title: HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 4

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.

data_processing:
Trimgalore was used to trim, and quality filter the newly generated reads.
Trimmed reads were mapped to the human reference genome hg19 (NCBI build 37.1 released 2009) using the RNA-Seq mapping software TopHat
annotated transcripts were quantified in units of FPKM using Cufflinks
Gene annotation used for the quantification was downloaded from ENSEMBL (version 81) and the file was filtered to remove all records from the gtf file whose molecular biotype was annotated as either ribosomal RNA (rRNA), or mitochondrial tRNA (Mt_tRNA).
Resultant files were used in cufflinks (arguments--GTF Hs_build-37.1.gtf (MT or RRNA filtered out) --compatible-hits-norm-M Hs_build 37.1_MT_RRNA.gtf (only MT and RRNA)) and cuffdiff (GTF argument set to Hs_build-37.1.gtf (MT or RRNA filtered out)) to ensure no ribosomal RNA or mitochondrial RNA that remained after efforts to remove them during the library prep would not influence the derived FPKM values

source_name: HaCaT

tag: cell line

value: HaCaT

value: Immortalized Human Keratinocytes

value: The cells were maintained for 28 weeks with 100 nM sodium arsenite


title: HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 2

status: Public on Jul 07 2021

type: SRA

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

country: USA

institute: University of Louisville

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

growth_protocol: HaCaT cells were cultured in 4 biological replicates in MEM alpha modification media supplemented with 10% fetal bovine serum, penicillin/streptomycin and glutamine. Cultures were maintained at 37°C in a humidified 5% CO2 atmosphere with 20% oxygen and were maintained separately for 3 and 7 weeks. A set of HaCaT cells maintained for 28 weeks (1 biological replicate) were obtained form Dr. Michael P. Waalkes.

extract_protocol:
Total RNA was purified from the cells using the mirVana™ miRNA Isolation Kit.
The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 1 μg total RNA. Libraries were validated on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems and the ABI7900HT real-time PCR instrument. All samples were pooled and run simultaneously on 4 flow cells, using 2x150 paired end sequencing with the 500 High-output v2 (300 cycles) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: cells maintained with and without 100 nM sodium arsenite from day 1 of plating.

tag: cell type

tag: treatment


title: HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 3


title: HaCaT cells-exposed sodium arsenite maintained for 28 weeks-replicate 1


title: Primary lens cells - DMOG_rep1

city: Boca Raton

first: Marc

last: Kantorow

state: FL

address: 777 Glades Road

institute: Florida Atlantic University

data_processing:
Cutadapt  was used to remove adaptor-contaminated reads, low quality bases and undetermined bases
Reads were mapped to galgal6 genome (ensemble version 96) using Bowtie2  and HISAT2
The mapped reads were assembled using StringTie
Comprehensive transcriptomes were generated using gffcompare and StringTie
The R package edgeR  was used to estimate the expression levels of all transcripts and to identify differentially expressed genes (log2 fold change FPKM > 0.6 or <-0.6) with parametric F-test comparing nested linear models (p < 0.05)
Genome_build: galgal6
Supplementary_files_format_and_content: DMOGvUntreated_RNAseq.txt file: 526 genes were found to be differentially expressed in DMOG-treated primary lens cells relative to untreated primary lens cell samples

organism: Gallus gallus

source_name: Primary lens cells

growth_protocol: Primary chick lens epithelial cell cultures were prepared from the lenses of Embryonic day 10 (E10) White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT). Briefly, primary lens cells were isolated from chicken lenses by trypsinization and agitation. Cells were plated onto dishes coated with mouse laminin (Invitrogen, prod no: 23017-015) and cultured in Medium 199 (Invitrogen, prod no: 11150) supplemented with 10% FBS (Invitrogen, prod no: 16140-071) and penicillin-streptomycin antibiotic mix (50 units/ml; Invitrogen, prod no: 15140-122)

extract_protocol:
Total RNA was isolated from primary lens cells using TRIZOL® reagent (Invitrogen, prod no: 15593018) according to the manufacturer’s instructions
Libraries were prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol

treatment_protocol: Primary lens cells were treated with the HIF1α activator dimethyloxalllyl glycine (DMOG, Santa Cruz Biotechnology, prod no: sc200755) (1 mM) for 4 hours at 37 °C

value: Embryonic day 10 primary lens cells

tag: strain

value: White leghorn

value: treated with 1mM DMOG for 4 hours


title: tRip-selected tRNAs - Bound tRNAs - tRNA/tRip=10

type: RNA

city: Charleston

first: Renaud

last: Geslain

state: SC

address: 58 Coming Street

department: Biology

institute: College of Charleston

hyb_protocol: Extracted radioactive tRNA were hybridized onto in-house printed human tRNA arrays. Each chip consists of 48 different probes, repeated 8 times (for a complete and generic protocol please refer to Emetu et al., 2018). Those probes hybridize either to a unique tRNA species (Arg-3h, Asn-1h, Asp-1h, Gly-2h, His-1h, Leu-3h, Lys-1h, Lys-3h, Lys4H, Met-1h, Sec-1h, Thr-3h, Thr-4h, Val-4h), a group of tRNA isodecoders (Arg-1h, Arg-4h, Glu-2h, Ile-2h, Leu-2hn, Leu-4h, Leu-6h, Lys-2h, Met-2h, Phe-1h, Ser-1h, Ser-3h, Thr-1h, Thr-2h, Thr-5h, Tyr-2h), several isoacceptors specific to the same amino acid (Ala-2h, Arg-2h, Glu-1h, Gly-1h, Leu-1h, Pro-1h, Ser-2h, Val-1h), or tRNAs specific to different amino acids (Glu-3h, Ser-4h, Thr6h, Tyr-1h, Val3H). Arrays were placed inside a hybridization cassette and loaded with radiolabeled tRNA samples. All subsequent steps were performed on an automated hybridization-washing station (DigiLab, Hyb10022) for maximum reproducibility: 1. Gasket conditioning for 2 min at 75 °C, 2. Probe introduction at 60 °C, 3. Probes and samples denaturation for 5 min at 90 °C., 4. Sample hybridization for 3 h at 60 °C, 5. Slides washing at 50 °C twice with 2 X SSC, 0.1% (w/v) SDS (flow 10 s and hold 20 s), 6. Slides washing at 42 °C twice with 0.1 X SSC, 0.1% SDS (flow 10 s and hold 20 s), and 7. Slides washing at 42 °C twice with 0.1 X SSC (flow 10 s and hold 20 s). microarray hybridizer as described in (Emetu et al., 2018).

scan_protocol: Arrays were exposed onto a storage phosphor screen in an exposure cassette at room temperature for 10 to 24 h depending on signal strength and scanned at 50 µm resolution using a Typhoon FLA 7000 IP phosphorimager.

data_processing: Radioactivity intensities at each probe spot were quantified using the free Image J software upgraded with a microarray profiler and background subtracted.

source_name: Human transfer RNAs, tRip-bound, tRNA/tRip=10

label_protocol: Radioactive labeling of the 3’ end of tRNAs was performed on 140 pmoles of tRNA/transcript with 20 µCi [32P]ATP in 50 mM Tris-HCl pH 8.0, 50 µM CTP, 10 mM MgCl2, 8 mM DTE and 6 ng/µl of yeast CCase for 20 min at 37°C according to Vlassov et al., 1980

growth_protocol: HeLa cells were washed in phosphate buffer sodium (PBS) and total RNA was extracted using Tri-Reagent (Sigma-Aldrich) according to the manufacturer’s instructions. Further fractionation was performed on a gel filtration column (Superdex 200) in 50 mM HEPES-KOH pH 7.5, 150 mM NaCl in order to isolate tRNAs from mRNAs and ribosomal RNAs.

extract_protocol: tRNAs were gel extracted using the crush & soak method (300 mM sodium acetate, 1 mM EDTA, 0.1% SDS according to Petrov et al., 2013

treatment_protocol: Increasing amounts of total tRNA purified from HeLa cells (8 µM, 20 µM and 40 µM) were incubated 20 min at 4ºC with 2 µM tRip dimers in a total volume of 100 µl with EMSA buffer. These mixtures were loaded on a 6% native gel and separated for 4 h at 140 V (10 ºC). Bands were visualized by UV shadowing

value: Cultured HeLa cells

tag: separated on non-denaturing polyacrylamide gel

value: Yes

tag: complexed to trip

tag: trna/trip ratio

tag: molecule subtype

value: Transfer RNA


title: DN, biological rep 1

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

description: miRNA expression data from differentiated mESC (Flk1-PDGFaR-)

hyb_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

scan_protocol: miRNA 4.1 strips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software and IPA

label: biotin

organism: Mus musculus

source_name: Differentiated mESCs

label_protocol: biotin

growth_protocol: mESCs were plated onto low-adherent 100 mm petri dish on a swirling rotator (50 rpmi/min) in IMDM (Thermo Fisher, Cat No: 12440053) supplemented with %15 FBS, 200 µg/ml Holotransferrin (Millipore, Cat No: 616424), 50 µg/ml Ascorbic Acid (Sigma, Cat No: A4403), 4.5 mM Monothioglycerol.  (Sigma, Cat No: M1753) at 37 °C in humidified atmosphere containing %5 CO2.

