002251 with C57BL/6J background, IMSR Cat# JAX:002251, RRID:IMSR_JAX:002251) and control wild-type (WT) mice (C57BL/6J, MGI Cat# 5657312, RRID:MGI:5657312, equal number of females and males was used) were obtained from The Jackson Laboratories (Bar Harbor, Maine).

extract_protocol:
The feces were collected once a week and stored at -80°C until processing. Mice were scuffed, and a 1.5 mL Eppendorf tube (Fisher Scientific, Waltham, MA) was placed under the anus to collect 3-5 fecal pellets. If sufficient feces were not collected after 30 seconds, the mouse was placed in a clean cage without beading until at least 3 pellets were obtained. Exosomal RNA was extracted and sequenced as follows. 2 fecal pellets (~60mg) were vortexed with 0.9-2.0 mm stainless steel beads (Next Advance, Troy, NY) with 60 μl Tris-HCl (10 mM) in a 1.5 mL microcentrifuge tube. Increasing amounts of Tris-HCl until 1 mL total volume was reached and subsequently vortexed. The resulting mixture was then centrifuged at 10,000Xg for 5 minutes. The supernatant was then filtered through a 0.2 μm syringe filter (ThermoFisher Scientific, Waltham, MA). Exosomes were isolated via ExoQuick TC (System Biosciences, Palo Alto, CA) according to manufacturer instructions. Purified exosomes were lysed and RNA was isolated using Quick-RNA Microprep Kit (Zymo Research, Irvine, CA). Quality and quantity of the extracted RNA were determined using TapeStation RNA ScreenTape (Agilent Technologies, Santa Clara, CA) and Qubit fluorometer (ThermoFisher Scientific).
SmRNA-sequencing libraries were prepared from 50 to 150 ng of total RNA using the QIAseq miRNA Library Kit (Qiagen, Germantown, MD) as per the manufacturer's instructions. This system offers a built-in Unique Molecular Identifier (UMI) application, which is used to eliminate possible PCR duplicates in sequencing datasets and therefore facilitate unbiased gene expression profiling. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol.
The denatured libraries were loaded onto an SP flow cell on an Illumina NovaSeq 6000 and run for 53-71 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: Each mouse was then housed conventionally and individually in polycarbonate cages, static, wire-top cages on corncob bedding (7092 Harlan Teklad, Madison, WI), and had ad lib access to irradiated rodent chow (2918, Harlan Teklad, Madison, WI) and tap water. The animal facility was programmed with a 12:12-h light: dark cycle. Room temperature was maintained at 20 ± 2ºC, and air humidity ranged between 30 to 60%. Environmental enrichment was provided in the form of an Enviropak (Lab Supply, Fort Worth, TX). Mice were free of ectromelia virus, Theiler’s encephalomyelitis virus, Hantaan virus, K virus, lactate dehydrogenase elevating virus, lymphocytic choriomeningitis virus, mouse adenovirus types 1 and 2, mouse cytomegalovirus, mouse hepatitis virus, mouse minute virus, murine norovirus, mouse parvovirus, mouse thymic virus, pneumonia virus of mice, polyoma virus, Reovirus 3, Rotavirus, encephalomyelitis virus, Sendai virus, Bordetella bronchiseptica, Flavum rodentium, Citrobacter rodentium, Clostridium piliforme, Corynebacterium kutscheri Corynebacterium bovis, Helicobacter spp., Mycoplasma pulmonis, Pasteurella spp., Salmonella spp., Streptobacillus moniliformis, Klebsiella pneumonia, Pneumocystis murina, Pseudomonas spp., Staphylococcus aureus, Streptococcus pneumonia, β-hemolytic Streptococcus spp., endo-and ectoparasites, enteric protozoa, and Encephalitozoon cuniculi. All experiments were conducted in accordance with institutional guidelines, the Guide for the Care and Use of Laboratory Animals (Institute for Laboratory Animal Research, 2011), and approved by the Penn State College of Medicine Institutional Animal Care and Use Committee.

tag: mouse individual id

value: IL-10 KO

tag: time point

value: end-point

value: F


title: 95Cb.del_rep1

description:
strand specific
total RNA (remove rRNA)


title: HUVEC_aza_5uM_rep3

city: Paris

first: Gwenneg

middle: Vincent

last: Kerdivel

address: 24 rue du faubourg saint jacques

institute: Institut Cochin

description: RNA-seq experiment performed on HUVEC cells treated with 5µM 5-azacytidine

