title: 5hmC-hMeDIP-seq-wt

description: hMeDIP

source_name: pituitary tissues of wild-type mice

value: pituitary tissue

value: female

value: Wild-type


title: Input DNA-hMeDIP-seq-pituitary-wt

status: Public on May 01 2020

type: SRA

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

country: China

institute: Capital Medical University

description: hMeDIP

library_source: genomic

data_processing:
Library strategy: hMeDIP
ChIP-seq and hMeDIP reads quality control performed using FastQC v0.11.5 and  cutadapt v1.8.3
ChIP-seq and hMeDIP reads were aligned to the mm10 genome assembly using Bowtie2 v2.2.5
ChIP-seq and hMeDIP peaks were called using macs2 v2.1.1.20160309
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq and hMeDIP bw files were generated using bamCoverage

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Pituitary tissues of wild-type or Foxk2 knockout mice

extract_protocol:
At least 100ng fragmented genomic DNA from pituitary tissues were performed for hMeDIP reactions. The DNA precipitated by polyclonal antibodies against 5hmC. The DNA samples were purified with the Active Motif's Chromatin IP DNA Purification Kit before in-depth whole genome DNA sequencing was performed by BGI (Wu Han, China). The process were validated by the instructions from Active Motif Kit. cat#55010
The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked mouse reference genome (mm10) using Bowtie2, and further analyzed by MACS.

tag: tissue

tag: strain

tag: age

tag: gender

tag: genotype

tag: antibodies


title: 32cell-3-rep

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

institute: Tongji University

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Drop-seq software (James Nemesh, McCarroll Lab) were used for data de-multiplexing, reads alignment and cellular molecular barcodes processing. Barcodes (9-16bp of read1) and UMI (17-25bp of read1) extracted from read1 were added to read2 as tags. Ploy(A) tail sequence and template switch oligo (TSO) sequence were trimmed. Only read2 were mapped to C.sav genome (CSAV2.0; ensembl). Gene exon were then labeled and attached to mapping output file. Genes of used exact barcodes were counted to get the final expression matrix.
Normalization of read count was performed in each cell by a scale factor estimated by DESeq2 (Anders and Huber 2010).
We considered a gene a differentially expressed gene (DEG) if its read count across all cells does not conform to a Poisson distribution. To remove batch effect of embryo, we excluded genes that have greater than two fold change on average expression between any pair of embryos at the same developmental stage.
Dimension reduction was implemented by t-distributed stochastic neighbor embedding (t-SNE) in Seurat (Macosko et al. 2015) to visualize and cluster cells at each stage using DEGs. Cell types were identified by the specific expression of tissue marker (Imai et al. 2006) on the clusters of t-SNE map at each stage.
Genome_build: CSAV 2.0
Supplementary_files_format_and_content: txt files include the raw count values of genes; xlsx files include barcode information of samples.

molecule: polyA RNA

organism: Ciona savignyi

source_name: 32-cell embryo

growth_protocol: Fecund C. sav animals were collected from the Jiaozhou Bay in Qingdao, Shandong and kept in 18c circulation sea water tank. Fertilization, dechorination and embryo cultures were done. For FGF drug inhibitor experiments, embryos were grown in sea water containing 2ug/ml U0126. C. sav embryo in situ experiments were done according to previous published methods.

extract_protocol:
All blastomeres from a single embryo were transferred to a new dish of fresh sea water at 4c. After that, cells were individually transferred using a glass capillary needle attached to mouth pippet to PCR tubes containing lysis buffer the same as smart-seq2 except that barcoded primer were used. Reverse transcription and pre-amplification were processed as smart-seq2 protocol. We use 12, 13, 14, 15, 16 and 17 cycles respectively for the amplification of 1/2-cell, 4-cell, 8-cell, 16-cell, 32-cell and 64/110-cell samples.
Equal amount of cDNA of the same stage and different barcodes were pooled together for Nextera XT sequencing library construction. 500 pg cDNA of each pooled sample was fragmented, tagged, and amplified according to the manufacturer’s instructions except that P5 and N7-index primers were used. Fragments were purified twice using 0.6x AMPure XP beads and once with 1x AMPure XP beads.

treatment_protocol: Staged embryos were transferred to Ca2+/Mg2+ free artificial sea water containing freshly prepared 0.1% trypsin (MP). Single embryos were gently pippeted using a mouth pippet until all blastomeres dissociate.

