title: LD_ZT47

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

description: processed data file: LD_ZT2_47_transcript_expr.txt

data_processing:
Low quality reads, which have less than 60% of bases with a quality score greater than 20, were filtered out
Gene expression abundances were measured and normalized based on their library sizes by computing the number of fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: long-day condition_seedling

growth_protocol: Seeds of Arabidopsis thaliana ecotype Columbia (Col-0) were surface-sterilized, and stratified for 2 days at 4°C, and then planted on a Murashige and Skoog (MS) plate. The seedlings were grown under long-day condition (16 h light /8 h dark) with a cool white fluorescent light at 24°C for 8 days.

extract_protocol:
Total RNA from seedings was isolated by Rneasy Plant Mini Kit (QIAGEN) and treated with TURBO DNA-free Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were either transferred to continuous light or kept under long-day condition at 24°C for additional 2 days to explore circadian and diurnal regulation.

tag: ecotype

value: 8 days

tag: growth condition

value: long-day condition (16 h ligh/8 h dark)

value: seedling


title: LD_ZT41

status: Public on Jan 14 2020

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

tag: age

tag: tissue


title: LD_ZT44


title: APP_WT_O_09

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

description: nm.mRNA.mmu.txt

data_processing:
Reads were pre-processed and mapped using BaseSpace SecondaryAnalysis (version 2.4.19.6, basespace.illumina.com), filtering out abundant sequences and trimming 2bp from the 5’ end. Reads were aligned against the mm10/GRCm38 Mus musculus reference genome by Tophat2 (version 2.0.7).
We found in 2 of the 12 APPtg-O mice a 46% lower expression levels of hsa-APPswe, a 26% lower expression of hsa-Psen1L166p and a 24% reduction in mmu-Thy1 gene, which drives the expression of the transgenes (see Suppl. Fig.1). In the absence of an explanation for this phenomenon, these two mice were excluded from all further analyses.
mRNAs with average raw read counts ≤ 5 in 10 out of 96 samples were discarded, leaving 15824 mRNAs for differential expression (DE) analysis. Non-biological variation due to library preparation technicalities (i.e. effects for library prep batch, RNA extraction group and RNA concentration) was removed by the removeBatchEffect function from limma package 3.22.7 Bioconductor/R (3). DE analysis was conducted using a 2-way interaction model (age, genotype, age*genotype) and performing Benjamini-Hochberg p-value adjustment for multiple testing.
Genome_build: mm10/GRCm38 Mus musculus reference genome
Supplementary_files_format_and_content: tab-delimited text file containing read counts after Limma Voom normalisation for all Samples

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice were co-housed and had ad libitum access to food and water.

extract_protocol:
Total RNA was extracted by homogenizing the left hippocampus in TRIzol (Invitrogen, Carlsbad, CA, USA) using 1ml syringes and 22G/26G needles and purified on mirVana spin columns according to the manufacturer’s instructions (Ambion, Austin, TX, USA). RNA purity (260/280 and 260/230 ratios) and integrity was assessed using  Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer with High Sensitivity chips (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), respectively.
Library preparation and sequencing was performed at the VIB Nucleomics Core (Leuven, Belgium) using 1 μg of total RNA per sample. Poly-A containing mRNA molecules were purified using Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E) and poly-T oligo-attached magnetic beads. After reverse transcription with random primers, different barcodes were introduced to each sample by ligating a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments and multiple indexing adapters and 10 cycles of PCR amplification were performed. 96 libraries were pooled and sequenced in 4 runs using NextSeq 500 High75 Output kits on an Illumina NextSeq 500 instrument (Illumina, San Diego, CA, USA).

treatment_protocol: Mice were sacrificed by cervical dislocation and the hippocampus was microdissected. Brain samples were snap frozen in liquid nitrogen and stored in -80°C until use.

value: hippocampus

tag: strain

tag: age (month)

tag: genotype

value: Wildtype


title: NAG rep 7

city: Richland

first: Daniel

middle: Torres

last: Naylor

state: WA

address: 3300 Stevens Drive, MSIN. J4-18

department: Biological Systems Division

country: USA

institute: Pacific Northwest National Laboratory

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + n-acetylglucosamine, rep 7.

data_processing:
Raw reads from all samples were aligned to a previously obtained soil metagenome using the Burrows Wheeler Aligner.
Resulting reads were converted to raw counts using HTSeq.
Only transcripts with at least 75 cumulative counts across the 15 samples, and with no more than 3 zero counts, were retained for downstream analysis.
The dataset was normalized using DESeq.
Statistical analyses were conducted using R.
Genome_build: Prosser soil metagenome, NCBI Bioproject PRJNA597444
Supplementary_files_format_and_content: tab-delimited text files include raw counts and variance-stabilized normalized counts for full dataset, as well as HTSeq output (raw counts) for each sample

organism: soil metagenome

source_name: Soil

extract_protocol:
Microbial cultures of a liquid culture were pelleted, flash frozen using liquid N2, and RNA was harvested using Trizol reagent. Ambien Turbo DNase was used to remove DNA, and MicrobExpress kit was used to deplete rRNA species before sending the purified mRNA to GENEWIZ for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: enrichment type

value: n-acetylglucosamine


title: NAG rep 8

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + n-acetylglucosamine, rep 8.


title: Pectin rep 3

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + pectin, rep 3.

value: pectin


title: APP_WT_O_10

description: nm.mRNA.mmu.txt


title: crz1hcm1dP_ET_60min_rep1

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
RNA-seq reads were aligned to the reference genome sacCer3 by using TopHat2 (version 2.1.1) with the maximal intron length set as 100 kb
A gene-level count summary table per sample was generated by using htseq-count (version 0.8.0)
Genome_build: sacCer3
Supplementary_files_format_and_content: A tab-delimited txt file for each sample: column 1 is yeast gene ID; column 2 is the raw read count at gene level generated by htseq-count

organism: Saccharomyces cerevisiae

growth_protocol: All strains are in the BY4741 background and were grown in synthetic media with ammonium chloride as a nitrogen source.

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
Ribo-Zero™ Magnetic Kit is used to remove RNA, remained RNA is then retrieved by ethonal precipitation. The retrieved RNA is fragmented using Ambion Fragmentation Solution. And according to Illumina solexa transcriptome sequencing protocol, random hexamer-primer was used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding A at 3’ end. After that, the fragments are ligated with sequencing adaptors. UNG is added before synthesizing the second cDNA strand. After the second strand degraded, dUTP is then converted to dTTP. Y-adaptor is added afterwards. Suitable fragments are selected as templates according to the agarose gel electrophoresis results for PCR amplification.

treatment_protocol: Yeast cells were pre-treated with ET buffer or 1μg/ml FK506 for 15 minutes prior to the addition of 200mM CaCl2. Samples were collected at 10-30 minute intervals following CaCl2 addition for RNA isolation.

tag: strain name

tag: strain information

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-∆PSIEIQ-3HA-HIS3

tag: pre-treatment

value: ET buffer

tag: time point

value: 60 minutes


title: APP_WT_O_08

description: nm.mRNA.mmu.txt


title: LD_ZT38


title: APP_WT_O_12

description: nm.mRNA.mmu.txt


title: APP_WT_O_07

description: nm.mRNA.mmu.txt


title: LD_ZT35


title: NAG rep 4

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + n-acetylglucosamine, rep 4.


title: Gentamycin rep 4

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + glucose + gentamycin, rep 4.

value: glucose+gentamycin


title: APP_WT_O_06

description: nm.mRNA.mmu.txt


title: LD_ZT32


title: APP_WT_O_05

description: nm.mRNA.mmu.txt


title: LD_ZT29


title: crz1hcm1dP_ET_90min_rep1

value: 90 minutes


title: LD_ZT26


title: crz1hcm1dP_ET_45min_rep1

value: 45 minutes


title: crz1hcm1dP_ET_0min_rep1

value: 0 minutes


title: LD_ZT23


title: crz1hcm1dP_ET_10min_rep1

value: 10 minutes


title: LD_ZT20


title: APP_WT_O_02

description: nm.mRNA.mmu.txt


title: APP_WT_O_03

description: nm.mRNA.mmu.txt


title: crz1_FK506_90min_rep1

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3


title: crz1hcm1dP_ET_30min_rep1

value: 30 minutes


title: crz1hcm1dP_ET_20min_rep1

value: 20 minutes


title: APP_WT_O_04

description: nm.mRNA.mmu.txt


title: crz1_FK506_60min_rep1


title: Gentamycin rep 2

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + glucose + gentamycin, rep 2.


title: U87-shPTPRN3-n1

city: Beijing

first: Liwei

last: Zhang

address: South 4th Ring West Road

department: Neurosurgery

institute: Beijing Tian Tan Hospital, Capital Medical University

data_processing:
Raw data was uploaded to usegalaxy website (https://usegalaxy.org/)
RNA-seq read quality was evaluated by FastQC (version 0.72)
Total RNA-seq reads were trimmed according to the standard parameters, then we got clean RNA-seq data
Clean RNA-seq data were mapped to the human reference genome (hg38) with RNA STAR (version 2.6.0b-1)
Gene expression levels were summaried as fragments per kilobase permillion reads sequenced (FPKM) using cufflinks (version 2.2.1.2). We used these processed data to do the informatic analysis
Genome_build: hg38
Supplementary_files_format_and_content: .csv flies include FPKM values for each sample

organism: Homo sapiens

source_name: U87 glioma cell

growth_protocol: Both shNC and shPTPRN U87 glioma cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (HyClone, Logan, UT, USA) and 100 IU/ml penicillin and streptomycin in a 5% CO2 incubator at 37°C

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-Seq Kit (KK8420) and NEB index primer (E7335S)

treatment_protocol: The empty FUGW-H1 vector and shPTPRN3 (GGAAGTCTGTATTCAGGATGG)  plasmids were packaged to lentiviruses. U87 cell line was infected by shNC and shPTPRN lentivirus, respectively

tag: cell type

value: glioma cell

tag: cell line

tag: shRNA


title: U87-shNC-n2

value: shNC


title: U87-shPTPRN3-n2


title: APP_WT_O_01

description: nm.mRNA.mmu.txt

value: hippocampus


title: Gentamycin rep 3

description: Enrichment of Prosser, WA soil microbes in liquid culture of M9 + glucose + gentamycin, rep 3.