data_processing:
RNAseq : After sequencing, a primary analysis based on AOZAN software64 was applied to demultiplex and control the quality of the raw data.
RNAseq : Mapping of the reads to the human reference genome hg19/GRCh37 was performed using STAR v2.5.3a65 with the following parameters: twopassMode, ‘Basic’; chimSegmentMin, 12; chimJunctionOverhangMin, 12; alignSJDBoverhangMin, 10; alignMatesGapMax, 100000000; alignIntronMax, 200000; alignSJstitchMismatchNmax, 5 -1 5 5.
RNAseq : FeatureCount66 was used to retrieve the gene-level raw read counts from aligned reads. Raw read counts were then normalized using the function RUVs from the R package “RUVSeq” (“remove unwanted variation” , v1.16.168) and then processed with DESeq2 (v1.22.2) without size factor normalization to find differentially expressed genes.
RRBS : Image analysis and base calling were performed using Illumina Real Time Analysis (3.4.4) with default parameters. Base calling was performed by using the Real-Time Analysis software sequence pipeline (3.4.4) with default parameters.
RRBS : RRBS data were mapped to the Human genome (hg19) using BS-Seeker2 (v2.1.8). The following parameters were used: -r (Map reads to the Reduced Representation genome), -c C-CGG (MspI: sites of restriction enzyme and specifying lengths of fragments ranging [40bp, 400bp]. One mismatch was allowed in the adaptor sequence. Allowing local/gapped alignment with Bowtie269 increased the mappability. BS-Seeker2 module bs_seeker2-call_methylation.py was used to call methylation levels from the mapping results with these parameters: --rm-SX (Removed reads which would be considered as not fully converted by bisulfite) and --rm-overlap (Removed one mate if two mates are overlapped). The methylation callings were saved in the ATCGmap/CGmap format.
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq : raw count files generated by feature counts (txt).   RRBS : Methylation callings in Cgmap format

source_name: vascular endothelium

growth_protocol: Human H295R cells were cultured in DMEM/F12 with 15 mM HEPES and sodium bicarbonate, without L-glutamine (Sigma-ALDRICH), supplemented with 2% NU-serum (Corning, France), 1% insulin, transferrin, and selenium (100U/ml; GIBCO), penicillin/streptomycin (100 U/ml; GIBCO) and 1ml plasmocin (2.5 mg/ml, Invivogen). The cells are grown in humidified 5% CO2 at 37°C. Human cell MUC-156 cultured in Advanced DMEM/F12 Medium (GIBCO) supplemented with  10% FBS and 1% penicillin/streptomycin and grown in humidified 5% CO2 at 37°C. Human HUVEC cells were cultured in DMEM medium with glutamax, 4.5 g D-glucose and pyruvate (Gibco), supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 U/ml; GIBCO) in a humidified incubator containing 5% CO2 at 37°C. H295R and HUVEC cell lines were purchased from the American Type Culture Collection (ATCC).

extract_protocol:
RNAseq : Total RNAs extractions were performed using TRIzol® Reagent (Invitrogen) according to manufacturer's protocol. Extracted RNAs were then treated with DNAse (TURBO DNA-freeTM kit, Invivogen) following provider’s instructions.     RRBS : Genomic DNA was extracted using QIAamp® Fast DNA Tissue Kit (Qiagen) according to manufacturer protocol.
RNAseq : 1% ERCC spike-in RNA (Life technologies) were added to 3µg of high quality total RNA samples. Sequencing libraries were then prepared using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, after purification of poly-A containing mRNA molecules, mRNA molecules were fragmented and reverse-transcribed using random primers. dTTP was replaced by dUTP during the second strand synthesis to achieve the strand specificity. Addition of a single A base to the cDNA (dA tailing) was followed by ligation of Illumina adapters. Libraries were quantified by Qubit fluorometer (Life Technologies) and library profiles were assessed using the DNA high Sensitivity LabChip kit on an Agilent Bioanalyzer 2100. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read chemistry in a paired-end mode. After sequencing, a primary analysis based on AOZAN software64 was applied to demultiplex and control the quality of the raw data.     RRBS : Reduced Representation Bisulfite Sequencing (RRBS) was performed by Integragen SA (Evry, France) with the Diagenode Premium RRBS kit. In brief, 100 ng of qualified genomic DNA were digested with MspI. After end-repair, A-tailing, and ligation to methylated and indexed adapters, the size selected library fragments were subjected to bisulfite conversion, amplified by PCR, and sequenced on an Illumina NovaSeq sequencer as Paired End 100 bp reads.

treatment_protocol: 5 days treatments were performed by replacing the medium with fresh medium containing 5µM 5-azacytidine or the control solvent (DMSO, 0.005%). Treatments were renewed everyday.

