title: SW-780-24hr-10,000 U/mL rhINFa2b-Rep3

city: San Diego

first: Robin

last: Osterhout

state: CA

address: 4245 Sorrento Valley Rd

institute: Ferring Pharmaceuticals

data_processing:
The assembly was performed using the nf-core/rnaseq pipeline (1.4.2) using default parameters. Reads were aligned with Hisat2 (2.1.0) to the human reference build GRCh38 and transcripts were quantified using featureCounts (1.6.4).
Differential expression analysis was performed using R(4.0.1)/Bioconductor with the edgeR (3.32.1) and Limma (3.46.0) packages.
Prior to differential expression analysis, low expression features were excluded and samples were adjusted by normalization factors and voom-normalized. Differential expression models were adjusted for correlations between technical replicates using the duplicateCorrelation function in Limma.
Genome_build: Homo_sapiens.GRCh38.dna_sm.toplevel.fa
Supplementary_files_format_and_content: raw counts output from featureCounts

growth_protocol: J82 was cultured in MEM with 10% fetal bovine serum (FBS); T24 & RT4 were cultured in McCoy’s 5a with 10% FBS; SV-HUC-1 was cultured in F-12K with 10% FBS; UM-UC-3, UM-UC-4, UM-UC-6, UM-UC-10, TCCSUP, HT-1376, HT-1197 and SCaBER were cultured in Eagle’s minimum essential mediuam with 10% FBS; SW-780 was cultured in L-15 with 10% FBS in sealed flasks to prevent air exchange. All cells were maintained in complete growth media at 37°C under 5% CO2 in a humid environment.

extract_protocol:
Following incubation, media was aspirated fully and 0.6mL RLT Buffer with β-mercaptoethanol (from Qiagen RNeasy Plus kit) was added to wells and plates were frozen at –20°C. Plates were thawed on ice, wells were scraped, and contents transferred to QIAshredder columns. RNA was isolated according to the RNeasy Plus kit instructions (Qiagen), RNA was eluted, quantified, aliquoted for RNAseq submission and/or qPCR, then frozen at –80°C.
RNA-seq libraries were prepared Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® NovaSeq to obtain 150-bp paired-end reads

treatment_protocol: Cells were seeded in six well TC-treated plates in triplicate. The following day, treatments were applied, and cells were incubated as indicated at 37°C in Assay Media with 10% FBS.

value: 10,000 U/mL rhINFa2b

tag: time

value: 24 hr


title: Pythium oligandrum self-confrontation replicate 3

status: Public on Oct 28 2021

type: SRA

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

country: China

institute: Jiangsu Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
Raw data (raw reads) were processed using Trimmomatic (Bolger, Lohse et al. 2014). The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
Downstream analysis of the cleaned reads was performed using the following software tool in UseGalaxy.eu (Afgan, Baker et al. 2018)
For all samples, reads that passed the filters were mapped using HISAT2 Galaxy Version 2.1.0 (Kim, Paggi et al. 2019) onto a composite reference genome that consisted of the genomes of both species. The composite genome was made by concatenating into a single file those Fasta files made of the sequences for the scaffolds of the genomes (see genome build).
Uniquely mapped read counts (at the MAPQ10 threshold) for each gene were calculated using HTSeq-count Galaxy version 0.9.1 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) (Anders, Pyl et al. 2015).
FPKM normalised read counts were defined originally by (Mortazavi, Williams et al. 2008). In our study, an FPKM value for a gene from a sample is the number of uniquely mapped (to the composite genome) fragments (counts) per kilobase of gene model per million uniquely mapped (to the composite genome) fragments (counts) onto gene models from that species.
Genome_build: For P. myriotylum, JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555) was used, and for P. oligandrum the ATCC 38472 strain genome (GCA_005966545.1_ASM596654v1) (Faure, Veyssiere et al. 2020) was used.
Supplementary_files_format_and_content: tab-delimited text files include read counts and FPKM values for each sample

molecule: total RNA

organism: Pythium oligandrum

source_name: mycelia

growth_protocol: Precultures were grown on 10 % V8 juice agar at 25°C.

extract_protocol:
The sample was mixed with 1 mL of Trizol before the addition of 200 µl chloroform: isoamyl alcohol (24:1). The RNA was precipitated by mixing 0.8 volume of isopropanol with the aqueous phase from the previous step and the resulting pellet was washed once with 70% EtOH before resuspension in DEPC-treated water. The RNA was then cleaned-up using a Tiangen Plant RNA extraction kit which included an on-column DNase treatment. RNA integrity was visualised using an agarose gel and a Bioanalyzer, and RNA quantity and purity using a nanodrop spectrophotometer.
A paired library 2x150 bp was prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

treatment_protocol: From the edge of the colony of P. myriotylum SWQ7 or P. oligandrum GAQ1, 0.5 cm mycelial plugs were transferred to 10 % V8 juice agar covered with a 14.2 cm diameter polycarbonate membrane with a 0.1 µm pore size (GVS filter technology, Cat. no. 1215304) in a 14 cm Petri dish. The mycelial plugs were placed equidistant from each other and from the edge of the Petri dish. The Petri dishes were inoculated with either two plugs of the same species (self-confrontation) or with one plug from each species (mixed species confrontation). The cultures were incubated at 25°C in the dark and mycelia from the confrontation zone was sampled. The mycelium was flash frozen in liquid nitrogen before being ground using a Tissue Lyser.

tag: isolate


title: aspc_D6_DMSO_0_24 ASPCPS3AD06_ACACGCCA

city: Athens

first: Eugene

last: Douglass

state: GA

address: 240 West Green Street

country: USA

institute: University of Georgia

description:
aspc_D6_DMSO_0_24
ASPC_dream_counts.csv

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Genome_build: hg38
Supplementary_files_format_and_content: 11 tab delinated text files (for 11 cell-lines) with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: pancreatic cancer

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

tag: treatment

value: DMSO

tag: cell line

tag: provider

value: ATCC

tag: vendor id

tag: age

tag: Sex

value: female


title: aspc_C6_DMSO_0_24 ASPCPS3AC06_AACAGTTG

description:
aspc_C6_DMSO_0_24
ASPC_dream_counts.csv


title: EF1-30-100ng

city: Rochester

first: Jin Sung

last: Jang

address: 200 1st st sw

institute: Mayo Clinic

description: EF1-30-100ng.FC000000000-JCB58_L1_R1_IGATAGAAACACC-GCTCGCCCACAA

data_processing:
The STAR (2.6.1d) aligner was used to perform alignment of reads to the hg38. After alignment, the final BAM files were quantified using Partek E/M algorithm by Ensembl annotations (Ensembl Transcripts release 92) after deduplicating UMI.
Genome_build: hg38, Ensembl Transcripts release 92
Supplementary_files_format_and_content: tab-delimited text files and gene counts

source_name: FFPE

extract_protocol:
Qiagen miRNeasy FFPE kit and Trizol
1ng to 100ng of total RNA from each sample was used. The RNA-Seq libraries were generated using QuantSeq 3’ mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria).

tag: input amounts

tag: protocol

value: Low Input


title: aspc_B4_Varlitinib_0.5_24 ASPCPS3AB04_ATGCCTCA

description:
aspc_B4_Varlitinib_0.5_24
ASPC_dream_counts.csv

value: Varlitinib


title: Pythium oligandrum self-confrontation replicate 2


title: aspc_D2_UNTREATED_0_24 ASPCPS3AD02_ATCATGTG

description:
aspc_D2_UNTREATED_0_24
ASPC_dream_counts.csv

value: UNTREATED


title: SW-780-24hr-Untreated-Rep2

molecule: polyA RNA

value: Untreated


title: aspc_E3_Regorafenib_5_24 ASPCPS3AE03_TTACCGTG

description:
aspc_E3_Regorafenib_5_24
ASPC_dream_counts.csv

value: Regorafenib


title: SW-780-24hr-Untreated-Rep3


title: Pythium oligandrum self-confrontation replicate 1


title: SW-780-24hr-10,000 U/mL rhINFa2b-Rep1


title: aspc_C2_UNTREATED_0_24 ASPCPS3AC02_TTTTACCG

description:
aspc_C2_UNTREATED_0_24
ASPC_dream_counts.csv


title: SW-780-24hr-Untreated-Rep1


title: aspc_F12_Ponatinib_0.135_24 ASPCPS2BF12_ATGTAACC

description:
aspc_F12_Ponatinib_0.135_24
ASPC_dream_counts.csv

value: Ponatinib


title: aspc_A2_DMSO_0_24 ASPCPS3AA02_CGTTGTCA

description:
aspc_A2_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_H11_UNTREATED_0_24 ASPCPS2BH11_CGGTGATA

description:
aspc_H11_UNTREATED_0_24
ASPC_dream_counts.csv


title: aspc_B2_DMSO_0_24 ASPCPS3AB02_CAGTACCT

description:
aspc_B2_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_G11_UNTREATED_0_24 ASPCPS2BG11_GTCGCACA

description:
aspc_G11_UNTREATED_0_24
ASPC_dream_counts.csv


title: SW-780-24hr-10,000 U/mL rhINFa2b-Rep2


title: aspc_E11_DMSO_0_24 ASPCPS2BE11_CTAGCATC

description:
aspc_E11_DMSO_0_24
ASPC_dream_counts.csv


title: SV-HUC1-24hr-10,000 U/mL rhINFa2b-Rep3


title: hAEC-CSE1

city: Chapel Hill

first: Yu

last: Mikami

state: NC

address: 125 Mason Farm Rd

department: Marsico lung institute

institute: The University of North Carolina at Chapel Hill

data_processing:
Sequence were read by BGISEQ500 and basecalling was processed.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
Gene expression levels were measured by counting numbers of reads in all the exons using featureCounts (v1.5.0-p1; -p -t exon -g gene_id -F GTF )
Differential gene expression was measured using TCC version 3.13
Genome_build: hg38

source_name: alveolar epithelial cells

growth_protocol: hAEC was cultured on a poly-L-lysine-coated six-well plate with alveolar epithelial cell medium (ScienCell)

extract_protocol:
RNA was extracted using Rneasy mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS or CSE were added into the medium for 48 h

value: CSE


title: hAEC-PBS2

value: PBS


title: hAEC-CSE2


title: SV-HUC1-24hr-10,000 U/mL rhINFa2b-Rep2


title: aspc_F11_DMSO_0_24 ASPCPS2BF11_ATTGTGGC

description:
aspc_F11_DMSO_0_24
ASPC_dream_counts.csv


title: hAEC-PBS1


title: SV-HUC1-24hr-Untreated-Rep3


title: LPS-treated PMX+FA-GM-MØ macrophage donor3 rep3

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing GM-CSF after an initial exposure (at day 0) to 50 nanomolar of the antifolate pemetrexed (PMX), 5 micomolar of folinic acid (FA) or both (PMX+FA). 7 days later, fully-differentiated macrophages were exposed to 10 ng/ml LPS for 3 hours and total RNA was extracted.