value: embryo

tag: developmental stage

value: 32-cell embryo


title: 7FC

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

data_processing:
Sequences were aligned to Rat Genome assembly (Rnor_6.0) using STAR-2.5.2a(26). rRNA reads were filtered using Bedtools intersectBed and rRNA annotation from Biomart.
Gene read counts generated by HTseq-count were used to compute fold changes and significance of expression differences using DESeq
DEGs were assessed through a generalized linear model implemented in limma, with phenotype (VS vs. control) and sex (male vs. female) as main factors for every brain region. The log expression values for each gene were averaged over each treatment group, and the log2 fold change was computed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: nucleus basalis of Meynert

extract_protocol:
RNA was extracted as detailed in SI methods. RNA quality was assessed using Qubit RNA HS assay and Bioanalyzer RNA 6000 Nano assay.
Libraries were prepared using NuGen Ovation RNA-Seq System v2 from total RNA.
Samples were barcoded for multiplexing and sequenced at 75 bp paired-end on Illumina HiSeq4000. Samples were pooled 16 per lane and sequenced at a depth of 130 million reads per sample.

value: Long Evans

value: Brain

value: 70+ days

value: ChAT::Cre rats

tag: Sex

value: Female

tag: group

value: Control


title: 32cell-2-rep


title: 238 FADD IEC-KO Zbp1 -/-

type: RNA

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

country: Germany

institute: University of Cologne

description: gene expression data from mouse ileum tissue at 11 weeks of age

hyb_protocol: accoring to GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) for 16h at 45°C, hybridization was performed in a GeneChip Hybridization Oven 645

scan_protocol: Gene chips were scanned using the GeneChip Scanner 7G

data_processing: Array analysis was performed using Affymetrix Expression Console and Transcriptome Analysis Console Software (TAC).

label: biotin

source_name: mouse ileum tissue at week 10-56

label_protocol: labelled ssc-DNA was prepared according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays protocol(thermo Fisher, 2017) from 100 ng total RNA

growth_protocol: Mice were maintained at an SPF animal facility uner a 12h light cycle and given a regular chow diet

extract_protocol: ileum tissues were disrupted using a Precellys 24 (Bertin technologies) and total RNA was extracted using a Nucelospin RNA kit (Macherey-Nagel) according to manufacturer's instructions. rDNAse treatment was increased to 45 minutes.

treatment_protocol: ileum tissues were frozen on dry ice immeadiately after collection.

value: FADD IEC-KO Zbp1 -/-


title: 12MS

value: Male

value: Stress


title: 6FC


title: Input_CHIP-Seq

first: xiong

last: wei

address: qinghuayuan street

institute: Tsinghua University

description: genomic DNA

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq  and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for RNA-seq and CHIP-Seq

source_name: NK cells

growth_protocol: freshly isolated NK cells

extract_protocol:
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit
RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L).   For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629).  For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA.  Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Eomes ChIP-seq, the RIPA buffer was diluted 1 to 10. The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq X-ten(Illumina).

treatment_protocol: freshly isolated NK cells from chronically CR treated mice

value: spleen

value: wt

tag: chip antibody

value: no


title: 32cell-1-rep


title: 16cell-2-rep

source_name: 16-cell embryo

value: 16-cell embryo


title: CR_wt_atac

description: genomic DNA


title: 4FS


title: 16cell-1-rep


title: 217 FADD IEC-KO Zbp1 -/-

source_name: mouse ileum tissue at week 10-55


title: 8FC


title: 35 FADD IEC-KO Zbp1 -/-

source_name: mouse ileum tissue at week 10-54


title: 32 FADD IEC-KO Zbp1 -/-

source_name: mouse ileum tissue at week 10-53


title: CR_ko_atac

description: genomic DNA

value: Eomes ko


title: 8cell-2-rep

source_name: 8-cell embryo

value: 8-cell embryo


title: Ctrl_ko_atac

description: genomic DNA


title: 2FS


title: 8cell-1-rep

value: embryo


title: 1FS


title: Ctrl_wt rep3

description: oligoT matrix facilitated


title: scrt1D

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of science

data_processing:
Quality control of the sequencing was performed with FastQC
Sequencing adaptors were removed using trimmomatic
An index of Rn6 cDNA was build for Kallisto
alignment of reads was performed using Kallisto
Subsequent analysis were performed with sleuth (differential expression analysis) and cluster profiller (annotation enrichment analysis)
Genome_build: Rno6
Supplementary_files_format_and_content: annotated count table with est counts, TPM, transcripts ID, gene ID,gene name, for each sample.