tag: cell type

value: HUVEC

tag: passages

tag: treatments

value: 5-azacytidine 5uM


title: HUVEC_aza_5uM_rep2


title: E_5

tag: Sex

value: M


title: E_6


title: PT_3, tumor_sc

tag: tissue

value: human breast cancer

value: female

value: Primary tumor

value: Invasive ductal carcinoma


title: Remission

value: Remission phase


title: E_4

tag: genotype


title: HUVEC_aza_5uM_rep1


title: PT_2, tumor_sc


title: 95Cc.del_rep2

description:
strand specific
total RNA (remove rRNA)


title: MUC-1_aza_5uM_rep3

description: RNA-seq experiment performed on MUC-1 cells treated with 5µM 5-azacytidine

source_name: adrenocortical carcinoma


title: MUC-1_aza_5uM_rep2


title: E_3


title: 95Ca.del_rep2

description:
strand specific
total RNA (remove rRNA)


title: 95Ca.del_rep1

description:
strand specific
total RNA (remove rRNA)


title: E_2


title: E_1


title: 82Eb.del_rep3

description:
strand specific
total RNA (remove rRNA)


title: 82Eb.del_rep2

description:
strand specific
total RNA (remove rRNA)


title: Sup-PR_1

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

description: Matrix with count and FPKM

data_processing:
First 5 steps were carried out by Novogene UK. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling)
Filter the raw reads and obtain the clean reads - (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
HISAT2 is selected to map the filtered sequenced reads to the reference genome.
Gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008)
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Therefore, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2) And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Assembly: GO analysis with BinGO in Cytoscape and GSEA analysis with GSEA Software (Broad Institute)
Supplementary files format and content: ensembl_homo_sapiens_grch38_p12
Supplementary files format and content: Processed data is in text matrix format (Sup_PRvsSup_B15_deg). It contains rows with all differentially expressed genes (Gene ID) (for later analysis 1.5 FC and adj p-value<0.05 were used), columns with the respective log2FoldChange, padj, and gene_name, as well as  columns with counts and FPKM values for each sample.

source_name: Blood

growth_protocol: IMDM with 15% FBS and 0,5% Pen/Strep. Splitting every 2-3 days.

extract_protocol:
Rneasy kit (Qiagen)
Sequencing was outsourced to Novogene UK -  NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used for library preparation with AMPure XP beads (Beckman Coulter, Beverly, USA) for size selection and PCR purification steps, both performed as instructed by the manufacturers.

treatment_protocol: No treatment.

value: Blood

value: Sup-PR

value: acute lymphoblastic leukaemia

value: Prednisolone-resistant sub-clone

tag: treatment


title: H295R_aza_5uM_rep3

description: RNA-seq experiment performed on H295R cells treated with 5µM 5-azacytidine


title: Sup-PR_2

description: Matrix with count and FPKM

tag: cell line


title: S_10

value: start-point


title: H295R_aza_5uM_rep2


title: 82Eb.del_rep1

description:
strand specific
total RNA (remove rRNA)

value: BDSC 5905

value: Larva L3

value: whole individual


title: 95Ca.del_rep3

description:
strand specific
total RNA (remove rRNA)


title: 21D.del_rep3

description:
strand specific
total RNA (remove rRNA)


title: H295R_aza_5uM_rep1


title: Sup-B15_2

description: Matrix with count and FPKM

value: Parental cell line


title: Sup-B15_1

description: Matrix with count and FPKM


title: S_8

value: IL-10 KO

value: F


title: S_9


title: HUVEC_DMSO_rep2

description: RNA-seq experiment performed on HUVEC cells treated with DMSO 0.005%

value: HUVEC

value: DMSO


title: S_7

value: M


title: HUVEC_DMSO_rep1


title: 21D.del_rep1

description:
strand specific
total RNA (remove rRNA)


title: 21D.del_rep2

description:
strand specific
total RNA (remove rRNA)


title: HUVEC_aza_5uM

description: RRBS experiment performed on HUVEC cells treated with 5µM 5-azacytidine

value: 5-azacytidine 5uM


title: MUC-1_DMSO_rep3

description: RNA-seq experiment performed on MUC-1 cells treated with DMSO 0.005%


title: Sup-PR_3

description: Matrix with count and FPKM


title: MUC-1_aza_5uM

description: RRBS experiment performed on MUC-1 cells treated with 5µM 5-azacytidine


title: S_6


title: MUC-1_aza_5uM_rep1


title: WT_rep3

description:
strand specific
total RNA (remove rRNA)

value: WT


title: MUC-1_DMSO_rep2


title: Sup-B15_3

description: Matrix with count and FPKM


title: H295R_aza_5uM

description: RRBS experiment performed on H295R cells treated with 5µM 5-azacytidine


title: WT_rep2

description:
strand specific
total RNA (remove rRNA)


title: S_4


title: MUC-1_DMSO_rep1


title: HUVEC_DMSO

description: RRBS experiment performed on HUVEC cells treated with DMSO 0.005%


title: S_3


title: H295R_DMSO_rep2

description: RNA-seq experiment performed on H295R cells treated with DMSO 0.005%