tag: cell type

value: Monocyte-derived GM-CSF macrophages

tag: agent

value: LPS-treated PMX+FA-GM-MØ


title: SV-HUC1-24hr-10,000 U/mL rhINFa2b-Rep1


title: aspc_C10_Dasatinib_0.345_24 ASPCPS2BC10_GAGTTACT

description:
aspc_C10_Dasatinib_0.345_24
ASPC_dream_counts.csv

value: Dasatinib


title: aspc_F10_Sunitinib_0.045_24 ASPCPS2BF10_AGATGCTA

description:
aspc_F10_Sunitinib_0.045_24
ASPC_dream_counts.csv

value: Sunitinib


title: LPS-treated PMX+FA-GM-MØ macrophage donor2 rep2


title: aspc_E10_Afatinib_0.09_24 ASPCPS2BE10_GTGGGACT

description:
aspc_E10_Afatinib_0.09_24
ASPC_dream_counts.csv

value: Afatinib


title: LPS-treated PMX+FA-GM-MØ macrophage donor1 rep1


title: SV-HUC1-24hr-Untreated-Rep2

value: 24 hr


title: aspc_G10_Sorafenib_4.5_24 ASPCPS2BG10_CCAGGCAA

description:
aspc_G10_Sorafenib_4.5_24
ASPC_dream_counts.csv

value: Sorafenib


title: aspc_D6_DMSO_0_24 ASPCPS2BD06_ACACGCCA

description:
aspc_D6_DMSO_0_24
ASPC_dream_counts.csv

value: DMSO

value: ATCC


title: SV-HUC1-24hr-Untreated-Rep1


title: aspc_F6_UNTREATED_0_24 ASPCPS2BF06_TCATTGGA

description:
aspc_F6_UNTREATED_0_24
ASPC_dream_counts.csv

value: female


title: aspc_E6_UNTREATED_0_24 ASPCPS2BE06_TTTCTCCC

description:
aspc_E6_UNTREATED_0_24
ASPC_dream_counts.csv


title: LPS-treated FA-GM-MØ macrophage donor3 rep3

value: LPS-treated FA-GM-MØ


title: aspc_C6_DMSO_0_24 ASPCPS2BC06_AACAGTTG

description:
aspc_C6_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_H4_Cabozantinib_1_24 ASPCPS2BH04_TTCAGTCC

description:
aspc_H4_Cabozantinib_1_24
ASPC_dream_counts.csv

value: Cabozantinib


title: LPS-treated FA-GM-MØ macrophage donor2 rep2


title: LPS-treated PMX-GM-MØ macrophage donor3 rep3

value: LPS-treated PMX-GM-MØ


title: aspc_D2_UNTREATED_0_24 ASPCPS2BD02_ATCATGTG

value: UNTREATED


title: aspc_B2_DMSO_0_24 ASPCPS2BB02_CAGTACCT

description:
aspc_B2_DMSO_0_24
ASPC_dream_counts.csv


title: LPS-treated FA-GM-MØ macrophage donor1 rep1


title: aspc_H2_Bosutinib_0.5_24 ASPCPS2BH02_GAGACCGA

description:
aspc_H2_Bosutinib_0.5_24
ASPC_dream_counts.csv

value: Bosutinib


title: aspc_C2_UNTREATED_0_24 ASPCPS2BC02_TTTTACCG


title: aspc_B3_Gefitinib_0.5_24 ASPCPS2BB03_CGACTTGT

description:
aspc_B3_Gefitinib_0.5_24
ASPC_dream_counts.csv

value: Gefitinib


title: aspc_H3_Lapatinib_2.5_24 ASPCPS2BH03_GCGCCTTA

description:
aspc_H3_Lapatinib_2.5_24
ASPC_dream_counts.csv

value: Lapatinib


title: LPS-treated PMX-GM-MØ macrophage donor2 rep2

value: Monocyte-derived GM-CSF macrophages


title: aspc_F12_Ponatinib_0.135_24 ASPCPS2AF12_ATGTAACC

value: Ponatinib


title: aspc_A2_DMSO_0_24 ASPCPS2BA02_CGTTGTCA

description:
aspc_A2_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_G8_Osimertinib_1_24 ASPCPS2BG08_TGTTACGT

description:
aspc_G8_Osimertinib_1_24
ASPC_dream_counts.csv

value: Osimertinib


title: aspc_H11_UNTREATED_0_24 ASPCPS2AH11_CGGTGATA


title: HT-1376-24hr-10,000 U/mL rhINFa2b-Rep3

value: 10,000 U/mL rhINFa2b


title: HT-1376-24hr-Untreated-Rep2

value: Untreated


title: aspc_G11_UNTREATED_0_24 ASPCPS2AG11_GTCGCACA


title: HT-1376-24hr-10,000 U/mL rhINFa2b-Rep1

value: 24 hr


title: HT-1376-24hr-10,000 U/mL rhINFa2b-Rep2


title: LPS-treated GM-MØ macrophage donor3 rep3

value: LPS-treated GM-MØ


title: HT-1376-24hr-Untreated-Rep1


title: UM-UC-4-24hr-10,000 U/mL rhINFa2b-Rep3


title: UM-UC-4-24hr-10,000 U/mL rhINFa2b-Rep2


title: HT-1376-24hr-Untreated-Rep3


title: LPS-treated GM-MØ macrophage donor2 rep2


title: aspc_F11_DMSO_0_24 ASPCPS2AF11_ATTGTGGC

value: DMSO


title: aspc_E11_DMSO_0_24 ASPCPS2AE11_CTAGCATC

value: ATCC


title: aspc_F10_Sunitinib_0.045_24 ASPCPS2AF10_AGATGCTA

value: Sunitinib

value: female


title: aspc_G10_Sorafenib_4.5_24 ASPCPS2AG10_CCAGGCAA

value: Sorafenib


title: LPS-treated GM-MØ macrophage donor1 rep1


title: aspc_C10_Dasatinib_0.345_24 ASPCPS2AC10_GAGTTACT

value: Dasatinib


title: UM-UC-4-24hr-Untreated-Rep3


title: UM-UC-4-24hr-10,000 U/mL rhINFa2b-Rep1


title: UM-UC-4-24hr-Untreated-Rep2


title: aspc_D6_DMSO_0_24 ASPCPS2AD06_ACACGCCA

description:
aspc_D6_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_G8_Osimertinib_1_24 ASPCPS2AG08_TGTTACGT


title: aspc_E6_UNTREATED_0_24 ASPCPS2AE06_TTTCTCCC

value: UNTREATED


title: aspc_H4_Cabozantinib_1_24 ASPCPS2AH04_TTCAGTCC

value: Cabozantinib


title: aspc_C6_DMSO_0_24 ASPCPS2AC06_AACAGTTG

description:
aspc_C6_DMSO_0_24
ASPC_dream_counts.csv


title: LPS-treated PMX-GM-MØ macrophage donor1 rep1

value: LPS-treated PMX-GM-MØ


title: aspc_E10_Afatinib_0.09_24 ASPCPS2AE10_GTGGGACT

value: Afatinib


title: J82-24hr-10,000 U/mL rhINFa2b-Rep3


title: GM-MØ macrophage donor3 rep3

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing GM-CSF after an initial exposure (at day 0) to 50 nanomolar of the antifolate pemetrexed (PMX).

tag: cell

value: Monocyte-derived GM-CSF macrophages

value: differentiated with GM-CSF (GM-MØ)


title: PMX-GM-MØ macrophage donor3 rep3

value: differentiated with GM-CSF (GM-MØ) in the presence of the antifolate pemetrexed (PMX)


title: PMX-GM-MØ macrophage donor1 rep1


title: aspc_B3_Gefitinib_0.5_24 ASPCPS2AB03_CGACTTGT

value: Gefitinib


title: PMX-GM-MØ macrophage donor2 rep2


title: UM-UC-4-24hr-Untreated-Rep1

value: Untreated


title: J82-24hr-10,000 U/mL rhINFa2b-Rep2

value: 10,000 U/mL rhINFa2b

value: 24 hr


title: aspc_F6_UNTREATED_0_24 ASPCPS2AF06_TCATTGGA


title: aspc_D2_UNTREATED_0_24 ASPCPS2AD02_ATCATGTG

description:
aspc_D2_UNTREATED_0_24
ASPC_dream_counts.csv


title: aspc_H3_Lapatinib_2.5_24 ASPCPS2AH03_GCGCCTTA

value: Lapatinib


title: aspc_B2_DMSO_0_24 ASPCPS2AB02_CAGTACCT

description:
aspc_B2_DMSO_0_24
ASPC_dream_counts.csv

value: DMSO

value: ATCC


title: aspc_G12_AZD5363_0.02_24 ASPCPS1BG12_GTCGACGA

description:
aspc_G12_AZD5363_0.02_24
ASPC_dream_counts.csv

value: female


title: GM-MØ macrophage donor2 rep2


title: aspc_H2_Bosutinib_0.5_24 ASPCPS2AH02_GAGACCGA

value: Bosutinib


title: aspc_G11_UNTREATED_0_24 ASPCPS1BG11_GTCGCACA


title: J82-24hr-Untreated-Rep2


title: J82-24hr-Untreated-Rep1


title: GM-MØ macrophage donor1 rep1


title: aspc_C2_UNTREATED_0_24 ASPCPS2AC02_TTTTACCG

description:
aspc_C2_UNTREATED_0_24
ASPC_dream_counts.csv


title: aspc_F11_DMSO_0_24 ASPCPS1BF11_ATTGTGGC


title: J82-24hr-10,000 U/mL rhINFa2b-Rep1


title: T24-24hr-10,000 U/mL rhINFa2b-Rep2


title: aspc_G9_Bafetinib_2_24 ASPCPS1BG09_CTGAGACG

description:
aspc_G9_Bafetinib_2_24
ASPC_dream_counts.csv

value: Bafetinib


title: aspc_B7_Quizartinib_1.5_24 ASPCPS1BB07_TTCACATG

description:
aspc_B7_Quizartinib_1.5_24
ASPC_dream_counts.csv

value: Quizartinib


title: aspc_E6_UNTREATED_0_24 ASPCPS1BE06_TTTCTCCC

value: UNTREATED


title: J82-24hr-Untreated-Rep3


title: aspc_F6_UNTREATED_0_24 ASPCPS1BF06_TCATTGGA


title: aspc_E12_Nilotinib_0.335_24 ASPCPS1BE12_TATCGGTC

description:
aspc_E12_Nilotinib_0.335_24
ASPC_dream_counts.csv

value: Nilotinib


title: T24-24hr-Untreated-Rep3


title: aspc_H11_UNTREATED_0_24 ASPCPS1BH11_CGGTGATA

description:
aspc_H11_UNTREATED_0_24
ASPC_dream_counts.csv


title: aspc_D6_DMSO_0_24 ASPCPS1BD06_ACACGCCA

description:
aspc_D6_DMSO_0_24
ASPC_dream_counts.csv


title: T24-24hr-10,000 U/mL rhINFa2b-Rep3


title: aspc_E11_DMSO_0_24 ASPCPS1BE11_CTAGCATC

description:
aspc_E11_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_D12_Vandetanib_0.11_24 ASPCPS1BD12_ATTGTCCT

description:
aspc_D12_Vandetanib_0.11_24
ASPC_dream_counts.csv

value: Vandetanib


title: aspc_C6_DMSO_0_24 ASPCPS1BC06_AACAGTTG

description:
aspc_C6_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_A2_DMSO_0_24 ASPCPS2AA02_CGTTGTCA

description:
aspc_A2_DMSO_0_24
ASPC_dream_counts.csv


title: T24-24hr-10,000 U/mL rhINFa2b-Rep1


title: aspc_G8_MGCD265_1_24 ASPCPS1BG08_TGTTACGT

description:
aspc_G8_MGCD265_1_24
ASPC_dream_counts.csv


title: aspc_C10_Crizotinib_0.19_24 ASPCPS1BC10_GAGTTACT

description:
aspc_C10_Crizotinib_0.19_24
ASPC_dream_counts.csv

value: Crizotinib


title: aspc_H10_Imatinib_5_24 ASPCPS1BH10_CACATTCC

description:
aspc_H10_Imatinib_5_24
ASPC_dream_counts.csv

value: Imatinib


title: aspc_G4_Dovitinib_2_24 ASPCPS1BG04_GGAAATTG

description:
aspc_G4_Dovitinib_2_24
ASPC_dream_counts.csv

value: Dovitinib


title: T24-24hr-Untreated-Rep2


title: aspc_E3_AEE788_0.17_24 ASPCPS1BE03_TTACCGTG

description:
aspc_E3_AEE788_0.17_24
ASPC_dream_counts.csv


title: T24-24hr-Untreated-Rep1


title: UM-UC-3-24hr-10,000 U/mL rhINFa2b-Rep3


title: s082845

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
UMI-tools was used to extract and add the 8bp cell barcode sequence and unique molecular identifiers (UMIs) to read name of sequencing read pairs.
Subsequently we trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1 and removed low-quality bases using costumed script and seqtk tool.
The clean read1 reads were aligned to mm10 reference genome using STAR.
Then, genomic features were added to reads using featureCounts of subread in order to count uniquely aligned reads with genes.
Finally, we used "count" tool in UMI-tools to obtain UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

organism: Mus musculus

source_name: mouse germ cells

extract_protocol:
Cells were randomly selected into precooled lysate. Then, the lysate were shocked at 72℃ for 3min to release RNA and Initial denaturation.
We used an improved Smart seq2 method. In brief, single-cell suspension is firstly prepared, and then single cells are selected into a PCR tube containing oligo(dT) primers and lysates through a suction tube.After cDNA amplification, the single cells labeled with different barcodes can be pooled together for subsequent library construction and sequencing. We add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’ terminal of cDNAs. Then the library was constructed by using Kapa Hyper Prep Kit(Thermo Fither) and run on illumina Hiseq X Ten for 150bp pair-end reads.