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

treatment_protocol: Not Applicable

tag: genotype/variation


title: HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 4

value: The cells were maintained for 19 weeks with 100 nM sodium arsenite


title: 10-11-21_B

city: Rehovot

first: Robert

last: Fluhr

address: hertzl 234, 17

department: Plant and environmental sciences

country: Israel

institute: Weizmann institute of science

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6G

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using cutadapt, (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to the barley genome (Mascher et al. 2017) using STAR,  v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Araport annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis is done for genes having minimum 5 read in at least one sample.
Genome_build: barley genome (Mascher et al. 2017)
Supplementary_files_format_and_content: Normalization of the counts and differential expression analysis was performed using DESeq2 , with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.

organism: Hordeum vulgare

source_name: flag leaf

growth_protocol: plants were grown in a small randomized block design in a glasshouse. Plants were kept at ~22 °C during the day and ~18 °C during the night; days were extended to a 16-hour photoperiod when required, using GE Multi-Vapor MVR1000/C/U lights (General Electric, Cleveland, OH, USA). Plants in potting soil were fertilized with 250 ml Peter's Professional General Purpose fertilizer (4 g l-1; Scotts-Sierra Horticultural Products Company, Marysville, OH, USA) per 4-liter pot with three plants. Fertilizer was applied every alternate week until anthesis, starting at 2 weeks after germination. Additionally, a treatment with 100 ml 16 mM KNO3 (Sigma-Aldrich, St. Louis, MO, USA) was applied twice per week, per pot, from germination to anthesis.

extract_protocol:
Each sample/replicate consisted of at least 10 flag leaves, and three independent samples/replicates were harvested for both 'Karl' and '10_11' at each time point. the samples were immediately shock-frozen in liquid nitrogen and RNA was extracted separately from frozen tissues using a standard Trizol extraction method (Sigma-Aldrich).
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Once plants reached anthesis, each shoot utilized for further experimentation was tagged with its exact anthesis date. Flag leaves were harvested at 7, 14, and 21 days past anthesis and immediately shock-frozen in liquid nitrogen

tag: cultivar

tag: tissue

value: flag leaf

tag: age

value: 21 days post anthesis


title: frog_oocyte_water_TAIL_seq

city: Cambridge

first: David

last: Bartel

address: 455 Main Street

institute: Whitehead Institute

description:
C01
no rRNA depletion

data_processing:
Library strategy: TAIL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

organism: Xenopus laevis

source_name: Xenopus laevis stage VI oocyte

growth_protocol: All mammalian cells were cultured at 37°C with 5% CO2. HeLa cells were cultured in DMEM (VWR, 45000-304) with 10% FBS (TaKaRa, 631106). HCT116 OsTIR1 cells were cultured in McCoy’s 5A media (Thermo Fisher, 16600082) supplemented with 10% FBS, 2mM L-glutamine (Thermo Fisher, 25030081). NIH3T3 cells were cultured in DMEM with 10% BCS (Sigma, 12133C).

extract_protocol:
To prepare lysate from mammalian cells, cycloheximide (CHX) was added to each plate at final concentration 100 µg/ml. Plates were immediately moved to a cold room and culture media were removed. Cells were washed twice with ice-cold PBS supplemented with 100 µg/ml CHX. After the last wash, 1 ml buffer RLL (20 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2, 1% (v/v) Triton X-100, 100 µg/ml cycloheximide, 500 unit/ml RNasin Plus (Promega, N2615), 2 mM DTT, cOmplete protease inhibitor cocktail (Sigma, 11836170001, 1 tablet per 10ml buffer)) was added to each 15 cm plate, and cells were scraped off and incubated on ice for 10 min. The resulting lysates were passed through a 26-gauge needle six times and cleared by centrifugation at 1300g at 4°C for 10 min. To prepare lysate from frog oocytes, injected oocytes were washed once with complete OR-2 buffer and three times with buffer RLL. After removing all wash buffer, oocytes were lysed in buffer RLL (10 µl/oocyte) by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5,000g at 4°C for 10 min. One tenth of each cleared lysate was added to 10 volumes of Tri Reagent for total-RNA preparation, following the manufacturer’s protocol. Another small portion (~10 µl) was taken for western analysis. The remainder was aliquoted, flash frozen in liquid nitrogen, and stored at –80°C.
Sequencing libraries were prepared as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)
Library strategies were as described previously (Subtelny et al., 2014) and (Eisen et.al, 2020)

treatment_protocol: For 5EU labeling: 48 h after siRNA transfection, HeLa cells were incubated with pre-warmed fresh media with 400 µM 5-ethynyl uridine (5EU, Jena Biosciences) for 1, 2, 4, and 8 h. For IAA-indcued degradation, HCT116 cells were incubated with 1 µg/ml doxycycline and 0.2 mM auxinole (Aobious, AOB8812), an inhibitor of OsTIR1 for 6 h, after which fresh media with 1 µg/ml doxycycline and 0.5 mM IAA were added. Cells were collected after 0.5, 1, and 3 h of induction.

value: oocyte

tag: Stage

value: VI

tag: manipulation

value: water-injected

tag: time after 5eu labeling (h)

tag: time after iaa addition (h)

tag: rna population

value: cytoplasmic RNA

tag: library type

value: TAIL-seq


title: HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 3

tag: cell line

value: HaCaT

tag: cell type


title: frog_oocyte_ePAB_no_rRNA_depeletion_ribo_seq

description:
B06
no rRNA depletion

data_processing:
Library strategy: ribo-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq)

value: ePAB-overexpressed

value: ribo-seq (ribosome footprint profiling)


title: frog_oocyte_eGFP_no_rRNA_depeletion_ribo_seq

description:
B05
no rRNA depletion

value: eGFP-expressed


title: HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 1

value: Immortalized Human Keratinocytes

tag: treatment


title: 10-11-14_C

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6E

value: 14 days post anthesis


title: Cecum contents, CNP4

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

country: China

institute: Jinan University

description:
16S rDNA (v3-v4 region)
allsample.all.abundance
allsample.all.reabundance
allsample.otu

library_source: genomic

data_processing:
Raw data were trimmed by Trimmomatic v0.33 and cutadapt 1.9.1 to produce high qualified raw reads.
The high qualified raw reads were processed (overlap) with FLASH v1.2.7 to produce clean reads.
Chimeric sequences were identified and removed with UCHIME v4.2 to produce effective tags.
The effective tags were then used to produce OTUs and taxonomic annotation with Usearch.
Genome_build: SILVA
Supplementary_files_format_and_content: allsample.all.abundance, allsample.all.reabundance, allsample.otu

molecule: genomic DNA

organism: rat gut metagenome

source_name: rat cecum content

extract_protocol:
Cecum contents were collected at 4 0C. the microbial genome DNA of rat cecum contents was extracted and purified. Then, the V4 region of 16S rDNA was amplified by PCR. After agarose gel electrophoresis, gel extraction, quantification, and library preparation, sequencing was performed on Illumina HiSeq with MiSeq Reagent Kit.
DNA libraries were prepared with Agilent SureSelectXT Methyl-seq Library Pre kit and then hybridized with hybridization reagents, blocking agents and the SureSelect capture library.
Illumina HiSeq

tag: strain

value: SD

value: cecum

tag: gender

value: male

tag: condition

value: CNP


title: 10-11-21_A

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6F

value: flag leaf


title: Cecum contents, CNP6


title: HaCaT cells-exposed sodium arsenite maintained for 19 weeks-replicate 2

value: The cells were maintained for 19 weeks with 100 nM sodium arsenite


title: Cecum contents, CNP5


title: tRip-selected tRNAs - Bound tRNAs - tRNA/tRip=4

source_name: Human transfer RNAs, tRip-bound, tRNA/tRip=4

value: Cultured HeLa cells

tag: separated on non-denaturing polyacrylamide gel

value: Yes

tag: complexed to trip

tag: trna/trip ratio

tag: molecule subtype

value: Transfer RNA


title: frog_oocyte_ePAB_ribo_seq

description:
B04
rRNA depletion with custom oligos

value: oocyte

value: VI

value: cytoplasmic RNA


title: 10-11-14_A

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6C

tag: cultivar

tag: tissue

tag: age


title: 10-11-14_B

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6D


title: Cecum contents, CNP3


title: frog_oocyte_PABPC1_ribo_seq

description:
B03
rRNA depletion with custom oligos

tag: Stage

tag: manipulation

tag: time after 5eu labeling (h)


title: Cecum contents, CNP2


title: HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 3

value: HaCaT

value: The cells were maintained for 7 weeks with 100 nM sodium arsenite


title: frog_oocyte_eGFP_ribo_seq

description:
B02
rRNA depletion with custom oligos

value: eGFP-expressed

tag: time after iaa addition (h)

tag: rna population

tag: library type

value: ribo-seq (ribosome footprint profiling)


title: 10-11-7_3

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X12B

value: 7 days post anthesis


title: frog_oocyte_water_ribo_seq

description:
B01
rRNA depletion with custom oligos

tag: cell type

value: water-injected


title: Cecum contents, CNP1

tag: strain

value: SD

value: cecum


title: HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 1

tag: cell line

value: Immortalized Human Keratinocytes

tag: treatment


title: Cecum contents, CTL6

tag: gender

value: male

tag: condition

value: CTL


title: 10-11-7_2

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X12A

value: flag leaf


title: 10-11-7_1

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X11H


title: frog_oocyte_eGFP_no_rRNA_depletion_matched_RiboZeroGold_RNA_seq

description:
A07
rRNA depletion with RiboZero Gold kit

data_processing:
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq)

value: ribo-seq matched RNA-seq


title: HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 4

value: The cells were maintained for 28 weeks without 100 nM sodium arsenite


title: HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 4


title: K21_B

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6A

value: Karl

value: 21 days post anthesis


title: K21_C

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X6B


title: Cecum contents, CTL4


title: K21_A

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X5H


title: frog_oocyte_eGFP_no_rRNA_depletion_RNA_seq

description:
A05
no rRNA depletion

value: oocyte

value: VI

value: cytoplasmic RNA


title: frog_oocyte_PABPC1_RiboZeroGold_RNA_seq

description:
A03
rRNA depletion with RiboZero Gold kit


title: Cecum contents, CTL2


title: Cecum contents, CTL3


title: frog_oocyte_ePAB_no_rRNA_depletion_RNA_seq

description:
A06
no rRNA depletion

value: ePAB-overexpressed


title: K14_C

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X5G

value: 14 days post anthesis


title: HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 1

description:
A generous gift from Dr. Tai Hao Quan, University of Michigan
Permanent epithelial cell line from adult human maleskin, aneuploid, immortal, has a transformed phenotype in vitro but remains nontumorigenic.