title: LD_ZT17

value: 8 days

value: long-day condition (16 h ligh/8 h dark)

value: seedling


title: U87-shNC-n1


title: LD_ZT14


title: APP_TG_Y_12

description: nm.mRNA.mmu.txt

value: Transgenic


title: LD_ZT11


title: APP_TG_Y_11

description: nm.mRNA.mmu.txt


title: HMEC_ALKBH5

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: Cells were cultured in Medium 171 supplemented with MEGS: S0155. ALKBH5 overexpression was induced with the addition of 1 ug/mL doxycycline to media for 48 hours before collecting cells. Total RNA was extracted with a Direct-zol kit. See manufacturer's protocol, Zymo Research

data_processing:
Oxford Nanopore's Albacore and Guppy base-callers
Reads were aligned and resquiggled with Tombo v1.4
Coverage and fraction modified files were obtained using Tombo's text_output commands. Bedobs was used to convert the wig files to bed files before being interescted with the coverage file using bedtools.
Genome_build: hg19 and hg38(cDNA)
Supplementary_files_format_and_content: bedgraph and wig

extract_protocol:
Total RNA was poly-A selected with oligo dT magnetic resin before being used a input for Oxford Nanopore's direct RNA sequecing kit. See manufacturer's protocol
See manufacturer's protocols, Oxford Nanopore

value: Human Mammary Epithelial Cells (HMEC)

tag: genotype/variation


title: crz1_FK506_45min_rep1


title: crz1_FK506_20min_rep1


title: APP_TG_Y_10

description: nm.mRNA.mmu.txt


title: LD_ZT5

tag: ecotype


title: HEK293_shMETTL3

description: Cells were cultured in DMEM + 10% FBS. Total RNA was extracted with Trizol


title: HMEC_WT

description: Cells were cultured in Medium 171 supplemented with MEGS: S0155. Total RNA was extracted with a Direct-zol kit. See manufacturer's protocol, Zymo Research

value: WT


title: crz1_FK506_30min_rep1


title: LD_ZT8

tag: growth condition


title: crz1_FK506_0min_rep1


title: crz1_ET_90min_rep1

value: ET buffer


title: HEK293_WT


title: APP_TG_Y_09

description: nm.mRNA.mmu.txt


title: crz1_FK506_10min_rep1


title: APP_TG_Y_07

description: nm.mRNA.mmu.txt


title: LL_CT47

description: processed data file: LL_CT2_47_transcript_expr.txt

source_name: continuous light_seedling

tag: age

value: continuous light


title: APP_TG_Y_08

description: nm.mRNA.mmu.txt

tag: tissue


title: crz1_ET_60min_rep1

value: 60 minutes


title: APP_TG_Y_06

description: nm.mRNA.mmu.txt

tag: strain


title: LL_CT44


title: A3_NHG_293-WG

city: Cambridge

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

description: DMS-modified RNA

data_processing:
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu)
RNAstructure (v6.0.1) folding and VARNA (v3.93) visualization
.sam files generated with bowtie2, .dot files generated by RNAstucture, _Mu.txt files produced by DREEM clustering algorithm. The five processed data files reflect clustering on 5 distinct regions of the HIV-1 using DREEM and the whole-genome data as the input. The regions of interest were specified by the user and only reads that align to that region were used by DREEM for clustering to produce that corresponding file.
Genome_build: GRCh38;  HIV-1NHG(Genbank accession number JQ585717.1)
Supplementary_files_format_and_content: _Mu.txt files produced by DREEM clustering algorithm

organism:
Homo sapiens
Human immunodeficiency virus 1

source_name: HEK293t cells transfected with HIV-1 NHG

growth_protocol: HEK293t were grown in T75 and cultured in DMEM+ 10% FBS + Penn/strep. Transfections were done in 6-well plates with X-tremegene9.

extract_protocol:
For RING1B, SUZ12, JARID2, PCL2, AEBP2, EPOP, PCGF2, PCGF1 and PCGF6, cChIP-seq was performed as described previously (Fursova et al., 2019). Briefly, 5 x 10^7 mouse ESCs (untreated or following 72 hours OHT treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C with 2 mM DSG (Thermo Scientific) for 45 minutes, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched with 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 minutes at 4˚C. Released nuclei were washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 minutes at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 minutes using a BioRuptor Pico (Diagenode), shearing genomic DNA to an average size of 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST, D22F2, 3 ul), anti-SUZ12 (CST, D39F6, 3 ul), anti-PCGF1 (in-house, 5 ul), anti-PCGF2 (Santa Cruz, sc-10744, 3 ul), anti-JARID2 (CST D6M9X, 3 ul), anti-PCL2 (GenWay GWB-FA7207, 2 ul), anti-AEBP2 (CST #D7C6X, 10 ul), anti-PCL2 (Active motif #61753, 5 ul), or anti-PCGF6 (3 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 1 hour at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al., 2012). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65oC with 200 mM NaCl and 2 ul RNase A (Sigma). A matched input sample (10% of original ChIP reaction) was identically treated. The following day, ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56oC and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). Native cChIP-seq for H2AK119ub1, H3K27me3, and H3K4me3 was performed as described previously (Fursova et al., 2019). Briefly, 5 x 10^7 mouse ESCs (both untreated and following 72 hours OHT treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitor cocktail (Roche)). Each sample was incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4oC with 5 ul of anti-H2AK119ub1 (CST D27C4), 5 ul of anti-H3K27me3 (in-house), or 3 ul anti-H3K4me3 (in-house) antibody. Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform.

treatment_protocol: DMS-treatment for RNA secondary structure analysis,  2% DMS at 37C for 5 minutes

tag: human cell type or cell line

tag: infection or transfection

value: transfected with HIV-1 NHG


title: LL_CT41


title: 9665_RRECD4

data_processing:
library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu)
RNAstructure(v6.0.1) folding and VARNA (v3.93) visualization
Genome_build: GRCh38;  HIV-1NL4-3 (Genbank accession number AF324493.1)
Supplementary_files_format_and_content: .sam files generated with bowtie2, .dot files generated by RNAstucture, _Mu.txt files produced by DREEM clustering algorithm. Multiple Mu files were generated for RREmutA and RREmutB by computationally mixing reads from the two samples in specified proportions in order to validate the ability of DREEM to accurately deconvolute the separate structures.

source_name: HIV-1 NL4-3 infected CD4 + T cells

growth_protocol: CD4+ T cells were grown in T75 flasks and cultured in RPMI1640 + 10%FBS + Penn/strep, maintained at a concentration of ~1-3million/mL. CD4+ T cells were activated with 10ug/mL PHA and 100U/mL IL-2.

extract_protocol:
DMS-treated cells were pelleted and resuspended in 1 mL Trizol, RNA was extracted by chloroform extraction and isopropanol precipitation.
3'Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. rRNA was subtracted with RiboZero, and RT was performed with TGIRT-III. cDNAs were isolated by gelextraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer.

treatment_protocol: DMS-treatment for RNA secondary structure analysis, between 0.2-2% DMS at 37C for 5 minutes

value: CD4+ T Cells

tag: molecule subtype

value: DMS-modified RNA


title: crz1_ET_45min_rep1

value: MATa ura3∆0 leu2∆0 his3∆0 met15∆0 crz1∆::KanMx Hcm1-3HA-HIS3

value: 45 minutes


title: 9666_RRECD4


title: APP_TG_Y_05

description: nm.mRNA.mmu.txt

tag: age (month)

tag: genotype


title: LD_ZT2


title: APP_TG_Y_03

description: nm.mRNA.mmu.txt


title: LL_CT38


title: APP_TG_Y_04

description: nm.mRNA.mmu.txt


title: LL_CT35


title: crz1_ET_30min_rep1

tag: strain name

tag: strain information

value: 30 minutes


title: LL_CT32


title: crz1_ET_10min_rep1

tag: pre-treatment

tag: time point

value: 10 minutes


title: APP_TG_Y_02

description: nm.mRNA.mmu.txt

value: hippocampus


title: LL_CT26

value: 8 days


title: APP_TG_Y_01

description: nm.mRNA.mmu.txt


title: APP_TG_O_12

description: nm.mRNA.mmu.txt


title: LL_CT20


title: crz1_ET_0min_rep1

value: 0 minutes


title: 360 minute incubation RepC

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

data_processing:
Analysis with FastQC followed by trimming if a nucleotide had a Phred score of < 25.  Adaptors were not present in the reads and so adaptor trimming was unnecessary
Alignment to the Neisseria gonorrhoeae FA1090 genome using the Burrows Wheeler Aligner
Counting using HTSeq
Normalization of raw counts and determination of differentially expressed genes using DESeq2
Genome_build: Neisseria gonorrhoeae FA1090 (NCBI: NC_002946.2)
Supplementary_files_format_and_content: Normalized_Expression_Levels_PMNs

organism: Neisseria gonorrhoeae 1291

source_name: 360 minute incubation

growth_protocol: N. gonorrhoeae 1291 wild-type was harvested from isovitalex supplemented GC medium base plates after overnight growth and transferred into GC broth.  They were grown to early log phase and harvested for PMN infections when they reached an optical density of 0.3 at 600 nm wavelength.

extract_protocol:
RNA was extracted with TRIzol
rRNA depletion with Epicentre MetaScript Ribo-Zero rRNA removal kit.  cDNA was generated with the NuGen Ovation RNA-Seq system, v2 and was sheared using a Covaris E220 to give an average fragment size of 300 bp.  500 ng of each cDNA were used to generate indexed libraries using the KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA, Cat. No. KK8500).  The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into a pool for sequencing. The concentration of the pool was measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA)
The sequencing pool was loaded into a single lane of an Illumina HiSeq 2500 flow cell running 150 bp paired-end SBS v4 sequencing chemistry

treatment_protocol: N. gonorrhoeae 1291 was fed to PMNs at 10:1 MOI for 10 minutes followed by removal of unbound bacteria then incubation at 37 °C for 10 minutes and 180 minutes.