treatment_protocol: BVSC transgenic mice were used in our study. Adult female C57BL/6 mice in natural estrus were cooped up with male BVSC mice at a ratio of 2:1. The mating status of mice was checked in the morning of the next day, and the female mice with vaginal suppository were retained. At noon of the day, the embryonic period was set at 0.5 days (E0.5).Germ cells are collected from E6.5 and collection methods for E6.5 and E7.5 were referenced in the published protocols. The germ cells from E8.5 to E18.5 were collected through flow sorting, and the whole embryo was digested directly from E8.5 to E10.5 to separate the BVSC+ cells. Gonads were separated from E11.5 to E18.5, and BVSC+ and negative cells were separated after digestion. Among them, E11.5 identified the Sry gene to distinguish male from female, and E13.5 to E16.5 divided the male gonads into three segments, defined as proximal, central and distal, according to their relative positions to mesonephroi.From E14.5 to E18.5, BV signal was gradually down-regulated, and SC+ positive cells were collected as germ cells. After flow cytometry enrichment, the samples before birth were examined by fluorescence microscopy for fluorescence signal, and then were selected into the 8-row PCR tube containing lysate. The day of birth was defined as P0. After mechanical and trypsin digestion of the gonads (testes), cells were transferred into 1% HSA.

tag: library


title: aspc_B4_Cediranib_0.22_24 ASPCPS1BB04_ATGCCTCA

description:
aspc_B4_Cediranib_0.22_24
ASPC_dream_counts.csv

value: Cediranib


title: s082844

description: polyA RNA


title: s082842

description: polyA RNA


title: aspc_B2_DMSO_0_24 ASPCPS1BB02_CAGTACCT

description:
aspc_B2_DMSO_0_24
ASPC_dream_counts.csv


title: UM-UC-3-24hr-10,000 U/mL rhINFa2b-Rep2


title: s082843

description: polyA RNA


title: aspc_A3_Icotinib_7.5_24 ASPCPS1BA03_TGAATCAG

description:
aspc_A3_Icotinib_7.5_24
ASPC_dream_counts.csv

value: Icotinib


title: aspc_G12_AZD5363_0.02_24 ASPCPS1AG12_GTCGACGA


title: aspc_D12_Vandetanib_0.11_24 ASPCPS1AD12_ATTGTCCT


title: aspc_F2_Dacomitinib_0.05_24 ASPCPS1BF02_CAGGCGTA

description:
aspc_F2_Dacomitinib_0.05_24
ASPC_dream_counts.csv

value: Dacomitinib


title: UM-UC-3-24hr-10,000 U/mL rhINFa2b-Rep1

value: 10,000 U/mL rhINFa2b

value: 24 hr


title: UM-UC-3-24hr-Untreated-Rep3

value: Untreated


title: aspc_F4_Crenolanib_0.145_24 ASPCPS1BF04_GTGTACAC

description:
aspc_F4_Crenolanib_0.145_24
ASPC_dream_counts.csv

value: Crenolanib

value: ATCC


title: UM-UC-3-24hr-Untreated-Rep2


title: s082838

description: polyA RNA


title: aspc_G11_UNTREATED_0_24 ASPCPS1AG11_GTCGCACA

description:
aspc_G11_UNTREATED_0_24
ASPC_dream_counts.csv

value: female


title: aspc_F11_DMSO_0_24 ASPCPS1AF11_ATTGTGGC

description:
aspc_F11_DMSO_0_24
ASPC_dream_counts.csv

value: DMSO


title: aspc_C2_UNTREATED_0_24 ASPCPS1BC02_TTTTACCG

description:
aspc_C2_UNTREATED_0_24
ASPC_dream_counts.csv


title: s082840

description: polyA RNA


title: UM-UC-3-24hr-Untreated-Rep1


title: aspc_D2_UNTREATED_0_24 ASPCPS1BD02_ATCATGTG

description:
aspc_D2_UNTREATED_0_24
ASPC_dream_counts.csv


title: s082841

description: polyA RNA


title: s082839

description: polyA RNA


title: HT-1197-24hr-10,000 U/mL rhINFa2b-Rep2


title: aspc_H10_Imatinib_5_24 ASPCPS1AH10_CACATTCC


title: aspc_E11_DMSO_0_24 ASPCPS1AE11_CTAGCATC


title: aspc_E12_Nilotinib_0.335_24 ASPCPS1AE12_TATCGGTC

description:
aspc_E12_Nilotinib_0.335_24
ASPC_dream_counts.csv


title: s082837

description: polyA RNA


title: HT-1197-24hr-Untreated-Rep3


title: aspc_C10_Crizotinib_0.19_24 ASPCPS1AC10_GAGTTACT


title: aspc_G9_Bafetinib_2_24 ASPCPS1AG09_CTGAGACG

description:
aspc_G9_Bafetinib_2_24
ASPC_dream_counts.csv

value: Bafetinib


title: aspc_A2_DMSO_0_24 ASPCPS1BA02_CGTTGTCA

description:
aspc_A2_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_H11_UNTREATED_0_24 ASPCPS1AH11_CGGTGATA

description:
aspc_H11_UNTREATED_0_24
ASPC_dream_counts.csv

value: UNTREATED


title: HT-1197-24hr-10,000 U/mL rhINFa2b-Rep3


title: aspc_B7_Quizartinib_1.5_24 ASPCPS1AB07_TTCACATG

description:
aspc_B7_Quizartinib_1.5_24
ASPC_dream_counts.csv

value: Quizartinib


title: HT-1197-24hr-Untreated-Rep2


title: aspc_G8_MGCD265_1_24 ASPCPS1AG08_TGTTACGT

description:
aspc_G8_MGCD265_1_24
ASPC_dream_counts.csv


title: HT-1197-24hr-Untreated-Rep1


title: aspc_E6_UNTREATED_0_24 ASPCPS1AE06_TTTCTCCC

description:
aspc_E6_UNTREATED_0_24
ASPC_dream_counts.csv


title: s082835

description: polyA RNA


title: s082834

description: polyA RNA


title: s082833

description: polyA RNA


title: HT-1197-24hr-10,000 U/mL rhINFa2b-Rep1


title: aspc_D6_DMSO_0_24 ASPCPS1AD06_ACACGCCA

description:
aspc_D6_DMSO_0_24
ASPC_dream_counts.csv


title: aspc_G4_Dovitinib_2_24 ASPCPS1AG04_GGAAATTG


title: s082836

description: polyA RNA


title: aspc_C6_DMSO_0_24 ASPCPS1AC06_AACAGTTG

description:
aspc_C6_DMSO_0_24
ASPC_dream_counts.csv


title: s082832

description: polyA RNA


title: aspc_B4_Cediranib_0.22_24 ASPCPS1AB04_ATGCCTCA


title: aspc_F4_Crenolanib_0.145_24 ASPCPS1AF04_GTGTACAC


title: UM-UC-10-24hr-10,000 U/mL rhINFa2b-Rep3


title: UM-UC-10-24hr-10,000 U/mL rhINFa2b-Rep2


title: s082831

description: polyA RNA


title: aspc_A3_Icotinib_7.5_24 ASPCPS1AA03_TGAATCAG


title: aspc_E3_AEE788_0.17_24 ASPCPS1AE03_TTACCGTG


title: UM-UC-10-24hr-10,000 U/mL rhINFa2b-Rep1


title: UM-UC-10-24hr-Untreated-Rep3


title: s082829

description: polyA RNA


title: aspc_F2_Dacomitinib_0.05_24 ASPCPS1AF02_CAGGCGTA


title: aspc_F6_UNTREATED_0_24 ASPCPS1AF06_TCATTGGA

description:
aspc_F6_UNTREATED_0_24
ASPC_dream_counts.csv


title: s082830

description: polyA RNA


title: aspc_D2_UNTREATED_0_24 ASPCPS1AD02_ATCATGTG


title: UM-UC-10-24hr-Untreated-Rep2


title: s082828

description: polyA RNA


title: aspc_C2_UNTREATED_0_24 ASPCPS1AC02_TTTTACCG


title: UM-UC-10-24hr-Untreated-Rep1


title: aspc_B2_DMSO_0_24 ASPCPS1AB02_CAGTACCT

description:
aspc_B2_DMSO_0_24
ASPC_dream_counts.csv


title: Control_Flag_2

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: Flag_Rep2 for RIP-seq

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

source_name: embryonic kidney

growth_protocol: The HEK293T cells with forced expression of METTL3, METTL14, and METTL16 were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin and plasmocin prophylactic for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish

extract_protocol:
After cross-link with 0.75 % formaldehyde, the cells were collected by trypsinization, lysed in 1 ml M-PER buffer (78501, Thermo Fisher Scientific) with 100 U/ml RNase inhibitor and 1 × protease inhibitor on ice for 20 min, and sonicated in a Bioruptor Pico device (Diagenode) with 30s on/30s off for 10 cycles. Then the lysates were collected and subject to RIP with Flag antibody and Protein A/G Magnetic Beads. The RIP RNAs were recovered from the beads with RNeasy mini kit (74104, Qiagen). Both Input and RIP RNAs were used for sequencing.
KAPA Stranded mRNA-Seq Kit (Illumina Platforms) was utilized to construct library and sequencing was performed on an Illumina Hiseq 2500.

treatment_protocol: Without special treatment

value: Flag (SigmaAldrich, Cat# F3165)


title: aspc_A2_DMSO_0_24 ASPCPS1AA02_CGTTGTCA

description:
aspc_A2_DMSO_0_24
ASPC_dream_counts.csv


title: s082827

description: polyA RNA


title: s082826

description: polyA RNA


title: Control_Flag_1

description: Flag_Rep1 for RIP-seq


title: UM-UC-6-24hr-10,000 U/mL rhINFa2b-Rep2


title: UM-UC-6-24hr-10,000 U/mL rhINFa2b-Rep3


title: Control_input_2

description: Input_Rep2 for RIP-seq


title: s082825

description: polyA RNA


title: sgM16.3.2_m6A-IP

description:
This is sgMETTL16-3_m6A-IP_Rep2
sgNS.2_sgM16.3.2_diff_peak.xls.xlsx

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the GRCh38 genome assembly using STAR
peaks were called using exomePeak.
the m6A peaks were annotated using an ad hoc perl script.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files were generated using exomePeak

growth_protocol: The HEK293T cells with METTL3, METTL14, and METTL16 knockout, plasmocin prophylactic, 10ug/ml blasticidin (for Cas9) and 100ug/ml hygromycin (for sgRNAs) for 10 days and the cells were collected at 70-80% confluency in 150 mm dish.

extract_protocol:
Total RNAs were isolated from the whole cells with QIAzol and poly(A) RNAs were enriched from total RNA with  oligo(dT) polystyrene beads.The anti-m6A antibody (202003, Synaptic Systems) was applied for m6A immunoprecipitation
Both input and m6A IP samples were utilized for next-generation sequencing (NGS). The library preparation was constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and was quantified by BioAnalyzer High Sensitivity DNA chip, and then was deeply sequenced on the Illumina HiSeq 2500.

