title: Sample_04-00099

value: Mononuclear Cells

value: Peripheral Blood

value: CML, TKI resistant


title: Parent_28_1

status: Public on Jul 28 2021

type: SRA

city: Wuxi

first: Nai-Xin

last: Lin

address: lihu avenue

country: China

institute: Jiangnan University

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and  is currently the most commonly used method for estimating gene expression levels.
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000223565.1/

molecule: total RNA

organism: Komagataella phaffii GS115

source_name: cell pellet

growth_protocol: Flask-batch fermentation in BMGY/BMMY medium

extract_protocol: Standard illumina protocols

treatment_protocol: Induction temperature: 28℃ and 37℃

tag: genotype

value: parent

tag: treatment

value: induction temperature 28 degrees C

tag: time


title: LRNA_SL_rep3

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
mapping reads to mm9 using STAR/v2.7.3a with parameters --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --outFilterMismatchNmax 1 --alignEndsType EndToEnd --outSAMattributes NH HI NM MD  (>80% uniquely mapped rates)
kallisto/0.46.2
rtracklayer/1.46.0, Rsamtools/2.2.3
GemonicRanges/1.38.0, GenomicAlignments/1.22.1, STAN/2.14.0
generate bigwig files using deepTools/v3.3.1 bamCoverage command with default settings
Genome_build: mm9
Supplementary_files_format_and_content: Genomic tracks in bigwig format with spike-in normalization

organism: Mus musculus

source_name: mESC

growth_protocol: Serum medium was used to culture mouse embryonic stem cells (mESCs) with feeder-free in 0.1% gelatin-coated flasks (Sigma, G1890) under standard conditions (10% CO2, 90% humidity, 37 °C) in KnockOut DMEM (LifeTechnologies, 10829018), 2 mM Alanyl-glutamine (Sigma, G8541), 0.1 mM non-essential amino acids (Sigma, M7145) 15% fetal bovine serum (FBS) (Sigma, F7524), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333).

extract_protocol:
TT-seq was performed as described before (Schwalb et al., 2016). In short, cells were seeded in 5 million per 15 cm dish for 2 days. After recording the cell number, cells were supplemented with 500 µM of 4-thiouracil (4sU) (Sigma-Aldrich, T4509) for 5 min at 37°C and 5\% CO2, then immediately quenched 4sU incorporation with TRIzol (ThermoFisher, 15596018). Total RNA extraction were fragmented to about 1 kb with Bioruptor (Diagenode), then incubated with HPDP-Biotin (ThermoFisher, 21341) for 2 hours at room temperature. A small aliquot was saved as fragmented total RNA and the rest was subjected to µMACS streptavidin beads (Miltenyi Biotec, 130-074-101) and purified with miRNeasy Micro Kit (Qiagen, 217084) with DNase digestion (Qiagen, 79254).
Ovation Universal RNA-Seq System 1-16 (NuGEN, #0348).
Stranded Ribo-minus RNA-Seq

treatment_protocol: mESCs were switched to 2i medium with ESGRO Complete Basal Medium (Millipore, SF002), 1 μM MEK inhibitor PD0325901 (Sigma, PZ0162) and 3 μM GSK3 inhibitor CHIR99021 (Sigma, SML1046), 0.1 mM β-mercaptoethanol (Sigma, M3148), ESGRO Leukemia Inhibitory Factor (LIF) (Millipore, ESG1107), Penicillin-Streptomycin (Sigma, P4333). mES mTORi cells were treated with 200nM INK128 (VWR, CAYM11811) in the serum LIF medium as described above.

tag: strain

tag: cell type

value: mouse embryonic stem cells

tag: assay

value: TT-seq labeled RNA

tag: culture

value: culture in SL medium


title: LRNA_2i_2d_rep1

value: 2 days culture in 2i medium


title: 42634-P1-D8

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the Mmul_8.0.1 genome sequence using STAR-2.5.2b with --quantMode GeneCounts --outSAMtype None and all other paramters default
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: tab-delimited text files (STAR output) include transcript raw count values for each sample

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from PBMC using RNEasy Mini kit reagents on a QIAcube instrument
cDNA libraries were constructed from 300 ng total RNA using Lexogen QuantSeq 3' FWD and sequenced on an Illumina HiSeq 4000 acquiring single-strand 65-bp reads (targeting > 10M reads/sample).

value: SIP-Isolated

tag: tissue

value: Peripheral blood mononuclear cells


title: FRNA_mTORi_2d_rep2

value: Fragmented total RNA

value: 2 days culture in mTORi medium


title: Sample_04-00083

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
bam files are converted to fastq files
Reads were mapped to ABL1 exon sequences using bowtie2 (v.2.1.1)
Counted the reads mapped to exon-exon, exon-intron boundaries
Supplementary_files_format_and_content: ABL1 alternative splicing reads quantification.xlsx
Supplementary_files_format_and_content: FASTA BCR-ABL1 splice variant junctions.txt

organism: Homo sapiens

source_name: Peripheral Blood

growth_protocol: Following informed consent, primary research specimens were collected from Ph+ leukemia patients by peripheral blood draw, bone marrow aspirate, or leukapheresis.

extract_protocol:
For mononuclear cells, cells were isolated by Ficoll gradient from other blood components by centrifugation, multiply washed with IMDM, aliquotted, and flash frozen and stored at -80C as either cell pellets or frozen GTC cell lysate. These were later thawed on ice and total RNA was isolated by Qiagen RNeasy protocol. For samples derived from total white blood cells, peripheral blood was colleted and lysed directly in PAXgene tubes to stabilize total RNA, and RNA was subsequently also extracted by Qiagen protocol. Sample RNA concentrations were determined by Nanodrop spectrophotometer and then flash frozen and stored at -80C until sequencing.
CML patient RNA was subjected to 2x125 bp paired-end Illumina sequencing using the KAPA Stranded Total RNASeq kit at the New York Genome Sequencing Center.

treatment_protocol: Samples were not treated ex vivo prior to other processing and extraction of RNA.

tag: disease state


title: Sample_04-00043


title: 42634-P1-D2


title: KO4-Stim

city: Miami

first: Haritha

last: Desu

state: Florida

address: 1095 NW 14th Terrace

institute: University of Miami

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequences using TrimGalore
Trimmed reads were aligned to the GRCm38.81 genome and read counts were generated using STAR
Fragments per kilobase mean (FPKM) and differential gene expression were calculated using edgeR software package in R
Genome_build: GRCm38.81
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Oligodendrocyte precursor cells

growth_protocol: OPCs were isolated from p2-p5 mouse pup cortices using the neural dissociation kit from Miltenyi according to manufacturers protocol. Half the media in each well was changed the day after plating and then every other day consequently

extract_protocol:
RNA was isolated and purified using the Arcturus PicoPure RNA Extraction kit according to manufacturer's protocol
Libraries were prepared according to standard Illumina protocols

treatment_protocol: After culturing 3 days in vitro, the cells were stimulated with a cytokine cocktail containing TNF, IFNgamma and IL1beta at 25ng/mL each

value: primary mouse OPCs

value: TNFR2 KO

tag: stimulation

value: Stimulated with TNF, IFNg, and IL1b for 3 hours


title: KO5-Stim


title: 42634-P1-FC


title: FRNA_mTORi_2d_rep1


title: FRNA_mTORi_1d_rep2

value: 1 day culture in mTORi medium


title: 42585-P2-D13

value: SIP-JuvenilePartnered


title: Sample_04-00014

source_name: Bone Marrow Aspirate

value: Mononuclear Cells

value: Bone Marrow Aspirate


title: Sample_03-00181

value: CML, TKI resistant


title: KO4-NS

value: Non-stimulated


title: Sample_03-00229

value: Peripheral Blood

value: CML, Newly diagnosed / TKI naive


title: KO5-NS


title: 42585-P2-D8


title: FRNA_SL_rep3

value: mouse embryonic stem cells

value: culture in SL medium


title: FRNA_mTORi_1d_rep1


title: 42585-P2-D2


title: 42585-P2-FC


title: FRNA_SL_rep2


title: KO2-NS


title: Sample_03-00175


title: sample39_PAH8_treatment1_Input

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

description: processed data file: diffReps_H3K27ac_siALDH1A3_vs_siCTRL_nb_NSD2.txt

library_source: genomic

data_processing:
diffReps
ChIP-seq: https://github.com/ny-shao/chip-seq_preprocess  diffReps
Genome_build: hg38
Supplementary_files_format_and_content: Normalized log2-transformed expression of genome-wide genes for RNA-seq.
Supplementary_files_format_and_content: Differentially enrich regions (DER) recognized by diffReps in ChIP-seq.

molecule: genomic DNA

source_name: pulmonary arterial smooth muscle cells

extract_protocol:
RNAseq: RNA was exracted using the Rneasy Mini Kit (QIAGEN, Hilden, Germany). ChIPseq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNAseq:Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) and subjected to sequencing on 1-2 Illumina HiSeq 2000 lanes to obtain an average of approximately 100-150 million uniquely mapped reads for each sample. ChIPseq: ChIP-DNA was treated with RNase A (Qiagen) and proteinase K (ThermoFisher Scientific) and then purified. The ChIP-DNA samples were end repaired and A-tailed. The Illumina TruSeq adapters (Illumina, San Diego, CA) were ligated and size-selected from the gel before PCR amplification. PCR products were purified and size selected in the gel again. The final purified samples were sequenced on HiSeq4000 (Illumina).

treatment_protocol: treatment 1: ALDH1A3 siRNA (sialdh1a3); treatment 2: control siRNA (sictrl).

tag: subject status/phenotype

value: idiopathic pulmonary arterial hypertension patient

value: pulmonary arterial smooth muscle cells

tag: passage


title: WT4-Stim

value: Wild Type


title: NoV：suckling BALB/c 3dpi

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Supplementary_files_format_and_content: mapping results

source_name: hindlimb muscle

extract_protocol:
Total RNA was extracted from mice hindlimb muscle tissue or 293T cells using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

value: BALB/c

value: WT

value: NoV virus


title: FRNA_SL_rep1

value: Fragmented total RNA


title: sample38_PAH2_treatment1_Input

value: mutant pulmonary arterial hypertension patient


title: 42585-P1-D13

value: SIP-Isolated

value: Peripheral blood mononuclear cells


title: KO2-Stim

value: primary mouse OPCs

value: TNFR2 KO

value: Stimulated with TNF, IFNg, and IL1b for 3 hours


title: WT3-Stim


title: 42585-P1-D8


title: FRNA_2i_7d_rep1

value: 7 days culture in 2i medium


title: sample37_PAH1_treatment1_Input


title: WT2-Stim


title: FRNA_2i_2d_rep2

value: 2 days culture in 2i medium


title: WT4-NS

value: Non-stimulated


title: FRNA_2i_2d_rep1

value: mouse embryonic stem cells


title: sample36_PAH8_treatment2_Input

value: idiopathic pulmonary arterial hypertension patient


title: 42585-P1-D2


title: 42585-P1-FC


title: WT3-NS


title: WT2-NS


title: 42557-P2-D13

value: SIP-JuvenilePartnered


title: 42557-P2-D8


title: sample33_PAH8_treatment1_H3K27ac

value: pulmonary arterial smooth muscle cells

tag: chip antibody


title: 42557-P2-D2


title: RORa_HA

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
All sequencing reads were mapped to the mouse genome mm10 by bowtie2
PCR duplicates were removed using picard MarkDuplicates
The uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
ChIPseeker was used for peak annotation and HOMER was used for motif discovery
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

source_name: in vitro Th17

growth_protocol: Naïve T cells were activated cultured with anti-IFN-γ and anti-IL-4 for 24 hours before retrovirus infection. One day after infection, the RFP+ infected cells were sorted and cultured with TGF-β+IL-6 +IL-1β+IL23 for 2 days.