source_name: siSCRT1_FACS sorted pancreatic beta-cells

growth_protocol: Islet isolation, dispersion and cell sorting: Islets were isolated by collagenase digestion of the pancreas (Gotoh et al., 1987) followed by Histopaque density gradient and hand-picking to separate them from digested exocrine tissue. At the end of the isolation, islets were incubated for 2h in RPMI 1640 GlutaMAXTM medium (Invitrogen) containing 11 mM glucose and 2 mM L-glutamine and supplemented with 10% fetal calf serum (Gibco), 10 mM Hepes pH 7.4, 1 mM sodium pyruvate, 100 µg/mL streptomycin and 100 IU/mL penicillin. Dissociated islet cells were obtained by incubating the islets in Ca2+/Mg2+ free phosphate buffered saline, 3 mM EGTA and 0.002% trypsin for 5 min at 37°C. For some experiments, rat islet cells were separated by  Fluorescence-Activated Cell Sorting (FACS) based on β-cell autofluorescence, as previously described (Guay et al., 2019; Kohler et al., 2012). Sorted islet cells were seeded on plastic dishes coated with extracellular matrix secreted by 804 G rat bladder cancer cells (804 G ECM) (Parnaud et al., 2008). Enrichment of α - and β-cells was evaluated by double immunofluorescence staining using polyclonal guinea pig anti-insulin (dilution 1:40, PA1-26938 Invitrogen) and polyclonal mouse anti-glucagon (dilution 1:1000, Abcam Ab10988), followed by goat anti-guinea pig Alexa-Fluor-488 and goat anti-mouse Alexa-Fluor-555 (diluted 1:400, Thermofisher A11073 and A21422, respectively) secondary antibodies. On average, β-cell fractions contained 99.1 ± 0.9% insulin-positive cells and 0.6 ± 0.6% glucagon-positive cells and α-cell-enriched fractions contained 10.6 ± 8.2% insulin-positive cells and 88.8 ± 8.2% glucagon-positive cells.

extract_protocol:
RNA was extracted using miRNeasy micro kit (Qiagen) followed by DNase treatment (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell transfection– Dispersed rat islet cells or FACS-sorted β-cells were transfected with a pool of 4 siRNAs directed against rat Scrt1 or negative control (On-Target plus #081299-02 and #001810-10 respectively, Dharmacon) using Lipofectamine RNAiMAX (Thermofisher). RNA extraction was performed 48h after transfection.

tag: strain background

value: Sprague-Dawley

value: adult

tag: genotype/variation

tag: cell type

value: FACS sorted pancreatic beta-cells


title: 1cell-rep

source_name: 1-cell embryo

value: 1-cell embryo


title: scrt1E


title: Eomes_CHIP-Seq

description: genomic DNA

value: sc-69269(Santa Cruz)


title: 212 CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-51

value: CASP8 IEC-KO Mlkl -/-


title: Ctrl_wt rep2

description: oligoT matrix facilitated


title: Ctrl_wt_atac

description: genomic DNA


title: scrt1C


title: 40 CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-50


title: 36 CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-47


title: 39 CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-49


title: Ctrl_wt rep1

description: oligoT matrix facilitated


title: drug_64cell-6

source_name: 64-cell embryo

value: 64-cell embryo U0126


title: 3FS

value: Long Evans

value: Brain

value: 70+ days

value: ChAT::Cre rats

value: Female


title: drug_64cell-5


title: Ctrl_ko rep2

description: oligoT matrix facilitated

value: spleen


title: 38 CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-48


title: ctrl5

source_name: control_FACS sorted pancreatic beta-cells

value: Control


title: drug_64cell-3


title: scrt1A


title: scrt1B


title: 31 FADD IEC-KO Zbp1 -/-

source_name: mouse ileum tissue at week 10-52

value: FADD IEC-KO Zbp1 -/-


title: 45 FADD IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-46

value: FADD IEC-KO Mlkl -/-


title: drug_64cell-4

value: embryo


title: Ctrl_ko rep1

description: oligoT matrix facilitated

source_name: NK cells

value: Eomes ko


title: 44 FADD IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-45


title: drug_64cell-2


title: ctrl4

value: Sprague-Dawley

value: adult


title: drug_64cell-1


title: ctrl2

value: FACS sorted pancreatic beta-cells


title: 43 FADD IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-44


title: CR_wt rep1

description: oligoT matrix facilitated

value: wt


title: ctrl3


title: CR_wt rep2

description: oligoT matrix facilitated


title: 110cell-15

source_name: 110-cell embryo

value: 110-cell embryo


title: CR_ko rep2

description: oligoT matrix facilitated


title: ctrl1


title: 110cell-14


title: 110cell-13


title: Second Replicate RNA-seq sample OD600=4.0

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
RNA-seq sample
Supplementary Table 1.xlsx

data_processing:
Raw sequencing reads in fastq files were processed using a pipeline developed by Sander Granneman, which uses tools from the pyCRAC package (Webb et al., 2014a). pyCRAC versions. 1.3.2 to 1.4.4 were used for the analyes. The entire pipeline is available at https://bitbucket.org/sgrann/). The CRAC_pipeline_PE.py pipeline first demultiplexes the data using pyBarcodeFilter.py and the in-read barcode sequences found in the L5 5’ adapters. Flexbar then trims the reads to remove 3’-adapter sequences and poor quality nucleotides (Phred score <23). Using the random nucleotide information present in the L5 5’-adaptor sequences, the reads were collapsed to remove potential PCR duplicates. The reads were then mapped to the Escherichia coli MG1655 genome with Novoalign (www.novocraft.com). To determine which genes the reads overlapped with we generated an annotation file in the Gene Transfer Format (GTF). This file contains the start and end positions of each gene on the chromosome as well as what genomic features (i.e. sRNA, protein- coding, tRNA) it belongs to. To generate this file, we used the Rockhopper software (Tjaden, 2015) on E. coli  rRNA-depleted total RNA-seq data (generated by Christel Sirocchi), a minimal GTF file obtained from ENSEMBL (without UTR information). The resulting GTF file contained information not only on the coding sequences, but also complete 5’ and 3’ UTR coordinates. PyReadCounters then used the novoalign output file and the GTF file to count the total number of unique cDNAs that mapped to each gene. RNA-seq data was generated by Novogene using the Illumina TruSeq protocol. The data were processed using the CRAC_pipeline_PE.py. For all the CLASH and RNA-seq data, we normalized the counts to transcripts per million (TPM). Processed and raw data files for these counts are provided.
Genome_build: Escherichia coli MG1655
Supplementary_files_format_and_content: TPM