tag: merip antibody

value: m6A antibody (Cat#:202003, Synaptic Systems)


title: UM-UC-6-24hr-10,000 U/mL rhINFa2b-Rep1


title: sgM16.3.2_Input

description:
This is sgMETTL16-3_Input_Rep2
sgNS.2_sgM16.3.2_diff_peak.xls.xlsx


title: sgM16.3.1_m6A-IP

description:
This is sgMETTL16-3_m6A-IP_Rep1
sgNS.2_sgM16.3.1_diff_peak.xls.xlsx


title: sgM16.3.1_Input

description:
This is sgMETTL16-3_Input_Rep1
sgNS.2_sgM16.3.1_diff_peak.xls.xlsx


title: s082824

description: polyA RNA


title: sgM14.3.2_m6A-IP

description:
This is sgMETTL14-3_m6A-IP_Rep2
sgNS.2_sgM14.3.2_diff_peak.xls.xlsx


title: sgM14.3.1_m6A-IP

description:
This is sgMETTL14-3_m6A-IP_Rep1
sgNS.2_sgM14.3.1_diff_peak.xls.xlsx


title: s082822

description: polyA RNA


title: UM-UC-6-24hr-Untreated-Rep1


title: UM-UC-6-24hr-Untreated-Rep3


title: UM-UC-6-24hr-Untreated-Rep2


title: sgM3.3.2_m6A-IP

description:
This is sgMETTL3-3_m6A-IP_Rep2
sgNS.1_sgM3.3.2_diff_peak.xls.xlsx


title: s082821

description: polyA RNA


title: TCCSUP-24hr-10,000 U/mL rhINFa2b-Rep3

source_name: TCCSUP

value: TCCSUP


title: Control_input_1

description: Input_Rep1 for RIP-seq


title: sgM3.3.2_Input

description:
This is sgMETTL3-3_Input_Rep2
sgNS.1_sgM3.3.2_diff_peak.xls.xlsx


title: sgM3.3.1_m6A-IP

description:
This is sgMETTL3-3_m6A-IP_Rep1
sgNS.1_sgM3.3.1_diff_peak.xls.xlsx


title: s082820

description: polyA RNA


title: sgNS.2_m6A-IP

description: This is Negative Control_m6A-IP_Rep2


title: sgM3.3.1_Input

description:
This is sgMETTL3-3_Input_Rep1
sgNS.1_sgM3.3.1_diff_peak.xls.xlsx


title: TCCSUP-24hr-10,000 U/mL rhINFa2b-Rep2


title: s082819

description: polyA RNA


title: sgNS.1_m6A-IP

description: This is Negative Control_m6A-IP_Rep1


title: s082823

description: polyA RNA


title: sgM14.3.2_Input

description:
This is sgMETTL14-3_Input_Rep2
sgNS.2_sgM14.3.2_diff_peak.xls.xlsx


title: TCCSUP-24hr-Untreated-Rep3


title: sgNS.1_Input

description: This is Negative Control_Input_Rep1


title: sgNS.2_Input

description: This is Negative Control_Input_Rep2


title: s082818

description: polyA RNA


title: s082817

description: polyA RNA


title: TCCSUP-24hr-Untreated-Rep2


title: TCCSUP-24hr-Untreated-Rep1


title: s082816

description: polyA RNA


title: LNCaP_AU_24h_H3K27Ac (ChIP-seq)

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

library_source: genomic

data_processing:
ChIP-Seq reads were aligned to the human reference genome (GRC h38/hg38) with BWA. The SAM file obtained after aliment was converted into BAM format using SAMTools
Using deepTools bamCoverage a coverage file (bigWig format) for each sample was created. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows.
ChIP-Seq peak calling was done using MASC2
Genome_build: GRCh38
Supplementary_files_format_and_content: BED

molecule: genomic DNA

source_name: LNCaP

growth_protocol: All cell lines were purchased from ATCC and were grown in ATCC-suggested culture media. They were bimonthly tested for mycoplasma contamination, including within a week of NGS-experiments.

extract_protocol:
Treated cells were crosslinked using 1% PFA for 10 mins and then processed following instructions from the Diagenode HighCell ChIP Kit (Cat No. C01010063).
ChIP experiments were carried out using the HighCell# ChIP-Protein G kit (Diagenode) as per the manufacturer’s protocol. Chromatin from five million cells was used per ChIP reaction with 10 μg of the target protein antibody. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 8 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode) using the standard protocol. Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E. coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single A base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).
Crosslinked DNA from 5M cells was sheared to a 200-500bp size range, which was used for immunoprecipitation using 7-10ug of target antibody per ChIP.

treatment_protocol: Cell were plated at 70-80% confluence in a 150mm culture plate and treated with AU-15330 dissolved in DMSO at indicated concentrations (1uM) and for labeled durations (6-24h).

value: LNCaP

tag: dosage & duration

value: 1uM for 24h

tag: cancer type

value: prostate cancer


title: s082815

description: polyA RNA


title: LNCaP_DMSO_6h_CTCF (ChIP-seq)

value: vehicle control


title: LNCaP_DMSO_6h_FOXA1 (ChIP-seq)


title: s082814

description: polyA RNA


title: LNCaP_AU_6h_FOXA1 (ChIP-seq)

value: 1uM for 4h


title: TCCSUP-24hr-10,000 U/mL rhINFa2b-Rep1

value: 10,000 U/mL rhINFa2b

tag: time

value: 24 hr


title: s082813

description: polyA RNA


title: VCaP_AU_24h_H3K27Ac (ChIP-seq)

source_name: VCaP

value: VCaP


title: LNCaP_DMSO_24h_H3K27Ac (ChIP-seq)


title: SCaBER-24hr-10,000 U/mL rhINFa2b-Rep2

source_name: SCaBER

value: SCaBER


title: SCaBER-24hr-10,000 U/mL rhINFa2b-Rep3


title: SCaBER-24hr-10,000 U/mL rhINFa2b-Rep1


title: LNCaP_AU_6h_CTCF (ChIP-seq)


title: LNCaP_AU_6h_AR (ChIP-seq)


title: VCaP_DMSO_6h_CTCF (ChIP-seq)


title: sgM14.3.1_Input

description:
This is sgMETTL14-3_Input_Rep1
sgNS.2_sgM14.3.1_diff_peak.xls.xlsx


title: s082812

description: polyA RNA


title: LNCaP_DMSO_6h_AR (ChIP-seq)


title: VCaP_AU_6h_FOXA1 (ChIP-seq)


title: VCaP_DMSO_6h_ERG (ChIP-seq)


title: SCaBER-24hr-Untreated-Rep3

value: Untreated


title: RT4-24hr-100,000 U/mL mIFNa11-Rep3


title: SCaBER-24hr-Untreated-Rep1


title: VCaP_AU_6h_CTCF (ChIP-seq)


title: LNCaP_sgSMARCA2+shSMARCA4_R2_72h (ATAC-seq)

data_processing:
Paired-end .fastq.gz files were trimmed and uniquely aligned to the GRCh38/hg38 human genome assembly using Novoalign (Novocraft) (with the parameters -r None -k -q 13 -k -t 60 -o sam –a CTGTCTCTTATACACATCT), and converted to .bam files using SAMtools (version 1.3.1).
Reads mapped to mitochondrial or duplicated reads were removed by SAMtools and PICARD MarkDuplicates (version 2.9.0), respectively.
Filtered .bam files from replicates were merged for downstream analysis. MACS2 (2.1.1.20160309) was used to call ATAC-seq peaks.
The coverage tracks were generated using the program bam2wig (http://search.cpan.org/dist/Bio-ToolBox/) with the following parameters:–pe–rpm–span–bw.
Genome_build: hg38
Supplementary_files_format_and_content: BED files for called peaks

extract_protocol:
Nuclei extraction and tagmentation of open chromatin was performed as described in the Buenrostro et al. 2013 Nat Methods.
ATAC-seq was performed as previously described in Buenrostro et al. 2013 Nat Methods. In brief, 50,000 cancer cells were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5-8 min (depending on the cell line) with gentle mixing by pipetting every 2 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50μl of 1× TD buffer, then incubated with 2-2.5 μl Tn5 enzyme for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol27. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881). ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length).

treatment_protocol: Cell were plated at 70-80% confluence in a 6-well plate and treated with AU-15330 dissolved in DMSO at 1uM concentration for labeled durations (4-24h). For genetic models, LNCaP cells were treated with sgRNAs to stably knockout the SMARCA2 gene followed by dox-inducible shRNA-mediated knockdown of the SMARCA4 gene for 72h.

value: sgSMARCA2 (stable) + shSMARCA4 (dox-inducible)

value: 1ug/ml doxycycline for 72h


title: s082811

description: polyA RNA


title: VCaP_DMSO_6h_AR (ChIP-seq)


title: SCaBER-24hr-Untreated-Rep2


title: RT4-24hr-100,000 U/mL mIFNa11-Rep2


title: s082809

description: polyA RNA


title: s082807

description: polyA RNA


title: VCaP_AU_6h_AR (ChIP-seq)


title: VCaP_DMSO_24h_H3K27Ac (ChIP-seq)


title: s082808

description: polyA RNA


title: LNCaP_sgSMARCA4_R2 (ATAC-seq)

value: sgSMARCA4 (stable)

value: untreated


title: s082805

description: polyA RNA


title: LNCaP_sgNC+shNC_R2_72h (ATAC-seq)

value: sgNC (stable) + shNC (dox-inducible)


title: VCaP_AU_6h_ERG (ChIP-seq)


title: LNCaP_sgSMARCA2_R2 (ATAC-seq)

value: sgSMARCA2 (stable)


title: LNCaP_sgSMARCA2+shSMARCA4_R1_72h (ATAC-seq)


title: s082810

description: polyA RNA


title: LNCaP_sgSMARCA4_R1 (ATAC-seq)


title: RT4-24hr-10,000 U/mL mIFNa11-Rep3


title: RT4-24hr-10,000 U/mL mIFNa11-Rep1


title: LNCaP_sgNC+shNC_R1_72h (ATAC-seq)


title: RT4-24hr-1,000 U/mL mIFNa11-Rep3

value: 1,000 U/mL mIFNa11


title: s082802

description: polyA RNA


title: s082803

description: polyA RNA


title: VCaP_DMSO_6h_FOXA1 (ChIP-seq)


title: LNCaP_DMSO_R1_24h (ATAC-seq)

value: LNCaP


title: LNCaP_DMSO_R2_24h (ATAC-seq)


title: s082806

description: polyA RNA


title: LNCaP_AU_R2_24h (ATAC-seq)

value: 1uM for 24h


title: RT4-24hr-10,000 U/mL mIFNa11-Rep2


title: s082804

description: polyA RNA


title: VCaP_ZBC260_R1_24h (ATAC-seq)

value: ZBC-260 (BRD4 degrader)

value: 10nM for 24h

value: prostate cancer


title: VCaP_ZBC260_R1_8h (ATAC-seq)

value: 10nM for 8h


title: RT4-24hr-1,000 U/mL mIFNa11-Rep1

value: 24 hr


title: s082801

description: polyA RNA


title: RT4-24hr-100,000 U/mL mIFNa11-Rep1


title: LNCaP_sgSMARCA2_R1 (ATAC-seq)


title: LNCaP_AU_R1_24h (ATAC-seq)


title: LNCaP_AU_R2_12h (ATAC-seq)

value: 1uM for 12h


title: RT4-24hr-100 U/mL mIFNa11-Rep3

value: 100 U/mL mIFNa11


title: LNCaP_AU_R1_12h (ATAC-seq)


title: VCaP_ZBC260_R2_24h (ATAC-seq)

value: VCaP


title: RT4-24hr-100 U/mL mIFNa11-Rep2


title: s050589

description: polyA RNA


title: RT4-24hr-1,000 U/mL mIFNa11-Rep2


title: VCaP_ZBC260_R2_8h (ATAC-seq)


title: s050591

description: polyA RNA


title: VCaP_AU_R2_8h (ATAC-seq)

value: 1uM for 8h


title: VCaP_AU_R2_24h (ATAC-seq)


title: s050590

description: polyA RNA


title: VCaP_AU_R1_12h (ATAC-seq)


title: VCaP_AU_R1_24h (ATAC-seq)


title: RT4-24hr-100,000 U/mL rhIFNb-Rep3

value: 100,000 U/mL rhIFNb


title: s050588

description: polyA RNA


title: VCaP_AU_R2_4h (ATAC-seq)

value: 1uM for 4h


title: RT4-24hr-100 U/mL mIFNa11-Rep1


title: RT4-24hr-100,000 U/mL rhIFNb-Rep2


title: VCaP_AU_R1_4h (ATAC-seq)


title: s050584

description: polyA RNA


title: VCaP_AU_R1_8h (ATAC-seq)


title: VCaP_DMSO_R2_24h (ATAC-seq)

value: vehicle control


title: VCaP_DMSO_R1_8h (ATAC-seq)


title: HUVEC_10uMSIMVA_2

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Bulk RNA-seq

data_processing:
after QC and adapter trimming, alignment was performed using the 2-pass STAR aligner with the human reference genome, GRCh38
gene expression was quantified using the GENECODE gene model using HTseq-count method with -t transcript -m union options.
counts were normailzed for total read-depth using the DESeq2 method in the R Statistical Computing Environment
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include transcripts per million (TPM) values for each sample

source_name: human umbilical vein endothelial cells

growth_protocol: HUVEC were cultured in M199 (LONZA Bioscience) supplemented with 20% heat-inactivated fetal bovine serum (Millipore Sigma), 2 nM L-glutamine, 100 U/ml penicillin, 100 U/ml streptomycin and 0.1% ECGS (Alfa Aesar by Thermo Fisher Scientific).