extract_protocol:
The ChIP assay was performed using ChIP-IT Express Chromatin Immunoprecipitation Kits (Active Motif) according to manufacturer’s instructions with slight modifications.
ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

value: pRV_RORa_HA_ires_RFP transfected

value: in vitro Th17

tag: antibody

value: HA ChIP antibody (CST,3724)


title: sample34_PAH1_treatment2_Input


title: sample35_PAH2_treatment2_Input


title: sample32_PAH2_treatment1_H3K27ac


title: input


title: 42557-P2-FC


title: sample31_PAH1_treatment1_H3K27ac


title: sample30_PAH8_treatment2_H3K27ac


title: WT_IL6_IL1β_IL23_in vitro Th17

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore
The clean reads were aligned to mm10 by bowtie2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: counts

growth_protocol: For the in vivo isolated CD4+ T cells, naïve CD4+ T cells from Rora_fl/fl (WT) or Cd4_cre Rora_fl/fl (KO) mice were transferred into Tcrbd-/- recipient mice for 6 weeks, and the CD4+ T cells were isolated from colon tissues for sequencing. For in vitro polarized Th17 cells, naïve CD4+ T cells were activated with plate-bound anti-CD3 and anti-CD28 and cultured with TGF-β+IL-6 or IL-6+IL-1β+IL-23 for 4 days.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: The cells were re-stimulated with PMA and ionomycin for 2 hours before RNA extraction.


title: 42557-P1-D13


title: 42557-P1-D8


title: Rorα KO_IL6_IL1β_IL23_in vitro Th17

value: Cd4_cre Rora_fl/fl


title: Ctrl_KD_NT_Rep2

city: Mainz

first: Junaid

last: Akhtar

state: Rheinland-Pflaz

address: Johannes-Joachim-Becherweg, 32

department: Institute of Neurobiology and Developmental Biology

country: Germany

institute: University of Mainz

description:
Biotin enrichment
Ctrl nascent DRB-4SU-seq with steady state condition.

data_processing:
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila.
Genome_build: dm6 (Drosophila melanogaster)

organism: Drosophila melanogaster

source_name: cell culture

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

extract_protocol:
5,6-dichlorobenzimidazole 1-_-d-ribofuranoside (DRB) from Sigma (D1916) was used at a final concentration of 300_M, dissolved in water, for 5 hours. 4-thiouridine (4sU) was purchased from Sigma (T4509) and used at a final concentration of 100 _M. Control and Mago KD was performed as described before. All the samples were labeled for 8 minutes with 4-thiouridine, and transcription was allowed to proceed after DRB removal for 0, 2, 8 and 16 minutes along with one non-DRB treated control.A total of 100 to 130 _g RNA was used for the biotinylation reaction. 4sU-labeled RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2 h with rotation at room temperature. Two rounds of chloroform extractions removed unbound Biotin-HPDP. RNA was precipitated at 20,000 g for 20 min at 4¡C with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with 75% ethanol and precipitated again at 20,000 g for 10 min at 4¡C. The pellet was left to dry, followed by resuspension in 100 _L RNase-free water. Biotinylated RNA was captured using Dynabeads MyOne Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 50 _L Dynabeads with rotation for 15 min at 25¡C. Beads were magnetically fixed and washed with 1_ Dynabeads washing buffer. RNA-4sU was eluted with 100 _L of freshly prepared 100 mM dithiothreitol (DTT), and cleaned on RNeasy MinElute Spin columns (Qiagen).
Enriched nascent RNAs were converted to cDNA libraries with Drosophila Ovation Kit (Nugen) with integrated ribosomal depletion workflow
NebNext UltraII

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated three times and cells were harvested 7 days after the first treatment.

tag: sample type

value: Embryonic

value: S2R+ Cells


title: Mettl3_KD_NT_Rep2

description:
Biotin enrichment
Mettl3 depleted nascent DRB-4SU-seq with steady state condition.


title: Mettl3_KD_NT_Rep1


title: Ctrl_KD_NT_Rep1


title: sample29_PAH2_treatment2_H3K27ac

value: mutant pulmonary arterial hypertension patient


title: 42557-P1-D2

value: SIP-Isolated

value: Peripheral blood mononuclear cells


title: WT_TGFβ_IL6_in vitro Th17


title: Rorα KO_TGFβ_IL6_in vitro Th17


title: Ythdc1_KD_NT_Rep1

description:
Biotin enrichment
Ythdc1 depleted nascent DRB-4SU-seq with steady state condition.


title: K11a_benign prostatic hyperplasia_urinary exosome

city: Guangzhou

first: wen

last: tao

address: Tianhe Road 600

institute: The Third Affiliated Hospital, Sun Yat-sen University

data_processing:
CircRNA-seq
Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were subjected to trimming process with SOAPnuke (v.1.5.2)
High-quality reads were aligned to the Homo sapiens reference genome (GRCH37/hg19) by bowtie2 (v.2.2.9) and Tophat2(v.2.1.0). The resulted sequence alignment files (bam formatted file) were then sorted by reference position as required by SAMtools(v.2.6.2).
CircRNAs was identified and quantified by find_circ(v.1.2) and CIRCexplorer2(v.2.3.2)
differential analysis; R(v.3.5) DESeq2(v.1.22.2)
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: counts

extract_protocol:
The urinary samples were centrifuged at 3000 g for 15 min to remove cells and cell debris. Next, the supernatant was transferred to two 38.5-mL thinwall polyallomer centrifuge tube (Beckman Coulter, Fullerton, CA) and ultracentrifuged at 100,000 g for 2h at 4 °C (SW 70Ti rotor, Beckman Coulter, Brea, CA) to obtain exosome-enriched pellet. Subsequently, the pellets were diluted to 5 mL in 1x phosphate-buffered saline and mixed with 1mL ExoQuick-TC by inverting or flicking the tube. After incubating overnight at 4°C with no rotation, the mixture was centrifuged at 1500 g for 30min at 4°C. The supernatant was discarded, and then centrifuged for another 5 min to remove residual fluid.
The total RNA were treated with Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (illumine, MRZG12324) to delete rRNA according to the manufacturer’s instructions. Next, strand-specific libraries were constructed by using NEBNext Ultra II RNA Library Prep Kit (NEB, E7770) following the manufacturer’s instructions. In brief, The RNAs were fragmented using fragmentation buffer and then reverse transcribed into first-strand cDNA and second-strand cDNA in orderly. Then, the cDNA fragments were purified, subjected to end-repair, and modified to add poly (A) to the 3’ end. The sequencing adapters were ligated to the cDNA fragments. The double strand cDNA are digested by Second Strand Enzyme Mix (Nugen, S01531) to remove the second-strand cDNA before sequencing. The purified ligation products were performed PCR amplification, then the amplification products of cDNA purified with AMPure XP beads (Beckman, A63881).The quantitative of library and the distribution of fragment were assessed with Qubit HS DNA kit (life, Q32854) and 2100 DNA high sensitivety kit (Agilent, 5067-4626), respectively. The RNA-seq conducted by Illumina Hiseq X Ten system (Illumina, San Diego, CA, USA) on paired-end (PE) mode with length 150 bases following the vendor’s recommended protocol.  and distribution of fragment.

tag: disease status

value: benign prostatic hyperplasia

value: urine


title: Ythdc1_KD_NT_Rep2


title: 42557-P1-FC


title: sample27_PAH8_treatment1

description: processed data file: siALDH1A3_DESeq2_exp_normalized.txt


title: KO_colitis_colon CD4+ T cells_rep2

value: colon CD4+ T cells


title: 42555-P2-D13


title: sample26_PAH2_treatment1


title: 42555-P2-D8


title: K8a_benign prostatic hyperplasia_urinary exosome


title: WT_colitis_colon CD4+ T cells_rep2


title: K9a_benign prostatic hyperplasia_urinary exosome


title: KO_colitis_colon CD4+ T cells_rep1


title: K7a_benign prostatic hyperplasia_urinary exosome


title: 42555-P2-D2


title: sample24_PAH8_treatment2


title: sample25_PAH1_treatment1


title: sample28_PAH1_treatment2_H3K27ac


title: K6a_benign prostatic hyperplasia_urinary exosome


title: sample23_PAH2_treatment2


title: 42555-P2-FC


title: 42555-P1-D13


title: K5a_benign prostatic hyperplasia_urinary exosome


title: K4a_benign prostatic hyperplasia_urinary exosome


title: 04_VPC220010_DHT_rep2

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

data_processing:
Base calling was performed using the BGISeq500 platform. The raw reads were pre-filtered by removing adaptor sequences, contamination and low-quality reads.
The high quality of the filtered reads was confirmed using the FastQC (Andrews, 2014) quality control tool.
Reads were quantified using Salmon version 1.1.0  (Patro, R., et al. 2017)
Differential gene expression analysis for different treatments was performed using the DESeq2 (Love, Huber, & Anders, 2014).
Genome_build: hg38 transcriptome
Supplementary_files_format_and_content: DESeq2 Differential Expression Analyses of DHT vs Ethanol, Enzalutamide vs DHT and VPC-220010 vs DHT, as a Microsoft Excel Spreadsheet.

source_name: LNCaP cells

growth_protocol: LNCaP cells (6 x 10^6) were seeded in RPMI 1640 media containing 10% FBS and 1% penicillin/streptomycin. Following O/N incubation, the media was changed to RPMI 1640 containing 5% CSS and the cells were then grown for 48hrs at 37C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol and the Qiagen RNeasy RNA Extraction Kit. Three biological replicas were collected for each condition.  The concentrations and the qualities of the RNA samples were checked by Nanodrop and tape station. All RIN values were between 9.5 and 10.
Library was constructed by BGI using library construction methods underlying the BGISEQ-500 platform.