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli grown in LB

extract_protocol:
Total RNA was extracted using the Guanidium thiocyanate phenol method. RNA integrity was assessed with the Prokaryote Total RNA Nano assay on a 2100 Bioanalyzer (Agilent). Genomic DNA was removed by incubating 10 μg of total RNA with 2U Turbo DNase (Ambion) in a 50 μl final volume for 30 minutes at 37°C in the presence of 10 U SuperaseIn RNase Inhibitor (Ambion). RNA was subsequently phenol-chloroform extracted and purified by ethanol-precipitation.
The  RNA-seq libraries were generated using the Illumina TrueSeq protocol according to manufacturer's procedures.

value: wildtype

tag: optical density


title: CR_ko rep1

description: oligoT matrix facilitated


title: 110cell-12


title: Wt rep2

description: oligoT matrix facilitated


title: Second Replicate RNA-seq sample OD600=2.4


title: Second Replicate RNA-seq sample OD600=3.0


title: 110cell-11


title: Wt rep1

description: oligoT matrix facilitated


title: CR_wt rep3

description: oligoT matrix facilitated


title: 42 FADD IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-43


title: 110cell-10


title: 41 FADD IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-42


title: Second Replicate RNA-seq sample OD600=1.8


title: 54 FADD IEC-KO

source_name: mouse ileum tissue at week 10-40

value: FADD IEC-KO


title: 52 FADD IEC-KO

source_name: mouse ileum tissue at week 10-38


title: 51 FADD IEC-KO

source_name: mouse ileum tissue at week 10-37


title: 221 FADD IEC-KO

source_name: mouse ileum tissue at week 10-41


title: 110cell-9


title: 208 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse ileum tissue at week 10-36

value: FADD IEC-KO RIPK3 IEC-KO


title: Tbx21_ko rep1

description: oligoT matrix facilitated

value: Tbx21 ko


title: Second Replicate RNA-seq sample OD600=1.2


title: Eomes_ko rep2

description: oligoT matrix facilitated


title: Second Replicate RNA-seq sample OD600=0.8


title: 53 FADD IEC-KO

source_name: mouse ileum tissue at week 10-39


title: Eomes_ko rep1

description: oligoT matrix facilitated


title: 110cell-6


title: 110cell-7


title: First Replicate  RNA-seq sample OD600=4.0


title: 202 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse ileum tissue at week 10-35


title: 75 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse ileum tissue at week 10-33


title: SC13

city: Nanjing

first: Zhaoyu

last: lin

state: Jiangsu

address: 12 Xuefu Road

institute: Nanjing University

data_processing:
base calling were performed with Illumina CASAVA-1.8.2
This yielded about 10M usable reads per sample. Short read sequences were mapped to a UCSC mm10 reference sequences
Differential gene expression analysis, statistical testing and annotation were performed using the number of uniquely mapped reads per kilobase transcriptome per million mapppable reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include RPKM values and Coverage for each Sample

source_name: PC iPS-13

growth_protocol: MEF were maintained in 90% DMEM + 10% FBS. Mouse ES and iPSCs were maintained in M15 medium, which is composed of Dulbecco’s modified Eagle’s medium (DMEM; Gibco Invitrogen, Carlsbad, CA)supplemented with 15% FBS (Gibco), 100 μM -mercaptoethanol (Sigma-Aldrich, St. Louis, MO), 2 mM non-essential amino acids(Gibco), 2 mM L-glutamine(Gibco), 1 mM sodium pyruvate (Gibco),and 10 ng/ml leukemia inhibitory factor (LIF; Chemicon, Temecula, CA) on feeder cells composed of mitomycin C-treated primary mouse embryonic fibroblast (MEF) cells.

extract_protocol:
Total RNA was isolated from cells by RNAiso Plus (Takara, Dalian, China).
Libraries were prepared from 100-1000ng total RNA using the VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s protocol. Libraries were validated by the 2100 BioAnalyzer (Agilent, Beijing, China), normalized, and pooled for sequencing.