extract_protocol:
Cells were lyzed in RLT buffer (Qiagen, Hilden, Germany) and total RNA was isolated using MyOne Silane Dynabeads (Thermo Fisher, Tewksbuy, MA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Simvastatin (Sigma-Aldrich, St. Louis, MO) was dissolved in ethanol and diluted with 0.9% sodium chloride solution to yield a final concentration of 10 µg/ml. Simvastatin was added to HUVEC at a concentration of 1 µM or 10 µM for 24 hours.

value: human umbilical vein endothelial cells

value: 10 µM simvastatin for 24h

tag: replicate

value: replicate 2


title: RT4-24hr-100,000 U/mL rhIFNb-Rep1

tag: treatment


title: s050586

description: polyA RNA


title: s050580

description: polyA RNA


title: VCaP_DMSO_R2_8h (ATAC-seq)

tag: cell line


title: HUVEC_10uMSIMVA_1

description: Bulk RNA-seq

value: replicate 1


title: s050581

description: polyA RNA


title: VCaP_AU_R2_12h (ATAC-seq)


title: VCaP_DMSO_R1_24h (ATAC-seq)


title: RT4-24hr-10,000 U/mL rhIFNb-Rep2

value: 10,000 U/mL rhIFNb


title: HUVEC_NT_2

description: Bulk RNA-seq


title: s050579

description: polyA RNA


title: HUVEC_1uMSIMVA_1

description: Bulk RNA-seq

value: 1 µM simvastatin for 24h


title: s050578

description: polyA RNA


title: HUVEC_1uMSIMVA_2

description: Bulk RNA-seq


title: RT4-24hr-10,000 U/mL rhIFNb-Rep3


title: RT4-24hr-1,000 U/mL rhIFNb-Rep3

value: 1,000 U/mL rhIFNb


title: s050577

description: polyA RNA


title: HUVEC_NT_1

description: Bulk RNA-seq


title: s050576

description: polyA RNA


title: RT4-24hr-1,000 U/mL rhIFNb-Rep2


title: METTL3-2.rip

description:
ribozero RNA
METTL3-bound transcripts  RIP-seq RIP 2
METTL3.tpm

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

tag: rip antibody

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

tag: overexpression


title: METTL3-2.input

description:
ribozero RNA
METTL3-bound transcripts  RIP-seq input 2
METTL3.tpm


title: RT4-24hr-1,000 U/mL rhIFNb-Rep1


title: RT4-24hr-10,000 U/mL rhIFNb-Rep1


title: METTL14-1.input

description:
ribozero RNA
METTL14-bound transcripts  RIP-seq input 1
METTL14.tpm


title: METTL3-1.input

description:
ribozero RNA
METTL3-bound transcripts  RIP-seq input 1
METTL3.tpm


title: METTL14-2.rip

description:
ribozero RNA
METTL14-bound transcripts  RIP-seq RIP 2
METTL14.tpm


title: METTL14-2.input

description:
ribozero RNA
METTL14-bound transcripts  RIP-seq input 2
METTL14.tpm


title: s050575

description: polyA RNA


title: s050573

description: polyA RNA


title: METTL14-1.rip

description:
ribozero RNA
METTL14-bound transcripts  RIP-seq RIP 1
METTL14.tpm


title: METTL16.input

description:
ribozero RNA
METTL16-bound transcripts  RIP-seq input
METTL16.tpm


title: s050574

description: polyA RNA


title: METTL16-1.rip

description:
ribozero RNA
METTL16-bound transcripts  RIP-seq RIP 1
METTL16.tpm


title: RT4-24hr-100 U/mL rhIFNb-Rep1

value: 100 U/mL rhIFNb


title: RT4-24hr-100 U/mL rhIFNb-Rep3

value: 24 hr


title: METTL3-1.rip

description:
ribozero RNA
METTL3-bound transcripts  RIP-seq RIP 1
METTL3.tpm


title: RT4-24hr-100 U/mL rhIFNb-Rep2


title: sgMETTL16-3.ribo

description:
ribozero RNA
sgMETTL16-3 ribo-seq

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

growth_protocol: The Cas9 single clone of HEK293T cells with sgRNA against METTL16 (and scramble control) were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin, plasmocin prophylactic, 10 ug/ml blasticidin, and 2 ug/ml puromycin for at least one week and the cells were collected at 70-80% confluency in 150 mm dish.

extract_protocol:
The ribosomes from the cell lysates were collected by ultracentrifugation and the ribosome footprints (17-34nts) were recovered from polyacrylamide TBE-Urea gel.
The end structures of the RNA fragments were repaired by T4 polynucleotide kinase (T4 PNK, M0201S, New England Biolabs): (1) 3’ end healing reaction (10 μl): 7 μl RNA sample, 1 μl 10×T4 PNK buffer, 1 μl T4 PNK, and 1 μl SUPERase In RNase Inhibitor were mixed and incubated for 1 h at 37 ℃; (2) 5’-end phosphorylation: 1 μl 10 mM ATP and 1 μl extra T4 PNK were added to the reaction and the mixture was kept for 30 min at 37 ℃. The RNA was purified by ethanol precipitation. The libraries were constructed after depletion of rRNA, and sequenced on Illumina Hiseq2500 with single end 51-bp read length.

treatment_protocol: The cells were treated with 100 μg/ml cycloheximide for 5 min at 37 ℃ to prevent translation before standard ribosome profiling protocol.

tag: rna fragment

value: ribosome footprint RNA

tag: guide rna


title: s050572

description: polyA RNA


title: RT4-24hr-100,000 U/mL rhINFa2b-Rep3

value: 100,000 U/mL rhINFa2b


title: sgMETTL16-2.ribo

description:
ribozero RNA
sgMETTL16-2 ribo-seq


title: s050571

description: polyA RNA


title: sgMETTL16-3.input

description:
ribozero RNA
sgMETTL16-3 input

value: Input RNA


title: RT4-24hr-100,000 U/mL rhINFa2b-Rep2


title: s050570

description: polyA RNA


title: s050569

description: polyA RNA


title: sgMETTL16-1.ribo

description:
ribozero RNA
sgMETTL16-1 ribo-seq


title: sgMETTL16-2.input

description:
ribozero RNA
sgMETTL16-2 input


title: sgNS.ribo

description:
ribozero RNA
Negative control sgRNA ribo-seq

value: Negative control sgRNA


title: METTL16-2.rip

description:
ribozero RNA
METTL16-bound transcripts  RIP-seq RIP 2
METTL16.tpm


title: RT4-24hr-10,000 U/mL rhINFa2b-Rep3

value: 10,000 U/mL rhINFa2b


title: RT4-24hr-100,000 U/mL rhINFa2b-Rep1


title: Nuclear-shMETTL16-2.input

description:
shMETTL16-2 input, nuclear polyA RNA
nuc.ns_nuc.m16.2.diff_peak.txt

growth_protocol: The HEK293T cells with METTL16 knockdown were expanded in DMEM medium with 10% FBS, 1 X penicillin-streptomycin, plasmocin prophylactic, and 2 ug/ml puromycin for 1-2 weeks and the cells were collected at 70-80% confluency in 150 mm dish.

extract_protocol:
Total RNAs were extracted from the cells treated with 4sU and then the total RNAs were subjected to biotinylation. The nascent RNAs were isolated from  biotinylated RNA with uMACS microbeads. Nuclear RNAs were extracted from nuclear pellets with miRNeasy Mini Kit and nuclear poly(A) RNAs were enriched from nuclear RNAs with  oligo(dT) polystyrene beads accordingly.The anti-m6A antibody (202003, Synaptic Systems) was applied for m6A immunoprecipitation
Both input and m6A IP samples were utilized for next-generation sequencing (NGS) on the Illumina HiSeq 2500.

treatment_protocol: In terms of nascent RNA, the cells were treated with 400 μM 4sU (T4509, Sigma Aldrich) for 1 h.

tag: knockdown

tag: rna population

value: nuclear polyA RNA


title: RT4-24hr-10,000 U/mL rhINFa2b-Rep2


title: sgNS.input

description:
ribozero RNA
Negative control sgRNA input


title: s050568

description: polyA RNA


title: Nuclear-shMETTL16-2.ip

description:
shMETTL16-2 ip, nuclear polyA RNA
nuc.ns_nuc.m16.2.diff_peak.txt

value: m6A antibody (Cat#:202003, Synaptic Systems)


title: s050567

description: polyA RNA


title: Nuclear-shMETTL16-1.ip

description:
shMETTL16-1 ip, nuclear polyA RNA
nuc.ns_nuc.m16.1.diff_peak.txt


title: RT4-24hr-10,000 U/mL rhINFa2b-Rep1


title: Nuclear-shMETTL16-1.input

description:
shMETTL16-1 input, nuclear polyA RNA
nuc.ns_nuc.m16.1.diff_peak.txt


title: Nuclear-shNS.ip

description: Negative control shRNA ip, nuclear polyA RNA

value: negative control shRNA


title: s050566

description: polyA RNA


title: Nuclear-shNS.input

description: Negative control shRNA input, nuclear polyA RNA


title: s050565

description: polyA RNA


title: Nascent-shMETTL16-2.ip

description:
shMETTL16-2 ip, Nascent RNA
nas.ns_nas.m16.2.diff_peak.txt

value: Nascent RNA


title: sgMETTL16-1.input

description:
ribozero RNA
sgMETTL16-1 input


title: RT4-24hr-1,000 U/mL rhIFNa2b-Rep2

value: 1,000 U/mL rhIFNa2b


title: s050564

description: polyA RNA


title: RT4-24hr-1,000 U/mL rhIFNa2b-Rep1


title: Nascent-shMETTL16-1.ip

description:
shMETTL16-1 ip, Nascent RNA
nas.ns_nas.m16.1.diff_peak.txt


title: Nascent-shMETTL16-1.input

description:
shMETTL16-1 input, Nascent RNA
nas.ns_nas.m16.1.diff_peak.txt


title: Nascent-shMETTL16-2.input

description:
shMETTL16-2 input, Nascent RNA
nas.ns_nas.m16.2.diff_peak.txt


title: s050563

description: polyA RNA


title: RT4-24hr-100 U/mL rhIFNa2b-Rep3

value: 100 U/mL rhIFNa2b


title: Nascent-shNS.ip

description: Negative control shRNA ip, Nascent RNA


title: RT4-24hr-1,000 U/mL rhIFNa2b-Rep3


title: s050561

description: polyA RNA


title: Endosperm 2

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
Gene expression analysis was done using RNA-Seq analysis tool in CLC Genomics Workbench (Qiagen) version 20.0.3.
Good quality reads were aligned to the reference genome of Oryza sativa variety indica genome assembly ASM465v1 (Ensembl). For most of the analysis CLC Standard Settings or default settings of the program were used. For mapping the reads to the genome, the default value was that at least 90 % of the bases of the read need to align with 80% similarity to the reference genome.
The expression levels were normalized as RPKM (reads per kilobase of exon model per million reads) values.
To identify differentially expression genes (DEGs) Statistical test “Tests on proportions” was performed on different pair of samples, and p-values were corrected using FDR (False Discovery Rate).
We considered a gene DEG, when it exhibited a log2 FC (Fold Change) of more than 2 compared with an FDR corrected p-value of <0.05.
Genome_build: Oryza sativa variety indica genome assembly ASM465v1 (Ensembl)
Supplementary_files_format_and_content: xlsx file having gene IDs and read count for each biological replicates

organism: Oryza sativa

source_name: Seed

growth_protocol: Plants were grown in field conditions

extract_protocol:
RNA extractions were done using PicoPure RNA Isolation Kit (Applied Biosystems, Thermo Fisher Scientific) according to the providers protocol.
Using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: No any treatments were done

tag: tissue-type

value: Endosperm


title: Nascent-shNS.input

description: Negative control shRNA input, Nascent RNA


title: Endosperm 3


title: s050562

description: polyA RNA


title: Endosperm 1


title: AZ-T-10

city: Montpellier

first: Timothy

middle: John

last: TRANBARGER

address: 911 avenue agropolis BP 64501

department: Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)