treatment_protocol: Cells were treated with 10nM DHT and either DMSO (Control) or 1.5µM Enzalutamide, or 6µM VPC-220010 for 6 hours before RNA isolation.

value: LNCaP cells


title: sample22_PAH1_treatment2


title: sample21_PAH11

description: processed data file: Donors_vs_Patients_DESeq2_exp_normalized.txt


title: 04_VPC220010_DHT_rep3


title: K10a_benign prostatic hyperplasia_urinary exosome


title: K3a_benign prostatic hyperplasia_urinary exosome


title: 04_VPC220010_DHT_rep1


title: sample20_PAH7


title: 42555-P1-D8


title: 03_Enzalutamide_DHT_rep3


title: K2a_benign prostatic hyperplasia_urinary exosome


title: 42555-P1-FC


title: 42555-P1-D2


title: sample19_PAH5


title: 03_Enzalutamide_DHT_rep2


title: WT_colitis_colon CD4+ T cells_rep1


title: K1a_benign prostatic hyperplasia_urinary exosome


title: K11_prostate cancer_urinary exosome

source_name: prostate cancer_urinary exosome

value: prostate cancer

tag: grade

value: Gleason score 7 or greater


title: 03_Enzalutamide_DHT_rep1


title: 42514-P2-D13

value: SIP-JuvenilePartnered


title: 42514-P2-D8


title: sample17_PAH9

value: idiopathic pulmonary arterial hypertension patient

value: pulmonary arterial smooth muscle cells


title: 02_DMSO_DHT_rep3


title: 42514-P2-D2


title: sample16_PAH10


title: 42514-P2-FC


title: 02_DMSO_DHT_rep2


title: K9_prostate cancer_urinary exosome


title: 02_DMSO_DHT_rep1


title: K8_prostate cancer_urinary exosome


title: sample14_PAH2


title: sample13_PAH4


title: 42514-P1-D13


title: 01_DMSO_ETOH_rep3


title: sample18_PAH6


title: sample15_PAH8


title: 01_DMSO_ETOH_rep2


title: K6_prostate cancer_urinary exosome


title: 42514-P1-D2


title: K7_prostate cancer_urinary exosome


title: sample12_PAH3


title: 01_DMSO_ETOH_rep1


title: K5_prostate cancer_urinary exosome


title: sample11_PAH12


title: 42514-P1-FC


title: K4_prostate cancer_urinary exosome


title: K10_prostate cancer_urinary exosome


title: sample10_PAH1

value: mutant patient


title: K3_prostate cancer_urinary exosome


title: 42402-P2-D8


title: sample09_donor8

value: donor control


title: E0771 - ADZ6

type: RNA

city: Sheffield

first: Penelope

last: Ottewell

address: Beech Hill road

department: Oncology and Metabolism

country: United Kingdom

institute: University of Sheffield

data_processing: The raw data were processed in nSolverTM 4.0 and Advanced Analysis 2.0 (NanoString Technologies). Cell-type deconvolution across treatment groups was performed in R; gene expression intensities were mean-centered across all samples before calculating raw cell-type signature scores as the mean average of log2 expression intensities for all genes in each cell-type signature.

source_name: breast cancer

extract_protocol: Primary tumours were homogenised using QIAshredder (Catalogue number: 79654, Qiagen) and RNA isolated using RNeasy mini kit (Cat number: 74101, Qiagen). 150 ng RNA (50 ng/µl) was used for NanoString analysis, according to the manufacturer’s recommended protocols.

value: primary tumour

tag: cell line

value: Breast cancer

tag: mouse strain

tag: mouse age when tumour cell injection was performed

value: 6-8 week old

tag: Sex

value: Female

value: Anakinra+Dox+Zol


title: E0771 - ADZ5

tag: cell type

tag: treatment


title: K2_prostate cancer_urinary exosome


title: E0771 - ADZ4


title: E0771 - ADZ3


title: E0771 - ADZ2


title: K1_prostate cancer_urinary exosome


title: 42402-P2-D2

value: Peripheral blood mononuclear cells


title: 42514-P1-D8

value: SIP-Isolated


title: 42402-P2-FC


title: 42402-P1-D2


title: E0771 - DZ5

value: Dox+Zol


title: 42402-P1-D8


title: 42402-P1-FC


title: sample04_donor7


title: sample03_donor3


title: sample08_donor2


title: 42402-P2-D13


title: E0771 - DZ4


title: sample05_donor1


title: sample07_donor4


title: E0771 - DZ3


title: sample02_donor9


title: E0771 - ADZ1


title: E0771 - DZ6


title: sample06_donor6


title: 42402-P1-D13


title: 42299-P2-D8


title: PR8ΔNS1: 293T-Dicer KO +hDicer +ZIKV NS1

source_name: 293T Dicer KO cells

tag: genotype

value: Dicer-/-

value: PR8ΔNS1 virus


title: E0771 - DZ2

tag: tissue


title: E0771 - DZ1


title: 42299-P2-D13


title: p38a-KO_IL-1{alpha}_rep2

city: Charlestown

first: JIn Mo

last: Park

state: Massachusetts

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
Basecalls were performed using  bcl2fastq v2.20.0.422 (Illumina).
Read alignment was performed on the hg19 assembly of the human genome using the genome mapper STAR for RNA-Seq.
Normalized values as reads per kilobase per million mapped reads (rpkm) was calculated by HOMER software.
Genome_build: hg19
Supplementary_files_format_and_content: txt (normalized values as reads per kilobase per million mapped reads)

source_name: HaCaT

growth_protocol: Cultured in DMEM with 10% FBS and penicillin-streptomycin (50 unit/ml and 50 mg/ml, Thermo Fisher Scientific)

extract_protocol:
Trizol Reagent (Thermo Fisher Scientific), further purified using the RNeasy Mini Kit (Qiagen)
Trueseq stranded mRNA sample prep kit (Illumina)

value: HaCaT

value: Immortalized keratinocytes

value: IL-1{alpha} in PBS for 4h


title: 42299-P2-FC

value: SIP-JuvenilePartnered


title: 42299-P2-D2


title: E0771 - A5

value: Anakinra


title: E0771 - A4


title: sample01_donor5

value: pulmonary arterial smooth muscle cells


title: p38a-KO_IL-1{alpha}_rep1


title: PR8ΔNS1: 293T-Dicer KO +hDicer


title: E0771 - A3


title: 42299-P1-D8


title: T47D_ETV7_rep3

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
Raw reads were adapter-trimmed with BBDuk (sourceforge.net/projects/bbmap/) and aligned using STAR (Dobin et al., 2013) version 2.5.3a to build version hg38 of the human genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package (Liao et al., 2014) and R (version 3.3.1).
Normalization and differential expression analysis were carried out using edgeR R package (Robinson et al., 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Expression matrix of raw counts for each sample

source_name: Cell line derivative

growth_protocol: Cells were grown in DMEM medium (Gibco, ThermoFisher Scientific, Milan, Italy) supplemented with 10% FBS (Gibco), 2mM L-Glutamine (Gibco) and a mixture of 100U/ml Penicillin / 100μg/ml Streptomycin (Gibco). Cells were cultured at 37°C with 5% CO2 in a humidified atmosphere. Selction was maintained  growing MCF7 and T47D cells in growth medium additioned with Puromycin (Life Technologies) 0.75 and 1.5 μg/ml, respectively.

extract_protocol:
Total RNA was extracted using the Illustra RNA spin Mini Kit (GE Healthcare, Milan, Italy), checkd for quality and purity the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) selecting RNA extracts with a RIN (RNA integrity number) value > 8.
RNA (1 mg) was then converted into cDNA libraries according to the Illumina TruSeq Stranded mRNA Sample Preparation Guide (Illumina, San Diego, CA, USA) following manufacturer’s instructions.

treatment_protocol: Cells were plated cultured as above and no treatment was applied.

value: Luminal Breast Cancer


title: 42299-P1-D2


title: p38a-KO_US

value: Unstimulated (PBS for 4h)


title: E0771 - A2

value: primary tumour

value: Breast cancer


title: T47D_Empty_rep3

value: Empty


title: WT_IL-1{alpha}_rep2

value: WT


title: T47D_ETV7_rep2


title: PR8ΔNS1: 293T-Dicer KO +hDicer +WSN NS1


title: E0771 - A1

value: 6-8 week old

value: Female


title: 42299-P1-D13

value: SIP-Isolated

value: Peripheral blood mononuclear cells


title: 42299-P1-FC


title: WT_IL-1{alpha}_rep1


title: E0771 - P6

value: Placebo


title: 42021-P2-D13


title: T47D_Empty_rep2


title: WT_US

value: HaCaT


title: T47D_ETV7_rep1


title: Ctrl2

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

institute: Università degli studi di Milano

data_processing:
The sequencing readings were paired to the human genome (Build GRCh38) with software Salmon (v.0.13.1)
The transcriptional analysis was performed by mean of DeSeq2 software, using the library R DESeq2 (v.1.24.0).
A selection of all transcripts was performed, to exclude those not expressed in our conditions, and selecting only the transcripts which sum of 6 expression values produced more than 20 reads.
Two samples per condition were used to identify differentially expressed genes and GSEA
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for genes with at least 20 reads.

source_name: Swhannoma cells

growth_protocol: The cells were maintained  in Dulbecco's modified Eagle's medium (DMEM)- fetal bovine serum (FBS) 10% (Gibco-Life Technologies, Milan, Italy).

extract_protocol:
RNA was extracted from whole cells by using Trizol protocol
500ng total RNA has been processed to obtain a library of indexed fragments by using Illumina Stranded mRNA kit (San Diego, CA, USA). Equimolar quantities of indexed library for each sample were loaded for sequencing on two flowcells Illumina MidOutput 150 cycles and sequenced by using Illumina NextSeq550dx (RUO mode).

treatment_protocol: Treated cells were exposed to 50 Hz 0.1 T EMF, 5 repeated 10-min exposures, at 37 °C, every 24 hours.