value: HaCaT


title: frog_oocyte_ePAB_RiboZeroGold_RNA_seq

description:
A04
rRNA depletion with RiboZero Gold kit


title: HaCaT cells-exposed sodium arsenite maintained for 7 weeks-replicate 2

value: The cells were maintained for 7 weeks with 100 nM sodium arsenite


title: HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 2


title: K14_B

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X5F


title: HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 3

value: The cells were maintained for 19 weeks without 100 nM sodium arsenite


title: HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 4


title: Cecum contents, CTL1

value: SD

value: cecum


title: frog_oocyte_water_RiboZeroGold_RNA_seq

description:
A01
rRNA depletion with RiboZero Gold kit

value: water-injected


title: frog_oocyte_eGFP_RiboZeroGold_RNA_seq

description:
A02
rRNA depletion with RiboZero Gold kit

value: eGFP-expressed


title: K14_A

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X5E

value: flag leaf


title: Cecum contents, CTL5

description:
16S rDNA (v3-v4 region)
allsample.all.abundance
allsample.all.reabundance
allsample.otu

value: male

value: CTL


title: HaCaT cells-unexposed sodium arsenite maintained for 28 weeks-replicate 3

value: Immortalized Human Keratinocytes

value: The cells were maintained for 28 weeks without 100 nM sodium arsenite


title: HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 1


title: PRR_iLECS_MUT-2

city: New Orleans

first: Stryder

last: Meadows

state: LA

address: 6400 Freret

department: Cell and Molecular Biology

institute: Tulane University

description: Raw counts

data_processing:
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: Endothelial cells

extract_protocol:
Lungs were harvested at P7, minced and digested in Collagenase-I (Fisher scientific, 17-100-17)/Dispase (Corning, 354235) buffer at 37◦C for 30 min under constant rotation. The digested tissue was triturated ten times through 18G needle to dissociate the clumps and filtered using a 70µm nylon mesh (VWR, 10199-656) to remove any cell debris. The cell suspension was centrifuged at 1200 rpm, 4◦C for 5 min. Single cell suspension were incubated with sheep anti-rat IgG dynabeads (Invitrogen, 11035) coated with CD31 antibody (BD Pharmingen, 553370) at room temperature for 20 min with agitation. Lastly, CD31+ cells were isolated using a magnetic rack separator and RNA was extracted using Genejet RNA purification kit.
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 1 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).

treatment_protocol: Tamoxifen (100µg) was adminstered to new born pups at postnatal days 1,2 and 3.

value: Lung

value: Postnatal day 7

tag: genotype

value: PRR (Atp6ap2)fl/Y; Cdh5-CreERT2+


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 4

value: The cells were maintained for 7 weeks without 100 nM sodium arsenite


title: tumor tissue of high fat diet-fed mouse liver #1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: murine liver tumor tissue

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Mice were treated with DMBA at neonatal stage (4 to 5 days old) and fed normal diet or high fat diet for 30 weeks until euthanized.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Mice were treated with DMBA at neonatal stage (4 to 5 days old) and fed normal diet or high fat diet for 30 weeks until euthanized (ref. Yoshimoto et al. Nature 499, 97–101, 2013)

value: tumor tissue of DMBA-treated, high fat diet-fed mouse liver #1


title: PRR_iLECs_WT-3

description: Raw counts

value: PRR (Atp6ap2)fl/Y


title: PRR_iLECS_MUT-1

description: Raw counts


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 3

value: HaCaT


title: Myometrial Stem Cell Vehicle 3

city: San Antonio

first: Thomas

last: Boyer

state: TX

address: 7703 Floyd Curl Dr.

institute: University of Texas Health San Antonio

data_processing:
aligned to human genome hg19 using TopHat2
read count data was performed using R version 3.6.3
Genome_build: hg19
Supplementary_files_format_and_content: allSamples_Genes_ReadCount

source_name: myometrium stem cells

extract_protocol:
RNA was extracted using Total RNA extraction kit from Zymo. RNA quality and integrity were checked using Fragment Analyzer RNA assay (Agilent Technologies, Santa Clara, CA).
Approximately 500ng Total RNA was used for RNA-seq library preparation by following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. No: KR1151, KAPA Biosystems, USA). The first step in the workflow involved the depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA and original DNA oligonucleotides, respectively. Following rRNA removal, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library. RNA-Seq libraries were subjected to quantification process by the combination of Qubit and Fragment Analyzer, pooled for cBot amplification and subsequent sequenced with 50 bp single read sequencing run with Illumina HiSeq 3000 platform. After the sequencing run, demultiplexing with Bcl2fastq2 will be employed to generate the fastq file for each sample. The average of 25-30M reads were obtained for this set of samples.

tag: agent

value: DMSO


title: PRR_iLECs_WT-2

description: Raw counts


title: PRR_iLECS_MUT-3

description: Raw counts


title: Myometrial Stem Cell Vehicle 2


title: PRR_iLECs_WT-1

description: Raw counts


title: HaCaT cells-unexposed sodium arsenite maintained for 19 weeks-replicate 2

value: The cells were maintained for 19 weeks without 100 nM sodium arsenite


title: K7-3

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X11G

tag: cultivar

value: Karl

value: 7 days post anthesis


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 2


title: pulse_expression_nc85_3

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
(pulse expression) Reads were filtered and trimmed with BBDuk. Mapping and read counting was done with READemption pipeline 0.4.3 (5). Normalization and enrichment analysis was done with edgeR version 3.28.1 (7). To calculate normalization factors the trimmed means of M values (TMM) method was used between pulse expression and empty vector libraries.  All features that had more than 10 read counts in at least two libraries were included in the analysis. Transcripts with log2 fold change of >1 or <-1 and an FDR of < 0.1 were considered as significant.
Genome_build: CP010905.2
Supplementary_files_format_and_content: wiggles

organism: Clostridioides difficile 630

source_name: German Collection of Microorganisms and Cell Cultures GmbH

growth_protocol: C. difficile 630 grown to late-exponential growth phase in TY

extract_protocol:
(pulse expression): Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95 % ethanol, 5 % phenol) and snap-frozen at – 80 °C if not directly processed. The bacterial solution was centrifuged for 20 min, 4500 rpm at 4 °C and the supernatant was completely discarded. Cells were suspended in 600 μl of 10 mg/ml lysozyme in TE buffer (pH 8.0) and incubated at 37 °C for 10 min. Next, 60 μl of 10 % w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64 °C, 1-2 min before adding 66 μl 3 M NaOAc, pH 5.2. Next, 750 μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5 min. at 64 °C. Samples were briefly placed on ice to cool before centrifugation for 15 min, 13,000 rpm at 4 °C. The aqueous layer was transferred into a 2 ml phase lock gel tube (Eppendorf), 750 μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12 min, 13,000 rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3 M NaOAc, pH 6.5) was added and incubated overnight at -20 °C. Precipitated RNA was harvested by centrifugation, washed with cold 75 % v/v ethanol and air-dried. Purified RNA was resuspended in 50 µl RNase-free water and stored at -80 °C.
(pulse expression) Sequencing was accomplished by Vertis Biotechnology GmbH. In brief, RNA was analyzed on a Shimadzu MultiNA microchip. Ribosomal RNA was depleted using an in-house developed depletion protocol. Fragmentation was done with ultrasound (1 pulse of 30s at 4°C). 3’end adapter was ligated and first-strand cDNA synthesis was performed using M-MLV reverse transcriptase with 3’ adapter as primer. cDNA was purified and 5’Illumina TruSeq adapter was ligated to the 3’ end of the antisense cDNA. Amplification of cDNA (10-20 ng/µl) was done by PCR with high fidelity polymerase and 15 PCR cycles. Purification of cDNA was done with Agencourt AMPure XP kit. The samples were pooled in approximately equimolar amounts and size fractionated (range 200 – 600 bp) with an preparative agarose gel. Sequencing was done on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: the induction was performed through the addition of 100ng/ml of anhydrotetracycline for the duration of 20min.

tag: growth


title: K7-1

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X11E

tag: tissue

tag: age


title: tumor tissue of high fat diet-fed mouse liver #186

value: tumor tissue of DMBA-treated, high fat diet-fed mouse liver #186


title: Myometrial Stem Cell Inhibitor 3


title: TA scRNAseq sample 6

city: San Francisco

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

institute: University of California, San Francisco

description:
COMET_1145
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv

data_processing:
Read count matrices were generated through the 10X genomics cellranger pipeline v3.0. All samples were merged into a cell by gene count matrix. This contains the raw data no filtering was applied. Metadata containing calculated QC metrics, COVID Status, Study Day, Identity and cell indexes were generated
Cell barcodes were then determined based upon UMI count distribution.
The h5ad object was processed and analyzed using Scanpy v1.649.
Cells that had <300 genes and had greater than 30,000 counts were filtered.
Data was scaled and mitochondrial genes and total counts were regressed out
Genome_build: GRCh38
Supplementary_files_format_and_content: raw cell by gene count matrix and metadata file containing sample name and corresponding cell index, study day collection, qc metrics  and COVID status are added. An additional h5ad object processed using Scanpy v1.649  has been added that contains log2 normalized and scaled counts.