country: France

institute: Institut de Recherche pour le Développement

data_processing:
Reads obtained by Illumina NovaSeq sequencing (single reads, 100 cycles) were demultiplexed and trimmed using Bcl2fastq (v2.20.0.422). Total trimmed reads per sample are indicated in the Table S1. All the trimmed reads passed the FastQC quality checks and were then mapped using the BWA-MEM package with default parameters [1] to a reference transcriptome derived from the genomic sequence of the African oil palm (E. guineensis - Eg) for which a fully annotated genome sequence is currently available [2]. The latest version of the oil palm transcriptome released by NCBI was used for mapping (http://genomsawit.mpob.gov.my; GCF_000442705.1_EG5_rna.fna, July 2019). Read counts were obtained from the resulting bam files by means of the program Samtools-idxstats [3]. For each sample, the total reads aligned to reference genome is indicated in the Table S1. Counts corresponding to different transcripts of the same locus were then merged. The R-based software DESeq package (default parameters, version 1.28.1 [4] was used to identify genes displaying significantly different expression levels in the Sd and NSd palms, applying padj cutoff < 0.01 and log2 fold change (LFC) cutoff (-1 > LFC > 1). After mapping to the reference transcriptome, the number of reads per kilobase and million reads (RPKM) in each sample were then calculated.                                                                                1. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013, 1303.3997.  2. Singh, R.; Ong-Abdullah, M.; Low, E.T.L.; Manaf, M.A.A.; Rosli, R.; Nookiah, R.; Ooi, L.C.L.; Ooi, S.E.; Chan, K.L.; Halim, M.A.; et al. Oil palm genome sequence reveals divergence of interfertile species in Old and New Worlds. Nature 2013, 500, 335-339, doi:Doi 10.1038/Nature12309.  3. Li, H.; Handsaker, B.; Wysoker, A.; Fennell, T.; Ruan, J.; Homer, N.; Marth, G.; Abecasis, G.; Durbin, R.; Genome Project Data Processing, S. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25, 2078-2079, doi:10.1093/bioinformatics/btp352.  4. Love, M.I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014, 15, 550, doi:10.1186/s13059-014-0550-8.
Supplementary_files_format_and_content: xlsx; RPKM read counts

organism: Elaeis oleifera

source_name: Base of fruit containing Abscission zone (AZ)

growth_protocol: American oil palm (Elaeis oleifera) fruits were collected from a palm population of 152 individuals from 18 progenies planted at the Colé station (DANEC) in Ecuador since 2006.

extract_protocol:
For RNA extractions, the fruit bunches were collected and the base of fruits containing the AZ were sampled as follows: the spikelets were removed from the bunches, rinsed in water, then individual fruit containing the base of the fruit containing the AZ were removed with scalpel, then the base of the fruit containing the AZ were dissected (approximately 50 AZ pieces were collected per sample), weighed at approximately 3 grams then froze immediately in liquid nitrogen.
Construction of cDNA libraries and llumina (NovaSeq 6000) sequencing of the RNA samples was carried out by MGX platform (Montpellier Genomix, http://www.mgx.cnrs.fr/).

treatment_protocol: The fruit were derived from an open pollination amongst the population. We estimated the stage of ripeness of the fruit by observing the position of the fruit bunch attachment within the whorl, and based on the color of the fruit. The ripe fruit bunch was that which was positioned the lowest in the whorl of fruit bunches, and had the fruit colored orange, at which time the fruit could be easily loosened and separated from the bunch. This is the typical stage at which fruit bunches are harvested for oil extraction. The fruit bunch po-sitioned just higher than the ripe bunch in the whorl had less orange colored fruit, and was at the pre-ripe (PR) stage, and fruit were more firmly attached to the fruit bunch.

tag: tissue

tag: developmental stage

value: ripe stage

tag: sample id

value: individual code 28-7


title: AZ-T-11

value: Base of fruit containing Abscission zone (AZ)


title: s050559

description: polyA RNA

tag: library


title: s050560

description: polyA RNA


title: RT4-24hr-100 U/mL rhIFNa2b-Rep2


title: RT4-24hr-100 U/mL rhIFNa2b-Rep1


title: AZ-T-8

value: pre-ripe stage


title: RT4-24hr-Untreated-Rep1

value: Untreated

value: 24 hr


title: RT4-24hr-Untreated-Rep3


title: AZ-T-12


title: s050557

description: polyA RNA


title: s050556

description: polyA RNA


title: AZ-T-9


title: AZ-T-7


title: s050558

description: polyA RNA


title: Aleurone 3

value: Aleurone


title: AZ-T-5

value: individual code 26-11


title: s050555

description: polyA RNA


title: RT4-24hr-Untreated-Rep2


title: RO070_J82-24hr-50ng/mL TRAIL

data_processing:
The assembly was performed using the nf-core/rnaseq pipeline (1.4.2) using default parameters. Reads were aligned with Hisat2 (2.1.0) to the human reference build GRCh38 and transcripts were quantified using featureCounts (1.6.4).
Differential expression analysis was performed using R(4.0.1)/Bioconductor with the edgeR (3.32.1) and Limma (3.46.0) packages.
Prior to differential expression analysis, low expression features were excluded and samples were adjusted by normalization factors and voom-normalized. Differential expression models were adjusted for correlations between technical replicates using the duplicateCorrelation function in Limma.
Genome_build: Homo_sapiens.GRCh38.dna_sm.toplevel.fa
Supplementary_files_format_and_content: Counts output from featureCounts

growth_protocol: J82 was cultured in MEM with 10% fetal bovine serum (FBS);  RT4 was cultured in McCoy’s 5a with 10% FBS. All cells were maintained in complete growth media at 37°C under 5% CO2 in a humid environment.

value: 50ng/mL TRAIL


title: RO069_J82-24hr-10,000 U/mL rhIFNa

value: 10,000 U/mL rhIFNa


title: RO068_J82-24hr-10,000 U/mL rhIFNa


title: Perciarp 3

value: Perciarp


title: s050552

description: polyA RNA


title: AZ-T-2


title: Embryo 2

value: Embryo


title: Perciarp 2


title: Embryo 3


title: RO072_J82-24hr-50ng/mL TRAIL


title: s050551

description: polyA RNA


title: AZ-T-1


title: Embryo 1


title: RO065_J82-24hr-1,000 U/mL rhIFNa

value: 1,000 U/mL rhIFNa


title: AZ-T-6


title: AZ-T-4


title: s050549

description: polyA RNA


title: s050553

description: polyA RNA


title: Aleurone 1


title: Y44-1ng

description: Y44-1.FCHGJWYBBXY_L6_R1_ITACGCCCACGTG-TCAGAAACAGTG

tag: input amounts

tag: protocol

value: Low Input


title: s050550

description: polyA RNA


title: RO071_J82-24hr-50ng/mL TRAIL

tag: time


title: RO067_J82-24hr-10,000 U/mL rhIFNa


title: RO066_J82-24hr-1,000 U/mL rhIFNa


title: s050554

description: polyA RNA


title: 84k poplar stem middle rep3 [PCS2]

city: Hangzhou

first: weti

state: China

address: WUSUSTREET NO.666

institute: zhejiang A&F university

data_processing:
The raw image data obtained from Illumina sequencing was transformed into sequence data by Base Calling and then stored in FASTQ file format.
Trim the raw data using Trimmomatic (v0.36): remove splice sequences, remove reads without inserted fragments; trim off bases with mass values less than 20 at the 3′ end, discard sequences containing bases with mass values less than 10; remove reads containing N ratios over 10%; discard reads after de-adapter and mass trimming sequences with length less than 70bp.
Trimmed clean reads were mapped to the reference genome using Hisat2 with default parameters and quality assessed using Qualimap (v2.2.1).
Genome_build: CNP0000339 in CNGB Nucleotide Sequence Archive (https://db.cngb.org/search/project/CNP0000339/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every samples

organism: Populus alba x Populus glandulosa

source_name: 84k poplar stem middle

growth_protocol: 84K poplar was obtained from annual seedlings from Renqiu, Hebei base of Chinese Academy of Forestry. Propagated in 1/2 MS rooting medium (half-strength Murashige and Skoog medium with 3% sucrose and 0.8% agar) using cuttings at pH 5.7-5.8, 16h/d of light, 50 umol*m-2*s-1 light intensity, and 25 centigrade. The plants were grown under natural conditions for 6 months with ~200cm height.

extract_protocol:
Total RNA was extracted from stems using TRIzol® Reagent (Invitrogen) and gDNA was removed using DNase I (TaKara), then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using NanoDrop ND-2000, of which high quality RNA samples were selected for sequencing library construction (OD260/280=1.8-2.2, OD260/230 great than or equal to 2.0, RIN great than or equal to 6.5, 28S:18S great than or equal to 1.0, great than 10μg).
Libraries were built with 1 μg total RNA starting volume using TruseqTM RNA sample prep Kit (Illumina). The mRNA with polyA was selectively isolated by oligo(dT) beads, and  fragmented by ion interruption using the TruseqTM RNA sample prep Kit (Invitrogen), followed by double-stranded cDNA synthesis, end-complementation repair, A-base addition at the 3′ end, and ligation of index junctions in sequence. Fifteen PCR cycles of PCR amplification using Phusion DNA polymerase (NEB) were performed to enrich the library, and the target bands of 200-300 bp were recovered from 2% agarose gel of Certified Low Range Ultra Agarose (Bio-Rad). After quantification using TBS380 Picogreen (Invitrogen), the data were mixed onto machine in proportion to data; bridge PCR amplification was performed using cBot Truseq PE Cluster Kit v3-cBot-HS (Illumina) to generate clusters; sequencing was performed using Illumina NovaSeq 6000 platform (150bp×2, Shanghai BIOZERON Co. Ltd) for sequencing Paired-end libraries Truseq SBS Kit (300cycles) (Illumina).

tag: cultivar

value: Poplar 84K

tag: age

value: 6 months

value: stem

tag: internodes

tag: height

tag: genotype

value: wild type


title: RO063_J82-24hr-Untreated

extract_protocol:
Following incubation, media was aspirated fully and 0.6mL RLT Buffer with β-mercaptoethanol (from Qiagen RNeasy Plus kit) was added to wells and plates were frozen at –20°C. Plates were thawed on ice, wells were scraped, and contents transferred to QIAshredder columns. RNA was isolated according to the RNeasy Plus kit instructions (Qiagen), RNA was eluted, quantified, aliquoted for RNAseq submission and/or qPCR, then frozen at –80°C.
RNA-seq libraries were prepared Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® NovaSeq to obtain 150-bp paired-end reads

tag: cell line

tag: treatment


title: UHR-100ng-standard

description: UHR-100.FCHGJWYBBXY_L6_R1_ICGGGAACCCGCA-AGGGCCAAAGAC

source_name: UHR

value: RIN 9.0

value: Standard


title: Perciarp 1


title: s050546

description: polyA RNA


title: 84k poplar stem bottom rep3 [PCS3]

description: 84K poplar was obtained from annual seedlings from Renqiu, Hebei base of Chinese Academy of Forestry. Propagated in 1/2 MS rooting medium (half-strength Murashige and Skoog medium with 3% sucrose and 0.8% agar) using cuttings at pH 5.7-5.8, 16h/d of light, 50 umol*m-2*s-1 light intensity, and 25 centigrade.

source_name: 84k poplar stem bottom


title: AZ-T-3

value: Base of fruit containing Abscission zone (AZ)

value: pre-ripe stage


title: Aleurone 2


title: 84k poplar stem middle rep2 [PBS2]


title: RO061_J82-24hr-Untreated

value: Untreated

value: 24 hr


title: s050543

description: polyA RNA


title: RO064_J82-24hr-1,000 U/mL rhIFNa


title: Y44-10ng

description: Y44-10.FCHGJWYBBXY_L6_R1_IATCGACTTGTGT-CTAGCATTGTGT


title: s050542

description: polyA RNA


title: s050548

description: polyA RNA


title: UHR-50ng-standard

description: UHR-50.FCHGJWYBBXY_L6_R1_IAAACGTTCATCC-CCCAGTTACTAA


title: 84k poplar stem top rep3 [PCS1]

source_name: 84k poplar stem top


title: RO062_J82-24hr-Untreated


title: 84k poplar stem bottom rep2 [PBS3]


title: s050541

description: polyA RNA


title: 84k poplar stem bottom rep1 [PAS3]


title: RO059_RT4-24hr-50ng/mL TRAIL


title: UHR-10-low input

description: UHR-10-low.FCHGJWYBBXY_L6_R1_ICCAAAGAGGGAT-AACCCGCGGGCT


title: RO058_RT4-24hr-50ng/mL TRAIL


title: UHR-1-low input

description: UHR-1-low.FCHGJWYBBXY_L6_R1_ITCCTCTCTTCTA-TAATATATTATC


title: RO060_RT4-24hr-50ng/mL TRAIL


title: 8B-10ng

description: 8B-10.FCHGJWYBBXY_L6_R1_IAGTCTCAGCAAA-CGTATACGACCC


title: s050539

description: polyA RNA


title: s050538

description: polyA RNA


title: 8B-1ng

description: 8B-1.FCHGJWYBBXY_L6_R1_IAGGTGGTTCTAC-CGGTGGTTATCA


title: RO057_RT4-24hr-10,000 U/mL rhIFNa


title: s050536

description: polyA RNA


title: 84k poplar stem top rep1 [PAS1]


title: 84k poplar stem top rep2 [PBS1]


title: RO056_RT4-24hr-10,000 U/mL rhIFNa


title: 6-1ng

description: 6-1.FCHGJWYBBXY_L6_R1_IAACCCTGGGAAG-CCAAATGGGCCG

source_name: FF


title: UHR-10ng-standard

description: UHR-10.FCHGJWYBBXY_L6_R1_ITTGTCCGATATG-TTGTAAGCTCTG


title: 6-10ng

description: 6-10.FCHGJWYBBXY_L6_R1_IGAAGGGTAAAGC-GCCGGGTCCCGA


title: RO055_RT4-24hr-10,000 U/mL rhIFNa


title: 84k poplar stem middle rep1 [PAS2]


title: RP5-998N21.4 overexpressed SK-N-SH cells_2

city: Guangzhou

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

data_processing:
The reads were aligned to the UCSC Homo sapiens reference genome hg19 with bowtie2  version 2.0.4, and multi-aligned reads were removed with Picard 2.21.6.
We then used Stringtie 2.1.6 to generate mapping counts for the known annotated genes
DEGs between RP5-998N21.4 overexpressed and wild type were identified with the DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated text file include gene expression level (Counts) for each Sample

source_name: SK-N-SH cells

growth_protocol: SK-N-SH cells were cultured at 37 ℃ and 5% CO2 concentrations in DMEM supplemented with 10% FBS (EX CELL) and antibiotics (penicillin and streptomycin, Gibco, USA).