value: Swhannoma cells


title: E0771 - P4


title: 42021-P2-D8


title: 42021-P2-D2


title: Ctrl1


title: 42021-P2-FC


title: MCF7_ETV7_rep3


title: E0771 - P3


title: EMF2

value: Repeated electromagnetic field


title: E0771 - P2


title: EMF1


title: MCF7_Empty_rep3


title: 42021-P1-D13


title: E0771 - P5


title: MCF7_ETV7_rep2


title: T47D_Empty_rep1


title: MCF7_Empty_rep2


title: G2_Bloodvessels3

city: Chennai

first: Suresh

middle: Kumar

last: Subbiah

address: 173, Agaram Main Rd, Selaiyur, Chennai, Tamil Nadu 600073, India

country: India

institute: Bharath university

description: Dengue virus Infected, HSC and EPC treated

data_processing:
Illumina MiSeq Next Generation Sequencer was used to generate output data from run.
Transcriptome assembly and analysis were completed using Tuxedo software. The libraries sequenced were mapped to the updated genomic annotation file of the mouse genome (Mus musculus, NCBI ref. database: GCF_000001635.26¬_GRCm38.p6_genomic.gff) using Tophat v2.0.9. Transcripts were assembled following conformation of reads quality control via the FASTQ format and quantified by Cufflinks 2.0.2 analysis. Isoforms assembled by Cufflinks from all the sample groups were further merged to create a single transcriptome annotation file in gtf using Cuffmerge. The results were analyzed using Cuffdiff to identify differentially expressed genes and transcripts. The relative expression of genes was determined based on FPKM (total fragments per kilobase of exon per million mapped reads) values.
The results obtained were used to generate density and scatter volcano plots using CummeRbund software. Heat maps showing the relative expression of the differentially expressed genes following treatment with stem cells were also generated utilizing the Morpheus heat map generator (https://software.broadinstitute.org/morpheus/)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each sample

source_name: Blood Vessels

growth_protocol: HSC cells were routinely generated by re-plating the non-adherent cultures  on uncoated plastic in high-glucose DMEM supplemented with 15% FBS, 1% penicillin-streptomycin (Biowest), 100 ng/mL murine SCF (BioVision), 6 ng/mL murine IL-3 (BioVision), and 10 ng/mL human IL-6 (BioVision). EPC were routinely generated by re-plating the adherent cultures on  gelatin coated T75 flask in Cell Biologics cell culture medium supplemented with 10% FBS, hydrocortisone, VEGF, EGF, endothelial cell growth factor (ECGS), heparin, L-glutamine and antibiotic-antimycotic solution. DPSC cells were also routinely generated by re-plating the non-adherent cultures  on uncoated plastic in high-glucose media

extract_protocol:
Liver and blood vessels were removed and preserved in RNALater. The RNA was harvested using the RNeasy mini kit (Qiagen, Hilden, Germany). The qiaseq stranded mrna select kit (Cat No./ID: 180773) was with 1 ug of total RNA to produce the sequencing libaries.
RNA libraries were prepared for sequencing using standard Qiagen RNeasy Mini kit protocols that are made compatible with the Illumina system

treatment_protocol: The stem cells were transplanted intraperitoneally in BALB/C mice at a desired concentration of HSCs (2.5 × 105 cells per mouse) and EPCs (1 × 106 cells per mouse) (suspended in Hank's balanced saline solution) using syringe at different timepoint. The mice were sacrificed by cervical disloation before liver collection.

tag: strain

value: BALB/C

value: Blood Vessels tissue

tag: age

value: Post Natal week 8

value: Wild type

value: 21 days after infection


title: E0771 - P1

value: primary tumour


title: MCF7_ETV7_rep1

value: Luminal Breast Cancer


title: 42021-P1-FC


title: 42021-P1-D8


title: Control_Bloodvessels1

description: Healthy


title: 42021-P1-D2


title: 41917-P2-D13

value: SIP-JuvenilePartnered


title: G3_Bloodvessels3

description: Dengue virus Infected, HSC, EPC and DPSC treated


title: MCF7_Empty_rep1

value: Empty


title: G3_Bloodvessels2


title: HPVco_19

city: Rio de Janeiro

first: Ayslan

middle: Castro

last: Brant

state: Rio de Janeiro

address: Andre Cavalvanti 37

department: Genetics

country: Brazil

institute: National Institute of Cancer

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads with low quality scores (Q < 20 phred score), short reads with lengths < 30 nucleotides, and reads with a high fraction of base ambiguities (> 60% ambiguous bases) were discarded using PRINSEQ.
To analyze likely integration events a de novo transcriptome construction was carried out with Trinity. Subsequently, to identify chimeric transcripts, assembled transcript sequences were compared to the HPV database genomic sequence with Blast tools to obtain high-scoring segment pairs (HSPs) with e-values < 1x10-6 and identity score ≥ 98%. Selected transcripts were additionally compared to the human genome (HG38) using Blast online to identify the Human/HPV chimeric transcripts.
Genome_build: X55964  X74462  X00203  X74463  X74465  M14119  X62843  K02718  AY262282  X74472  X74473  U31783  U31784  X74474  J04353  X74475  M12732  X74476  X74477  M62849  X74478  M73236  AJ620205  U31788  X74479  M62877  X74481  X74482  U37488  X74483  X55965  D90400  X77858  U31793  AY395706  U31794  D21208  DQ080079  AB027020  U21941  AB040456  X94164  X94165  AF436130  Y15175  KC138720  AJ620209  AB027021  AF151983  AF293960  AF131950  AF349909  AJ400628  AF436128  AY057438  AF419318  AJ620211  DQ080080  DQ080083  DQ080082  GQ244463  GQ246950  FN547152 and GRCh38
Supplementary_files_format_and_content: Fasta file from chimerics contigs obtained from de novo assembly and blast selection, only for samples with HPV integration to host genome.  Txt files with count of reads covering each nucleotides from HPV genomes.

source_name: uterine cervix tumor with multiple HPV genotype infection

growth_protocol: All biopsies were collected from patientes at Brazilian National Cancer Institute hospital in Rio de Janeiro, Brazil

extract_protocol:
DNA and RNA were isolated from each sample and cell line with Qiagen Allprep DNA/RNA mini kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. DNA and RNA were quantified and stored at -20°C and -80°C, respectively.
Libraries were prepared with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer´s recommendations.

treatment_protocol: All biopsies were collected before patient treatment and stored in RNAlater (Qiagen) at -80°C until mRNA isolation.

value: Uterine cervix

tag: hpv infection

value: Multiple HPV genotypes infected

tag: histological tumor classification

value: Squamous cell carcinoma


title: 41917-P2-D2

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: G3_Bloodvessels1


title: 41917-P2-D8


title: HPVco_18


title: A12h-2

city: Hengyang

first: Yating

last: Wen

state: Hunan

address: No. 28, Changsheng West Road

institute: University of South China

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HeLa cells were cultured and maintained in Dulbecco's Modified Eagle Medium (DMEM; Hyclone, Logan, UT) supplemented with 10% fetal bovine serum (FBS; Gibco, Waltham, MA). Cells were grown at 37°C, 5% CO2.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: C. trachomatis were diluted in complete DMEM. After the incubation for 2 hours, the medium was replaced with complete DMEM containing 10% FBS and 2 μg/ml cycloheximide. The cell samples were cultured at 37°C in a CO2 incubator and collected at 12, 24, and 40h after infection.

value: HeLa

tag: tissue source

value: Cervical epithelium

tag: source gender

value: Female

tag: infectected with

value: Chlamydia trachomatis


title: G2_Liver3

source_name: Liver

value: BALB/C

value: Liver tissue


title: HPVco_17


title: 41917-P2-FC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the Mmul_8.0.1 genome sequence using STAR-2.5.2b with --quantMode GeneCounts --outSAMtype None and all other paramters default
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: tab-delimited text files (STAR output) include transcript raw count values for each sample

extract_protocol:
Total RNA was extracted from PBMC using RNEasy Mini kit reagents on a QIAcube instrument
cDNA libraries were constructed from 300 ng total RNA using Lexogen QuantSeq 3' FWD and sequenced on an Illumina HiSeq 4000 acquiring single-strand 65-bp reads (targeting > 10M reads/sample).


title: HPVco_16


title: A24h-2


title: A24h-1


title: HPVco_15

value: Unknown


title: Control-1

value: Non-infected


title: 41917-P1-D8

value: SIP-Isolated


title: A40h-2


title: 41917-P1-D13


title: Control-2


title: A12h-1


title: A40h-1


title: G2_Bloodvessels2

value: Blood Vessels tissue

value: Post Natal week 8

value: Wild type

value: 21 days after infection


title: Control_Liver3

description: Healthy


title: 41917-P1-D2


title: G2_Bloodvessels1


title: HPVco_14

value: Uterine cervix


title: Human Myeloma Cell Line OPM2_AZD4785 treated_rep3

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G

data_processing: All the following analyses were performed in R Bioconductor (version 3.5.1). Robust Multichip Average (RMA) processing was applied on raw data, based on the platform design (pd.clariom.d.human), allowing background subtraction, quantile normalization and median-polish summarization on core probe sets, by using oligo package.Global expression levels of 138.745 total transcripts were extracted from the ExpressionSet. Following Affymetrix Human Clariom D annotation (clariomdhumantranscriptcluster.db, version 8.7.0, org.Hs.eg.db, version 3.7.0 ) and filtering based on Entrez Gene Identifier and the exclusion of non-coding or uncharacterized protein transcripts (by subtracting microRNA, long non-coding RNA, long intergenic non-coding RNA, small nucleolar RNA, antisense, intronic, uncharachterized protein transcripts), 20.558 total features were further considered.

label: biotin

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA)

growth_protocol: The Human MM cell lines MM.1S, U266, KMS20 and OPM2 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA) and kept in culture according to manufacturer’s instructions.

extract_protocol: RNA was extracted from MM cell lines using RNeasy Mini kit (Qiagen)