source_name: Tracheal aspirate

extract_protocol:
After collection, fresh tracheal aspirate (TA)  was transported to a BSL-3 laboratory at ambient temperature to improve neutrophil survival. 3mL of TA was dissociated in 40mL of PBS with 50ug/mL collagenase type 4 (Worthington) and 0.56 ku/mL of Dnase I (Worthington) for 10 minutes at room temperature, followed by passage through a 70mM filter. Cells were pelleted at 350g 4C for 10 minutes, resuspended in PBS with 2mM EDTA and 0.5% BSA, and manually counted on a hemocytometer. Cells were stained with MojoSort Human CD45 and purified by the manufacturer’s protocol (Biolegend). After CD45 positive selection, cells were manually counted with trypan blue on a hemocytometer.
Using a V(D)J v1.1 kit according to the manufacturer’s protocol, samples were loaded on a 10X Genomics Chip A without multiplexing, aiming to capture 10,000 cells (10X Genomics). Libraries underwent paired end 2x150 base pair sequencing on an Illumina NovaSeq 6000.

value: Tracheal aspirate

tag: disease state

value: COVID-ARDS

tag: subject id


title: K7-2

description:
Barley flag leaves at increasing stage of senescence, from 7 to 21 days post anthesis
X11F

value: flag leaf


title: 015.88-M2s

city: Houston

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Adaptors were trimmed
Alignment was performed using the STAR algorithm
Unaligned reads were then aligned using Bowtie 2 v 2.1.0
Aligned reads from both alignment steps were then combined
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm in the Partek Flow software
Pseudocount of 1.0 was given to offset transcripts with 0 reads
miRNAs were filtered out
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample. Data from all 12 samples are in one file

source_name: Macrophages

extract_protocol:
RNA was isolated using the RNeasy kit from Qiagen according to the manufacturer's protocol. Concentrations of RNA samples were quantified using the NanoDrop 2000 spectrophotometer (Thermofisher) according to the manufacturer’s protocol. Quality was assessed by computing RNA integrity numbers (RINs) using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.
Total RNA (800 ng) was ribosomal RNA (rRNA) depleted using the Low Input RiboMinus™ Eukaryote System v2 (Thermofisher) according to the manufacturer’s instructions. Samples were then vacuum concentrated and whole-transcriptome and barcoded libraries were prepared using the Ion Total RNA-Seq Kit v2 (Thermofisher) according to the manufacturer’s instructions. Size distribution of samples was assessed using the Agilent 2100 Bioanalyzer and 6000 RNA Pico kit. Library concentrations were quantified using the Agilent DNA 1000 assay and the 2100 Bioanalyzer according to the manufacturer’s instructions. Barcoded whole-transcriptome libraries were diluted to a 66 pM concentration and combined in equal volumes (13 µl each, 26 µl total) for sequencing with two samples per template preparation. All template reactions were performed on the Ion Chef Instrument using the Ion PI Hi-Q Chef kit (Thermofisher) according to the manufacturer’s instructions. Reactions were loaded onto Ion PI Chips v3 (Thermofisher) for sequencing on an Ion Proton sequencer according to the manufacturer’s protocol.

tag: donor

value: Donor 8

tag: differentiation

value: GM-CSF


title: 015.88-Mobs

value: M. obuense


title: Myometrial Stem Cell Inhibitor 2


title: pulse_expression_nc85_2

value: grown to late-exponential growth phase in TY


title: non-tumor tissue of high fat diet-fed mouse liver #186

source_name: murine liver tissue

value: non-tumor tissue of DMBA-treated, high fat diet-fed mouse liver #186


title: non-tumor tissue of high fat diet-fed mouse liver #117

value: non-tumor tissue of DMBA-treated, high fat diet-fed mouse liver #117


title: TA scRNAseq sample 5

description:
COMET_1107
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv


title: pulse_expression_nc85_1


title: normal diet-fed mouse liver #120

value: DMBA-treated, normal diet-fed mouse liver #120


title: normal diet-fed mouse liver #117

value: DMBA-treated, normal diet-fed mouse liver #117


title: Myometrial Stem Cell Inhibitor 1


title: non-tumor tissue of high fat diet-fed mouse liver #1

value: non-tumor tissue of DMBA-treated, high fat diet-fed mouse liver #1


title: Myometrial Stem Cell Vehicle 1

value: DMSO


title: 013.87-Mobs

value: Donor 7


title: tumor tissue of high fat diet-fed mouse liver #117

value: tumor tissue of DMBA-treated, high fat diet-fed mouse liver #117


title: HaCaT cells-unexposed sodium arsenite maintained for 7 weeks-replicate 1

value: HaCaT

value: Immortalized Human Keratinocytes

value: The cells were maintained for 7 weeks without 100 nM sodium arsenite


title: TA scRNAseq sample 4

description:
COMET_1089
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv

value: Tracheal aspirate

value: COVID-ARDS


title: pulse_expression_control_3

value: emtpy vector


title: TA scRNAseq sample 3

description:
COMET_1072
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv


title: Rb1_3

city: 济南市

first: li

last: hongshi

state: 山东

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室

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
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: white adipose

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the control (CTR) group（intraperitoneally (ip) administered with saline）, the Rb1 group（ip administered with Rb1, 14 mg/kg/d）. Body weight was monitored every day. Mice were housed on a 12-h light/dark cycle.

value: adipose

value: intraperitoneall yadministered with Rb1


title: 014.87-M2s

value: GM-CSF


title: Rb1_2

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室


title: 012.87-M1s

value: M-CSF


title: TA scRNAseq sample 2

description:
COMET_1002
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv


title: pulse_expression_control_1

value: grown to late-exponential growth phase in TY


title: pulse_expression_control_2


title: Rb1_1

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室


title: TA scRNAseq sample 1

description:
COMET_1001
Artik_AnnData_041221_Pos_LogNorm_QCFiltered.h5ad
count_matrix_raw_pos_ARDS.csv
meta_data_pos_ARDS.csv


title: 016.88-M1s

value: Donor 8


title: 007.86-Mobs

value: Donor 6

value: M. obuense


title: CTR3

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室

value: intraperitoneally  administered with saline


title: 011.86-M2s


title: RIP-seq_ST_Hfq-ctrl_2

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to stationary growth phase (3 h post entry); sample was subjected to RIP-seq protocol; biological replicate 2

data_processing:
all: Reads were trimmed for the NEBNext adapter sequence using Cutadapt version 2.5 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two colour sequencing chemistry. Reads that were trimmed to length=0 were discarded.The READemption pipeline version 4.5 (Förstner et al., 2014) with segemehl version 0.2 (Otto et al., 2014) was used for read mapping and calculation of read counts. Reads were mapped on CP010905.2 with additional annotations for ncRNAs, 3’UTRs and 5’UTRs.
dRNA-seq: For the prediction of transcriptional start sites (TSS) and small regulatory RNAs (sRNA), we used the modular, command-line tool ANNOgesic (Yu et al., 2018). All parameters were kept at the default setting, unless stated otherwise. The TSS prediction algorithm was trained using parameters that were derived from manual curation of the first 200 kb of the genome. Secondary TSSs were excluded if a primary TSS was within seven nucleotides distance. For annotation of 5’ untranslated regions (5’UTRs) the default settings for maximum length was corrected to 500 nt.  For the prediction of sRNA, we used the default settings, that is, the transcript must have a predicted TSS or PS at their 5’end, form a stable secondary structure (calculated with RNAfold from Vienna RNA package), and a length between 30 to 500 nt. For 5’UTR-derived sRNA the transcripts must have a processing site (PS) at their 3’end. For 3’UTR-derived sRNA the transcript can either have a TSS or PS at their 5’end and share its terminator with the parental gene.
RIP-seq: Normalization and enrichment analysis was done with the edgeR version 3.28.1 (Robinson et al., 2010). To calculate normalization factors the trimmed means of M values (TMM) method was used between flag-tagged and non-flag-tagged Hfq libraries of each growth phase individually. All features that considered more than 10 read counts in at least two replicates were included in the analysis. Only features with a Benjamini-Hochberg corrected P-value of ≤ 0.1 and a log2 fold-change of ≥ 2 were considered as significantly enriched.
RNAtag-seq: Reads were demultiplexed using fastX toolkit (v0.0.14) prior do further
Genome_build: CP010905.2
Supplementary_files_format_and_content: wiggles