title: MUC-1_DMSO

description: RRBS experiment performed on MUC-1 cells treated with DMSO 0.005%


title: Esophagus Keap1 cKO

city: Sendai

first: Keiko

last: Taguchi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba

department: Tohoku Medical Megabank Organization

institute: Tohoku University

data_processing:
Basecalls performed using ZebraCallV2 version 1.0.8.208
CellRanger v6.0.1 used for sequence assembleing, alignment and quality check
R v4.1.1 package Seurat v4.0.2 is used for cell and gene selection. Cell with mitochondrion < 5% and detected gene 200~8000 will be selected. The gene is detected across at least 3 cells will be selected.
Cell clustering(resolution = 0.5) performed based on scaling gene expression. Gene knockout cells is recognized by marker gene Nqo1 >1.6(scaled)
Perform GSEA v4.1.0 with parameter: Chip platform = Mouse Gene Symbol Remapping Human, Gene sets database = hallmark gene sets.
Genome_build: mm10
Supplementary_files_format_and_content: all gene/Cell matrix csv file
Supplementary_files_format_and_content: all cell annotation csv file

source_name: Esophageal cells

extract_protocol:
Esophagi were extracted from mice and muscle layers were removed, then the tissues were cut into small pieces. These tissues were treated 0.25% trypsin-EDTA and were dispersed into single cells with gentleMACS dissociator.
cDNA libraries were prepared using 10xGenomics protocol Chromium Next GEM Single Cell 3' Reagent Kits (Dual Index) (CG000315 Rev A)

value: Esophagus

value: Hybrid of C57BL/6J and BALB/c

value: K5CreERT2::Keap1 floxB/floxB


title: S_2


title: H295R_DMSO_rep1


title: H295R_DMSO

description: RRBS experiment performed on H295R cells treated with DMSO 0.005%


title: S_1


title: WT_rep1

description:
strand specific
total RNA (remove rRNA)


title: H2BL-L3P.3

status: Public on Feb 18 2023

first: Dade

last: Song

address: No.1239,Siping Road

institute: Advanced Institute of Qingdao,Tongji University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to hg19 transcripts genome using hisat2 v2.1.0 with default parameters, and then filtered by samtools v1.9 with  parameters -f 3 -F 256 to reserve paired and primary aligment reads
Reads count for genes were counted by featureCounts v1.6.1 with parameter -p, and then were normalized by the size of the library and removed the batch effect using R packages for futher analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene reads count values.

source_name: Liver cancer cells

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% FBS, at 37℃ with 5% CO2.

extract_protocol:
Culture medium was removed and the cells were washed by PBS twice. Total RNA was extracted by RNAiso (Takara). 1μg total RNA was used for the construction of libraries.
Libraries was constructed using TruSeq RNA Sample Prep Kit v2 for Illumina.

tag: overexpression


title: H2BL-L3P.1


title: H2BL-L3P.2


title: H2BL.1


title: H2BL.2


title: H2BL.3


title: H2BG.3


title: H2BG.2


title: H2BG.1


title: Esophagus Control

value: Keap1 floxB/floxB


title: MSTN-treated 24h rep2

city: Vancouver

first: Yuyin

last: Yi

address: 4500 Oak St

country: Canada

institute: University of British Columbia, BC Children’s Hospital Research Institute

data_processing:
De-multiplexed sequences were aligned to the Homo sapiens (UCSC hg19) reference sequence using STAR aligner
Fragments per kilobase of exon per million reads (FPKM) estimation of reference genes and transcripts using Cufflinks 2
Assembly of novel transcripts with Cufflinks 2
Differential expression of novel and reference transcripts with Cuffdiff 2
Assembly: GRCh37 (hg19)
Supplementary files format and content: *.genes.fpkm_tracking: Tab-delimited text files include FPKM values for each gene.

source_name: First-trimester Placenta Trophoblast

extract_protocol:
Total RNA from human primary trophoblasts was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Sample quality control was performed using the Agilent 2100 Bioanalyzer.
Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs).

value: First-trimester Placenta Trophoblast

value: MSTN

tag: time

value: 24 hrs


title: MSTN-treated 24h rep4


title: MSTN-treated 24h rep3


title: MSTN-treated 24h rep1


title: SKNMC, OE, NFIB, wt, rep2

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using STAR v.2.4.0h with default settings.
The aligned fragments quantification was computed by featureCounts, and FPKM expression values were calculated for hg19 RefSeq genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw gene expression counts for each sample

source_name: Ewing sarcoma cells

growth_protocol: SKNMC was grown in RPMI-1640 (Gibco, 11875). All media were supplemented with 10% FBS and cells were cultured at 37°C with 5% CO2.