tag: protocol

value: incubated with human PMNs

tag: time

value: 360 minutes


title: 360 minute incubation RepD


title: APP_TG_O_10

description: nm.mRNA.mmu.txt

value: Transgenic


title: crz1_ET_20min_rep1

value: 20 minutes


title: 360 minute incubation RepB


title: LL_CT29

value: seedling


title: 360 minute incubation RepA


title: APP_TG_O_09

description: N.A.


title: LL_CT17

value: continuous light


title: 180 minute incubation RepD

source_name: 180 minute incubation

value: 180 minutes


title: LL_CT23


title: APP_TG_O_08

description: nm.mRNA.mmu.txt


title: APP_TG_O_11

description: nm.mRNA.mmu.txt


title: 180 minute incubation RepB


title: APP_TG_O_06

description: nm.mRNA.mmu.txt


title: LL_CT14


title: LL_CT11


title: LL_CT8


title: APP_TG_O_05

description: nm.mRNA.mmu.txt


title: 180 minute incubation RepA


title: Activated cardiac fibroblasts of MI hearts 5 days post MI. Biological Rep. 3

type: RNA

city: Duesseldorf

first: Christoph

last: Owenier

address: Universitätsstraße 1

department: Molecular Cardiology

country: Germany

institute: Uniklinik Duesseldorf

hyb_protocol: After fragmentation labeled cDNA was hybridized to Applied Biosystems™ Clariom™ S Mouse Gene Expression Microarrays for 16 hr at 45°C and stained by streptavidin/phycoerythrin conjugate, according to the manufacturer's protocol. Fluidics Station 450 was used.

scan_protocol: Using the Affymetrix Calvin Scan Acquisition on the Affymetrix GeneChip Scanner 3000 7G with the Affymetrix GeneChip Command Console Scan Control Version 4.0.0.1567.

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by GeneSprings’ ExonSSTRMAWithoutStabilization algorithm after quantile normalization of probe-level signal intensities across all samples to reduce interarray variability (Bolstad et al., 2003). Input data preprocessing was concluded by baseline transformation to the median of all samples. After grouping of samples (five biological replicates each) according to their respective experimental condition, a given probe set had to be expressed above background (i.e., fluorescence signal of that probe set was detected within the 20th and 100th percentiles of the raw signal distribution of a given array) in all five replicates in at least one of three conditions to be further analyzed in pairwise comparisons.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps
sst-rma from GeneSpring GX software (Vers. 12.5; Agilent Technologies), normalized log scale

label: biotin

source_name: Wild-type murine heart

label_protocol: According to the manufacturer's protocol: 1 ng of total RNA were converted to cDNA, amplified to complementary RNA (cRNA) followed by in vitro transcription and biotin labeling of cDNA.

growth_protocol: Isolated fibroblasts and epicardial stromal cells isolated from unstressed control mouse hearts (CF1-5) and infarcted hearts 5 days post MI (EpiSC1-5; aCF1-5)

extract_protocol: For the simultaneous isolation of aCFs and EpiSCs from the infarcted murine heart (5 days post-MI), a novel isolation technique was developed, which combines the enzymatic digestion of the isolated perfused heart (Langendorff) with the simultaneous enzymatic removal of EpiSCs from the cardiac surface by applying mild shear forces. Isolated hearts were digested with collagenase solution [1200 U/mL collagenase CLS II (Biochrom, Berlin, Germany) in PBS] for 8 min at 37°C. Simultaneously, the heart was immersed in a 5 mL Eppendorf tube containing pre-warmed collagenase solution. Small plastic rods glued to the tube permitted shaking of the tube by a motor-driven eccentric disc at 80 rpm. The tip of the tube was continuously moved by approximately 15mm from its original position, which creates moderate shear forces to ensure epicardial cell removal from the heart surface.For the isolation of CFs from uninjured hearts it was not necessary to apply shear forces due to the absence of the activated epicardial layer.    In case of CFs/aCFs, the atria of the heart were removed and the digested ventricular tissue was transferred into Dulbecco’s modified eagle medium containing 10% fetal calf serum to stop collagenase activity. The digested tissue was then gently pulled apart with forceps and dispersed by pipetting 10 times up and down using a 5 mL pipette to achieve a single cell suspension (within 1 min). The cell suspension was passed through a 100 µm cell strainer (BD Biosciences, Franklin Lakes, NJ, USA) followed by 1 min centrifugation at 55 g at room temperature (RT) to separate the non-myocyte fraction, containing CFs/aCFs, from cardiomyocytes. The supernatant with the non-myocytes fraction was passed through a 40 µm cell strainer and centrifuged for 7 min at 300 g and RT. Supernatant was discarded and the cell pellet was resuspended in PBS supplemented with 2% FCS and 1 mM EDTA. In case of EpiSCs, the collected overflow was centrifuged for 7 min at 300 g at RT and the cell pellet was resuspended in PBS supplemented with 2% FCS and 1 mM EDTA. Cell purification was performed by FACS for cells positive for the markers CD90.2, Mefsk-4, and Pdgfr-α but negative for CD31, CD45, and 7-AAD (viability marker). CFs from healthy control hearts as well as aCFs and EpiSCs from hearts 5 days post-MI were isolated as described above. Total RNA samples were isolated with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol and were quantified and quality measured by capillary electrophoresis Bioanalyzer assay (Eukaryote Total RNA Pico, Agilent, Santa Clara, CA, USA) prior Microarray Analysis.

treatment_protocol: EpiSC and aCF samples were isolated from infarcted hearts. Myocardial infarction was induced 5 days prior isolation.

value: 8-12 weeks

value: Heart

tag: cell type


title: LL_CT2

tag: ecotype


title: LL_CT5

tag: growth condition


title: Activated cardiac fibroblasts of MI hearts 5 days post MI. Biological Rep. 5

tag: age


title: Activated cardiac fibroblasts of MI hearts 5 days post MI. Biological Rep. 2

tag: tissue


title: APP_TG_O_04

description: nm.mRNA.mmu.txt

tag: strain


title: 180 minute incubation RepC


title: non-model organism

city: Xiamen

first: Runwei

state: Fujian

address: No.43, yindou road

department: Fisheries College

institute: Jimei University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Assembling of the clean reads were carried out by using CLC Genomics Workbench version:6.0.4
Unigene abundance measurements were generationed and normalized  using Reads Per Kilobase of exon per Megabase of library size (RPKM)
Genome_build: no reference genomics
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values and raw fragment counts for each Sample

organism: Epinephelus coioides

source_name: Heart, muscle, gill filament, spleen, intestine, liver, gonad, kidney,hepatopancreas

extract_protocol:
RNA was harvested using RNAiso Plus Total RNA extraction reagent (Cat#9109).
Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: tag

value: tissue

value: 3 months


title: Activated cardiac fibroblasts of MI hearts 5 days post MI. Biological Rep. 4


title: Activated cardiac fibroblasts of MI hearts 5 days post MI. Biological Rep. 1


title: Epicardial stromal cells of MI hearts 5 days post MI. Biological Rep. 5


title: APP_TG_O_03

description: N.A.


title: APP_TG_O_07

description: nm.mRNA.mmu.txt


title: 10 minute incubation RepA

source_name: 10 minute incubation


title: 9349_RREvirion

organism: Human immunodeficiency virus 1

source_name: HIV-1 NL4-3 virions isolated from infected CD4 + T cells

growth_protocol: CD4+ T cells were grown in T75 flasks and cultured in RPMI1640 + 10%FBS + Penn/strep, maintained at a concentration of ~1-3million/mL. CD4+ T cells were activated with 10ug/mL PHA and 100U/mL IL-2. Virions were isolated from supernatant by ultracentrifugation.

tag: human cell type or cell line

value: CD4+ T Cells

value: DMS-modified RNA


title: APP_TG_O_02

description: nm.mRNA.mmu.txt


title: 10 minute incubation RepB

value: 10 minutes


title: APP_TG_O_01

description: nm.mRNA.mmu.txt

value: hippocampus


title: Epicardial stromal cells of MI hearts 5 days post MI. Biological Rep. 4


title: 8461rreUT

source_name: gBlock

tag: sample type

value: in vitro transcribed

tag: molecule subtype

value: RNA


title: SAMPLE 4: Tumor, patient 1

city: Shenyang

first: Ming

last: He

state: Liaoning

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/au/analyze/
For the normalization it uses the average of five housekeeping genes: 18S rRNA, ACTB, B2M, GAPDH, HPRT1.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (tumor/adjacent) ratios.

label: SYBR Green

source_name: Osteosarcoma

label_protocol: PCR assays were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Hilden, Germany). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: Adjacent tissues and tumor tissues were collected simultaneously. All the resected or biopsy specimens were placed immediately into liquid nitrogen and stored at - 80°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) followed by Ribonuclease R treatment (RNase R; Epicenter, Madison, USA).