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

treatment_protocol: SK-N-SH cells had been seeded into a 100-mm dish in normal DMEM with 5% fetal bovine serum and  we overexpressed a recombinant lentivirus carrying lncRNA-RP5-998N21.4 in SK-N-SH cells

value: SK-N-SH

tag: cell type

value: neuroblastoma

value: RP5-998N21.4 overexpressed

value: treated with a recombinant lentivirus carrying lncRNA-RP5-998N21.4


title: WT SK-N-SH cells_2

value: treated with an empty lentivirus vector with no insert


title: RP5-998N21.4 overexpressed SK-N-SH cells_1


title: s050532

description: polyA RNA


title: S_Brain

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

description:
exosome encapsulated RNA
Brain

data_processing:
Removed adapter sequences with cutadapt (v.1.9.1) Discarded reads that do not have adapters as these fragments are too long for a small RNA library.
cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC --discard-untrimmed
Trimmed the first 4 and last 4 bases of the reads
Reads were aligned to the human genome (hg38) and features were quantified with Genboree's exceRpt pipeline v4.6.2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated raw-count matrix, where rows are genes (miRNAs) and columns are samples. The file is a plain-text .tsv

source_name: Exosomes extracted from brain tissue

extract_protocol:
Exosomes were extracted from 2mL of plasma using size exclusion chromatography, and further enriched for those of neuronal origin using an immunoassay. Small non-coding RNA was isolated using miRNeasy kit
Librarys were constructed using the 4N library prep protocol from the Galas lab. (Giraldez et al., 2018) First, degenerative adapters are added to the miRNA. These adapters are used to eliminate the problem of bias in small RNA library construction. The product is then reverse transcribed and amplified.

value: Exosomes extracted from brain tissue

tag: disease state

tag: patient id

tag: week

tag: treatment response

tag: Sex

value: M

tag: sequencing batch

tag: madrs score at week 0

tag: madrs score at week 8


title: RO053_RT4-24hr-1,000 U/mL rhIFNa

value: 1,000 U/mL rhIFNa

tag: time


title: WT SK-N-SH cells_1


title: s050530

description: polyA RNA

tag: library


title: s050529

description: polyA RNA


title: RO051_RT4-24hr-Untreated


title: RO052_RT4-24hr-1,000 U/mL rhIFNa


title: s050535

description: polyA RNA


title: HD4 WB

city: Bethesda

first: Amanda

last: Henning

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina BaseSpace applications were used for data processing. Specifically, alignment and transcript quantification were performed using the RNA-Seq Alignment application (v2.0.1). This application utilizes the STAR aligner and Salmon for transcript quantification. These analyses were conducted using the default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.quant.sf is the transcript quantification output file from Salmon. There are plain-text, tab-separated files with a single header line.

source_name: Blood

extract_protocol:
RNA was isolated from freshly collected whole blood using the Quick-RNA Whole Blood kit (Zymo Research), and from PBMC and isolated B cells using the RNeasy Plus Mini kit (Qiagen). B cells had previously been isolated from PBMC using the EasySep Human B cell Isolation kit (StemCell Tech).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina) following manufacturer's protocol. For whole blood and PBMC samples, an input of 300ng RNA was used, and for isolated B cells 100ng of RNA was used.

tag: donor

value: Donor 4

tag: diagnosis

value: Healthy

value: Whole blood


title: s050533

description: polyA RNA

source_name: mouse germ cells


title: S59_NRES_W8

description:
exosome encapsulated RNA
59_W8

source_name: Neuronal-derived exosomes from plasma

tag: tissue

value: Neuronal-derived exosomes from plasma

value: depressed

value: Non-responder

tag: age

value: F


title: HD4 Bcells

value: B cells


title: S60_RES_W0

description:
exosome encapsulated RNA
60_W0

value: Responder


title: s050526

description: polyA RNA


title: HD4 PBMC

value: PBMC


title: S59_NRES_W0

description:
exosome encapsulated RNA
59_W0


title: HD3 WB

value: Donor 3


title: RO054_RT4-24hr-1,000 U/mL rhIFNa

tag: cell line

value: 24 hr


title: RO050_RT4-24hr-Untreated

tag: treatment

value: Untreated


title: S58_RES_W8

description:
exosome encapsulated RNA
58_W8


title: RO049_RT4-24hr-Untreated


title: s050524

description: polyA RNA


title: RO048_J82-8hr-50ng/mL TRAIL

value: 50ng/mL TRAIL

value: 8 hr


title: HD3 PBMC

tag: cell type


title: S60_RES_W8

description:
exosome encapsulated RNA
60_W8

tag: disease state

value: M


title: RO047_J82-8hr-50ng/mL TRAIL


title: s050523

description: polyA RNA


title: S57_NRES_W8

description:
exosome encapsulated RNA
57_W8

tag: patient id


title: s050527

description: polyA RNA


title: s050521

description: polyA RNA


title: HD3 Bcells


title: HD2 WB

value: Donor 2


title: RO046_J82-8hr-50ng/mL TRAIL


title: S57_NRES_W0

description:
exosome encapsulated RNA
57_W0

tag: week


title: RO043_J82-8hr-10,000 U/mL rhIFNa

value: 10,000 U/mL rhIFNa


title: RO045_J82-8hr-10,000 U/mL rhIFNa


title: S58_RES_W0

description:
exosome encapsulated RNA
58_W0

tag: treatment response


title: HD2 Bcells

value: Healthy


title: S56_NRES_W8

description:
exosome encapsulated RNA
56_W8

tag: Sex


title: s050519

description: polyA RNA


title: HD2 PBMC


title: HD1 WB

value: Donor 1

value: Whole blood


title: S56_NRES_W0

description:
exosome encapsulated RNA
56_W0

value: Neuronal-derived exosomes from plasma

value: depressed

tag: sequencing batch


title: RO044_J82-8hr-10,000 U/mL rhIFNa


title: s050514

description: polyA RNA


title: RO042_J82-8hr-1,000 U/mL rhIFNa

value: 1,000 U/mL rhIFNa


title: s050513

description: polyA RNA


title: S54_NRES_W8

description:
exosome encapsulated RNA
54_W8

value: Non-responder

value: F

tag: madrs score at week 0


title: s050515

description: polyA RNA


title: RO039_J82-8hr-Untreated


title: HD1 PBMC

value: PBMC


title: S54_NRES_W0

description:
exosome encapsulated RNA
54_W0

tag: madrs score at week 8


title: RO040_J82-8hr-1,000 U/mL rhIFNa

tag: time


title: S55_RES_W8

description:
exosome encapsulated RNA
55_W8

value: Responder


title: HD1 Bcells

value: B cells


title: s050517

description: polyA RNA

tag: library


title: RO041_J82-8hr-1,000 U/mL rhIFNa


title: S55_RES_W0

description:
exosome encapsulated RNA
55_W0


title: s050510

description: polyA RNA


title: RO038_J82-8hr-Untreated

value: Untreated


title: s050509

description: polyA RNA


title: B10

first: Aristidis

last: Veves

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

data_processing:
Library strategy: GeoMX-Seq
Adapter trimming with trim galore, trimGaloreOpts = " --hardtrim5 26 --dont_gzip"  If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"  Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"  Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"  Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes), see attached Alpha_CTA_v2.0.pkc file
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode). Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

source_name: Foot skin

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures (CD45, aSMA, panCK). Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Each collection of oligo tags from one well (representing an area of illumination-AOI- from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio. Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers.