extract_protocol:
Total RNAs were isolated from cells using the NucleoSpin RNA Plus kit (Takara, 740984.50).
RNAs were used to prepare sequencing libraries with CORALL Total RNA-Seq Library Prep Kit (LEXOGEN, 146) and were sequenced with the Nextseq 500 Illumina genome analyzer.

treatment_protocol: untreated

value: Ewing sarcoma cells

value: SKNMC

value: NFIB wildtype expression vector


title: SKNMC, OE, NFIB, wt, rep1


title: SKNMC, OE, NFIB, del, IDR, rep1

value: NFIB deletion expression vector


title: SKNMC, OE, EV, rep2

value: empty expression vector


title: SKNMC, OE, NFIB, del, IDR, rep2


title: SKNMC, OE, EV, rep1


title: 3T3-L1 preadipocyte cells_SQ treatment 14days_rep1

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: SQ 1

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, mouse; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).
algorithm: RMA (SST-RMA, Transcriptome Analysis Console, version 4)

source_name: 3T3-L1 preadipocytes were treated with 5 μM SQ for 14 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: Murine 3T3-L1 preadipocytes were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). 3T3-L1 preadipocytes were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA).

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Squalene was purchased from Tokyo Chemical Industry Co., Ltd., four ethylene glycol squalene derivatives  (0.5µM-80µM) were synthesized by National Institute of Advanced Industrial Science and Technology. 3T3-L1 preadipocytes were seeded into a 96-well plate at density of 5x104 cells/mL and and upon 2 days post-confluency at 37 °C. In induction medium (IBMX, Dexamethasone and Insulin with or without SQ or derivatives treatment) and then maintained in differentiation medium (Insulin with or without SQ or derivatives treatment). Medium change was done every 48 hours.

value: Murine 3T3-L1 preadipocytes (Riken Tsukuba, Japan)

value: SQ-induced for 14 days


title: 3T3-L1 preadipocyte cells_tri-SQ treatment 14days_rep1

description: tri-SQ 1

source_name: 3T3-L1 preadipocytes were treated with 5 μM tri-SQ for 14 days

value: tri-SQ-induced for 14 days


title: 3T3-L1 preadipocyte cells_mono-SQ treatment 14days_rep2

description: mono-SQ 2

source_name: 3T3-L1 preadipocytes were treated with 5 μM mono-SQ for 14 days

value: mono-SQ-induced for 14 days


title: SKNMC, shGFP, NFIB

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using bwa v.0.7.12 with default settings.
Duplicate reads were removed using picard-tools v.1.95. Aligned reads were extended to 150 bp to approximate fragment sizes
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedtools; scores show fragments normalized to 10M mapped fragments.

growth_protocol: NCI-H446 was grown in specific RPMI 1640 Medium (Gibco, A1049101) and SKNMC was grown in RPMI-1640 (Gibco, 11875). All media were supplemented with 10% FBS and cells were cultured at 37°C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the specified antibodies using standard protocol.
Precipitated DNA samples were used to prepare sequencing libraries with Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, 0344NB-A01), and DNA samples were sequenced with the Nextseq 500 Illumina genome analyzer.

value: shGFP control

tag: chip antibody

value: NFIB (Sigma, HPA003956)


title: SKNMC, TFAP2

value: wildtype

value: AP2a (Santa Cruz, sc-12726X)


title: 3T3-L1 preadipocyte cells_tri-SQ treatment 14days_rep2

description: tri-SQ 2


title: MSTN-treated 24h rep5


title: 3T3-L1 preadipocyte cells_tetra-SQ treatment 14days_rep1

description: tetra-SQ 1

source_name: 3T3-L1 preadipocytes were treated with 5 μM tetra-SQ for 14 days

value: tetra-SQ induced for 14 days


title: 3T3-L1 preadipocyte cells_di-SQ treatment 14days_rep1

description: di-SQ 1

source_name: 3T3-L1 preadipocytes were treated with 5 μM di-SQ for 14 days

value: di-SQ-induced for 14 days


title: HIF1a-sg2-Hypoxia-3

city: Chicago

first: Simon

last: Schwoerer

address: 900 E 57th St

institute: University of Chicago

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Adapter sequences were trimmed with 'Trimmomatic' and validated read pairs were aligned to the mouse genome with 'STAR' with default parameters.
Uniquely aligned reads were used to count gene features with 'featureCounts'.
Normalization and differential expression was determined using the 'DESeq2' package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text of raw count values per gene

source_name: Pancreatic stellate cells

growth_protocol: Pancreatic stellate cells were isolated and immortalized by spontaneous outgrowth. They were cultured in DMEM containing 10% FBS and 1% P/S and infected with lentivirus to express R26 sg1, HIF1a sg2 and Cas9.  Infected cells were selected with 2 ug/mL Puromycin. Polycolonal cells were used for experiments.