tag: gender

value: male

value: tibia

value: circular RNAs


title: SAMPLE 6: Tumor, patient 3

description: Test

value: female

value: femur


title: SAMPLE 3: Adjacent, patient 3

description: Control

source_name: Adjacent tissue


title: 9648_RREshort


title: SAMPLE 5: Tumor, patient 2

description: Test


title: RREmutB


title: Epicardial stromal cells of MI hearts 5 days post MI. Biological Rep. 3


title: Add_ribo_NOADD

data_processing:
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu)
RNAstructure(v6.0.1) folding and VARNA (v3.93) visualization
Genome_build: Adenosine deaminase (add) riboswitch corresponds to nucleotides 1590535-1590663 of V.vulnificus strain (Genbank Accession code CP037932.1). The U4/6 core-domain RNA construct is based on the interface of the U4 and U6 snRNA (Genbank accession code 2N7M_X).
Supplementary_files_format_and_content: _Mu.txt files produced by DREEM clustering algorithm

organism: Vibrio vulnificus

growth_protocol: In vitro transcribed and DMS modified RNA

tag: treatment

value: No adenine

value: In vitro transcribed RNA


title: Epicardial stromal cells of MI hearts 5 days post MI. Biological Rep. 2

value: 8-12 weeks


title: SAMPLE 2: Adjacent, patient 2

description: Control


title: Add_ribo_ADD

value: 5 mM adenine


title: Epicardial stromal cells of MI hearts 5 days post MI. Biological Rep. 1

value: Heart


title: cardiac fibroblasts of unstressed control hearts. Biological rep. 5


title: 9652_RREshort


title: RREmutA

value: In vitro transcribed


title: MM254-RNAseq

status: Public on Jan 13 2020

city: Toronto

first: Ali

last: Mahdipour Shirayeh

state: Ontario

address: 101 College St

department: Princess Margater Cancer Centre / Faculty of Medicine

country: Canada

institute: University Health Network / University of Toronto

description: Single cell RNA-seq (10X Genomics) profiles of plasma cells and B cells from the bone marrow of a patient with multiple myeloma (MM). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage. For the processed file, cells other than MM plasma cells (MMPCs) were excluded. MMPC were identified by gene expression-based clustering and their identity was confirmed by their expression of specific plasma cell markers and clonal immunoglobulin isotype.

data_processing:
Raw sequencing reads of single cell RNA-seqs were de-multiplexed using Illumina bcl2fastq software and then mapped to the GRCh38 human genome reference using the gene model available at the 10X Genomics online resource.
Then raw sequencing reads were filtered and consolidated into unique mRNA counts per gene per cell using the CellRanger 2.1.0 pipeline (10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: txt

source_name: Bone marrow

extract_protocol:
Research bone marrow samples were obtained from MM patients at The Princess Margaret Cancer Centre at the time of routine clinical biopsy following informed consent in compliance with the Declaration of Helsinki and a protocol approved by the University Health Network Research Ethics board. Cells were collected in heparinized tubes and processed by Ficoll-Plaque gradient. Plasma cells and B cells were enriched on a Beckman Coulter FACSAria by FSC-SSC characteristics, negative selection for duplets (by FSC and SSC height versus area), negative selection for lineage markers (CD14, CD2, GYPA) and non viable cells (7AAD); and by positive selection for CD38, CD138 or for CD20, as described1. Cell viability was >95% post FACS.
Single cell RNA-sequencing libraries were prepared from FACS-purified plasma cells and B cells (pooled) using the 10X Genomics Chromium Single Cell 3’ or 5’ library performed by Illumina Hiseq 2500 & Gel bead kit v2 and Chromium Single Cell Controller according to the user guide, targeting 3-6,000 cells per sample. Library constituents incorporated a 26bp read 1, 98bp read 2 and an 8bp sample index.
Whole exome sequencing libraries were prepared from FACS-purified bone marrow plasma cells as well as from buccal swab cells. DNA was sheared using a Covaris instrument, and 200ng of the sheared product was used for library preparation utilizing the SureSelectXT low input reagent kit. Library quantity and quality were verified by Bioanalyzer. Whole exome sequencing was performed using an Illumina Hiseq 2500.

value: Plasma cells

tag: chip antibody


title: MM283-RNAseq


title: cardiac fibroblasts of unstressed control hearts. Biological rep. 4


title: MM199-Buccal-WES

description: Whole exome sequencing (WES) profile of genomic DNA of oral mucosal cells from buccal swab of a patient with multiple myeloma (MM199-Buccal-WES). Used as a control for comparison with tumor cell sequencing.

library_source: genomic

molecule: genomic DNA

source_name: Buccal swab

value: Oral mucosal cells


title: cardiac fibroblasts of unstressed control hearts. Biological rep. 3


title: cardiac fibroblasts of unstressed control hearts. Biological rep. 2


title: MM241-RNAseq


title: MM296-RNAseq


title: SAMPLE 1: Adjacent, patient 1

description: Control


title: MM207-RNAseq


title: cardiac fibroblasts of unstressed control hearts. Biological rep. 1


title: MM237-RNAseq

description: Single cell RNA-seq (10X Genomics) profiles of plasma cells and B cells from the bone marrow of a patient with multiple myeloma (MM). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage.

value: B cell lineage


title: MM244-RNAseq


title: MM199-RNAseq


title: MM238-RNAseq/NormalPCs-RNAseq

description:
Single cell RNA-seq (10X Genomics) profiles of plasma cells and B cells from the bone marrow of a patient with multiple myeloma (MM). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage.
Single cell RNA-seq (10X Genomics) profiles of plasma cells and B cells from the bone marrow of a patient with multiple myeloma (MM) , more precisely from sample 2 (MM238-RNAseq). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage. For the processed file, cells other than normal plasma cells (NPCs) were excluded. NPCs were identified by gene expression-based clustering and their identity was confirmed by their expression of specific plasma cell markers and the absence of tumor clone CNV. Cells expressing the MM clone immunoglobulin isotype were excluded.


title: MM199-WES

description: Whole exome sequencing (WES) of DNA from plasma cells from the bone marrow of a patient with multiple myeloma (MM199-WES). FACS was used to isolate plasma cells from other bone marrow cells.  WES was performed on 200ng DNA, purified from 1.9x10^6 cells.


title: H1201852

city: harbin

first: Lishuang

last: Qi

address: No. 157, Baojian Road, Nangang District

department: College of Bioinformatics Science and Technology

institute: Harbin Medical University

description: processed data file: readcounts_featurecounts.txt, FPKM_normalized.txt

data_processing:
Paired-end reads were filtered and trimmed using software fastp
Clean fastq reads were aligned to human HG38 reference genome using software HISAT2 with default settings
Raw read count estimation using featureCounts 1.6.3 with gene annotation from GENCODE v32, gencode.v26.annotation.gtf, Settings: -g gene_id -t exon
The Fragments per Kilobase of transcript per Million mapped reads (FPKM) calculation normalizes read count by dividing it by the gene length and the total number of reads mapped to all genes
Genome_build: GRCh38 (HG38)
Supplementary_files_format_and_content: Tab-separated matrices with FPKM and read counts, respectively.

source_name: lung adenocarcinoma

extract_protocol:
Total RNA was extracted using RNeasy FFPE Kit (Cat#73504, QIAamp) according to the manufacture’s protocol. The purity and concentration of total RNA was determined by Nano Drop One spectrophotometer according to OD260/280 reading and Qubit 3.0 fluorescence quantifier, respectively. The Agilent 4200 bioanalyzer was used to assess RNA Integrity Number (RIN).
RNA-seq libraries were constructed using NEBNext UItra Directional RNA Library Prep Kit (NEB USA) according to the manufacturer’s protocol.

tag: histology

value: lung adenocarcinoma

value: Male

tag: Stage

value: IB

tag: t

tag: n

tag: time to last followup (month)

tag: survstatus

tag: chemotherapy

value: No

tag: radiotherapy


title: H1219341

tag: age

value: Female


title: H1309040

value: IA


title: H1214854


title: H1410722


title: H1404057


title: H1207164


title: H1315723


title: H1214577


title: H1207062


title: H1200782


title: H1306068


title: H1205324


title: H1117322


title: H1212849


title: H1207362


title: H1128468


title: H1224785


title: H1117899


title: MDA-MB-231_siControl

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from MDA-MB-231 cells treated with control siRNA

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hours at 45C on Affymetrix GeneChip (Human Gene 1.0ST Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: MDA-MB-23 cells treated with siControl

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human breast cancer MDA-MB-231 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MDA-MB-231 cells were transfected with siRNA for 48 hours.

tag: sirna treatment

value: siControl


title: MDA-MB-231_siNONO

description: Gene expression data from MDA-MB-231 cells treated with siRNA targeting NONO

source_name: MDA-MB-23 cells treated with siNONO

value: siNONO


title: MCF-7_E2(+)_siControl

description: Gene expression data from MCF-7 cells treated with control siRNA in the presence of E2

source_name: MCF-7 cells treated with siControl in the presence of E2

growth_protocol: Human breast cancer MCF-7cells were maintained in phenol red-free Dulbecco's modified Eagle's medium (DMEM) with charcoal stripped-FBS.

treatment_protocol: MCF-7 cells transfected with siRNA were treated with 10 nM E2 (17-beta estradiol) or vehicle (ethanol) for 12 hours.

tag: estrogen treatment


title: MCF-7_E2(+)_siPSF

description: Gene expression data from MCF-7 cells treated with siRNA targeting PSF in the presence of E2

source_name: MCF-7 cells treated with siPSF in the presence of E2

value: siPSF


title: MCF-7_E2(+)_siNONO

description: Gene expression data from MCF-7 cells treated with siRNA targeting NONO in the presence of E2

source_name: MCF-7 cells treated with siNONO in the presence of E2


title: H1203610


title: MCF-7_E2(-)_siPSF

description: Gene expression data from MCF-7 cells treated with siRNA targeting PSF in the absence of E2

source_name: MCF-7 cells treated with siPSF in the absense of E2


title: MCF-7_E2(-)_siControl

description: Gene expression data from MCF-7 cells treated with control siRNA in the absence of E2

source_name: MCF-7 cells treated with siControl in the absense of E2


title: MCF-7_E2(-)_siNONO

description: Gene expression data from MCF-7 cells treated with siRNA targeting NONO in the absence of E2

source_name: MCF-7 cells treated with siNONO in the absense of E2


title: H1119662


title: H1203616


title: H1116430


title: H1109702


title: H1109081


title: H1110269


title: H1108343


title: H1112431


title: H1111618


title: Low dose [E2]

city: Shanghai

first: Hailong

last: Ma

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic v0.36
HISAT2 v2.1.0 was used to map the clean reads with Homo_sapiens.GRCh38 whole genome
In order to achieve high-quality data, five tools (CPC2, PLEK, CNCI, Pfam and CPC2) were used to identify the candidate lncRNAs. Transcripts prediction with coding potential by any of the five tools was filtered out. And those without coding potential were retained. Then the shared lncRNAs by those five tools were selected as high confidence lncRNAs, and was used for further analysis.
The direct expression of a gene expression level is the abundance of its transcript, and then transcripts abundances were quantified by StringTie (version 1.3.3b). The software was used to calculate Transcripts Per Million (TPM) of both protein-coding genes and lncRNAs in each sample.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: HNSCC cell line