extract_protocol:
dRNA-seq and RNAtag-seq: Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95 % ethanol, 5 % phenol) and snap-frozen at – 80 °C if not directly processed. The bacterial solution was centrifuged for 20 min, 4500 rpm at 4 °C and the supernatant was completely discarded. Cells were suspended in 600 μl of 10 mg/ml lysozyme in TE buffer (pH 8.0) and incubated at 37 °C for 10 min. Next, 60 μl of 10 % w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64 °C, 1-2 min before adding 66 μl 3 M NaOAc, pH 5.2. Next, 750 μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5 min. at 64 °C. Samples were briefly placed on ice to cool before centrifugation for 15 min, 13,000 rpm at 4 °C. The aqueous layer was transferred into a 2 ml phase lock gel tube (Eppendorf), 750 μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12 min, 13,000 rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3 M NaOAc, pH 6.5) was added and incubated overnight at -20 °C. Precipitated RNA was harvested by centrifugation, washed with cold 75 % v/v ethanol and air-dried. Purified RNA was resuspended in 50 µl RNase-free water and stored at -80 °C.
RIP-seq: For each condition, 50 OD were harvested by centrifugation for 20 min at 4000 rpm at 4 °C, snap frozen and resuspended in 800 µl lysis buffer (20 mM TRIS pH 8.0, 1 mM MgCl2, 150 mM KCl, 1 mM DTT). Subsequently, each sample was mixed with 1 µl DNase I (Fermentas, 1U/µl) and 800 µl of 0.1 mm glass beads and lysed in a RETSCH's Mixer Mill (30 Hz, 10 min, 4°C). Bacterial lysates were cleared by centrifugation for 10 min at 14,000 x g and 4 °C. Approximately 900 µl supernatant was transferred to a new tube and incubated with 25 µl (1/2 * OD in µl) of mouse-anti-FLAG antibody (clone M2, Merck/Sigma-Aldrich #F1804) at 4 °C for 45 min (rocking). Immunoprecipitation of FLAG-tagged Hfq was performed by incubating each sample with 75 µl pre-washed (3 x resuspended in 1 ml lysis buffer and centrifuged at 10,000 rpm for 1 min) protein A sepharose beads (Merck/Sigma-Aldrich #P6649) for 45 min at 4 °C (rocking). Beads and captured proteins were washed 5 x with 500 µl lysis buffer (mixed by inversion and centrifuged at 10,000 rpm for 1 min) and resuspended in 500 µl lysis buffer. Finally, RNA, co-immunoprecipitated with antibodies and protein A sepharose beads, was eluted by adding the same volume of Phenol:Chloroform:Isoamylalcohol (25:24:1, pH 4.5, Roth). The solution was mixed for 20 s, transferred to PLG tubes (Eppendorf) and incubated at room temperature for 3 min. Following centrifugation (30 min, 15,200 x g, 15 °C) the aqueous phase was transferred to new tubes and RNA was precipitated over night at -°20 °C by adding 30 µg Glycoblue and 800 µl isopropanol. Precipitated RNA was pelleted (centrifugation for 45 min, 15,200 rpm, 4 °C), washed with 80 % and 100 % ethanol (centrifugation for 10 min, 15,200 rpm, 4 °C) and resuspended in 15,5 µl nuclease-free water (65 °C, 1 min, 600 rpm). For DNase treatment, purified RNA was incubated with 2 µl DNase I, 0.5 µl RNase inhibitor and 2 µl 10 x DNase buffer for 30 min at 37 C. To each sample, 100 µl nuclease free water was added and DNase treated RNA was purified by Phenol:Chloroform:Isoamylalcohol treatment, as described before. Precipitation was performed overnight at – 20 °C by mixing the samples with 3 x the volume of sodium-acetate/ethanol (1:30), followed by centrifugation and washing with 80 % and 100 % ethanol. Finally, air-dried pellets were resuspended in 20 µl nuclease-free water (65 °C, 1 min, 600 rpm).
dRNA-seq: Library preparation for dRNA-seq was accomplished by Vertis Biotechnology AG. In brief, total RNA was analyzed on a Shimadzu MultiNA microchip electrophoresis system. 23S/16S ratio for all samples was 1.3. RNA was fragmented via ultrasound (4 pulses a 30 sec, 4 °C) and subsequently treated with T4 Polynucleotide Kinase (NEB). Half of the samples were then treated with terminator exonuclease (TEX) for dRNA-seq. For the cDNA synthesis, the RNA fragments were poly(A)-tailed and 5’PPP structures were removed with RNA 5’ Polyphosphatase (Epicentre). The RNA sequencing adapter with the barcodes were ligated to the 5’-monophosphate of the fragments. First strand cDNA was synthesized with an oligo(dT)-adapter primer and M-MLV reverse transcriptase. Amplification of cDNA was done via PCR to an approximate amount of 10 20 ng/µl. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed with Shimadzu MultiNA microchip electrophoresis. Equimolar amounts of the samples were pooled for sequencing. cDNAs had a size between 200 and 550 bp. The library pool was fractionated via differential clean-up with the Agencourt AMPure kit. The cDNA pool was checked with capillary electrophoresis as stated above. Libraries were sequenced on an Illumina NextSeq 500 system using 75 bp read length.
RNAtag-seq: Total RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies) and rRNA was detected. Equal amounts of samples (~ 500 ng) were used for the preparation of cDNA libraries with the RNA-tag-Seq protocol as previously published by Shishkin et al. (Shishkin et al., 2015) with minor modifications. Briefly, the RNA samples were fragmented with FastAP buffer at 94˚C for 3 min and were dephoshorylated using the FastAP enzyme (Thermo Scientific) at 37 ˚C for 30 min followed by bead purification with 2 volumes of Agencourt RNAClean XP beads. Fragmentation profiles were checked using RNA 6000 pico kit (Agilent) with a 2100 Bioanalyzer. The RNA fragments were ligated with 3´- barcoded adaptors at 22˚C for 1 hour and 30 min using T4 RNA Ligase (NEB). Barcoded RNA samples were pooled together, the ligase was inhibited by RTL buffer (Qiagen RNeasy Min Elute Cleanup Kit) and purified with RNA Clean & Concentrator-5 column (Zymo). rRNA were depleted from pools using Ribo-Zero (Bacteria) Kit (Illumina) and purified with RNA Clean & Concentrator-5 column (Zymo). The profiles before and after rRNA depletion were analysed with RNA 6000 pico kit (Agilent) with a 2100 Bioanalyzer. The rRNA depleted RNA were reverse transcripted and the first strand of the cDNA were synthsized using a custom AR2 oligo (Sigma-Aldrich) and the AffinityScript multiple temperature cDNA synthesis kit (Agilent) at 55°C for 55 minutes. The RNA was degraded with 1M NaOH at 70 °C for 12 minutes, the reactions were neutralized with Acetic acid and were purified with 2 volumes of MagSi-NGSPREP Plus beads (AMSBIO). A second 3Tr3 adaptor were ligated to the cDNA using T4 RNA Ligase (NEB) overnight at 22°C followed with two bead purification steps with 2 volumes of MagSi-NGSPREP Plus beads (AMSBIO). A PCR enrichment test was performed in order to determine the number of PCR cycles that are nesessery for each pool followed by a bead purification step and a QC with DNA HS kit (Agilent). Then, the final PCR was performed with the number of cycles determined from the previous step using P5 and P7 primers. Two sequential bead purification steps were performed with 1.5 and 0.7 respectively. Libraries were quantified with the Qubit 3.0 Fluometer (ThermoFisher) and the library quality and size distribution (~480 bp peak size) was checked using a 2100 Bioanalyzer with the High Sensitivity DNA kit (Agilent). Sequencing of pooled libraries, spiked with 5% PhiX control library, was performed with ~8 million reads / sample in single-end mode on the NextSeq 500 platform (Illumina) with the High Output Kit v2.5 (75 Cycles).
RIP-seq: RNA quality was controlled using a 2100 Bioanalyze

value: grown in TY to stationary growth phase


title: CTR2

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室


title: MOLT-3 cells, Compound E rep 3

city: Zhengzhou

first: Hui

last: Yu

address: 100 Kexue Road

institute: Zhengzhou University

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MB3

data_processing:
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Index of the reference genome was built using Hisat2 v2.0.5
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Supplementary_files_format_and_content: MA vs MB gene_count, MA vs MB gene_fpkm

source_name: Cultured MOLT-3 cells

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Compound E


title: CTR1

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室


title: MOLT-3 cells, Compound E rep 2

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MB2


title: RIP-seq_ST_Hfq-ctrl_1

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to stationary growth phase (3 h post entry); sample was subjected to RIP-seq protocol; biological replicate 1


title: MOLT-3 cells, DMSO rep 3

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MA3

value: DMSO


title: 007.85-M2s

value: Donor 5


title: RIP-seq_ST_Hfq-FLAG_1

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to stationary growth phase (3 h post entry); sample was subjected to RIP-seq protocol; biological replicate 1


title: 010.85-Mobs


title: MOLT-3 cells, Compound E rep 1

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MB1


title: 008.85-M1s


title: RIP-seq_ST_Hfq-FLAG_2

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to stationary growth phase (3 h post entry); sample was subjected to RIP-seq protocol; biological replicate 2


title: MOLT-3 cells, DMSO rep 2

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MA2


title: RIP-seq_LE_Hfq-ctrl_2

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to late-exponential growth phase (OD600=0.9); sample was subjected to RIP-seq protocol; biological replicate 2


title: MSL3 CTR_2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
Sequencing reads were aligned to the dm6 version of the D. melanogaster genome using bowtie2 (version 2.3.5) allowing only unique matches
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: dm6 (mel) and caf1 (vir)
Supplementary_files_format_and_content: bigwig files with coverage

organism: Drosophila melanogaster

source_name: KC cells

growth_protocol: D. melanogaster embryonic Kc167 cell line was obtained from the Drosophila Genomic Resource Center (https://dgrc.bio.indiana.edu/Home). D. melanogaster S2 (subclone L2-4) cell line was a kind gift of P Heun (Villa et al., 2016). D. virilis 79f7Dv3 cell line was a kind gift of BV Adrianov (Albig et al., 2019). The identity of cell lines was verified by high-throughput sequencing. Cells were subjected to mycoplasma testing. Cells were maintained at 26°C in Schneider’s Drosophila Medium (Thermo-Fischer, Cat. No 21720024) supplemented with 10% FBS (Kc167 and S2) or 5% FBS (79f7Dv3) and 1% Penicillin-Streptomycin solution (Sigma-Aldrich, Cat No P-4333). Spodoptera frugiperda 21 (SF21) cells (Gibco) were used for amplification of recombinant baculoviruses and baculovirus-driven expression of recombinant proteins. SF21 cells were cultured at 26°C in Sf-900 II medium (Gibco) supplemented with 10% fetal calf serum and gentamycin.

extract_protocol:
Pellet from 6 × 107 S2 or virilis cells was suspended in 1.2 ml of lysis buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA pH 8, 0.5% SDS, 0.15 mg/ml of proteinase K) and incubated at 56°C overnight. After addition of sodium acetate to a final concentration of 0.3 M, the nucleic acids were extracted with phenol–chloroform and precipitated with an equal volume of isopropanol at −20°C for 1 h. Precipitated nucleic acids were centrifuged and washed with 70% ethanol. Dried pellets were resuspended in TE buffer and sonicated with Covaris AFA S220 (microTUBEs, Peak Incident Power 175 W, Duty Factor 10%, Cycles per Burst 200, 430 s) to generate 200 bp fragments. After RNAse digestion (0.1 mg/ml, 1 h at 37°C), DNA was purified with the GenElute kit (Sigma-Aldrich). DNA immunoprecipitation (DIP) experiments were performed as in (Villa et al. 2016) with few modifications. Briefly, 400 ng of genomic DNA (gDNA) was incubated with 80nM of recombinant proteins at 26°C for 30 min in 100 μl of binding buffer (100 mM KCl, 2 mM MgCl2, 2 mM Tris–HCl pH 7.5, 10% Glycerol, 10 μM ZnCl2). Ten percent of the reaction was taken as input material. DNA–protein complexes were immunoprecipitated using 30 μl of anti-FLAG M2 beads (SIGMA) and washed twice with 100 μl of binding buffer to eliminate unbound DNA. After proteinase K digestion (0.5 mg/ml, 1 h at 56°C), DNA was purified with AMPure beads (Beckman Coulter).
Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465).