extract_protocol:
RNA was isolated from cells using Trizol reagent
Libraries were prepared from poly-A+ RNA with the NEBNext Ultra RNA library prep kit.

treatment_protocol: Cells were seeded at 0.25e6 cells per mL in DMEM containing 10% FBS and 1% P/S.  The next day cells were cultured in 20% O2 (regular TC incubator) or in 0.5% O2 (Hypoxia glove box). Cells were cultured for 48h before RNA isolation.

value: Pancreatic stellate cells

tag: strain

value: 0.5% Oxygen

tag: group

value: Hypoxia HIF1a-ko


title: HIF1a-sg2-Hypoxia-2


title: 3T3-L1 preadipocyte cells_SQ treatment 14days_rep2

description: SQ 2


title: SKNMC, shFLI1, NFIB

value: Ewing sarcoma cells

value: SKNMC

value: EWS-FLI1 knockdown


title: 3T3-L1 preadipocyte cells_tetra-SQ treatment 14days_rep2

description: tetra-SQ 2

value: tetra-SQ-induced for 14 days


title: 3T3-L1 preadipocyte cells_di-SQ treatment 14days_rep2

description: di-SQ 2

value: Murine 3T3-L1 preadipocytes (Riken Tsukuba, Japan)


title: 3T3-L1 preadipocyte cells_No treatment_rep1

description: control 1

source_name: 3T3-L1 preadipocytes differentiated with no induction for 14 days

value: without induction for 14 days


title: 3T3-L1 preadipocyte cells_mono-SQ treatment 14days_rep1

description: mono-SQ 1


title: HIF1a-sg2-Hypoxia-1


title: SKNMC, OE, NFIB, wt, V5

value: NFIB wildtype expression vector

value: V5 (Cell Signaling, 13202)


title: SKNMC, OE, NFIB, wt, Input

value: no antibody for Input


title: R26-Hypoxia-sg1-3

value: control

value: Hypoxia


title: SKNMC, OE, NFIB, wt, H3K27ac

value: H3K27ac (ACTIVE MOTIF, 39133)


title: R26-Hypoxia-sg1-2


title: R26-Hypoxia-sg1-1


title: R26-Normoxia-sg1-3

value: 20% Oxygen


title: Liver, AAV8-GFP, 314

source_name: Liver

value: Liver

value: Wild-type

tag: diet

value: NASH diet


title: S_5

value: IL-10 KO

value: start-point

value: M


title: SKNMC, OE, NFIB, del, IDR, Input

value: Ewing sarcoma cells

value: SKNMC

value: NFIB deletion expression vector


title: SKNMC, OE, NFIB, del, IDR, V5


title: SKNMC, OE, NFIB, del, IDR, H3K27ac


title: R26-Normoxia-sg1-2

value: Pancreatic stellate cells


title: SKNMC, NFIB

value: wildtype

value: NFIB (Sigma, HPA003956)


title: SKNMC, H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: vpcLneg

city: Palo Alto

first: Liming

last: Zhao

address: G3105, Lokey Stem Cell Research Building, 265 Campus Drive, 450 Serra Mall, Stanford

institute: Stanford University

data_processing:
cellranger count (version 3.1.0) to perform alignment, filtering, barcode counting, and UMI counting of fastq files
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output of filtered matrix files: tab separated barcodes, tab separated features, matrix files of genes vs cells and their read counts.

source_name: Vessel progenitor cells

extract_protocol:
Two vessel forming mesenchymal stromal cell populations were FACS sorted according to their surface markers, P1 is CD45-Ter119-Tie2+PDGFRa-CD31+CD105highSca1low and P2 is CD45-Ter119-Tie2+PDGFRa+CD31-CD105lowSca1high.
Single cell libraries were prepared following the user guide for Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) from 10X Genomics (10x Genomics Inc San Francisco, CA).
10X Genomics single cell RNA-Seq

value: Lung


title: vpcFpos

value: Fat


title: vpcFneg


title: vpcLpos


title: H446, shNFIB, NFIB

source_name: small cell lung cancer cells

value: small cell lung cancer cells

value: NFIB knockdown


title: H446, shNFIB, Input

value: no antibody for Input


title: SKNMC, OE, EV, H3K27ac

value: empty expression vector

value: H3K27ac (ACTIVE MOTIF, 39133)


title: SKNMC, OE, EV, V5

value: V5 (Cell Signaling, 13202)


title: H446, shNFIB, H3K27ac


title: H446, shGFP, Input

value: shGFP control


title: CCTaggedRP_HEK293T_HA_1

city: Charlottesville

first: Jesse

last: Cochran

state: Virginia

address: 1221 Lee St

institute: University of Virginia

description: Configuration: 2x150 bp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Normalized transcipt abundance was determined via DeSeq2 (V3.16)
Assembly: GRCh38/hg38
Supplementary files format and content: .csv file containing each sample's normalized transcript abundance derived from DeSeq2 analysis.