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Approximately 3 μg RNA per sample was used as input material for the RNA sample preparations. First, ribosomal RNA was removed by using an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, Madison, WI, USA), and rRNA-free residue was removed by ethanol precipitation. Subsequently, the high strand-specificity of the libraries was generated using the rRNA-depleted RNA of the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA), following manufacturer’s recommendations. Briefly, fragmentation was conducted using divalent cations under elevated temperature in NEB Next. First-strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNaseH-). Second-strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of the DNA fragments, NEB Next adaptors with a hairpin loop structure were ligated to prepare for hybridization. To preferentially select cDNA fragments of 150–200 bp in length, the library fragments were purified with an AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μL USER Enzyme (NEB, Ipswich, MA, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then,PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers, and Index (X) Primers. Finally, the PCR products were purified (AMPure XP system), and library quality was assessed on an Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA), following the manufacturer’s instructions

tag: group

value: Low dose


title: High dose [F2]

value: High dose


title: Low dose [E1]


title: High dose [F1]


title: H1112116


title: High dose [C2]


title: Control [D2]

value: Control


title: Control [D1]


title: Control [A1]


title: Low dose [B1]


title: High dose [C1]


title: OB_3

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Pairend reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a)
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and normalized using DESeq2 (v1.20.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: Olfactory bulb

extract_protocol:
The olfactory bulb, hippocampus, cortex, and brainstem from 16-week old Aldh1l1–eGFP mice was dissected, dissociated, and FAC sorted into QIAGEN RLT lysis buffer (Cat# 74004) with 1% ß-Mercaptoethanol. RNA was isolated using the RNeasy Micro Kit (74004, QIAGEN).
Illumina sequencing libraries were constructed from 5ng of total RNA using the Trio RNA-Seq System (0507-96, NuGEN).

tag: cell type

value: Aldh1l1-GFP positive astrocytes

tag: strain

tag: tissue

value: Olfactory bulb


title: OB_2


title: BS_3

source_name: Brainstem

value: Brainstem


title: BS_1


title: HC_3

source_name: Hippocampus

value: Hippocampus


title: CX_1

source_name: Cortex

value: Cortex


title: BS_2


title: CX_2


title: HC_1


title: Control [A2]


title: HC_2


title: Low dose [B2]


title: Oscillation Ex5 Time Point 15 [Mm]

city: Kyoto

first: Cantas

last: Alev

address: Medical Faculty Bldg. B, Yoshida-Konoe-cho, Sakyo-ku

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the mm10 mouse reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE vM20 annotation gtf file.
The uniquely mapped reads (MAPQ>=20) were counted using HTSeq (version 0.6.1) with the human GENCODE vM20 annotation gtf file (protein_coding genes).
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file includes raw counts of sequenced reads for each sample obtained with HTSeq-count.

source_name: Hes7-luciferase Epi-SC reporter derived murine PSM Ex5

growth_protocol: Mouse epiblast stem cells (EpiSCs) were obtained from RIKEN BRC (#AES0204) (Sugimoto et al., Stem Cell Reports, 2015) and maintained on fibronectin coated dish with DMEM/HamF12 containing 15% KSR, nonessential amino acids (0.1 mM), β-mercaptoethanol (0.1 mM), Activin A (20 ng/ml), bFGF (10 ng/ml) and IWR-1-endo (2.5 µM).

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were generated from 200 ng total RNA using  the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's instructions

treatment_protocol: EpiSCs were seeded on 35 mm dishes coated with fibronectin and cultured overnight with the medium containing Y27632 (10 µM), Activin A (20 ng/ml) and bFGF (10 ng/ml) but without IWR-1-endo. Then the medium was changed into CDMi containing SB431542 (10 µM), LDN193189 (250 nM), CHIR99021 (10 µM) and bFGF (20 ng/ml). After 30 hours, the medium was changed again into CDMi containing SB431542 (10 µM), LDN193189 (250 nM), CHIR99021 (1 µM) and bFGF (20 ng/ml). The luminescence was continuously monitored with Kronos Dio Luminometer using one sample, and the other 16 samples were frozen at each time point.

tag: background line

value: AES0204 based Hes7-reporter

value: PSM (presomitic mesoderm)

tag: time

value: 405 min


title: Oscillation Ex5 Time Point 16 [Mm]

value: 425 min


title: OB_1


title: GFP-negative rep1

city: Iowa City

first: Robert

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
Sequencing reads were trimmed with Trimmomatic (0.35).
Trimmed paired reads were pseudoaligned and quantified with kallisto (v0.41; default parameters)
The output datasets from kallisto were normalized and compared using the sleuth program
Genome_build: danRer10
Supplementary_files_format_and_content: TPM.csv, kallisto_abundance.tsv

organism: Danio rerio

source_name: Tg(krt4:GFP) embryos

extract_protocol:
Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit (Ambion, Foster City, CA) and treated with Turbo DNase I (Ambion, Austin, TX) to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM-5 Kit (Zymo Research, Irvine, CA).
1 ug of RNA was subjected to first-strand cDNA synthesis and cDNA amplification using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio, Kusatsu, Shiga, Japan). Purified cDNA was quantified using Qubit, and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, CA), following the manufacturer’s instructions.

treatment_protocol: FACS sort GFP-positive and GFP-negative cells

value: 4-somite stage

tag: gfp

value: negative

value: non-periderm


title: GFP-negative rep2


title: Oscillation Ex5 Time Point 14 [Mm]

tag: Stage

value: 385 min


title: GFP-negative rep3


title: Oscillation Ex5 Time Point 10 [Mm]

value: 305 min


title: Oscillation Ex5 Time Point 12 [Mm]

value: 345 min


title: Oscillation Ex5 Time Point 11 [Mm]

value: 325 min


title: GFP-positive rep2

value: positive

value: periderm


title: GFP-positive rep3


title: Oscillation Ex5 Time Point 13 [Mm]

value: 365 min


title: Oscillation Ex5 Time Point 8 [Mm]

value: 270 min


title: GFP-positive rep1


title: Oscillation Ex5 Time Point 7 [Mm]

value: 255 min


title: Oscillation Ex5 Time Point 9 [Mm]

value: 285 min


title: Oscillation Ex5 Time Point 2 [Mm]

value: AES0204 based Hes7-reporter

value: 180 min


title: Oscillation Ex5 Time Point 5 [Mm]

value: PSM (presomitic mesoderm)

value: 225 min


title: Oscillation Ex5 Time Point 4 [Mm]

value: 210 min


title: Oscillation Ex5 Time Point 6 [Mm]

value: 240 min


title: Oscillation Ex5 Time Point 1 [Mm]

value: 165 min


title: Oscillation Ex4 Time Point 16 [Mm]

source_name: Hes7-luciferase Epi-SC reporter derived murine PSM Ex4

value: 405 min


title: Oscillation Ex4 Time Point 15 [Mm]

value: 385 min


title: Oscillation Ex4 Time Point 14 [Mm]


title: Oscillation Ex4 Time Point 13 [Mm]

value: 345 min


title: Oscillation Ex4 Time Point 10 [Mm]

value: 292 min


title: Oscillation Ex4 Time Point 11 [Mm]

value: 310 min


title: Oscillation Ex4 Time Point 12 [Mm]

value: 327 min


title: sCJD_50752_smallRNASeq

city: London

first: Simon

last: Mead

address: 33 Cleveland St

department: MRC Prion Unit at UCL

country: United Kingdom

institute: University College London

data_processing:
Base-calling carried out by Illumina MiSeq.
Removal of adapter sequences and trimming of reads to minimum length 15bp with minimum quality score 25.
Reads aligned to Hg38 using Bowtie v2.2.5: seed length of 10 with 1 mismatch.
Quantification and normalization carried out with Cufflinks v2.2.1 default settings.
Genome_build: Hg38

source_name: PAX preserved peripheral whole blood

extract_protocol:
Total RNA extracted from 1ml PAX preserved whole blood using Norgen Biotek Preserved Blood RNA Purification Kit II followed by DNAse I digestion using Zymo Research RNA Clean & Concentrator-5 columns.
Illumina TruSeq Small RNA Library Prep Kit followed by size selection using the Sage Science PippinPrep system

tag: disease status

value: sCJD

tag: Sex

value: Male

tag: age at sampling

value: whole blood

tag: rna integrity number (rin)

tag: sample age proxy

tag: prnp codon 129 genotype

value: VV

tag: mrc scale score


title: sCJD_47015_smallRNASeq

value: MM


title: sCJD_48884_smallRNASeq


title: sCJD_48466_smallRNASeq


title: sCJD_47981_smallRNASeq

value: Female


title: sCJD_46880_smallRNASeq


title: sCJD_48573_smallRNASeq


title: sCJD_49585_smallRNASeq


title: sCJD_47537_smallRNASeq


title: sCJD_48487_smallRNASeq


title: sCJD_51022_smallRNASeq


title: sCJD_46954_smallRNASeq

value: MV


title: sCJD_47923_smallRNASeq


title: Oscillation Ex4 Time Point 9 [Mm]

value: AES0204 based Hes7-reporter

value: PSM (presomitic mesoderm)

value: 275 min


title: sCJD_46829_smallRNASeq


title: sCJD_46408_smallRNASeq


title: Oscillation Ex5 Time Point 3 [Mm]

value: 195 min


title: Oscillation Ex4 Time Point 8 [Mm]

value: 260 min


title: sCJD_46364_smallRNASeq


title: Oscillation Ex4 Time Point 7 [Mm]

value: 245 min


title: sCJD_46307_smallRNASeq


title: Oscillation Ex4 Time Point 6 [Mm]