value: palmitoylcarnitine induced pluripotent stem cell


title: SC7

source_name: Control iPS-7

value: normal induced pluripotent stem cell


title: Tbx21_ko rep2

description: oligoT matrix facilitated

source_name: NK cells

value: spleen


title: 110cell-4


title: First Replicate  RNA-seq sample OD600=2.4


title: SC5

source_name: PC iPS-5


title: First Replicate  RNA-seq sample OD600=1.8


title: SC3

source_name: Control iPS-3


title: 110cell-3

source_name: 110-cell embryo


title: 78 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse ileum tissue at week 10-34


title: First Replicate  RNA-seq sample OD600=1.2

source_name: Escherichia coli grown in LB


title: Second Replicate RNA-seq sample OD600=0.4


title: 110cell-2


title: 228 Fadd fl/fl

source_name: mouse ileum tissue at week 10-31

value: Fadd fl/fl


title: 62 FADD IEC-KO RIPK3 IEC-KO

source_name: mouse ileum tissue at week 10-32


title: MEF

source_name: MEF

value: mouse embryonic fibroblast


title: 110cell-1


title: 110cell-5


title: First Replicate RNA-seq sample OD600=0.8


title: B6

value: embryonic stem cell


title: 64cell-10

source_name: 64-cell embryo

value: embryo

value: 64-cell embryo


title: 220 Fadd fl/fl

source_name: mouse ileum tissue at week 10-30


title: First Replicate RNA-seq sample OD600=0.4


title: R12_IP2_V5

city: New York

first: James

last: Gregory

state: NY

address: 101 Ave of the Americas

institute: New York Genome Center

description: V5 IP from Sample 4 lysate

data_processing:
basecalls were performed using bcl2fastq
fastqs were trimeed with trimGalore
fastqs were aligned to an hg38/mm20/GFP/mCherry combined reference using STAR (v2.5.2)
reads were counted with Samtools or FeatureCounts
Genome_build: mm20/hg38
Supplementary_files_format_and_content: Gene count files were generated using featureCounts

organism:
Homo sapiens
Mus musculus

source_name: HEK293 & NIH3T3 co-culture

growth_protocol: standard cell culture

extract_protocol:
RNA from standard extracts or immunoprecipitation with the indicated antibody
SMART-seq cDNA prep followed by Nextera DNA Flex

tag: cell line

value: HEK293 & NIH3T3 co-culture

tag: target ip cell type

tag: ip antibody

tag: ip order

value: second


title: 59 Fadd fl/fl

source_name: mouse ileum tissue at week 10-28


title: 64cell-9

tag: tissue


title: 209 Fadd fl/fl

source_name: mouse ileum tissue at week 10-29


title: U2OS_plus_Aphidicolin_RNA_replicate_2

city: Hangzhou

first: Fang

last: Ji

state: Zhejiang

address: Zijingang campus of Zhejiang University, No.866 of Yuhangtang Road

institute: Zhejiang University

data_processing:
Reads were trimmed using Trim Galore with default settings and mapped to the human genome (hg38) by HISAT2.
Mapped reads were counted by FeatureCounts for exons according to the latest version of human gene annotation (Release 32, GRCh38.p13) by the GENCODE database.
Read counts were normalized into reads per kilobase per mega reads (RPKM) using R.
Supplementary_files_format_and_content: csv file containing expression matrix of the two samples.

organism: Homo sapiens

source_name: Osteosarcoma cell

growth_protocol: U2OS Cells were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (Gibco).  supplemented with 1% penicillin-streptomycin (Invitrogen). Cells were grown at 37˚C under 5% CO2.

extract_protocol:
Add Trizol directly to the plate to lyse cells.To each Trizol-lysed sample, add 0.2 ml chloroform per1 ml of Trizol used initially and shake vigorously for 5–10 s. Centrifuge at 4°C for 15 min at 12,000g and Transfer the upper aqueous layer to a new EP tube and add 0.5 ml isopropanol per 1 ml of Trizolused initially.Incubate at room temperature for 10 min before centrifuging at 4°C for 10 min at 12,000g to pellet RNA. Remove supernatant and wash pellet by adding 1 ml of 75%ethanol per 1 ml of Trizol used initially. Centrifuge at 4°C for 5 min at 7500g. Remove supernatant and invert tube to allow pellet to dryslightly. Resuspend the pellet in 200ll DEPC-water andincubate at 55°C for 10 min to ensure RNA is fully dissolved.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular.

treatment_protocol: RNA from asynchronously growing U2OS cells being treated with 0.3uM aphidicolin for 18h was sequenced commercially by BGI Genomics (BGI-SHENZHEN).