treatment_protocol: All HMCLs were exposed to 3 µM AZD4785 for 48 hours

value: Human Myeloma Cell Line


title: 41917-P1-FC

first: Steve

last: Cole

institute: UCLA School of Medicine


title: HPVco_13

value: Multiple HPV genotypes infected


title: G1_Bloodvessels3

description: Dengue virus Infected


title: Human Myeloma Cell Line OPM2_AZD4785 treated_rep1


title: G1_Bloodvessels2

description: Dengue virus Infected


title: Human Myeloma Cell Line OPM2_untreated_rep3

source_name: Human Myeloma Cell Line OPM2_untreated

value: control


title: HPVco_10

value: Squamous cell carcinoma


title: 41764-P2-D13

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: G1_Bloodvessels1

description: Dengue virus Infected


title: Control_Liver1

description: Healthy


title: HPVco_12


title: 41764-P2-FC


title: Human Myeloma Cell Line OPM2_AZD4785 treated_rep2


title: Human Myeloma Cell Line OPM2_untreated_rep2


title: 41764-P2-D2


title: Control_Liver2

description: Healthy


title: HPVco_9


title: 41764-P1-D13


title: HPVco_8


title: Human Myeloma Cell Line OPM2_untreated_rep1


title: G2_Liver1


title: 41764-P1-D8


title: Human Myeloma Cell Line KMS20_AZD4785 treated_rep3


title: HPVco_7


title: Human Myeloma Cell Line KMS20_AZD4785 treated_rep2


title: 41764-P1-D2


title: Human Myeloma Cell Line U266_AZD4785 treated_rep3


title: 41764-P1-FC


title: Human Myeloma Cell Line KMS20_AZD4785 treated_rep1


title: Human Myeloma Cell Line KMS20_untreated_rep3

source_name: Human Myeloma Cell Line KMS20_untreated


title: HPVco_6

value: Adenocarcinoma


title: 40579-P2-D13


title: G3_Liver1

value: BALB/C


title: G3_Liver2

value: Liver tissue


title: G1_Liver3

description: Dengue virus Infected


title: Human Myeloma Cell Line KMS20_untreated_rep1


title: HPVco_5


title: HPVco_4


title: HPVco_3


title: Human Myeloma Cell Line U266_AZD4785 treated_rep2


title: 40579-P2-D8


title: G3_Liver3


title: Human Myeloma Cell Line KMS20_untreated_rep2


title: 40579-P2-D2


title: G1_Liver2

description: Dengue virus Infected


title: HPVco_2


title: Human Myeloma Cell Line U266_AZD4785 treated_rep1


title: G1_Liver1

description: Dengue virus Infected


title: 40579-P2-FC


title: HPVco_1


title: 40579-P1-D13


title: experiment_1_input replicate 1

city: SEATTLE

first: Wei

last: Zhou

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: genome sciences

institute: University of Washington

description:
plasmid DNA
yeast three hybrid system
exp1_processed.txt

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/ 2.16.0.10 tolerating one mismatched base in barcodes (edit distance (ED) < 2). Read1 and read2 are merged using SeqPrep/2016. Low quality reads were filtered based on the exact match of the first 10bp common sequence in the plasmid. Puf repeat ID was determined by the 5-14bp sequence of merged reads. RNA code and protein code sequenced were extracted from the related location on the sequence.
Supplementary_files_format_and_content: Processed data files are in txt format; exp1 and exp2 content include Puf_repeat,TRM_combination,RNA_code,mutation_type,input_1_reads,input_2_reads,select_1_reads,select_2_reads; exp 3 include Puf_design,RNA_target,input_reads,select_1_reads,select_2_reads

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: The yeast strain constitutively expresses the fusion protein LexA–MS2 coat and a HIS3 reporter gene under the control of multiple LexA operators. The genotype of YBZ-1 is MATa, ura3-52, leu2-3, 112, his3-200, trp1-1, ade2, LYS2 :: (LexAop)-HIS3, ura3 :: (lexA-op)-lacZ, LexA-MS2 coat (N55K). We collected transformants from plates containing SC-Leu media18.

extract_protocol:
We collected cells and extracted their plasmids (Zymoprep Yeast Plasmid Miniprep II kit; Cat 11-315).
The region including each PUF repeat was amplified through sequential reactions. Internal PCR was carried out through primers with sequences that anneal to each repeat (primers 623-654) and external PCR was carried out to add an Illumina sequencing adapter (primers 419-422). Phusion polymerase was used for these reactions, and each reaction was performed on a BioRad MiniOpticon and monitored to avoid over-amplification. The PCR products were sequenced using the Nextseq 550 platform. Downstream analyses were performed in R.

treatment_protocol: For the three-hybrid selection, we plated the transformants onto plates containing SC-Leu media and plates with SC-Leu-His + 0.5mM 3-AT media. Colonies were grown for four days.

tag: yeast strain

value: YBZ strain

tag: expression method

value: plasmid overexpression

tag: group setting

tag: replicate

value: replicate 1


title: Human Myeloma Cell Line U266_untreated_rep3

source_name: Human Myeloma Cell Line U266_untreated

tag: cell line


title: Human Myeloma Cell Line U266_untreated_rep2


title: 40579-P1-D8

city: Los Angeles

address: 11-934 Factor Bldg, UCLA

value: SIP-Isolated


title: SacCer_800U_RNaseI

city: Zürich

first: Puneet

last: Sharma

state: Zürich

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH

description:
Ribosome profiling
processed data file: SacCer_supplementary_count_table.txt

data_processing:
Library strategy: Ribo-Seq
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13.
Processed yeast reads were mapped to tRNA, rRNA, snRNA and snoRNA; reads from human samples were mapped to rRNA using bowtie version 1.2.1.1.
Residual reads were uniquely mapped to non-dubious ORFs (hg38; SacCer3; C_albicans_SC5314_version_A22;Pombe_ASM294v2) extended by 18 nt into the UTRs.
Genome_build: hg38 (GRCh38); SacCer3 (R64); C_albicans_SC5314_version_A22 (ASM18296v3); Pombe_ASM294v2 (ASM294v2)
Supplementary_files_format_and_content: *_count_table.txt: Tab-delimited text files include raw counts for each sample.

source_name: Yeast

growth_protocol: HEK 293T cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37C. Yeast cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4–0.5) at 30C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).

extract_protocol:
For HEK 293T cells, total RNA is extracted using phenol:chloroform method. For yeast, total RNA is extracted using the hot-acid-phenol method.
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.

treatment_protocol: (+/+) samples are pre-treated with CHX and lyzed in buffer containing CHX; (-/+) samples are lyzed in buffer containing CHX WITHOUT CHX pre-treatment; (-/-) samples are lyzed without CHX pre-treatment in buffer devoid of CHX.

value: 800U RNaseI


title: Human Myeloma Cell Line U266_untreated_rep1


title: 40579-P1-D2


title: Isolated_stromal cells_Peritoneum_mouse_1_(AL349)

city: Montpellier

first: Damien

last: Grégoire

address: 1919, route de Mende

country: France

institute: CNRS

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: Athymic nude mice stromal cells

growth_protocol: BMEL (Bipotential Mouse Embryonic Liver) cell line was isolated from C57B/6_C3H mouse. Cells were grown on collagen-coated plates in RPMI medium (Gibco/Life Technologies) supplemented with 10% fetal calf serum (Pan-Biotech), insulin 10 ug/mL (Sigma), IGFII 30 ng/mL (Peprotech), EGF 50 ng/mL (Peprotech), 100 units/ml penicillin, and 100 mg/ml streptomycin. Cells were grown under standard conditions at 37°C in a humidiﬁed incubator containing 5% CO2. All cells were routinely tested to confirm absence of mycoplasma contamination. Liver and peritoneal tumors were dissociated using mouse tumor dissociation kit (Milteny 130-096-730) and OCTOdissociator based on manufacturer instructions. Tumoral and stromal cells were isolated from cell suspensions based on GFP positivity  with an ARIA IIU BECTON DICKINSON sorter.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit following manufacturer instructions. DnaseI treatment (Qiagen) was used to remove residual genomic DNA. RNA integrity was assessed by Agilent BioAnalyser NuGen Universal Plus mRNAseq kit (Cat#0520-A01)   was used with 250ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No

value: Athymic nude mice stromal cells

tag: processing

value: Isolated from peritoneum metastasis


title: Human Myeloma Cell Line MM.1S_AZD4785 treated_rep3

tag: cell type


title: Isolated_stromal cells_Peritoneum_mouse_2_(AL355)


title: SacCer_400U_RNaseI

tag: treatment

value: 400U RNaseI


title: Isolated_stromal cells_Peritoneum_mouse_4_(AL387)


title: Isolated_stromal cells_Peritoneum_mouse_3_(AL373)


title: SacCer_600U_RNaseI

value: 600U RNaseI


title: SacCer_minus_minus_3

value: Not pre-treated with CHX, not lyzed in buffer containing CHX


title: Human Myeloma Cell Line MM.1S_AZD4785 treated_rep2

value: Human Myeloma Cell Line


title: 40579-P1-FC


title: 39916-P2-D8


title: DS-MHCII-CD64+Ly6C-inter

city: Houston

first: Jahan

last: Alam

address: One Baylor Plaza, MS: BCM-706,  Room C 505D,, MS: BCM-706,  Room C 505D,

department: Ophthalmology

institute: Baylor College of Medicine, Ocular-surface Center Lab

description:
Sorted Cells for NanoString
MWF-DS3

hyb_protocol: One hundred nanograms of total RNA were hybridized with the Nanostring Technologies nCounter Gene Expression Mouse Myeloid Innate Immunity Panel codeset (NS_MM_Myeloid_V2.0+Pls) containing 770 Unique pairs of 35-50bp reporter probes, 12 custom probe pairs and biotin-labeled capture probes, including internal refereance controls. overnight hybridization occured for 20hours at 65C.

scan_protocol: The cartridge containing immobilized sample was transferred to the nCounter Digital Analyzer (Software v3.0.1.4) and scanned at 555 field of view (FOV).

data_processing: Data was processed using the nCounter Software nSolver 4.0

source_name: Mouse conjuctiva

label_protocol: The samples were labeled according to the condition in which the mice were kept and according to the gating strategy

growth_protocol: Mice were purchased from Jackson lab and maintained at BCM animal facilities until use

extract_protocol: Immune cells were sorted from the conjuctiva from each group and the RNA was extracted using the standard protocol provided by the manufactorer, we use the Qiagen RNA preparation kit

treatment_protocol: Mice were either kept at normal condition or subjected to dessication stress under the standard protocol

tag: experimental group

value: Dessication stress

tag: Sex

value: Female

value: conjuctiva


title: SacCer_minus_minus_2

tag: strain


title: DS-MHCII-CD64+Ly6C-low

description:
Sorted Cells for NanoString
MWF-DS4

tag: age

tag: tissue


title: 39916-P2-D2

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: Isolated_stromal cells_Liver_mouse_2_(AL353)

value: Isolated from liver xenograft


title: Isolated_stromal cells_Liver_mouse_4_(AL385)


title: Isolated_stromal cells_Liver_mouse_3_(AL371)


title: Human Myeloma Cell Line MM.1S_AZD4785 treated_rep1


title: DS-MHCII-CD64+Ly6C-high

description:
Sorted Cells for NanoString
MWF-DS2


title: SacCer_minus_minus_1


title: 39916-P2-D13


title: SacCer_minus_plus_3

value: Not pre-treated with CHX, lyzed in buffer containing CHX


title: Isolated_stromal cells_Liver_mouse_1_(AL347)


title: Isolated_tumor cells_Peritoneum_mouse_4_(AL386)

source_name: bipotential embryonic mouse liver cells

value: bipotential embryonic mouse liver cells


title: 39916-P2-FC


title: DS-MHCII+

description:
Sorted Cells for NanoString
MWF-DS1

value: DS-MHCII+


title: N-MHCII-CD64+Ly6C-low

description:
Sorted Cells for NanoString
MWF-NS4

value: No dessication stress


title: N-MHCII-CD64+Ly6C-inter

description:
Sorted Cells for NanoString
MWF-NS3


title: 39916-P1-D13

value: SIP-Isolated


title: SacCer_minus_plus_2


title: Human Myeloma Cell Line MM.1S_untreated_rep2

source_name: Human Myeloma Cell Line MM.1S_untreated

value: control


title: 39916-P1-D8


title: Isolated_tumor cells_Peritoneum_mouse_3_(AL372)

value: Isolated from peritoneum metastasis


title: N-MHCII-CD64+Ly6C-high

description:
Sorted Cells for NanoString
MWF-NS2


title: SacCer_minus_plus_1


title: 39916-P1-D2


title: Isolated_tumor cells_Peritoneum_mouse_2_(AL354)


title: SacCer_plus_plus_3

value: Pre-treated with CHX, lyzed in buffer containing CHX


title: SacCer_plus_plus_2


title: 39916-P1-FC


title: Isolated_tumor cells_Peritoneum_mouse_1_(AL348)


title: PSPC1-9h-EU-seq-2

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version
CLIP-seq Reads were filtered and pre-processed and the exact sequence duplicates were collapsed to remove PCR duplicates. EU-seq reads were trimmed by trim_galore
Reads obtained from CLIP-seq library sequencing were aligned to the mm9 genome assembly using novoalign program with parameters described before. Reads from EU-seq library sequencing were aligned to the mm9 genome assembly using Hisat2.
Peaks of CLIP-seq were called using Piranha
bedgraph files containing the sequencing signals of CLIP-seq or EU-seq were generated by samtools
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing the sequencing signals of CLIP-seq or EU-seq