value: 230 min


title: sCJD_46339_smallRNASeq


title: Oscillation Ex4 Time Point 5 [Mm]

value: 215 min


title: sCJD_46191_smallRNASeq


title: Oscillation Ex4 Time Point 4 [Mm]

value: 200 min


title: Oscillation Ex4 Time Point 3 [Mm]

value: 185 min


title: sCJD_46159_smallRNASeq

value: sCJD


title: Oscillation Ex4 Time Point 2 [Mm]

value: 170 min


title: sCJD_44896_smallRNASeq

value: whole blood


title: sCJD_42515_smallRNASeq

value: Male


title: sCJD_45334_smallRNASeq

value: MM


title: sCJD_42223_smallRNASeq

value: Female


title: sCJD_43040_smallRNASeq

value: VV


title: sCJD_45066_smallRNASeq


title: sCJD_42330_smallRNASeq

value: MV


title: Oscillation Ex4 Time Point 1 [Mm]

value: AES0204 based Hes7-reporter

value: PSM (presomitic mesoderm)

value: 155 min


title: RNAseq_K562_10ug_untreated_3

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (https://github.com/BrendelGroup/GoSTRIPES)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
TSS bedgraphs and TSR beds derived from TSRchitect were CPM normalized via edgeR (v3.28.0) and exported with rtracklayer (v1.42.1)
For human and yeast RNA-seq samples, rRNA reads were first removed using tagdust (v2.33.0) with additional settings -fe 3 -dust 97
STAR (v2.7.0e) was used to generate genome indices (with the additional setting --genomeSAindexNbases 10 for yeast) and align reads to coordinate sorted bam files.
Rsubread (v1.6.4) featureCounts was utilized to count fragments overlapping annotated exons.
RNA-seq bigwigs were generated with deepTools (3.3.0) bamCoverage using the settings -bs 1 --normalizeUsing CPM --smoothLength 25. RNA-seq libraries were constructed using the dUTP method, so coverage of positively-stranded transcripts was obtained with --filterRNAstrand forward, which excludes positively-stranded reads, as negatively-stranded reads correspond to positively-stranded transcripts in the dUTP protocol. Similarly, coverage of negatively-stranded transcripts was obtained with --filterRNAstrand reverse.
Genome_build: human (GRCh38.p13), yeast (R64-1-1)
Supplementary_files_format_and_content: CPM-normalized RNA-seq signal (.bw), CPM-normalized TSS signal (.bedgraph), CPM-normalized TSR signal (.bed).

molecule: polyA RNA

growth_protocol: DMEM + 10% FBS & 1x penicillin/streptomycin at 37°C with 5% CO2

extract_protocol:
Invitrogen TRIzol
RNA-seq (Illumina TruSeq Stranded mRNA Library Prep Kit)
stripe-seq-library-construction-2ivgce6.pdf

tag: cell line

tag: treatment

value: untreated

tag: input to technology

value: 10 ug


title: sCJD_44890_smallRNASeq


title: RNAseq_K562_10ug_untreated_1


title: STRIPEseq_K562_100ng_untreated_3

data_processing:
Library strategy: STRIPE-seq
Human and yeast STRIPE-seq samples were processed from .fastq to coordinate sorted .bam files using the GoSTRIPEs computational workflow (https://github.com/BrendelGroup/GoSTRIPES)
TSSs and TSRs were called using TSRchitect (v1.8.9) as part of the GoSTRIPES workflow. TSSs with less than 3 reads were filtered out, and TSSs within 40 bases were clustered into TSRs.
TSS bedgraphs and TSR beds derived from TSRchitect were CPM normalized via edgeR (v3.28.0) and exported with rtracklayer (v1.42.1)
For human and yeast RNA-seq samples, rRNA reads were first removed using tagdust (v2.33.0) with additional settings -fe 3 -dust 97
STAR (v2.7.0e) was used to generate genome indices (with the additional setting --genomeSAindexNbases 10 for yeast) and align reads to coordinate sorted bam files.
Rsubread (v1.6.4) featureCounts was utilized to count fragments overlapping annotated exons.
RNA-seq bigwigs were generated with deepTools (3.3.0) bamCoverage using the settings -bs 1 --normalizeUsing CPM --smoothLength 25. RNA-seq libraries were constructed using the dUTP method, so coverage of positively-stranded transcripts was obtained with --filterRNAstrand forward, which excludes positively-stranded reads, as negatively-stranded reads correspond to positively-stranded transcripts in the dUTP protocol. Similarly, coverage of negatively-stranded transcripts was obtained with --filterRNAstrand reverse.
Genome_build: human (GRCh38.p13), yeast (R64-1-1)
Supplementary_files_format_and_content: CPM-normalized RNA-seq signal (.bw), CPM-normalized TSS signal (.bedgraph), CPM-normalized TSR signal (.bed).

extract_protocol:
Invitrogen TRIzol
STRIPE-seq
stripe-seq-library-construction-2ivgce6.pdf


title: sCJD_42003_smallRNASeq


title: STRIPEseq_K562_100ng_untreated_1


title: STRIPEseq_K562_100ng_untreated_2


title: Day 13  endodermal progenitor

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description: Day 13

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38
Supplementary_files_format_and_content: the processed  files are the standard output from combining the four libraries with the cellranger aggr pipeline in HD5 format

source_name: C17 NKX2-1-GFP

growth_protocol: Surrogate wells of differentiated iPSCs (C17 NKX2-1GFP) towards endodermal lineages from a single MF differentiation were isolated at day 6 and day 13

extract_protocol:
Cells were disassociated and brought to a single cell suspension with AccuMax, counted and resuspended in appropriate volume.  Cell isolation, capture, and library prep followed the 10x Genomics scRNA-Seq (V2) protocol
Library prep followed the 10x Genomics scRNA-Seq (V2) protocol

tag: developmental stage

value: Day 13 endodermal progenitor

value: Human iPSC directed differentiation


title: sCJD_41716_smallRNASeq


title: Day 6 endodermal progenitor

description: Day 6

value: Day 6 endodermal progenitor


title: sCJD_41573_smallRNASeq


title: Single cell mRNA-seq_PC9_DMSO_invitro

first: Kari

last: Kurppa

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
cellranger 3.0.2 was used to process bcl files and convert them all to fastq files followed by aligning the fastq files to human GRCh38 transcriptome using standard cellranger pipeline
The filtered features matrix was used to perform downstream  analysis using Seurat V3. The following preprocessings were performed. First we filtered out cells with mitochondria percentages greater than 20 or expressed less than  200 genes
Raw counts was normalized using LogNormalize method with scaling factor 10000
Genome_build: GRCh38
Supplementary_files_format_and_content: tab deliminated, row names and column names corresponding to gene name amd cell barcodes, respectivley.

source_name: EGFR-mutant NSCLC cell line

extract_protocol:
Cell preparation: Cells were washed twice, trypsinized, and loaded onto a 10X Chromium instrument (10X Genomics) per the manufacturer’s instructions.
Single-cell RNA libraries were generated using the Single Cell 3’ Reagent Kit (10X Genomics) per user guide.  Quality control of the completed libraries was performed using Bioanalyzer High Sensitivity DNA Kit (Agilent)

treatment_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were treated with 0.1% DMSO for 48h.

value: EGFR-mutant NSCLC cell line

value: DMSO

tag: condition

value: in vitro


title: sCJD_41591_smallRNASeq

value: sCJD

tag: tissue

value: whole blood


title: Single cell mRNA-seq_PC9_OSI_TRAM_invitro

treatment_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were treated with 100nM osimertinib and 30nM trametinib for three weeks.

value: osimertinib + trametinib


title: sCJD_42618_smallRNASeq

value: Female


title: RNAseq_K562_10ug_untreated_2


title: sCJD_40661_smallRNASeq

value: Male

value: VV


title: sCJD_41542_smallRNASeq

value: MV


title: sCJD_40403_smallRNASeq


title: sCJD_40572_smallRNASeq

value: MM


title: sCJD_35821_smallRNASeq


title: sCJD_36250_smallRNASeq


title: sCJD_35846_smallRNASeq


title: sCJD_38803_smallRNASeq


title: sCJD_40363_smallRNASeq


title: sCJD_34727_smallRNASeq


title: PDAC-C inDrop1

city: New York

first: Itai

last: Yanai

state: NY

address: 435 E. 30th Street, 8th Floor

institute: Institute for Computational Medicine, NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the ST method were processed using a custom-built pipeline, available online (https://github.com/yanailab/celseq2). The pipeline was adapted to ST sequencing data using the following three steps: 1) Tagging and demultiplexing: the left-most 25 nucleotides (nt) of the R1 sequence contains the 18 nt for the spot-specific barcode and then 7 nt for UMI. The R2 sequence contains the transcript sequence, and its left-most 35 nt are used. The name of every read in the R2 file is tagged with the spot-specific barcode and UMI sequence that are extracted from the paired R1 read. The R2 file is demultiplexed to create the 1007 spot-specific FASTQ files. If the detected spot-specific barcode of a read is not present in the pre-defined barcodes list, the read is excluded from the downstream analysis. 2) Alignment of demultiplexed FASTQ files using Bowtie2. 3) Counting UMI using HTSeq. The reads that are aligned to a user-defined feature (by default: “gene_name”) are collapsed to count only once if they have same UMI. Here we used the version 2.3.1 of Bowtie2 with default parameters and the 0.9.1 version of HTSeq in the “union” mode. For demultiplexing spatial barcodes, PDAC-A ST1 was demultiplexed using the lot10001 barcode file, and PDAC-B ST1 was demultiplexed using the lot10003 barcode file (barcode files included in submission, and is also available at https://spatialtranscriptomics.com/resources/
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns. For ST data: tab-delimited files with genes as rows  and spots as columns (with first row is the coordinate of each spot along the array)

source_name: pancreatic adenocarcinoma tissue

extract_protocol:
For single-cell RNA-seq (inDrop platform), cell suspension was generated by incubating minced pancreatic cancer tissue with trypsin for 15' at 37C prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For spatial transcriptomics of pancreatic cancer tissue, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation.
For single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England Biolabs). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For spatial transcriptomics (ST) library construction, we followed the previously published ST protocol from Stahl et al. Science 2016, with minor changes. Briefly, after brightfield imaging of stained tissue, tissue was permeabilized with collagenase and 0.1% pepsin prior to an overnight RT step with SuperScript III on the ST slide. Tissue was digested away with proteinase K and 1% 2-mercaptoethanol prior to cleavage of probes from the slide surface with USER enzyme. Second strand synthesis was performed with DNA Pol I and RNase H (New england biolabs) followed by an in vitro transcription amplification step with the MEGAScript T7 kit (Thermofisher). Amplified RNA then underwent a second RT with random hexamers and SuperScript II (Invitrogen), eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).