value: Bone


title: U2OS_plus_Aphidicolin_RNA_replicate_1


title: 58 Fadd fl/fl

source_name: mouse ileum tissue at week 10-27


title: 64cell-8


title: R8_IP_V5

description: V5 IP from Sample 1 lysate

value: first


title: 64cell-7


title: 207 FADD IEC-KO CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-26

value: CASP8 IEC-KO Mlkl -/-


title: R7_IP1_HA

description: HA IP from Sample 1 lysate

value: HA


title: HC6 LV

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We mapped all reads to the Human genome version HG38/GRCh38.96, downloaded from the Ensembl database, using a 2-steps approach. First, we aligned reads against the whole genome, by STAR (v.2.7.0f); then, the unmapped reads were locally mapped by Bowtie2 (version 2.3.5). We set the default parameters for both tools, except for --chimSegmentMin 18, --chimScoreMin 12 (STAR) and --local --very-sensitive-local, -q, --mm (Bowtie2).
Gene expression quantification was performed by the featuresCount tool (v. 1.6.4), taking into account genes annotated in the GRCh38.96 release.
We filtered out genes with less than 10 counts in at least 6 samples.
Genome_build: HG38/GRCh38.96
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample. The header of the files reports gene name,  sample identifiers.

source_name: heart left ventricle

growth_protocol: C-MSC were obtained by collagenase digestion from ventricular tissues, expanded and mantained in culture medium.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific), following manufacturer's instructions, precipitated through ammonium acetate/ethanol method, and  treated with DNAse (Turbo-DNAse; Thermo Fisher Scientific) to remove genomic DNA contamination.
Poly(A)+ RNA enrichment followed the Dynabeads™ mRNA DIRECT Micro Kit protocol (Thermo Fisher Scientific). Libraries were prepared and pooled together (6 samples per sequencing run) using multiplex library RNA Barcoding reagents and Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: No treatment applied.

value: Mesenchymal Stromal Cells

tag: subject

value: heart left ventricle

value: Female

tag: age (years)

tag: country of origin

value: Italy


title: 205 FADD IEC-KO CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-24

tag: genotype


title: R1_input_control

description: co-culture of HEK293 and NIH3T3 expressing RPL22-HA and RPL22-V5, respectively


title: 201 FADD IEC-KO CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-23


title: 64cell-5

tag: developmental stage


title: HC4 LV

tag: Sex

value: Male


title: 64cell-4


title: 64cell-3


title: HC3 LV


title: HC2 LV


title: R11_IP2_HA

description: HA IP from Sample 5 lysate


title: HC1 LV


title: 214 CASP8 IEC-KO

source_name: mouse ileum tissue at week 10-21

value: CASP8 IEC-KO


title: HC5 LV


title: 64cell-2


title: 64cell-6


title: 200 FADD IEC-KO CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-22


title: 64cell-1


title: HC6 RV

source_name: heart right ventricle

value: heart right ventricle


title: HC5 RV


title: Pat_48_tga

city: Erlangen

first: Arif

middle: B

last: Ekici

address: Schwabachanlage 10

institute: Institute of Human Genetics

description: miRNA expression data from TGA patient

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The data were analyzed using the Partek Genomics Suite version 6.6. The data were RMA normalized.

source_name: whole blood

label_protocol: Labeling was performed using the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

extract_protocol: Total RNA was extracted using the Qiasymphony PAXGene Blood RNA kit (Qiagen).

value: whole blood

tag: surgery type

value: TGA

tag: condition

value: tga


title: 206 FADD IEC-KO CASP8 IEC-KO Mlkl -/-

source_name: mouse ileum tissue at week 10-25


title: 210 CASP8 IEC-KO

source_name: mouse ileum tissue at week 10-20


title: 48 CASP8 IEC-KO

source_name: mouse ileum tissue at week 10-19


title: Pat_47_tga

description: miRNA expression data from TGA patient


title: 32cell-3

source_name: 32-cell embryo

value: embryo

value: 32-cell embryo


title: 47 CASP8 IEC-KO

source_name: mouse ileum tissue at week 10-18


title: Pat_46_non-PLE

description: miRNA expression data from non-PLE Fontan patient

value: Fontan

value: non-PLE


title: 32cell-2


title: HC4 RV


title: 46 CASP8 IEC-KO

source_name: mouse ileum tissue at week 10-17


title: HC3 RV


title: 32cell-4


title: HC2 RV


title: 236 Casp8 fl/fl

source_name: mouse ileum tissue at week 10-16

value: Casp8 fl/fl


title: Pat_45_non-PLE


title: 69 Casp8 fl/fl

source_name: mouse ileum tissue at week 10-14


title: Pat_44_tga

description: miRNA expression data from TGA patient


title: Pat_43_non-PLE


title: 32cell-1


title: 16cell-2

source_name: 16-cell embryo

value: 16-cell embryo


title: 16cell-1


title: HC1 RV


title: RNAseq of Bordetella pertussis BPSM DBvgA 2

city: Lille

first: loic

last: coutte

address: 1 rue du Pr Calmette, U1019 INSERM

department: microbiology

country: France

institute: INSERM

data_processing:
The RNAseq data of each sample were analyzed using Rockhopper v2.0.3 with the default parameters to calculate the RPKM value for each coding sequence with the B. pertussis Tohama I BX470248 genome annotation.
To avoid false positive and to increase clarity, RNAseq results were considered with LogFC<-2 or LogFC>2.
Genome_build: B. pertussis Tohama I BX470248
Supplementary_files_format_and_content: excel file with gene, Product, Synonym, Log FC BPSM Mg vs BPSM, Log FC BPSM DBvgA vs BPSM, qValue BPSM vs BPSM Mg, qValue BPSM vs BPSM BvgA, RPKM BPSM, RPKM BPSM Mg, RPKM BPSM DBvgA