treatment_protocol: Cells were transfected with the plasmid of interest plus 1:20 of pCoBlast (Thermo Fischer, Cat. No K5150-01) using Effectene transfection reagent (QIAgen, Cat. No 301425). 72h after transfection cells were diluted 2-3 times and Blasticidin was added to the medium at a final concentration of 50ng/ul for 7 or 10 days. For the DIP experiments in presence of RNA we pre-incubated the recombinant proteins with different amount of RB4 (GGUUAACGUUAUACAAGCCGAG) or ctrl (GACGUUGUAAUAUGUACGGGAU) RNA oligos and proceeded with the normal DIP protocol.

tag: ip target

tag: assay type

value: ChIP

tag: experimental series


title: MOLT-3 cells, DMSO rep 1

description:
MA vs MB gene_count.txt
MA vs MB gene_fpkm.txt
MA1

tag: cell line


title: Colon CTL rep 3

city: New York

first: Andrea

last: Ventura

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were aligned to the standard mouse genome (mm10) using the STAR aligner (v2.5.3a).
Mapped reads were counted at each gene locus and differential gene expression was calculated using DESeq2 V1.20.0
Log2Fold Change and adjusted pvalues were calculated by comparing T6B vs control tissues.
Genome_build: mm10
Supplementary_files_format_and_content: single csv file containing log2Foldand statistics for all expressed genes.

source_name: Colon

growth_protocol: Mice were bred and housed in the pathogen-free animal facility at Memorial Sloan-Kettering Cancer Center and were used in accordance with institutional guidelines. Mouse experiments were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center.

extract_protocol:
Total RNA was extracted from homogenyzed tissues using the TRIzol reagent (Invitrogen) according to  manufacturer's instructions
After Ribogreen quantification and quality control, 500 ng of total RNA with RIN values of 7.0-10 underwent polyA selection and TruSeq library preparation according to instructions  provided by Illumina (TruSeq Stranded mRNA LT Kit). An Average of 34 million paired reads was generated per samples. Libraries generated from the colon were run on an Illumina HiSeq  2500 machine and generated using the HiSeq SBS Kit v4 generating single reads 50 bp long.

treatment_protocol: Mice were fed chow containing doxycycline (625mg/Kg)

tag: strain

tag: treatment

value: doxycycline


title: RIP-seq_LE_Hfq-ctrl_1

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to late-exponential growth phase (OD600=0.9); sample was subjected to RIP-seq protocol; biological replicate 1


title: MSL3 CTR_1


title: RIP-seq_LE_Hfq-FLAG_2

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to late-exponential growth phase (OD600=0.9); sample was subjected to RIP-seq protocol; biological replicate 2


title: Colon CTL rep 2


title: D112PrTz_Fib

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

data_processing:
Illumina's RTA version 2 was used for basecalling followed by bcl2fastq version 2.20 to generate fastq files.
Reads were mapped to GRCh38 using HISAT2.
Duplicates were removed using SAMtools.
Mapped reads were counted using FeatureCount using annotations from Gencode V20.
Genes identified as Goblins, rRNAs, and pseudogenes were removed.
Counts were normalized to FPKM with edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: Viable human prostate transition zone fibroblasts

extract_protocol:
Total RNA from 500K FACS-purified cells was extracted using RNEasy micro columns (Qiagen). RNA quality and quantity were measured by a TapeStation and NanoDrop.
Library prep was performed using Takara Bio SMARTer Stranded Total RNA sample prep kit according to the manufacturer's instructions.

treatment_protocol: Fibroblasts from dissociated health prostates from organ donors were isolated by FACS.

tag: patient phenotype

value: Donor (Normal)

tag: prostatic zone

value: Transition Zone + Urethra

tag: digestion enzyme

value: 5mg/mL Collagenase I 4hr

tag: facs ab profile

value: Via- CD326- CD45- CD200- PDPN+

tag: cell type

value: Fibroblasts from normal human prostate transition zone tissue


title: RIP-seq_LE_Hfq-FLAG_1

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to late-exponential growth phase (OD600=0.9); sample was subjected to RIP-seq protocol; biological replicate 1

tag: growth


title: MSL3 VIR_6

tag: transfection

value: GFP-MSL2 vir


title: Colon CTL rep 1

tag: genotype


title: D112PrPz_Fib

source_name: Viable human prostate peripheral zone fibroblasts

value: Peripheral Zone

value: Fibroblasts from normal human prostate peripheral zone tissue


title: 010.86-M1s

value: Donor 6

value: M-CSF


title: RIP-seq_ME_Hfq-ctrl_2

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to mid-exponential growth phase (OD600=0.5); sample was subjected to RIP-seq protocol; biological replicate 2

value: emtpy vector


title: MSL3 VIR_2


title: Colon T6B rep 3

value: R26-rtTA; T6B


title: D107PrTz_Fib


title: MSL3 MEL_2

value: GFP-MSL2 mel


title: RIP-seq_ME_Hfq-ctrl_1

description: Strain expressing un-tagged Hfq (FFS-38) grown in TY to mid-exponential growth phase (OD600=0.5); sample was subjected to RIP-seq protocol; biological replicate 1


title: MSL2vir RB4_80 DIP

source_name: S2 cells sheared genomic DNA

value: MSL2 Drosophila virilis

value: DIP


title: RIP-seq_ME_Hfq-FLAG_2

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to mid-exponential growth phase (OD600=0.5); sample was subjected to RIP-seq protocol; biological replicate 2


title: Colon T6B rep 1


title: RIP-seq_ME_Hfq-FLAG_1

description: Strain expressing 3xFLAG tagged Hfq (FFS-50) grown in TY to mid-exponential growth phase (OD600=0.5); sample was subjected to RIP-seq protocol; biological replicate 1


title: D103PrTz_Fib


title: D107PrPz_Fib


title: Colon T6B rep 2


title: MSL2vir DIP 7


title: D103PrPz_Fib


title: NIH3T3_siPABPC1_48h_PAL_seq

description:
C19
no rRNA depletion

data_processing:
Library strategy: PAL-seq
Illumina 1.5; Conventional base calls
Read trimming: Cutadapt (v1.18). For ribo-seq and ribo-seq matched RNA-seq: cutadapt -m 15 -u 4 --match-read-wildcards -e 0.1 -a TCGTATGCCGTCTTCTGCTTG -O 1; For PAL-seq: cutadapt -m 15 -u 12 --match-read-wildcards -e 0.05 -a NNNNATCTCGTATGCCGTCTTCTGCTTG -O 7
Read mapping: STAR (v2.4.2a): STAR --runThreadN 23 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate
Transcript modle: human (release 25, GRCh38.p7, main annotation) and mouse (release 10, GRCh38.p4, primary assembly) gene annotations were downloaded from the GENCODE website. X. laevis gene annotations (v9.1 assembly, v1.8.3.2 primary transcript) were downloaded from the Xenbase website, and only chromosomal annotations were used. X. laevis mitochondrial gene annotations were curated based on the information obtained from the NCBI website (NC_001573.1) and appended. For all species, annotations for protein-coding genes were extracted, and for each gene, the isoform with the longest open reading frame (ORF) was selected to represent that gene. In cases in which multiple isoforms had ORFs of the same length, the isoform with the longest transcript was selected as the reference annotation.
Assigning reads to genes: htseq-count (0.11.0) and bedtools (v2.26.0). For ribo-seq and ribo-seq matched RNA-seq: htseq-count -f bam -t CDS; for NEXTflex RNA-seq: htseq-count -s reverse -f bam -t exon; for TAIL-seq: intersect -wa -wb -bed -s; for PAL-seq: intersect -wa -wb -bed -S
Genome_build: Human (GRCh38.p7), Mouse (GRCh38.p4), Frog (Xenbase X. laevis v9.1)
Supplementary_files_format_and_content: tab delimited text file with gene id and read count (for RNA-seq and Ribo-seq); tab delimited text file with gene id, cluster id and tail length (for PAL-seq and TAIL-seq); *hits.txt files are raw signal intensities from Hiseq 2000 sequencing which are used with a custom algorithm to call poly(A) tail lengths

source_name: NIH3T3 cells

value: cell line

tag: Stage

tag: manipulation

value: transfected with siRNAs targeting PAPBPC1 for 48h

tag: time after 5eu labeling (h)

tag: time after iaa addition (h)

tag: rna population

value: cytoplasmic RNA

tag: library type

value: PAL-seq v3


title: NIH3T3_siControl_48h_PAL_seq

description:
C18
no rRNA depletion

value: transfected with non-targeting siRNAs for 48h


title: D098PrPz_Fib

value: Donor (Normal)

value: 5mg/mL Collagenase I 4hr

value: Via- CD326- CD45- CD200- PDPN+


title: D094PrTz_Fib

value: Transition Zone + Urethra

value: Fibroblasts from normal human prostate transition zone tissue


title: MSL2vir DIP 6

tag: ip target

tag: assay type

tag: experimental series


title: H4K16ac VIR_ROX_5

value: ChIP

value: GFP-MSL2 vir + roX2


title: D094PrPz_Fib

tag: patient phenotype

value: Peripheral Zone

value: Fibroblasts from normal human prostate peripheral zone tissue


title: DIP input 3

value: input control


title: BPH556PrSN_Fcol

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 and v3 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Populations of single-cells dissociated from diseased prostates from BPH patients were isolated by FACS