value: pancreatic adenocarcinoma

tag: tissue preparation

value: single-cell suspension of tissue


title: sCJD_34587_smallRNASeq


title: SM MESP2-KO 2

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
The low-quality bases at the 3' read ends and the adaptor sequences were trimmed by cutadapt-1.14.
The sequenced reads were mapped to the hg38 human reference genome plus the luciferase reporter sequence using HISAT2 (version 2.1.0) with the human GENCODE v25 annotation gtf file.
The uniquely mapped reads were counted using HTSeq (version 0.6.1) with the human GENCODE v25 annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include raw counts of sequenced reads for each sample obtained with HTSeq-count.

source_name: SM MESP2-KO clone 11

growth_protocol: Human iPSCs (patient, rescue and control lines) were maintained without feeder cells and cultured on iMatrix-511-silk (Nippi) coated dishes or plates with StemFit® AK02N (Ajinomoto) medium supplemented with 50 U penicillin and 50 mg/ml streptomycin (Gibco).

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
RNA-seq libraries were generated from 200-300 ng total RNA with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Human iPSCs (patient, rescue and control lines) were seeded on iMatrix-511 silk-coated plates or dishes at appropriate densities as single cells (e.g. 1.3 × 104 cells/well into 6 well plate; 8.0 × 104 cells/dish into 10cm dish) 5 days before induction. All differentiation and induction steps were performed in chemically defined medium with insulin (CDMi). Human primitive streak (PS) cells were induced by treatment of iPSCs with bFGF (20 ng/ml), CHIR99021 (10 µM) and Activin A (50 ng/ml) for 24 hours. Presomitic mesoderm (PSM) cells were induced from PS cells by exposure to SB431542 (10 µM), CHIR99021 (3 µM), LDN193189 (250 nM) and bFGF (20 ng/ml) for 24 hours. Subsequently, somitic mesoderm (SM) cells were induced from PSM cells using PD173074 (100 nM) and XAV939 (1 µM) for 24 hours. Following initial step-wise somitic mesoderm (SM) induction, human sclerotome (SCL) cells were induced with combination of SAG (100 nM) and LDN193189 (600 nM) for 72 hours. Dermomyotome (DM) cells were induced from human somitic mesoderm, using a combination of CHIR99021 (3 µM), GDC0449 (150 nM) and BMP4 (50 ng/ml) for 48 hours.

tag: background line

value: knock-out iPSC line (201B7 reporter)

value: SM (somitic mesoderm)

tag: original source

value: 201B7 (Hes7-luciferase reporter)


title: PDAC-C inDrop3


title: SCL MESP2-KO 2

source_name: SCL MESP2-KO clone 11

tag: Stage

value: SCL (sclerotome)


title: PDAC-C inDrop2


title: DM MESP2-KO 1

source_name: DM MESP2-KO clone 7

value: DM (dermomyotome)


title: sCJD_25868_smallRNASeq

tag: disease status


title: sCJD_27241_smallRNASeq

tag: Sex


title: sCJD_28042_smallRNASeq

tag: age at sampling


title: iPSC MESP2-KO 2

description:
MESP2_KO_11_iPS
re-analysis of GSM3264473

source_name: iPSC MESP2-KO clone 11

value: iPSC (induced pluripotent stem cell)


title: PDAC-C inDrop4


title: PSM MESP2-KO 2

description:
MESP2_KO_11_PSM
re-analysis of GSM3264485

source_name: PSM MESP2-KO clone 11

value: PSM (presomitic mesoderm)


title: sCJD_25652_smallRNASeq

value: sCJD

tag: rna integrity number (rin)


title: sCJD_41427_smallRNASeq

value: whole blood

tag: sample age proxy


title: sCJD_25632_smallRNASeq

tag: prnp codon 129 genotype


title: SCL MESP2-KO 1

source_name: SCL MESP2-KO clone 7


title: SM MESP2-KO 1

source_name: SM MESP2-KO clone 7


title: PSM MESP2-KO 1

description:
MESP2_KO_7_PSM
re-analysis of GSM3264484

source_name: PSM MESP2-KO clone 7


title: sCJD_24863_smallRNASeq

tag: mrc scale score


title: sCJD_22883_smallRNASeq


title: sCJD_35218_smallRNASeq


title: DM MESP2-KO 2

source_name: DM MESP2-KO clone 11


title: sCJD_18764_smallRNASeq


title: sCJD_28130_smallRNASeq


title: sCJD_15385_smallRNASeq


title: iPSC MESP2-KO 1

description:
MESP2_KO_7_iPS
re-analysis of GSM3264472

source_name: iPSC MESP2-KO clone 7


title: 48h_2DF_Slug

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

growth_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
For ChIP, Cells were washed in phosphate-buffered saline (PBS) and crosslinked with 1% Formaldehyde for 10 minutes (H3K27Ac) or crosslinked with two agents startingwith 2 mM DSG (Pierce) for 45 min at RT, followed by 1 ml 1% Formaldehyde for 10 min (YAP and TEAD4). Crosslinked Cell lines were quenched with 0.125 M glycine for 5 min at room temperature. After quenching, the material was resuspended in 1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 5 minutes with a Covaris E220 instrument, 5% duty cycle, 140 Peak Incident Power, 200 Cycles per burst, in 1ml AFA Fiber milliTUBEs. Soluble chromatin was immunoprecipitated with 10 μg of H3K27ac antibody, 7 μg of YAP antibody, 1.5 μg of SLUG antibody, or 1.5 μg of TEAD antibody. 5 µg of chromatin was used for H3K27Ac ChIP, and 40 µg for YAP, TEAD4 and SLUG ChIPs. For ATAC-seq, 50000 cells / sample were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at max speed for 5 min in a pre-chilled (4 C) fixed-angle centrifuge. After centrifugation supernatant was carefully aspirated.  Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at max speed in a pre-chilled (4 C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (Corces et al., 2017): 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen columns.
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. ATAC-seq libraries were amplified as described previously (Buenrostro et al., 2015).

treatment_protocol: For ChIP, Cells were treated either with DMSO or with the combination of 100 nM osimertinib and 30nM trametinib for 48h. Cells were trypsinized, and cryopreserved in FBS + 8% DMSO in -80C until processing. For ATAC-seq, cells were treated with DMSO, 100 nM osimertinib or with the combination of 100 nM osimertinib and 30nM trametinib. DMSO-treated control cells were harvested 24h later. Osimertinib and osimertinib/trametinib treated cells were harvested after 2 weeks of treatment. Rebound samples were obtained by withdrawing drugs from three additional osimertinib/trametinib-treated plates and harvesting the cells once the plates reached 60-70% confluence. Cells were trypsinized at timepoints, and cryopreserved in FBS + 8% DMSO in -80C until processing.

value: osimertinib + strametinib

tag: cell line

tag: cell type

value: Non-small cell lung cancer cell line

tag: chip antibody

value: Slug (Cell signaling #9585)


title: DMSO_2F_H3K27ac

tag: treatment

value: DMSO

value: H3K27ac (Diagenode cat# C15410196)


title: sCJD_12355_smallRNASeq

value: Female

value: MM


title: Control_55097_smallRNASeq

value: Control

value: Male


title: DMSO_2DF_TEAD4

value: TEAD4 (ab58310, Abcam)


title: DMSO_2DF_YAP

value: YAP (Cell signaling #14074)


title: Control_52863_smallRNASeq

value: MV


title: Control_52783_smallRNASeq


title: DMSO_1DF_YAP


title: DMSO_2DF_Slug


title: Control_48898_smallRNASeq


title: DMSO_1DF_TEAD4


title: Control_52641_smallRNASeq


title: DMSO_1DF_Slug


title: Control_51045_smallRNASeq


title: Control_52345_smallRNASeq

value: VV


title: Control_47708_smallRNASeq


title: 48h_2F_H3K27ac


title: 48h_2DF_YAP


title: Control_47082_smallRNASeq


title: 48h_2DF_TEAD4


title: 48h_1F_H3K27ac


title: Control_46909_smallRNASeq


title: Control_46480_smallRNASeq


title: Control_46286_smallRNASeq


title: 48h_1DF_TEAD4


title: Control_55093_smallRNASeq


title: 48h_1DF_Slug


title: rebound_ATAC_3

value: osimertinib + strametinib, then drugs withdrawn


title: Control_46181_smallRNASeq


title: Control_45947_smallRNASeq


title: Control_47716_smallRNASeq


title: rebound_ATAC_2


title: rebound_ATAC_1


title: Control_46005_smallRNASeq


title: 48h_1DF_YAP


title: osimertinibplustrametinib_ATAC_3


title: osimertinibplustrametinib_ATAC_2


title: osimertinibplustrametinib_ATAC_1


title: Control_45418_smallRNASeq


title: osimertinib_ATAC_2

value: osimertinib


title: DMSO_ATAC_3


title: osimertinib_ATAC_1


title: osimertinib_ATAC_3


title: Control_43488_smallRNASeq


title: Control_43988_smallRNASeq


title: Control_42215_smallRNASeq


title: DMSO_ATAC_1


title: Control_45017_smallRNASeq


title: Control_44631_smallRNASeq


title: Control_40921_smallRNASeq


title: Control_41219_smallRNASeq


title: DMSO_ATAC_2


title: Control_40396_smallRNASeq


title: Control_37464_smallRNASeq


title: HCC4006 YAP1 KO OT rep2

data_processing:
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b)
Normalized read counts (FPKM) were calculated using cufflinks (v2.2.1)
Differential gene expression testing was performed by DESeq2 (v1.10.1)
Genome_build: GRCh37/hg19

source_name: EGFR-mutant NSCLC cells

extract_protocol:
Total RNA was extracted using Trizol reagent
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: The cells were treated with DMSO or with the combination of 100 nM osimertinib and 30 nM trametinib (OT) for 24h.