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells)

growth_protocol: ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
EU-seq was performed as described previously with modifications115. ESCs were labeled by 1 mM EU for 10 minutes. RNA extraction was performed with TRIzol (Life Technologies, Carlsbad, CA, USA). Labelled RNAs were further biotinylated and fragmented as previously described. The biotinylated RNAs were resuspended in 100 μl H2O and then were subjected to tandem affinity purification similar to TT-seq. M-280 dynabeads were washed twice using 1 × B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.005% Tween-20) followed by two times of washes using solution A (0.1 M NaOH, 50 mM NaCl) and solution B (0.1 M NaCl) respectively. 1 mg/ml yeast tRNA in 1 × HSWB (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1 M NaCl, 0.01% Tween-20) was used to block the beads and incubated at room temperature for 30 min. The blocked beads were washed twice using 1 × HSWB and resuspended in 100 μl 2 × HSWB. The biotinylated RNA was denatured at 65 ℃ for 10 minutes and incubated with blocked M-280 beads at room temperature for 30 minutes in an end-to-end rotator. Beads were washed twice with 800 μl of 10 × HSWB and incubated at 50 ℃ for 2 min, then washed twice with 50 ℃ water for 2 min. RNA was eluted by incubating the beads with 50 μl SDS washing buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS) at 95 °C for 5 min. The elution was repeated once ant two eluates were pooled together. M-280 beads were added to the eluted RNA for another affinity purification. RNAs were finally eluted in 10 μl H2O
RNAs were  reverse transcribed and used for library construction  by following manuals of Single-stranded DNA-seq Lib Prep Kit (Abconal, RK20222).

treatment_protocol: Cells were treated by adding 1 mM IAA, and culture at 37℃ for 9 hours

value: embryonic stem cells

value: IAA, 9 hours

tag: affinity purification

value: M280 Streptavidin Dynabeads (Invitrogen, 11205D)


title: SacCer_plus_plus_1


title: Isolated_tumor cells_Liver_mouse_4_(AL384)


title: PSPC1-9h-EU-seq-1


title: 39109-P2-D13


title: 39109-P2-D8


title: Isolated_tumor cells_Liver_mouse_3_(AL370)


title: wt biological replicate 3

city: Warsaw

first: Izabela

last: Rudzińska

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
Mapping to genome by TopHat2 v 2.0.11
Read counts using Genomic Alignments version 1.20.1
differential expresssion calculations using DESeq2 version 1.24.0
Genome_build: Saccharomyces_cerevisiae_EF4_Ensembl
Supplementary_files_format_and_content: Fold Change of gene expression between each strains calculated by DESeq2

growth_protocol: Yeast were grown in selective media o/n. Than were transfered to fresh complete medium (YPD) and diluted to OD600=0,15. Cultures were cultivated to log phase and harvested.

extract_protocol:
Total RNA was extracted from yeast cells using the Bead-beat Total RNA Mini kit (A&A Biotechnology, catalog no. 031-25BB ) and purified using Clean-Up RNA Concentrator (A&A Biotechnology, catalog no. 039-25C)
mRNA was enriched using oligo(dT) beads. The mRNA was fragmented randomly, and then cDNA was synthesized using an mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H, and DNA Pol I were added to initiate second-strand synthesis. After a series of terminal repair and ligation of sequencing adaptors, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: no treatment

tag: genotype

value: wt


title: PSPC1-3h-EU-seq-1

city: Beijing

treatment_protocol: Cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: IAA, 3 hours


title: PSPC1-3h-EU-seq-2


title: 41764-P2-D8


title: rpc128-1007[PRT1] biological replicate 3


title: Isolated_tumor cells_Liver_mouse_2_(AL352)


title: Human Myeloma Cell Line MM.1S_untreated_rep3

value: Human Myeloma Cell Line


title: Human Myeloma Cell Line MM.1S_untreated_rep1


title: Isolated_tumor cells_Liver_mouse_1_(AL346)


title: rpc128-1007[RBS1-R3H] biological replicate 3


title: PSPC1-0h-EU-seq-2

value: No IAA


title: 39109-P2-FC

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: rpc128-1007[RBS1] biological replicate 3


title: 39109-P2-D2


title: BMEL_RasHIGH_rep3_(AL417)

value: exponentially growing on collagen coated plates


title: PSPC1-CLIP-2

source_name: CJ9 mES cells stably express biotin-FLAG-tagged PSPC1

extract_protocol:
CLIP-seq assays were performed as previously described98,99. ESCs that carry a stably integrated transgene of PSPC1 (tagged with FLAG and biotin moiety) were harvested and resuspended with 4 mL cold PBS. The cells were plated back to the plate and crosslinked with 600 mJ/cm2 of 254 nm UV light. Cells were harvested and resuspended in 0.5 mL CLIP lysis buffer (1 × PBS, 0.5% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) and lysed at 4°C for 30 min. The lysate was treated with 30 µL of DNase I at 37 °C for 10 min and stopped by addition of 4 µL 0.5 M EDTA. The insoluble pellet was spun down and the supernatant was harvested. About 40 μl pre-equilibrated FLAG M2 resins (sigma) were used for each purification. The FLAG resins were incubated with lysate overnight at 4°C and washed twice with cold CLIP lysis buffer and two more times with high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% sodium deoxycholate, 0.1% SDS). The proteins were eluted with 200 ng/mL 3xFLAG peptide dissolved in CLIP lysis buffer (sigma) for three times. The eluents were pooled together and incubated with 60 μl pre-equilibrated streptavidin (M-280, Invitrogen) beads for 3 h. The samples were washed twice with SDS-urea wash buffer (50 mM Tris pH 7.4, 2% SDS, 1 M urea) and twice with SDS-high salt wash buffer (5XPBS, 0.5% NP-40, 0.5% SDS) at room temperature. The protein-RNA complex bound beads were washed four times with PNK buffer (50 mM Tris pH 7.4, 10 mM MgCl2, 0.5% NP-40). Then the RNAs were partially digested with MNase (NEB, 1:105 diluted) at 37°C for 10 min (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 s per 30 s). The reaction was stopped by PNK-EGTA buffer (PNK buffer with 2 mM EGTA). Then the beads were washed twice with SDS-urea wash buffer and twice with PNK buffer. To dephosphorylate the RNA, the beads were treated with CIP (NEB) for 10 min at 37°C (mixed with an Eppendorf Thermomixer at 1,200 rpm for 5 s per 30 s). After two more washes with PNK buffer, the pre-adenylated 3’ linker (rAppAGATCGGAAGAGCACACGTCT-NH2, TAKARA) was ligated with truncated T4 RNA ligase 2 (NEB) at 16°C overnight. The non-ligated 3′ linker was washed away with two washes of CLIP lysis buffer and two washes of PNK buffer. The RNAs were then phosphorylated by T4 PNK (NEB) for 10 min at 37°C. To elute the protein-RNA complex, the samples were treated with Proteinase K (50 mM Tris, pH 7.4, 150 mM NaCl, 0.5% SDS, and 20 μg Proteinase K) for 30 min at 37°C.
The RNAs were purified and ligated with 5′ RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNNNN, TAKARA) containing a 6-mer random barcode by T4 RNA ligase (Ambion). Then the RNAs were reverse transcribed by Superscript III with RT primer (AGACGTGTGCTCTTCCGATCT, TAKARA) and amplified for 20 cycles with Q5 DNA polymerase (NEB) (Primer_Forward: GTTCAGAGTTCTACAGTCCGACGATC; Primer_Reverse: AGACGTGTGCTCTTCCGATCT, TAKARA). Library index sequence was introduced by PCR with index primers for 8 more cycles. Forward: AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGAC; Reverse: CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (the underlined hexamer indicates Illumina index sequence, TAKARA).

value: M280 Streptavidin Dynabeads (Invitrogen, 11205D); FLAG M2 resins (sigma)


title: 39109-P1-D13


title: HPVco_11

value: Uterine cervix

tag: hpv infection

value: Multiple HPV genotypes infected

tag: histological tumor classification

value: Squamous cell carcinoma


title: N-MHCII+

description:
Sorted Cells for NanoString
MWF-NS1

value: No dessication stress

value: Female

value: conjuctiva

value: N-MHCII+


title: rpc128-1007[-] biological replicate 3


title: PSPC1-CLIP-1

value: embryonic stem cells


title: BMEL_RasHIGH_rep2_(AL398)

value: bipotential embryonic mouse liver cells


title: BMEL_RasHIGH_rep1_(AL392)


title: 39109-P1-D2

value: SIP-Isolated


title: wt biological replicate 2

value: wt


title: rpc128-1007[PRT1] biological replicate 2


title: 39109-P1-FC


title: BMEL_RasLOW_rep3_(AL399)


title: Wt_H3K36Me3_Rep1

city: Mainz

first: Junaid

last: Akhtar

address: Johannes-Joachim-Becherweg, 32

institute: University of Mainz

description: H3K36Me3 ChIP in control condition

data_processing:
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila.
Genome_build: dm6 (Drosophila melanogaster)

source_name: cell culture

extract_protocol:
S2R+ cells were fixed with 1% formaldehyde for 3 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4ºC. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4ºC.
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol
NebNext UltraII

tag: antibody

value: H3K36Me3 (Abcam Cat No-ab9050) Lot No GR75636-1

tag: sample type

value: Embryonic

value: S2R+ Cells


title: G2_Liver2

value: BALB/C

value: Liver tissue

value: Post Natal week 8

value: Wild type

value: 21 days after infection


title: rpc128-1007[RBS1-R3H] biological replicate 2


title: Input_H3K36Me3

description: Input control

value: Input Sample H3K36Me3


title: 38707-P2-D13

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: BMEL_RasLOW_rep1_(AL173)