value: BPH Stromal Nodule

tag: prostatic zone

value: Transition Zone

tag: 10x library type


title: MSL3 MEL_1

value: GFP-MSL2 mel


title: RNAtag-seq_LE-TY_2

description: C. difficile 630 grown to late-exponential growth phase in TY; samples treated according to adopted RNA-tag-seq protokol (Shishkin et al., 2015) to expose RNA 3' ends; biological replicate 2


title: H4K16ac VIR_5

value: GFP-MSL2 vir


title: RNAtag-seq_LE-TY_1

description: C. difficile 630 grown to late-exponential growth phase in TY; samples treated according to adopted RNA-tag-seq protokol (Shishkin et al., 2015) to expose RNA 3' ends; biological replicate 1


title: MSL2vir IRB_80 DIP

value: MSL2 Drosophila virilis

value: DIP

tag: treatment

value: IRB 80


title: BPH556PrGA2_Fcol

value: BPH Glandular Area

tag: digestion enzyme

tag: facs ab profile


title: dRNA-seq_LE-BHI_TEX-_2

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 2

value: untreated

tag: growth


title: H4K16ac VIR_ROX_4

tag: transfection


title: dRNA-seq_LE-BHI_TEX-_1

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 1


title: dRNA-seq_ST-TY_TEX-_3

description: C. difficile 630 grown to stationary growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 3

value: grown to stationary growth phase in TY


title: H4K16ac VIR_4


title: BPH556PrGA1_Fcol

value: 5mg/mL Collagenase I 4hr


title: BPH511PrPUr_Fcol_3GEX

value: BPH Peri-Urethral Fibrosis


title: RNAtag-seq_LE-TY_3

description: C. difficile 630 grown to late-exponential growth phase in TY; samples treated according to adopted RNA-tag-seq protokol (Shishkin et al., 2015) to expose RNA 3' ends; biological replicate 3


title: BPH511PrG_Fcol_3GEX

value: BPH Glandular Nodule


title: MSL2vir RB4_40 DIP


title: dRNA-seq_ST-TY_TEX-_2

description: C. difficile 630 grown to stationary growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 2


title: H4K16ac VIR_ROX_2

value: ChIP

value: GFP-MSL2 vir + roX2


title: H4K16ac VIR_ROX_3


title: TT-258_Solifenacin

city: South San Francisco

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: hg38 v.13
Supplementary_files_format_and_content: TXT

source_name: iPSC-CM

growth_protocol: iPSC Culture, iPSC-CM Differentiation, and Blasticidin Selection: WTC iPSCs and derivative lines were maintained under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences) and fed daily with E8 medium (STEMCELL Technologies) (Ludwig et al., 2006). Accutase (STEMCELL Technologies) was used to enzymatically dissociate iPSCs into single cells. To promote cell survival during enzymatic passaging, cells were passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10μM; Selleckchem) (Watanabe et al., 2007). iPSCs were frozen in 90% fetal bovine serum (HyClone) and 10% dimethyl sulfoxide (Sigma). iPSCs were differentiated into iPSC-CMs using the Wnt modulation-differentiation method (Lian et al., 2012) with 7μM CHIR (Selleckchem) and 5μM IWP2 (Sigma) in RPMI media supplemented with B27 (Thermo Fisher Scientific). iPSC-CMs were purified using 1μM blasticidin (Thermo Fisher Scientific). Then, 15 days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum (FBS) + 10% DMSO. iPSC-CMs were thawed in RPMI+B27+10% FBS directly onto Matrigel-coated 384-well plates at a density of 20,000 cells/well. The next day, the media was switched to Tenaya’s Cardiomyocyte (TCM) media for 6 days before screening. TCM media comprises Dulbecco's Modified Eagle Medium (DMEM) without glucose, 10% dialyzed FBS, 10mM D-(+)-galactose, and 1mM sodium pyruvate. Generation of Blasticidin-Selectable iPSC Line: A plasmid containing the Bsd open reading frame and a selectable marker containing Puromycin and green fluorescent protein was knocked into the 3’ end of the MYH6 locus of WTC iPSCs. Cells were selected with puromycin. After the first round of selection, the selectable marker was removed using a plasmid expressing Cre recombinase (Supplemental Figure 1A). Clones were isolated and verified using colony polymerase chain reaction (PCR) to ensure the presence of the Bsd marker and absence of the selectable cassette. Finalized clones showing the appropriate iPSC morphology were sent to WiCell for single-nucleotide polymorphism karyotyping (Figure S1B).

extract_protocol:
RNA Extraction: Approximately 10^5 to 10^6 iPSC-CMs were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 minutes at room temperature. cDNA was reverse transcribed from 1 μg of RNA through random hexamers using the SuperScript-III kit (Invitrogen) according to the manufacturer’s instructions. Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Applied Biosystems) with the TaqMan probes listed in Table S5 (Life Technologies).
Library Preparation: 100ng total RNA was extracted via polyA-tail specific protocol according to Illumina protocol. RNA library preparation was achieved by using TruSeq Stranded mRNA kit (Illumina) which also removes ribosomal RNA. The libraries were sequenced as 100bp single-end reads using Illumina NovaSeq SP with an average of 30M reads per sample.

treatment_protocol: Approximately 10^5 iPSC-CMs exposed to cardiotoxic drugs for 4 days.

value: Solifenacin

tag: media-timepoint

value: 1uM 4 days

tag: cell type

value: iPSC cardiomyocytes


title: H4K16ac VIR_2


title: dRNA-seq_LE-TY_TEX-_3

description: C. difficile 630 grown to late-exponential growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 3


title: dRNA-seq_LE-BHI_TEX-_3

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 3


title: HEK293T-Vehicle-HiC

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hi-C data process pipline. Reads were obtained following quality filtering and adaptor trimming using fastp(version  0.20.0) with default parameters. Hi-C mapping, filtering, correction, and binning were performed with the HiC-Pro(version 2.11.1) software. The reads were mapped to the hg38 human reference genome. Hi-C interactive loops were identified by Fit-Hi-C (version 2.0.7)  with parameters (-r 25000 -U 5000000 -L 50000) at resolution 25kb.Hi-C files were transfered from HiCPro results by using Juicertools (version 1.13.02).The popular format to store Hi-C data, .hic, can be converted into .cool files using hic2cool(version 0.8.3) software.We used coolpup.py(version 0.9.5) to pile-up normalized Hi-C signals at a 25kb resolution at loops previously identified.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks,and broadPeak files  were generated using MACS2.

source_name: HEK293T cells

growth_protocol: BJAB and HEK293T cells were cultured at 37℃ and 5% CO2 in  complete medium: RPMI 1640 or DMEM medium  supplemented with 10% fetal bovine serum, 100U ml-1 penicillin/streptomycin.

extract_protocol:
For HEK293T Hi-C, cells were crosslinked,digested and ligated. Then protein were degraded by protein K, precipitated by isopropanol.
Hi-C libraries were prepared using in-situ Hi-C protocol. Dynabeads MyOne Streptavidin C1 beads was washed once with 1×Tween Washing Buffer. The beads were added to Hi-C DNA and incubated at RT for 15 min with rotation. The beads were washed by adding 200μl of 1×TWB. Heat the tubes on a Thermomixer at 55°C for 2 min with mixing. The beads were reclaimed using a magnet, supernatant was discarded. Repeat washing. End-repair and dA tailing following the in situ Hi-C protocol, adapters were added to DNA fragments. PCR amplification was performed with thirteen to nineteen cycles using Illumina primers.

tag: cell line

value: embryonic kidney cell

value: Transient transfection with vehicle plasmid


title: TT-257_Solifenacin


title: dRNA-seq_LE-TY_TEX-_2

description: C. difficile 630 grown to late-exponential growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 2


title: dRNA-seq_LE-TY_TEX-_1

description: C. difficile 630 grown to late-exponential growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 1


title: HEK293T-EBNA2-full-HiC

value: Transient transfection with EBNA2(full) plasmid


title: TT-256_Nitrendipine

value: Nitrendipine


title: H4K16ac VIR_1

value: GFP-MSL2 vir


title: HEK293T-EBNA2-1-176-HiC

value: Transient transfection with EBNA2(1-176) plasmid


title: dRNA-seq_LE-BHI_TEX+_3

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 3

value: TEX treated


title: TT-255_Nitrendipine


title: BJAB-SCNG-ATAC-Rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq data process pipline.Clean reads  were obtained following quality filtering and adapter trimming using fastp(version  0.20.0) with default parameters, and reads were mapped to the hg38 genome assembly using bowtie2 (version 2.3.5.1) with parameters (-p 6 --sensitive -X 2000);Uniq mapped  ATAC-seq reads pairs were got after pcr duplication removing by Picard (version 2.22.8) and samtools (version 1.7);RPKM normalized BigWig files were generated by BEDtools (version 2.29.2);Peak files were got from Bam file by using MACS2(version 2.2.4) with parameters(-t input_file –q 0.01 -f BAM --nomodel --shift -100 --extsize 200 -keep-dup all).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks,and broadPeak files  were generated using MACS2.

source_name: BJAB cells

extract_protocol:
For HEK293T ATAC-seq, transient transfection of EBNA2 and vehicle plasmid into BJAB cell respectively, collect positive cells by fluorescence-activated cell sorting (FACS) after 48 hours. To profile open chromatin, a total of 5×104 cell pellets were washed once with cold PBS, cells lysed on ice for 3 minutes in 50 μL ice-cold Lysis Buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% TWEEN 20, 0.01% Digitonin in DEPC H2O), resuspended in 1mL ice-cold RBS-Wash (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% TWEEN 20) and pelleted at 4°C at 500 × g for 10 minutes. Tagmentation was performed in 1 × Tagmentation Buffer (10mM Tris pH 7.4, 5mM MgCl2, 10% DMF, 33% PBS, 0.1% TWEEN 20, 0.01% Digitonin) using 100nM Tn5 Transposase for 30 minutes at 37°C. Tagmentation was inactivated with the addition of 5 volumes SDS Lysis Buffer (100mM Tris pH 7.4, 50mM NaCl, 10mM EDTA, 0.5% SDS in H2O) and 100μg Proteinase K (Invitrogen, 25530015, USA) for 30 minutes at 55°C. Centrifuge at 500 × g to take the supernatant, DNA was size selected and purified using QIAquick PCR Purification Kit (QIAGEN, 28106, GERMANY) according to the manufacturer’s instructions.
ATAC library was prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 for Illumina (#TD501).