tag: genotype/variation

value: YAP1 KO

value: 100 nM osimertinib and 30 nM trametinib


title: HCC4006 YAP1 KO OT rep1


title: HCC4006 YAP1 KO OT rep3


title: Control_26445_smallRNASeq

tag: tissue

value: whole blood


title: Control_26927_smallRNASeq


title: HCC4006 YAP1 KO DMSO rep2


title: HCC4006 YAP1 KO DMSO rep1


title: HCC4006 YAP1 KO DMSO rep3


title: Control_25464_smallRNASeq


title: Control_26126_smallRNASeq


title: HCC4006 CTRL OT rep2

value: CTRL


title: HCC4006 CTRL OT rep3


title: HCC4006 CTRL DMSO rep2


title: HCC4006 CTRL DMSO rep3


title: HCC4006 CTRL DMSO rep1


title: HCC4006 CTRL OT rep1


title: Control_25190_smallRNASeq


title: PC9 YAP1 KO OT rep2


title: Control_24655_smallRNASeq


title: Control_24711_smallRNASeq


title: Control_24614_smallRNASeq


title: Control_23906_smallRNASeq


title: PC9 YAP1 KO OT rep1


title: PC9 YAP1 KO DMSO rep3


title: PC9 YAP1 KO DMSO rep2


title: Control_23817_smallRNASeq


title: Control_23759_smallRNASeq


title: Control_26192_smallRNASeq


title: PC9 YAP1 KO DMSO rep1


title: Control_23628_smallRNASeq

value: No data


title: PC9 CTRL OT rep3


title: Control_23518_smallRNASeq


title: PC9 CTRL OT rep2


title: PC9 CTRL OT rep1


title: Control_24771_smallRNASeq


title: Control_24955_smallRNASeq


title: Control_24717_smallRNASeq


title: Control_23472_smallRNASeq


title: PC9 CTRL DMSO rep3

value: DMSO


title: PC9 YAP1 KO OT rep3


title: Control_23463_smallRNASeq


title: PC9 CTRL DMSO rep2


title: HCC4006 Dormant rep2

description: RNAseq_DormantCells_FPKM_gene [HCC4006_MRD_S2]

treatment_protocol: Control cells were treated for 24h with DMSO; Dormant cells were treated for two weeks with the combination of 100nM EGFR inhibitor osimertinib and 30nM MEK inhibitor trametinib

value: 100nM EGFR osimertinib and 30nM MEK trametinib


title: HCC4006 Dormant rep1

description: RNAseq_DormantCells_FPKM_gene [HCC4006_MRD_S1]


title: Control_23466_smallRNASeq

value: Female


title: HCC4006 DMSO rep1

description: RNAseq_DormantCells_FPKM_gene [HCC4006_NT_S1]


title: HCC4006 DMSO rep2

description: RNAseq_DormantCells_FPKM_gene [HCC4006_NT_S2]


title: FurC_Minus_3hr_Rep2

city: Richland

institute: Pacific Northwest National Laboratory

data_processing:
Analysis with FastQC followed by trimming if a nucleotide had a Phred score of < 25.  Adaptors were not present in the reads and so adaptor trimming was unnecessary
Alignment to the Neisseria gonorrhoeae FA1090 genome using the Burrows Wheeler Aligner
Counting using HTSeq
Normalization of raw counts and determination of differentially expressed genes using DESeq2
Genome_build: Neisseria gonorrhoeae FA1090 (NCBI: NC_002946.2)
Supplementary_files_format_and_content: Normalized_Expression_Levels_Fur_3hour

organism: Neisseria gonorrhoeae F62

growth_protocol: All strains were plated on GCB plates, grown overnight at 37°C with 5% CO2, and inoculated into chemically defined medium (CDM) containing 0.042% Na2HCO3 with shaking until an O.D of 0.25 was reached.

extract_protocol:
RNA was extracted with TRIzol
RNA was depleted of rRNA using the Agilent Microbe Express kit.  Libraries were made using the BioChain High Yield Directional mRNA Sample Prep kit per the manufacturer's instructions. cDNA libraries were subject to electrophoresis on an 8% Tris-borate-EDTA (TBE) gel for 60 min at 140 V. cDNA fragments between 200 and 500 bp were extracted from the gel in Tris-EDTA (TE) buffer with agitation, and libraries were analyzed on an Agilent Technologies 2100 Bioanalyzer to confirm cDNA library size and quantity.
Libraries were sequenced using 72-bp single-end reads on an Illumina GAIIX machine

treatment_protocol: Subsequently, 100 μM ferric nitrate (for iron-replete [+Fe] conditions) or 100 μM desferal (for iron-depleted [−Fe] conditions) was added to the culture. The bacterial pellets were collected 3h after the addition of iron or desferal.

tag: genotype

value: Fur Knockout complemented

value: No Iron


title: FurC_Plus_3hr_Rep1

value: Plus Iron


title: FurC_Plus_3hr_Rep2


title: HCC827 Dormant rep2

description: RNAseq_DormantCells_FPKM_gene [HCC827_MRD_S2]


title: HCC827 Dormant rep1

description: RNAseq_DormantCells_FPKM_gene [HCC827_MRD_S1]


title: FurKO_Minus_3hr_Rep2

value: Fur Knockout


title: FurKO_Plus_3hr_Rep2


title: WT_Minus_3hr_Rep2

value: Wild Type


title: Control_23469_smallRNASeq

value: Control

value: MV


title: WT_Plus_3hr_Rep1


title: PC9 Dormant rep2

description: RNAseq_DormantCells_FPKM_gene [PC9_MRD_S2]


title: PC9 CTRL DMSO rep1


title: PC9 Dormant rep1

description: RNAseq_DormantCells_FPKM_gene [PC9_MRD_S1]


title: HCC827 DMSO rep1

description: RNAseq_DormantCells_FPKM_gene [HCC827_NT_S1]


title: PC9 DMSO rep1

description: RNAseq_DormantCells_FPKM_gene [PC9_NT_S1]


title: FurKO_Minus_3hr_Rep1


title: PC9 DMSO rep2

description: RNAseq_DormantCells_FPKM_gene [PC9_NT_S2]


title: PDAC-B inDrop3

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop method were processed using a custom-built pipeline, available online (https://github.com/flo-compbio/singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted (included in Read 1 together with transcript), and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the ST method were processed using a custom-built pipeline, available online (https://github.com/yanailab/celseq2). The pipeline was adapted to ST sequencing data using the following three steps: 1) Tagging and demultiplexing: the left-most 25 nucleotides (nt) of the R1 sequence contains the 18 nt for the spot-specific barcode and then 7 nt for UMI. The R2 sequence contains the transcript sequence, and its left-most 35 nt are used. The name of every read in the R2 file is tagged with the spot-specific barcode and UMI sequence that are extracted from the paired R1 read. The R2 file is demultiplexed to create the 1007 spot-specific FASTQ files. If the detected spot-specific barcode of a read is not present in the pre-defined barcodes list, the read is excluded from the downstream analysis. 2) Alignment of demultiplexed FASTQ files using Bowtie2. 3) Counting UMI using HTSeq. The reads that are aligned to a user-defined feature (by default: “gene_name”) are collapsed to count only once if they have same UMI. Here we used the version 2.3.1 of Bowtie2 with default parameters and the 0.9.1 version of HTSeq in the “union” mode. For demultiplexing spatial barcodes, PDAC-A ST1 was demultiplexed using the lot10001 barcode file, and PDAC-B ST1 was demultiplexed using the lot10003 barcode file (barcode files included in submission, and is also available at https://spatialtranscriptomics.com/resources/
Genome_build: hg38
Supplementary_files_format_and_content: for inDrop data: tab-delimited files with genes as rows and cells as columns.  Cell ID is composed of the word "cell" followed by two numbers which represent the sequence number of the barcodes available in the files inDrop_gel_barcode*txt. For example, cell_004-028 is represented by the 4th barcode sequence in inDrop_gel_barcode1_list.txt  and the 28th sequence in inDrop_gel_barcode2_list.txt.
Supplementary_files_format_and_content: For ST data: tab-delimited files with spots as rows (with first column is the coordinate of each spot along the array) and genes are columns.

value: pancreatic adenocarcinoma

tag: tissue preparation

value: single-cell suspension of tissue


title: HCC827 DMSO rep2

description: RNAseq_DormantCells_FPKM_gene [HCC827_NT_S2]


title: PDAC-B inDrop2


title: WT_Plus_3hr_Rep2


title: PDAC-A inDrop6


title: PDAC-A inDrop5


title: PDAC-A inDrop3


title: PDAC-B inDrop1


title: PDAC-A inDrop4


title: 2072 m6A-IP

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

description: m6A enriched RNA

data_processing:
Seequencing reads were aligned to reference genome by Hisat2
Read count of connected bins was quantified by R package RADAR.
Differential methylation sites detection by RADAR
Genome_build: hg38
Supplementary_files_format_and_content: differential methylation sites in BED12 file. Bins in text files are consecutive bins of 50 bp size on the longest isoform of a gene, which is by concatenating the exons of a gene.

source_name: ovary

extract_protocol:
TRIzol (Invitrogen)
Takara Pico-Input Strand-Specific Total RNA-seq for Illumina
MeRIP-seq

tag: group

value: normal Fallopian tube

tag: age


title: 1850 m6A-IP

description: m6A enriched RNA


title: 1917 m6A-IP

description: m6A enriched RNA


title: 2053 m6A-IP

description: m6A enriched RNA