organism: Bordetella pertussis

source_name: delta bvgA

growth_protocol: B. pertussis strains were grown on BG agar plates for 2 days at 37°C and then cultured in modified Stainer Scholte (SS) liquid medium supplemented when indicated with 50 mM MgSO4 at 37°C under agitation

extract_protocol:
Bacteria were pelleted, and total RNA was extracted using TriReagent (Invitrogen) following the manufacturer’s instructions. Genomic DNA was removed by DNase I treatment (Sigma Aldrich).
For each RNAseq sample, DNA-depleted total RNA was treated with the Ribo-Zero rRNA Removal Kit (Illumina) following the manufacturer’s recommendations. The rRNA-depleted RNA was then used to build the Illumina library using the TruSeq RNA Library Preparation Kit, followed by sequencing on an Illumina NextSeq 500 benchtop sequencer on SR150 high output run mode.

treatment_protocol: The bacterial cultures were stopped at mid exponential phase (OD600 =1.5-2) by adding 2 mL of a mixture of 5:95 phenol:ethanol (v:v) to 8 mL of bacterial suspensions.

tag: strain

value: BPSM

value: delta bvgA

tag: culture conditions

value: strain were cultivated in SS media to OD600 nm = 2.

value: Loic Coutte


title: 84 Casp8 fl/fl

source_name: mouse ileum tissue at week 10-15


title: 8cell-2

source_name: 8-cell embryo

value: 8-cell embryo


title: RNAseq of Bordetella pertussis BPSM DBvgA 1

tag: genotype/variation


title: Pat_42_non-PLE


title: 64 Casp8 fl/fl

source_name: mouse ileum tissue at week 10-13


title: First Replicate  RNA-seq sample OD600=3.0

source_name: Escherichia coli grown in LB

value: wildtype

tag: optical density


title: Pat_41_tga

description: miRNA expression data from TGA patient


title: Pat_40_non-PLE


title: αKO_Bmdms_Lps_24h_rep2

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

hyb_protocol: cRNA was hybridized to the GeneChip mouse Clariom S assay (Affymetrix) according to the manufacturer instructions.

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high-resolution scanner.

data_processing: Expression values were obtained after analysis of data with MAS5.0 algorithm.

source_name: cultured mouse bone marrow derived macrophage cell

label_protocol: Biotinylated cRNA was generated using two cycle target preparation kit (Affymetrix) following manufacturer's instructions and performed at the Servicio de Genomica, Universidad Complutense de Madrid

growth_protocol: BMDMs from LXR WT and LXRα-/- mice were generated in vitro as described by Ramón-Vázquez A et al. (Mol Cell Biol. 2019. Feb 15;39(5). BMDM cells were cultured for 7 days in RPMI 1640 medium containing 10% fetal bovine serum (FBS) supplemented with L929 conditioned medium (10%).

extract_protocol: 24h post treatment, RNA was harvested by column purification with RNeasy mini-kit (Qiagen). RNA was quantified and submitted for microarray analysis to the Unidad de Genomica, Universidad Complutense de Madrid (UCM)

treatment_protocol: BMDMs were cultured with PBS as control cells or LPS (100ng/ml) for 24 hours as a stimulus.

tag: cell type

value: bone marrow-derived macrophage cell (M-CSF)

tag: culture

value: cultured primary cells

value: LXR[alpha]-/-

tag: treatment

value: LPS (100ng/ml) for 24 hours


title: αKO_Bmdms_Lps_24h_rep1


title: 8cell-1


title: RNAseq of Bordetella pertussis BPSM MG 2

source_name: wild type

value: wild type

value: strain were cultivated in SS media with 50mM MgSO4 to OD600 nm = 2.


title: RNAseq of Bordetella pertussis BPSM 2


title: RNAseq of Bordetella pertussis BPSM MG 1


title: 1cell

source_name: 1-cell embryo

value: embryo

value: 1-cell embryo


title: Pat_37_tga

description: miRNA expression data from TGA patient

source_name: whole blood

value: whole blood

value: TGA

value: tga


title: αKO_Bmdms_untreated_rep2

value: untreated


title: Pat_38_non-PLE

value: Fontan

value: non-PLE


title: RNAseq of Bordetella pertussis BPSM 1

value: BPSM

value: strain were cultivated in SS media to OD600 nm = 2.