source_name: kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
2 ug of sample was used to construct libraries via Poly(A) selection method according to manufacturer's instructions.

value: kidney

value: Epithelial-like cells

tag: epitope tag

value: HA


title: CCTaggedRP_HEK293T_Flag_3

description: Configuration: 2x150 bp

value: Flag


title: CCTaggedRP_HEK293T_HA_3

description: Configuration: 2x150 bp


title: CCTaggedRP_HEK293T_HA_2

description: Configuration: 2x150 bp


title: CCTaggedRP_HEK293T_Flag_2

description: Configuration: 2x150 bp


title: CCTaggedRP_HEK293T_Flag_1

description: Configuration: 2x150 bp


title: H446, NFIB


title: H446, shGFP, H3K27ac


title: H446, Input


title: 3T3-L1 preadipocyte cells_No treatment_rep2

description: control 2

value: Murine 3T3-L1 preadipocytes (Riken Tsukuba, Japan)

value: without induction for 14 days


title: R26-Normoxia-sg1-1

value: Pancreatic stellate cells

value: control

value: 20% Oxygen


title: SKNMC, OE, EV, Input

value: Ewing sarcoma cells

value: SKNMC


title: H446, H3K27ac

value: small cell lung cancer cells

value: wildtype


title: GEM43

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: GRCh38
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: buccal

growth_protocol: Participants for this study were MZ twins recruited from the community-based Washington State Twin Registry (WSTR). Participants in the current study previously participated in a study of objective measures of physical activity (PA) and locations among individuals residing in the Puget Sound area around Seattle between 2012 and 2015. Follow-up data collection was conducted in 2018 and 2019, 72 pairs completed follow-up collection out of the 144 pairs who completed the baseline study.

extract_protocol:
Frozen human buccal samples were thawed for analysis. Genomic DNA from buccal samples was prepared as follows: The buccal brush was suspended in 750 μl of cell lysis solution and 3.5 µl of Proteinase K (20 mg/ml). This suspension was incubated at 55ºC for 3 hours, then vortexed and centrifuged briefly. The lysis solution was then transferred to a new 1.5 µl microcentrifuge tube. The microcentrifuge tube with the buccal brush was centrifuged again to retain any remaining solution which was combined with the transferred lysis solution. The buccal brush was discarded and 300 µl of protein precipitation solution (Promega, A795A, Madison, WI) was added to the lysis solution. The sample was incubated on ice for 15 minutes, then centrifuged at 4C for 30 minutes. The supernatant was transferred to a fresh 2 mL microcentrifuge tube and 1,000 µl ice cold isopropanol was added along with 2 µL glycoblue. This suspension was mixed thoroughly and incubated at -20 ºC overnight. The suspension was then centrifuged at 4ºC for 20 minutes, the supernatant was discarded, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 14,000rpm for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 C freezer for 1 hour to overnight. The precipitate was centrifuged at 14,000rpm for 20 min at 4 C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 C freezer for 15 min then centrifuged again at 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: Once participants were enrolled in the study, the study coordinator sent all study materials to the participant for remote data collection. Participants wore a Qstarz BT-Q1000XT (Qstarz International Co. Ltd, Taipei, Taiwan) GPS data logger and Actigraph GT3X+ accelerometer (Actigraph Inc. Pensacola, FL) attached to a belt worn around the waist for one week. They also completed questionnaires and provided a buccal sample, with 70 complete pairs provided buccal samples. The buccal cell collection procedure involved 30 second brushing of each cheek before putting in enclosed vial for shipment by mail and then stored at -80°C. Materials were sent to the Skinner lab at WSU Pullman after sample and data collection was completed. Buccal swab brushes were stored at -80°C until use. The study protocol was approved by the Washington State University Institutional Review Board (#16419), and informed written consent was obtained from all participants prior to receiving the study materials. All methods were carried out in accordance with relevant guidelines and regulations.

tag: twin pair_number

tag: srzyg

value: homozygote

value: male

value: buccal

tag: age

tag: average waist

tag: bmi

tag: obese call

value: non-obese


title: KYSE150-Luc-LM3 cells

city: guangzhou

first: xiaomei

last: yu

address: Harbour Road

institute: The Fifth Affiliated Hospital of Guangzhou Medical University

description: 150 bp paired-end reads

data_processing:
The quality of the original reads including sequencing error rate distribution and GC content distribution, is evaluated using bcl2fastq.Filter out reads with the number of N basesaccounting for.
And Clean Data were mapped to the reference genome using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments PerKilobase Millon Mapped Reads) were then calculated to represent the expression level of genes in each sample.
DESeq is used for data exploration. The output results can be used for cluster analysis and PCA (principal component analyses) analysis among lncRNA-seq samples, and the relationship among samples can be explored or the experimental design can be verified.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: esophagus

growth_protocol: KYSE150-Luc and KYSE150-Luc-LM3 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
A total amount of 3 μg RNA per sample was used as initial material for the RNA sample preparations. Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA) .
RNA libraries for lncRNA-seq were prepared using ruSeq PE Cluster Kit v4-cBot-HS (Illumina)  following manufacturer's protocols.