value: exponentially growing on collagen coated plates


title: 38707-P2-D8


title: rpc128-1007[RBS1] biological replicate 2


title: ythdc1_t10_R2

description:
Biotin enrichment
Ythdc1 (YT521) depleted nascent DRB-4SU-seq where the elongation inhibition was removed for 10 minutes

extract_protocol:
5,6-dichlorobenzimidazole 1-_-d-ribofuranoside (DRB) from Sigma (D1916) was used at a final concentration of 300_M, dissolved in water, for 5 hours. 4-thiouridine (4sU) was purchased from Sigma (T4509) and used at a final concentration of 100 _M. Control and Mago KD was performed as described before. All the samples were labeled for 8 minutes with 4-thiouridine, and transcription was allowed to proceed after DRB removal for 0, 2, 8 and 16 minutes along with one non-DRB treated control.A total of 100 to 130 _g RNA was used for the biotinylation reaction. 4sU-labeled RNA was biotinylated with EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2 h with rotation at room temperature. Two rounds of chloroform extractions removed unbound Biotin-HPDP. RNA was precipitated at 20,000 g for 20 min at 4¡C with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with 75% ethanol and precipitated again at 20,000 g for 10 min at 4¡C. The pellet was left to dry, followed by resuspension in 100 _L RNase-free water. Biotinylated RNA was captured using Dynabeads MyOne Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 50 _L Dynabeads with rotation for 15 min at 25¡C. Beads were magnetically fixed and washed with 1_ Dynabeads washing buffer. RNA-4sU was eluted with 100 _L of freshly prepared 100 mM dithiothreitol (DTT), and cleaned on RNeasy MinElute Spin columns (Qiagen).
Enriched nascent RNAs were converted to cDNA libraries with Drosophila Ovation Kit (Nugen) with integrated ribosomal depletion workflow
Nugen Ovation


title: ythdc1_t10_R1


title: 39109-P1-D8


title: 38707-P2-D2


title: rpc128-1007[-] biological replicate 2


title: BMEL_empty vector_rep3_(AL413)


title: 38707-P2-FC


title: BMEL_empty vector_rep2_(AL411)


title: Wt_H3K36Me3_Rep2

description: H3K36Me3 ChIP in control condition


title: wt biological replicate 1


title: 38707-P1-D13


title: ythdc1_t2_R2

description:
Biotin enrichment
Ythdc1 (YT521) depleted nascent DRB-4SU-seq where the elongation inhibition was removed for 2 minutes


title: ythdc1_t2_R1


title: rpc128-1007[PRT1] biological replicate 1


title: 38707-P1-D8


title: BMEL_empty vector_rep1_(AL410)


title: BMEL_RasLOW_rep2_(AL393)


title: Stat3_osx_cre_3

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Hisat2
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: Each counts file represent one sample

molecule: polyA RNA

source_name: parietal bone from OsxCre;Stat3fl/fl mice

growth_protocol: Parietal bone from newborn OsxCre;Stat3fl/fl and OsxCre littermates were collected

extract_protocol:
tissues were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

value: parietal bone


title: rpc128-1007[RBS1-R3H] biological replicate 1


title: ythdc1_t0_R2

description:
Biotin enrichment
Ythdc1 (YT521) depleted nascent DRB-4SU-seq where the elongation inhibition was not removed


title: rpc128-1007[RBS1] biological replicate 1


title: Stat3_osx_cre_1


title: 38707-P1-D2


title: 38707-P1-FC


title: rpc128-1007[-] biological replicate 1


title: ime4_t10_R2

description:
Biotin enrichment
Mettl3 (ime4) depleted nascent DRB-4SU-seq where the elongation inhibition was removed for 10 minutes


title: ythdc1_t0_R1


title: 38566-P2-D13


title: experiment_3_selected replicate 2

description:
plasmid DNA
yeast three hybrid system
exp3_processed.txt

tag: yeast strain

value: YBZ strain

tag: expression method

value: plasmid overexpression

tag: group setting

value: replicate 2


title: ime4_t10_R1

tag: cell line


title: 38566-P2-D8


title: ime4_t2_R2

description:
Biotin enrichment
Mettl3 (ime4) depleted nascent DRB-4SU-seq where the elongation inhibition was removed for 2 minutes

tag: cell type


title: experiment_3_selected replicate 1

tag: replicate

value: replicate 1


title: WT_osx_cre_2

source_name: parietal bone from OsxCre mice

value: OsxCre


title: experiment_3_input replicate 1


title: ime4_t2_R1

value: Embryonic


title: KO_microbiota_rep3

first: Chen

last: Dong

address: Haidian District

data_processing:
Raw reads were filtered to remove adaptors and low-quality and ambiguous bases, and then paired-end reads were added to tags by the Fast Length Adjustment of Short reads program (FLASH, v1.2.11) to get the tags.
The tags were clustered into OTUs with a cutoff value of 97% using UPARSE software (v7 .0.1090) and chimera sequences were compared with the Gold database using UCHIME (v4.2.40) to detect.
OTU representative sequences were taxonomically classified using RDP_11_5 database  with a minimum confidence threshold of 0.6, and trained on the Greengenes database v201305 by QIIME v1.8.0
The USEARCH_global was used to compare all Tags back to OTU to get the OTU abundance statistics table of each sample.
Alpha and beta diversity were estimated by MOTHUR (v1.31.2) and QIIME (v1.8.0) at the OTU level, respectively. Sample cluster was conducted by QIIME (v1.8.0) based on UPGMA.
Genome_build: Greengenes

growth_protocol: WT and Rorα KO littermates were housed in different cages after weaning, and the stools were isolated from cecums for DNA extraction.

extract_protocol: microbial DNA was isolated from cecum stools of indicated mice using QiAamp DNA Stool Mini Kit (QIAGEN) according to manufacturer’s instructions.

tag: treatment

value: steady state

value: Cd4_cre Rora_fl/fl

value: feces

tag: molecule type

value: microbial DNA


title: ime4_t0_R2

description:
Biotin enrichment
Mettl3 (ime4) depleted nascent DRB-4SU-seq where the elongation inhibition was not removed

growth_protocol: Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin

value: S2R+ Cells


title: KO_microbiota_rep2


title: Stat3_osx_cre_2

tag: strain


title: 38566-P2-D2


title: 38566-P1-D13

value: SIP-Isolated


title: experiment_2_input replicate 1

description:
plasmid DNA
yeast three hybrid system
exp2_processed.txt


title: experiment_2_selected replicate 1


title: 38566-P2-FC


title: 38566-P1-D8


title: WT_osx_cre_3


title: experiment_1_selected replicate 2


title: WT_microbiota_rep3


title: experiment_1_input replicate 2


title: Ctrl_t10_R1

description:
Biotin enrichment
Ctrl nascent DRB-4SU-seq where the elongation inhibition was removed for 10 minutes


title: Ctrl_t10_R2


title: WT_osx_cre_1


title: 38566-P1-D2


title: 38566-P1-FC


title: WT_microbiota_rep2


title: Ctrl_t2_R2

description:
Biotin enrichment
Ctrl nascent DRB-4SU-seq where the elongation inhibition was removed for 2 minutes


title: 37873-P2-D13


title: experiment_1_selected replicate 1


title: Ctrl_t2_R1


title: Cut & Run LSK IgG

city: Cincinnati

first: Zhaowei

last: Tu

address: 3333 Burnet Ave

institute: Cincinnati Children's Medical Center

data_processing:
Sequencing reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1. The trimmed reads were aligned to the Mus musculus reference genome version GRCm38/mm10 with the program STAR v2.6.1e for RNA-seq and with BOWTIE v2.3.4.1 for ATAC-seq and CUT&RUN-seq experiments. Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
For RNA seq, Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database. Read counting was done with the program feature Counts v1.6.2 from the Rsubread package. Raw counts were normalized as transcripts per million (TPM). Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0.
For ATAC seq, Peaks were called with MACS2 v2.1.2 using the --broad option. ATAC genomic regions among all samples were obtained by merging called peaks at 50% overlap using BEDtools v2.27.0 and in-house programs. This was done at two levels using, between replicates and between treatments. In the former, we require peaks to be present in all biological replicates, meaning a peak observed in one replicate has to have a peak present in all other replicates at the 50% cutoff. On the latter, we keep all peaks from different treatments (merging the peaks in common at 50%). The resulting set of peaks, originally in BED format, were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.6.2 (Rsubread package). Each feature in the GTF file has the value "peak" on the second column.
For Cut & Run, reads with an aligned length between 0 and 280bp were selected for peak calling. The cutoff was chosen to include the first peak in the histogram of read lengths between aligned read pairs. Aligned length is defined as the distance in base-pairs from beginning of alignment in read1 to end of alignment in read2. Peak calling was done with the program MACS v2.1.2 using the narrow peaks mode (default). CUT&RUN genomic regions were obtained using the same method used in the analysis of ATAC-seq data. Resulting peaks, originally in BED format, were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.6.2 (Rsubread package).
Genome_build: mm10
Supplementary_files_format_and_content: TPM expression files for RNA seq data and BigWig for ATAC seq and Cut&Run data.

source_name: LSK

growth_protocol: The cells were sorted from mice with different genotypes and directly used for prepareing libraries.

extract_protocol:
Trizol was used for RNA seq extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols, ATAC seq library was based on Illumina Tagment DNA Enzyme and Buffer Kit. Cut&Run was followed as published online protocols
RNA-Seq, ATAC seq and Cut &Run libraries werer prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina from New England Biolabs

treatment_protocol: pI;pC was injected to induce deletion in the mice. Cells were sorted for use without any culture or other treatment

value: WT

tag: harvest condition

value: 6 days post deletion

value: IgG, Cell Sinaling (#2729S)


title: Ctrl_t0_R2

description:
Biotin enrichment
Ctrl nascent DRB-4SU-seq where the elongation inhibition was not removed


title: 37873-P2-D8

source_name: Peripheral blood mononuclear cells

value: SIP-JuvenilePartnered

tag: tissue

value: Peripheral blood mononuclear cells


title: KO_microbiota_rep1


title: ime4_t0_R1


title: Patient 2 human liver organoid 2 (HLO2)

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: liver

growth_protocol: Huch et al., Cell 2015.

extract_protocol: Chromium Single Cell 3' Reagent Kit (10x Genomics)

treatment_protocol: Differentiated for 19 days.

tag: patient

value: Liver organoid


title: Patient 1 human liver organoid 1 (HLO1)


title: Cut & Run LSK CHD8

tag: genotype

value: CHD8, Abcam (ab84527)


title: 37873-P2-D2


title: 37873-P2-FC


title: Cut & Run KO H3K27me3

value: H3K27me3, Active Motif(#39157)


title: Ctrl_t0_R1

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated three times and cells were harvested 7 days after the first treatment.