value: BJAB

value: B cell line


title: TT-254_Daunorubicin

value: Daunorubicin


title: dRNA-seq_LE-BHI_TEX+_2

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 2


title: MSL3 VIR_5


title: BJAB-SCNG-ATAC-Rep1


title: dRNA-seq_ST-TY_TEX-_1

description: C. difficile 630 grown to stationary growth phase in TY; samples remain untreated with terminator exonuclease (Tex),  to capture both primary (5′- PPP) and processed (5′-P or 5′OH) 5’ ends of transcripts; biological replicate 1

value: untreated

value: grown to stationary growth phase in TY


title: VIR_ROX_5_input

value: input control

value: ChIP


title: dRNA-seq_ST-TY_TEX+_3

description: C. difficile 630 grown to stationary growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 3


title: TT-252_BI 2536


title: TT-253_Daunorubicin


title: BJAB-EBNA2-ATAC-Rep2

value: Transient transfection with EBNA2 plasmid


title: BJAB-EBNA2-ATAC-Rep1


title: TT-251_BI 2536

value: 1uM 4 days


title: H4K16ac VIR_ROX_1

value: GFP-MSL2 vir + roX2


title: VIR_5_input


title: MSL3 VIR_ROX_4


title: dRNA-seq_ST-TY_TEX+_2

description: C. difficile 630 grown to stationary growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 2


title: BJAB-SCNG-H3K27ac-Rep2

data_processing:
Library strategy: CUT&Tag
Illumina Casava1.7 software used for basecalling.
CUT&Tag data process pipline.Clean reads  were obtained following quality filtering and adapter trimming using fastp(version  0.20.0) with default parameters, and reads were mapped to the hg38 genome assembly using bowtie2 (version 2.3.5.1) with parameters (-p 6 --sensitive -I 10 -X 700 --phred33);Uniq mapped CUT&Tag reads pairs were got after pcr duplication removing by Picard (version 2.22.8) and samtools (version 1.7);RPKM normalized BigWig files were generated by BEDtools (version 2.29.2);Bed files of peaks were got from Bam file by using HOMER (version 4.10.4) with parameters (-style histone).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks,and broadPeak files  were generated using MACS2.

extract_protocol: BJAB cells CUT&Tag was carried out following manufacture’s instruction (Vazyme Biotech, TD901-01). In brief, transient transfection of EBNA2 and vehicle plasmid into BJAB cell respectively, collect positive cells by fluorescence-activated cell sorting (FACS) after 48 hours. Approximately 100,000 BJAB cells were processed by centrifugation between buffer exchanges at 600×g for 3 min and in a swinging bucked rotor at room temperature for the initial wash and incubation steps. Cells were collected and washed with 1 ml of Wash Buffer at room temperature. Cells were rotate and incubated in antibody (ab4729, Abcam, USA) diluted 1:50 in Antibody Buffer for 2 hours at room temperature. Permeabilized nuclei were then centrifuged once and incubated with anti-rabbit IgG antibody (FD0218, Fudebio, China, 1:100 dilution) in 1 ml of Dig-wash Buffer on a rotator at room temperature for 1 hour. Nuclei were washed twice with Dig-wash Buffer and incubated with 1:100 dilution of pG-Tn5 in Dig-300 Buffer for 1 h at room temperature on a rotator. Cells were washed two times with Dig-300 Buffer and resuspended in 300µl of Tagmentation Buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding Stop Buffer (each sample with 10μl 0.5M EDTA, 3μl 10% SDS and 2.5μl 20mg/ml Proteinase K), and the sample was held for 1 hour at 50 °C in incubator. The remaining steps are carried out according to the product manual.

tag: chip antibody

value: H3K27ac (Abcam, ChIP Grade ab4729)


title: TT-250_PHA-767491

value: iPSC cardiomyocytes


title: MSL3 VIR_4


title: TT-249_PHA-767491


title: BJAB-SCNG-H3K27ac-Rep1

value: Transient transfection with vehicle plasmid


title: MSL3 VIR_ROX_5


title: VIR_ROX_4_input


title: dRNA-seq_ST-TY_TEX+_1

description: C. difficile 630 grown to stationary growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 1


title: VIR_4_input


title: TT-248_WZ8040


title: TT-247_WZ8040


title: dRNA-seq_LE-TY_TEX+_3

description: C. difficile 630 grown to late-exponential growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 3


title: dRNA-seq_LE-TY_TEX+_1

description: C. difficile 630 grown to late-exponential growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 1


title: MSL3 VIR_ROX_3


title: dRNA-seq_LE-BHI_TEX+_1

description: C. difficile 630 grown to late-exponential growth phase in BHI; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 1


title: BJAB-EBNA2-H3K27ac-Rep1


title: dRNA-seq_LE-TY_TEX+_2

description: C. difficile 630 grown to late-exponential growth phase in TY; samples were treated with terminator exonuclease (Tex) leading to the specific degradation of processed (5′-P or 5′OH) RNAs, thus enriching primary transcripts; biological replicate 2


title: BJAB-EBNA2-H3K27ac-Rep2


title: TT-245_Tegretol

value: Tegretol


title: TT-246_Tegretol


title: ICC11664_R_3

city: Penrith

first: Krista

last: Plett

state: NSW

address: Locked Bag 1797

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

data_processing:
NovaSeq sequencing was performed at the Ramaciotti Centre for Genomics (University of New South Wales, Sydney, Australia)
Raw reads from the RNA-sequencing were trimmed and mapped to the C. arietinum genome (desi type - ICC4958) using CLC Workbench v.10. Genes that were not expressed or lowly expressed (<5 counts on average across each set of 3 replicates) were eliminated from the data set.
Genome_build: C. arietinum genome (desi type - ICC4958)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cicer arietinum

source_name: Roots

growth_protocol: Chickpea seeds from three genotypes forming low numbers of nodules (Jimbour, Boundary, ICC11664) and three genotypes with high nodulation (ICC9002, ICC2072 and ICC1510) were sterilized in 10% bleach, rinsed in sterile water and planted into vermiculite for two weeks. Seedlings were transplanted to sterilized soil and acclimatised to the new soil for a day prior to inoculation.

extract_protocol:
RNA was extracted from the chickpea roots (3 biological replicates per condition) using the Isolate II RNA Plant kit (Bioline, London, U.K.) according to manufacturer’s instructions.
RNA libraries were constructed using the SENSE total RNA-Seq library prep kit (Lexogen, Vienna, Austria)

treatment_protocol: Actively growing cultures of M. ciceri (~10,000 CFU per plant) was applied to half of the chickpeas while a mock solution without rhizobia was applied to the other half. Chickpea roots were harvested and frozen in liquid nitrogen 3 days after addition of live M. ciceri cultures or mock controls.

tag: genotype

tag: agent

value: Mesorhizobium ciceri


title: VIR_2

tag: ip target

value: GFP-MSL2 vir


title: BJAB-EBNA2-H3K27ac-IgG

value: Normal Rabbit IgG Control (R&D Systems AB-105-C)


title: ICC11664_R_2


title: GC3

city: wuxi

first: fangmei

last: an

state: jiangsu

address: NO 299,QingYang Road

institute: Wuxi Public Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM/counts for each Sample

source_name: gastric mucosa

extract_protocol: Total RNA extraction

tag: tissue

value: gastric mucosa

tag: tissue type

value: gastric cancer


title: TT-244_Bortezomib

value: Bortezomib


title: MSL3 VIR_1

tag: assay type

tag: experimental series


title: MSL3 VIR_ROX_1


title: ICC11664_R_1


title: GC2


title: TT-243_Bortezomib


title: ICC11664_C_3

value: Mock


title: TT-242_Doxorubicin

value: Doxorubicin


title: GC1


title: ICC11664_C_2


title: BJAB-SCNG-H3K27ac-IgG

value: BJAB

value: B cell line


title: VIR_2_input

value: input control

value: ChIP


title: Dys3

value: dysplasia


title: VIR_ROX_1_input

value: GFP-MSL2 vir + roX2


title: ICC11664_C_1


title: TT-241_Doxorubicin

value: 1uM 4 days

value: iPSC cardiomyocytes


title: Dys2


title: Dys1


title: TT-240_DMSO

value: DMSO

value: 0.1% DMSO


title: GFP-MSL2virCXCdrome ChiP 1

value: GFP

value: GFP-MSL2 virCXCdrome


title: Boundary_R_3

value: PBA Boundary

value: Mesorhizobium ciceri


title: GFP-MSL2vir ChiP 2

value: GFP-MSL2 vir


title: CAG+IM3

value: gastric mucosa

value: chronic atrophic gastritis + intestinal metaplasia


title: TT-238_DMSO


title: Boundary_R_2


title: CAG+IM2


title: GFP-MSL2mel ChiP 2

value: GFP-MSL2 mel


title: Boundary_C_3

value: Mock


title: GFP ChIP


title: VIR_ROX_2_input

value: input control


title: Boundary_C_2


title: GFP-MSL2vir ChiP 1

value: ChIP


title: TT-236_DMSO


title: TT-235_DMSO


title: N2

value: chronic superficial gastritis


title: GFP-MSL2mel ChiP 1


title: Boundary_C_1