tag: tissue

value: esophagus

tag: cell type

value: esophageal squamous cell carcinoma

value: highly metastatic KYSE150-Luc


title: GEM44

tag: Sex

value: obese (I)


title: H446, shGFP, NFIB

tag: cell line

tag: genotype

value: shGFP control

value: NFIB (Sigma, HPA003956)


title: SKNMC, shFLI1, ATAC

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using bwa v.0.7.12 with default settings.
Duplicate reads were removed using picard-tools v.1.95.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedtools; scores show fragments normalized to 10M mapped fragments.

extract_protocol:
DNAs from 50,000 cells were prepared by Tn5 tagmentation following the standard ATAC-seq protocol.
followed Nextera DNA Sample Prep Kit (Illumina)

value: EWS-FLI1 knockdown


title: KYSE150-Luc cells

description: 150 bp paired-end reads

value: WT


title: SKNMC, OE, NFIB, wt

value: NFIB wildtype expression vector


title: SKNMC, shGFP, ATAC

value: Ewing sarcoma cells


title: GEM42

description:
male.all.results.csv.gz
male.hetero.results.csv.gz

value: heterozygote

value: obese (II)


title: SKNMC, OE, EV

value: SKNMC

value: empty expression vector


title: GEM39

description:
male.all.results.csv.gz
male.homo.results.csv.gz

value: homozygote

value: male


title: GEM41

value: buccal

value: non-obese


title: GEM40


title: H446, shNFIB, ATAC

value: small cell lung cancer cells

value: NFIB knockdown


title: SKNMC, ATAC

value: wildtype


title: H446, ATAC


title: GEM37


title: GEM35


title: GEM36

value: obese (I)


title: Old adult CBA/CaJ mouse LW-2

city: Charleston

first: Jeremy

last: Barth

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out using Partek Flow. Alignment was conducted with TopHat2 using mouse genome (mm10) and the default option set
Aligned reads were quantified to annotation model (Partek E/M) using mm10 and RefSeq transcripts 83 (2017-11-01) with the settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed using DESeq2 to determine normalized expression measures and adjusted p-value (FDR step up) for old versus young samples
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Auditory nerve cells

extract_protocol:
Microdissections were performed to isolate the cochle lateral wall from mouse cochlear structures. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the miRNeasy Mini Kit per the manufacturer’s instructions. Quality of each total RNA isolation was assessed using the Agilent 2100 Bioanalyzer and low-quality samples showing degradation or contamination were excluded.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina's TruSeq RNA Library Prep Kit

value: Isolated lateral wall

value: CBA/CaJ


title: Old adult CBA/CaJ mouse LW-1


title: Young adult CBA/CaJ mouse LW-3

value: 2 mo


title: SKNMC, OE, NFIB, del, IDR

value: NFIB deletion expression vector


title: GEM33


title: GEM34


title: GEM32

value: obese (III)


title: GEM31

value: heterozygote


title: GEM30

value: obese (II)


title: GEM38


title: Young adult CBA/CaJ mouse LW-1


title: GEM29


title: Astrocyte LFS-2 YTHDF2 eCLIP

city: Houston

first: An

last: Xu

state: TX

institute: UThealth Houston

data_processing:
Data analysis was run through the eCLIP-v0.4.0 pipeline (Van Nostrand, E.L. et al. Methods Mol Biol 1648, 177-200 (2017))
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Astrocyte LFS-2

extract_protocol:
LFS astrocytes were UV crosslinked and then sonicated in lysis buffer on ice.
libraries were prepared using KAPA Hyper Prep Kit according to the manufacture's instruction

value: iPSC-derived astrocytes

value: Astrocyte LFS-2

tag: treatment

value: No

tag: disease state

value: LFS

tag: rip antibody

value: YTHDF2 (Aviva, ARP67917_P050)


title: Young adult CBA/CaJ mouse LW-2

tag: strain


title: H446, shGFP, ATAC

value: shGFP control


title: Astrocyte LFS-1 YTHDF2 input

source_name: Astrocyte LFS-1

value: Astrocyte LFS-1


title: Astrocyte LFS-2 YTHDF2 input


title: Astrocyte LFS-1 YTHDF2 eCLIP


title: GEM26

value: homozygote

value: male

value: buccal


title: GEM24

description:
female.all.results.csv.gz
female.homo.results.csv.gz

value: female


title: GEM25

value: non-obese