title: Cut & Run WT H3K27me3


title: Ythdc1PolII1_Rep1

description: Pol II ChIP in Ythdc1 KD

data_processing:
De-multiplexing and fastq file conversion was performed using blc2fastq (v.1.8.4)
Mapping was performed using bowtie2 (v. 2.3.3) against ensembl release 84 of BDGP6 for Drosophila.
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig  from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: dm6 (Drosophila melanogaster)
Supplementary_files_format_and_content: Ctrl_HA.bw: Replicate averaged, input normalized bigwig file of Control HA
Supplementary_files_format_and_content: Ctrl_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with LacZ depletion
Supplementary_files_format_and_content: Ctrl_KD_Ser2P.bw : Replicate averaged, input normalized bigwig file for Ser2P with LacZ depletion
Supplementary_files_format_and_content: Mettl14_HA_UCSC.bw : Replicate averaged, input normalized bigwig file of Mettl14HA
Supplementary_files_format_and_content: Mettl14_KD_PolII_ave.bw: Replicate averaged, input normalized bigwig file for Pol II with Mettl14 depletion
Supplementary_files_format_and_content: Mettl14_KD_Ser2P_ave.bw : Replicate averaged, input normalized bigwig file for Ser2P with Mettl14 depletion
Supplementary_files_format_and_content: Mettl3_HA.bw: Replicate averaged, input normalized bigwig file of Mettl3 HA
Supplementary_files_format_and_content: Mettl3_HA_Ime4KD.bw : Replicate averaged, input normalized bigwig file of Mettl3 HA, with Mettl3 depletion
Supplementary_files_format_and_content: Mettl3_HA_RNaseT1.bw: Replicate averaged, input normalized bigwig file of Mettl3 HA, with RNAseT1 treatment
Supplementary_files_format_and_content: Mettl3_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with Mettl3 depletion
Supplementary_files_format_and_content: Mettl3_KD_Ser2P.bw: Replicate averaged, input normalized bigwig file for Ser2P with Mettl3 depletion
Supplementary_files_format_and_content: Ythdc1_HA.bw: Replicate averaged, input normalized bigwig file of Ythdc1 HA
Supplementary_files_format_and_content: Ythdc1_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with Ythdc1 depletion
Supplementary_files_format_and_content: fl2d_HA.bw: Replicate averaged, input normalized bigwig file of fl2d HA
Supplementary_files_format_and_content: fl2d_KD_PolII.bw: Replicate averaged, input normalized bigwig file for Pol II with fl2d depletion
Supplementary_files_format_and_content: fl2d_KD_Ser2P.bw: Replicate averaged, input normalized bigwig file for Ser2P with fl2d depletion

treatment_protocol: dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated two times and cells were harvested 5 days after the first treatment.

value: RBP1 (Diagenode Cat No-15200004) / Lot No 001-11


title: 37873-P1-D13


title: Cut & Run KO H3K4me3

value: H3K4me3, Millipore (07-473)


title: 37873-P1-D8


title: Ythdc1PolII1_Rep2

description: Pol II ChIP in Ythdc1 KD

value: Embryonic


title: WT_microbiota_rep1

value: steady state


title: HCT116-CD276KO_3

city: Biberach (Riss)

first: Sibel

last: Durlanik

address: Birkendorferstr. 65

department: Cancer Immunology & Immune Modulation

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

data_processing:
Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in [ https://pubmed.ncbi.nlm.nih.gov/32180900/ ]): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner [https://doi.org/10.1093/bioinformatics/bts635] allowing for soft clipping of adapter sequences. For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) [ https://pubmed.ncbi.nlm.nih.gov/21816040/ ] and featureCounts (v1.5.1) [ https://pubmed.ncbi.nlm.nih.gov/24227677/ ]. Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) [ https://pubmed.ncbi.nlm.nih.gov/27769170/ ] at the respective steps.   Finally, differential expression analysis was performed on the human mapped counts derived from featureCount using limma/voom [https://pubmed.ncbi.nlm.nih.gov/25605792/ , https://pubmed.ncbi.nlm.nih.gov/24485249/ ].
Genome_build: Homo sapiens (human) genome hg38/GRCh38
Supplementary_files_format_and_content: tpm.txt contains expression levels (tpm) in tab-separated format.

growth_protocol: HCT116 colon cancer cells (ATCC, CCL-247) were propagated and maintained in McCoy’s 5A (Modified) medium (16600082, Gibco) with 10% FCS supplement.

extract_protocol:
RNA isolation and quality control   HCT116WT and HCT116CD276KO cells were cultured and maintained in different culture flasks for further propagation. Five biological replicates were used per group for a total of 10 samples. 1x106 cells per sample were collected, centrifuged, washed two times with PBS. After removal of supernatant completely, cell pellets were immediately frozen at -80C until further use. Total RNA extraction for Next-Generation Sequencing from cell pellets lysed in RLT plus buffer were performed by using the AllPrep DNA/RNA Mini Kit (80224, Qiagen) according to the company’s protocol. An on-column DNA digestion was performed and the final elution volume was 30 µL.  Total RNA was quantitatively and qualitatively assessed using the fluorescence-based RNA Broad Range Qubit Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 30 ng/µL while RIN were all >8.5.
Whole Transcriptome Sequencing  10 HCT116-derived RNA samples were normalized and 200 ng of input was used for library construction using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760), together with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) upstream and the NEXNext Multiplex Oligos for Illumina (E7600) downstream (all New England Biolabs). Sequencing libraries were quantified, normalized, pooled and spiked in with PhiX Control v3 (Illumina). The library pool was subsequently clustered with the HiSeq 3000/4000 SR Cluster Kit on a cBot; and sequenced on a HiSeq 4000 Sequencing System (Illumina) with dual index, single read at 50 bp length (Read parameters: Rd1: 51 Rd2: 8, Rd3: 8), reaching an average depth of 40 million Pass-Filter reads per sample (11.1% CV).

treatment_protocol: Crispr-Cas9 gene editing for HCT116 cells   Neon Transfection System (MPK1096 Invitrogen) was utilized to deliver the Cas9 (A36499, Invitrogen) - ribonuclear proteins (RNP) complex including guiding RNA against CD276 (A35533 -CRISPR806748_SGM, Invitrogen) or scrambled gRNA (A35526, Invitrogen) as control into the cell according to the company’s protocol with following modification.   HCT116 cells were treated with accutase (A6964, Sigma Aldrich) to detach and washed with PBS. For each transfection, 5x104 cells were electroporated with RNP complex (240 ng gRNA + 1.25 µg Cas9) in 10 µl reaction buffer with following setting on Neon: 1530V, 20ms, 1 pulse. After electroporation, cells were seeded in 24-well culture plate (142475, ThermoFisher) in McCoy’s 5A (modified) medium with 10% FCS supplement and cultured for 4 days. CD276 expression on the cell surface was analyzed by flow cytometry.


title: Cut & Run WT H3K4me3


title: Patient 4 human liver organoid 4 (HLO4)


title: 37873-P1-D2


title: Ythdc1HAChIP_Rep2

description: HA ChIP of Ythdc2

value: F-7 (anti-HA, Santa Cruz sc7392-x) / Lot No K1417


title: ATAC seq ko2-4


title: Ythdc1HAInput

description: Input control

value: Input Sample HA


title: PSPC1-0h-EU-seq-1

extract_protocol:
EU-seq was performed as described previously with modifications. ESCs were labeled by 1 mM EU for 10 minutes. RNA extraction was performed with TRIzol (Life Technologies, Carlsbad, CA, USA). Labelled RNAs were further biotinylated and fragmented as previously described. The biotinylated RNAs were resuspended in 100 μl H2O and then were subjected to tandem affinity purification similar to TT-seq. M-280 dynabeads were washed twice using 1 × B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.005% Tween-20) followed by two times of washes using solution A (0.1 M NaOH, 50 mM NaCl) and solution B (0.1 M NaCl) respectively. 1 mg/ml yeast tRNA in 1 × HSWB (10 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.1 M NaCl, 0.01% Tween-20) was used to block the beads and incubated at room temperature for 30 min. The blocked beads were washed twice using 1 × HSWB and resuspended in 100 μl 2 × HSWB. The biotinylated RNA was denatured at 65 ℃ for 10 minutes and incubated with blocked M-280 beads at room temperature for 30 minutes in an end-to-end rotator. Beads were washed twice with 800 μl of 10 × HSWB and incubated at 50 ℃ for 2 min, then washed twice with 50 ℃ water for 2 min. RNA was eluted by incubating the beads with 50 μl SDS washing buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS) at 95 °C for 5 min. The elution was repeated once ant two eluates were pooled together. M-280 beads were added to the eluted RNA for another affinity purification. RNAs were finally eluted in 10 μl H2O
RNAs were  reverse transcribed and used for library construction  by following manuals of Single-stranded DNA-seq Lib Prep Kit (Abconal, RK20222).

value: embryonic stem cells

value: No IAA

tag: affinity purification

value: M280 Streptavidin Dynabeads (Invitrogen, 11205D)


title: 37873-P1-FC

extract_protocol:
Total RNA was extracted from PBMC using RNEasy Mini kit reagents on a QIAcube instrument
cDNA libraries were constructed from 300 ng total RNA using Lexogen QuantSeq 3' FWD and sequenced on an Illumina HiSeq 4000 acquiring single-strand 65-bp reads (targeting > 10M reads/sample).

value: SIP-Isolated


title: Ythdc1HAChIP_Rep1

description: HA ChIP of Ythdc1

value: S2R+ Cells


title: HCT116-CD276KO_1


title: ATAC seq ko2-2

value: 6 days post deletion


title: HCT116-CD276KO_5


title: Input_Ythdc1_KD

description: Input Sample Pol II, with Ythdc1 depletion

value: Input Sample Pol II


title: HCT116-WT_5

value: WT


title: 36454-P2-D8

value: SIP-JuvenilePartnered

value: Peripheral blood mononuclear cells


title: HCT116-WT_4


title: 36454-P2-D13


title: ATAC seq wt2-3


title: Input_Mettl3_KD

description: Input Sample Pol II & Ser2P, with Mettl3 depletion

value: Input Sample Pol II & Ser2P


title: ATAC seq wt2-1


title: Input_fl2d_KD

description: Input Sample Pol II & Ser2P, with fl2d depletion


title: HCT116-WT_3


title: RNA seq dko3


title: 36454-P2-FC


title: HCT116-WT_2


title: HCT116-CD276KO_2


title: Input_Ctrl_KD

description: Input Sample Pol II & Ser2P, with LacZ depletion


title: 36454-P1-D13


title: RNA seq dko2


title: HCT116-WT_1


title: Input_Mettl14_KD

description: Input Sample Pol II & Ser2P, with Mettl14 depletion


title: RNA seq dko1


title: 36454-P1-D8