value: skin

tag: subject id

value: Subject 4

tag: ulcer location

value: plantar left foot

tag: roi location

value: Ulcer

tag: healing status

value: Healer


title: B11

tag: tissue

value: M

tag: age


title: S52_RES_W8

description:
exosome encapsulated RNA
52_W8


title: s050508

description: polyA RNA


title: RO036_RT4-8hr-50ng/mL TRAIL

first: Robin

institute: Ferring Pharmaceuticals

tag: cell line

tag: treatment

value: 50ng/mL TRAIL

value: 8 hr


title: s050512

description: polyA RNA


title: C01


title: S52_RES_W0

description:
exosome encapsulated RNA
52_W0

value: Neuronal-derived exosomes from plasma

tag: disease state

tag: patient id


title: s050511

description: polyA RNA


title: B12


title: RO035_RT4-8hr-50ng/mL TRAIL


title: S51_RES_W8

description:
exosome encapsulated RNA
51_W8

value: depressed

tag: week

tag: treatment response


title: S53_NRES_W0

description:
exosome encapsulated RNA
53_W0

tag: Sex

tag: sequencing batch


title: s050507

description: polyA RNA


title: RO034_RT4-8hr-50ng/mL TRAIL


title: RO033_RT4-8hr-10,000 U/mL rhIFNa

value: 10,000 U/mL rhIFNa


title: B06

value: Subject 3

value: Non-Healer


title: B08


title: RO037_J82-8hr-Untreated


title: B04

value: Non-ulcer

value: F


title: s050504

description: polyA RNA


title: s050505

description: polyA RNA


title: S53_NRES_W8

description:
exosome encapsulated RNA
53_W8

value: Non-responder

tag: madrs score at week 0

tag: madrs score at week 8


title: B05


title: S51_RES_W0

description:
exosome encapsulated RNA
51_W0

value: Responder


title: S50_C_W8

description:
exosome encapsulated RNA
50_W8

value: Control


title: B09

value: skin

value: Subject 4

value: Ulcer edge


title: RO032_RT4-8hr-10,000 U/mL rhIFNa

tag: time


title: S49_C_W8

description:
exosome encapsulated RNA
49_W8


title: RO030_RT4-8hr-1,000 U/mL rhIFNa

value: 1,000 U/mL rhIFNa


title: s050506

description: polyA RNA

tag: library


title: B02

tag: subject id

tag: ulcer location

value: plantar left foot


title: s050502

description: polyA RNA


title: B01

value: Subject 2

tag: roi location

value: Ulcer

tag: healing status

value: Healer


title: s030731

description: polyA RNA


title: RO029_RT4-8hr-1,000 U/mL rhIFNa

value: 8 hr


title: s050501

description: polyA RNA


title: RO028_RT4-8hr-1,000 U/mL rhIFNa


title: S48_C_W8

description:
exosome encapsulated RNA
48_W8

tag: tissue

value: Neuronal-derived exosomes from plasma

tag: age


title: S48_C_W0

description:
exosome encapsulated RNA
48_W0


title: S49_C_W0

description:
exosome encapsulated RNA
49_W0


title: RO027_RT4-8hr-Untreated

tag: cell line

tag: treatment

value: Untreated


title: A12


title: s030730

description: polyA RNA


title: S50_C_W0

description:
exosome encapsulated RNA
50_W0

tag: disease state

tag: patient id


title: B03

value: Subject 3

value: Non-Healer


title: RO031_RT4-8hr-10,000 U/mL rhIFNa

value: 10,000 U/mL rhIFNa


title: S47_C_W8

description:
exosome encapsulated RNA
47_W8

tag: week

tag: treatment response

value: M


title: s030728

description: polyA RNA


title: A10

tag: Sex

value: F


title: S47_C_W0

description:
exosome encapsulated RNA
47_W0

value: Control

tag: sequencing batch


title: s030727

description: polyA RNA


title: RO026_RT4-8hr-Untreated


title: s050503

description: polyA RNA


title: RO025_RT4-8hr-Untreated


title: A09

value: skin


title: S46_C_W8

description:
exosome encapsulated RNA
46_W8


title: RO024_J82-4hr-50ng/mL TRAIL

value: 50ng/mL TRAIL

value: 4 hr


title: S46_C_W0

description:
exosome encapsulated RNA
46_W0


title: A08


title: s030726

description: polyA RNA


title: A11

value: Epidermis


title: A07

value: Subject 1

value: plantar right foot

value: Non-Ulcer


title: s030725

description: polyA RNA


title: RO023_J82-4hr-50ng/mL TRAIL


title: S45_C_W8

description:
exosome encapsulated RNA
45_W8


title: A06

value: Ulcer


title: s030723

description: polyA RNA


title: RO022_J82-4hr-50ng/mL TRAIL


title: S45_C_W0

description:
exosome encapsulated RNA
45_W0


title: RO021_J82-4hr-10,000 U/mL rhIFNa


title: A05

value: Non-ulcer


title: s030722

description: polyA RNA


title: A04

value: Ulcer edge


title: RO020_J82-4hr-10,000 U/mL rhIFNa


title: s030721

description: polyA RNA


title: S44_C_W0

description:
exosome encapsulated RNA
44_W0

value: Neuronal-derived exosomes from plasma


title: RO018_J82-4hr-1,000 U/mL rhIFNa

value: 1,000 U/mL rhIFNa


title: A03

value: Non-Healer


title: RO019_J82-4hr-10,000 U/mL rhIFNa

value: 10,000 U/mL rhIFNa


title: A02


title: s030724

description: polyA RNA


title: RO017_J82-4hr-1,000 U/mL rhIFNa


title: S42_C_W8

description:
exosome encapsulated RNA
42_W8


title: s030720

description: polyA RNA


title: S43_C_W0

description:
exosome encapsulated RNA
43_W0


title: S43_C_W8

description:
exosome encapsulated RNA
43_W8


title: s030719

description: polyA RNA


title: s030718

description: polyA RNA


title: RO015_J82-4hr-Untreated

value: Untreated


title: s030716

description: polyA RNA


title: S42_C_W0

description:
exosome encapsulated RNA
42_W0

value: F


title: s030717

description: polyA RNA


title: S41_C_W8

description:
exosome encapsulated RNA
41_W8

value: Control


title: S44_C_W8

description:
exosome encapsulated RNA
44_W8


title: RO014_J82-4hr-Untreated


title: S41_C_W0

description:
exosome encapsulated RNA
41_W0


title: RO013_J82-4hr-Untreated


title: s030715

description: polyA RNA


title: s030713

description: polyA RNA


title: S40_C_W8

description:
exosome encapsulated RNA
40_W8

value: M


title: RO012_RT4-4hr-50ng/mL TRAIL

value: 50ng/mL TRAIL


title: s030709

description: polyA RNA


title: S40_C_W0

description:
exosome encapsulated RNA
40_W0


title: DKO_Input (HMCP)

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

data_processing:
Library strategy: HMCP
Single-end reads were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) indexed with spiked-in phage lambda, using Bowtie (V 1.1.2) (-S -p 3)
Reads that mapped to spike-ins were filtered out with samtools view; remaining mapped  reads in sam files were sorted and PCR duplicates were removed with Picard (V 2.7.1)
Peaks were called with MACS2 (callpeak --keep-dup all -g mm)
Peaks from the replicates from same condition were merged with mergePeaks from HOMER and kept only those that intersected between the replicates. Intersected peaks from the replicates were merged between the conditions to create the total number of peaks.
Genome_build: mouse genome mm10 GRCm38
Supplementary_files_format_and_content: Comma separated file with the rpkm normalized HMCP signal in G4 and Rloops union peaks

source_name: Spleen

growth_protocol: Primary YFP+ CD19 DKO B cells or CD19+ YFP- control B cells were isolated using flow sorting.

extract_protocol: 5hmC mapping was performed on purified genomic DNA using the 5hmC pull-down (HMCP) method (Cambridge Epigenetix) according to the manufacturer’s recommended protocol.

tag: strain

value: Spleen

tag: cell type

value: B cells

value: 10 weeks of age

tag: genotype

value: CD19 DKO


title: RO008_RT4-4hr-10,000 U/mL rhIFNa

city: San Diego

last: Osterhout

address: 4245 Sorrento Valley Rd

tag: time

value: 4 hr


title: S39_C_W8

description:
exosome encapsulated RNA
39_W8


title: s030707

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
UMI-tools was used to extract and add the 8bp cell barcode sequence and unique molecular identifiers (UMIs) to read name of sequencing read pairs.
Subsequently we trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1 and removed low-quality bases using costumed script and seqtk tool.
The clean read1 reads were aligned to mm10 reference genome using STAR.
Then, genomic features were added to reads using featureCounts of subread in order to count uniquely aligned reads with genes.
Finally, we used "count" tool in UMI-tools to obtain UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

extract_protocol:
Cells were randomly selected into precooled lysate. Then, the lysate were shocked at 72℃ for 3min to release RNA and Initial denaturation.
We used an improved Smart seq2 method. In brief, single-cell suspension is firstly prepared, and then single cells are selected into a PCR tube containing oligo(dT) primers and lysates through a suction tube.After cDNA amplification, the single cells labeled with different barcodes can be pooled together for subsequent library construction and sequencing. We add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’ terminal of cDNAs. Then the library was constructed by using Kapa Hyper Prep Kit(Thermo Fither) and run on illumina Hiseq X Ten for 150bp pair-end reads.

tag: library


title: RO010_RT4-4hr-50ng/mL TRAIL


title: Dfl1_IP (HMCP)

value: Dfl


title: RO011_RT4-4hr-50ng/mL TRAIL


title: RO009_RT4-4hr-10,000 U/mL rhIFNa


title: S38_C_W8

description:
exosome encapsulated RNA
38_W8


title: S37_C_W8

description:
exosome encapsulated RNA
37_W8


title: s030703

description: polyA RNA


title: S37_C_W0

description:
exosome encapsulated RNA
37_W0


title: Dfl2_IP (HMCP)


title: RO016_J82-4hr-1,000 U/mL rhIFNa


title: DKO2_IP (HMCP)


title: DKO1_IP (HMCP)


title: S39_C_W0

description:
exosome encapsulated RNA
39_W0


title: RO006_RT4-4hr-1,000 U/mL rhIFNa


title: S38_C_W0

description:
exosome encapsulated RNA
38_W0


title: Dfl_Input (HMCP)


title: RO007_RT4-4hr-10,000 U/mL rhIFNa


title: s030706

description: polyA RNA


title: s030702

description: polyA RNA


title: s030701

description: polyA RNA


title: S36_C_W8

description:
exosome encapsulated RNA
36_W8


title: Dko1 (RNA-seq)

data_processing:
Single-end (50bp) reads were mapped to the mouse genome mm10/GRCm38 using STAR (--runThreadN 8 --genomeLoad LoadAndRemove --outFilterMultimapNmax 1 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --outFilterMismatchNmax 0).
Counts were obtained with featureCounts (subread-1.4.3-p1 ) (-g gene_name  -s 1).
Differentially expressed genes were calculated with DESeq2, filtering out genes that did not have any count in any condition; cut off to define DEGs was an adjusted pvalue 0.05 and a log2 fold change >= +/-1
Genome_build: mouse genome mm10/GRCm38
Supplementary_files_format_and_content: Comma separated file with raw counts of genes, each column represent a sample; Excel file with the results from DESeq2

extract_protocol:
RNA from cells was isolated with Trizol (ThermoFisher, Waltham, MA) following manufacturer’s instructions. Isolated RNA was further purified using RNA clean up and concentrator kit (R1013, Zymo research) according to manufacturer’s instructions.
40 ng of purified RNA was then used for preparation of RNA-sequencing libraries with the Nugen ovation RNA-Seq V2 system (now Tecan Genomics) according to the manufacturer recommended protocol. Samples were sequenced on Illumina Hiseq 2500 (single-end 50 bp reads)


title: RO005_RT4-4hr-1,000 U/mL rhIFNa


title: s010304

description: polyA RNA


title: Dko2 (RNA-seq)


title: s030705

description: polyA RNA


title: RO004_RT4-4hr-1,000 U/mL rhIFNa


title: S35_RES_W8

description:
exosome encapsulated RNA
35_W8

value: depressed

value: Responder

tag: madrs score at week 0

tag: madrs score at week 8


title: RO003_RT4-4hr-Untreated


title: s010303

description: polyA RNA


title: Dflx1 (RNA-seq)

tag: tissue


title: Dflx2 (RNA-seq)

tag: age


title: S36_C_W0

description:
exosome encapsulated RNA
36_W0

value: Neuronal-derived exosomes from plasma


title: S34_C_W8

description:
exosome encapsulated RNA
34_W8


title: RO002_RT4-4hr-Untreated

tag: cell line


title: RO001_RT4-4hr-Untreated

tag: treatment


title: Klf5-KO Lgr5+ ISC rep 2

city: Stony Brook

first: Vincent

last: Yang

state: New York

address: 101 Nicolls Rd., HSC T17-090

department: Medicine

institute: Stony Brook University

data_processing:
The reads were aligned with STAR (version 2.5.2a).
Genes annotated in Gencode vM16 were quantified with featureCounts (v1.4.3-p1).
Normalization and differential expression was done with the Bioconductor package DESeq2 (v1.18.1).
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID (in ENSEMBL), coordinates, strand, length of the transcripts, and counts (=number of reads mapping to the exons of the gene).

source_name: Klf5-KO mouse intestinal stem cells

extract_protocol:
Proximal 1/3 of small intestine were resected, and crypts were isolated by villi scraping and 5mM EDTA incubation. Cells were dissociated with 4x TrpLE in DMEM for 45 minutes, and Lgr5-EGFPhi cells were sorted by flow cytometry. Total RNA was isolated using RNeasy Mini Kit (Qiagen) in combination with on-column DNase treatment.
Library was prepared using the KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) according to the manufacturer's instructions.

treatment_protocol: Mice were injected with tamoxifen (1mg in 0.1 mL corn oil per injection) for 5 consecutive days to activate Cre recombinase for initating lineage-tracing, and to delete Klf5 in Klf5-KO mice

value: Adult small intestinal stem cell; proximal 1/3 of intestine


title: Klf5-KO Lgr5+ ISC rep 3


title: Control Lgr5+ ISC rep 3

source_name: Control mouse intestinal stem cells


title: Klf5-KO Lgr5+ ISC rep 1


title: s010301

description: polyA RNA


title: TN-12

first: Yi

last: Feng

address: No.11,Xizhimen South Street, Xicheng District

department: Department of Anesthesiology

institute: Peking university people's hospital

data_processing:
Illumina RtaVersion v3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 software,tophat2 -a 8 -m 0 -i 50 -I 500000 -N 2 --read-gap-length 2 --read-edit-dist 2 -g --library-type fr-unstranded -p 8 -G -r 50 --microexon-search;For FPKM valuse analysis using RSEM software,RSEM --paired-end  --bowtie2 -p 8 --bowtie2-path.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample .

source_name: Whole blood cells in patients with trigeminal neuralgia

extract_protocol:
total RNA were extracted for using PAXgene Blood RNA Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole blood

tag: gender

value: Female

tag: condition

value: trigeminal neuralgia


title: S33_C_W8

description:
exosome encapsulated RNA
33_W8

tag: disease state

tag: patient id

tag: week

value: F


title: TN-15

value: Male


title: Control Lgr5+ ISC rep 2


title: S35_RES_W0

description:
exosome encapsulated RNA
35_W0

tag: treatment response

tag: Sex

tag: sequencing batch


title: S33_C_W0

description:
exosome encapsulated RNA
33_W0

value: Control