value: Loic Coutte


title: U2OS_plus_Aphidicolin_WGS

data_processing:
Library strategy: DNA-seq
Reads were trimmed using Trim Galore with default settings and mapped to the human genomes(hg38) by BWA to get bam format file.
Estimated copy numbers were called by Control-FREEC with the default configuration file.
Copy number variations (CNV) were filtered by the criteria that the estimated copy numbers were not in the range of 1 to 3 to get U2OS_plus_Aphidicolin_CNV.bed
Bam format file was transformed to BigWig format file via Deeptools with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bw files containing depth information of sequencing data. bed files containing location information of CNV sites.

source_name: Osteosarcoma cell

extract_protocol:
Genomic DNA was extracted according to TIANamp Genomic DNA Kit.
DNA library was constructed with the TruSeq DNA Sample Preparation Guide (Illumina 15026486 Rev.C).

treatment_protocol: Whole genomes from asynchronously growing U2OS cells being treated with 0.3uM aphidicolin for 18h were sequenced commercially by AnnoroadGene Technology Co., Ltd, Beijing, China.

value: Bone

tag: cell line


title: BPSM_dBvgA_a-BvgA_CHIPSEQ-RUN2_sample8

data_processing:
The ChIPseq data of each sample were analyzed using the ChIP-Seq Analysis module of CLC genomics v11.0 using the default parameters and the B. pertussis Tohama I BX470248 genome annotation to map reads, do the peak calling and calculate peak shape scores
To avoid false positive and to increase clarity, ChIPseq Peaks were considered informative if the CLC genomic peak shape score was > 5 and if the number of reads at the center of the peak was > 1,000.
The mapped read depth was calculated on ChIPseq CLC genomics output bamfiles using SAMtools depth module of SAMtools
Genome_build: B. pertussis Tohama I BX470248
Supplementary_files_format_and_content: excel file with Center of peak, Length of peak, Peak shape score, P-value and number of reads at specific ChIPseq site in each samples

source_name: Bordetella pertussis total lysate

extract_protocol:
The bacterial suspension was centrifuged at 5,000 x g for 10 min and washed twice with PBS. Cell pellets were resuspended in Immunoprecipitation buffer + Antiprotease. Bacteria were lysed by sonication with a refrigerated Diagenode Bioruptor at 4°C with specific TPX Diagenode tubes. Cell debris were removed by centrifugation (15 min, 4,000 rpm, 4ºC). IP was performed with anti-BvgA antibodies that recognize phosphorylated and non-phosphorylated BvgA and the samples were incubated at 4°C on a wheel for 16h. Protein G Magnetic Dynabeads were added to the IP samples and incubated for 4h at 4°C on the wheel. Beads were separated from the lysate with a magnet and washed with IP buffer. Beads were finally resuspended in TE buffer and incubated for 6h at 65ºC. The surpernatant was then treated with RNAseA and Proteinase K and the DNA fragments were extracted with Phenol-Choloform and precipitated with isopropanol.
The DNA fragments isolated by ChIP were used to build the Illumina library using the Illumina TruSeq ChIP Library Preparation Kit, followed by sequencing on an Illumina NextSeq 500 benchtop sequencer on SR150 high output run mode.

treatment_protocol: The bacterial cultures were stopped at mid exponential phase (OD600 =1.5-2) by adding 1% final concentration of formaldehyde (1% final conc.) and incubated for 30 min. at 37ºC with gentle shaking. 125 mM glycine was added to saturate the crosslinking reaction and incubated for 30 min. at 37ºC with gentle shaking.

tag: strains

value: BPSM delta bvgA

tag: antibody

value: anti-BvgA


title: Pat_36_non-PLE

tag: tissue


title: 63 Casp8 fl/fl

source_name: mouse ileum tissue at week 10-12

value: Casp8 fl/fl


title: BPSM_Mg_a-BvgA_CHIPSEQ-RUN2_sample7


title: BPSM_a-BvgA_CHIPSEQ-RUN2_sample6


title: 2cell_4cell

source_name: 2-cell 4-cell embryo

value: 2-cell 4-cell embryo


title: Pat_39_non-PLE


title: Pat_35_non-PLE


title: Pat_34_non-PLE


title: BPSM_WoAb_CHIPSEQ_sample5


title: αKO_Bmdms_untreated_rep1

value: bone marrow-derived macrophage cell (M-CSF)

value: cultured primary cells

value: LXR[alpha]-/-


title: WT_Bmdms_Lps_24h_rep1

value: WT

value: LPS (100ng/ml) for 24 hours


title: BPSM_dBvgA_a-BvgA_CHIPSEQ-RUN1_sample3


title: WT_Bmdms_Lps_24h_rep2


title: WT_Bmdms_untreated_rep1


title: Pat_31_non-PLE

value: whole blood


title: Pat_30_non-PLE


title: BPSM_Mg_a-BvgA_CHIPSEQ-RUN1_sample2

value: strain were cultivated in SS media with 50mM MgSO4 to OD600 nm = 2.


title: Platyphylline 3.3 mg/kg/bw_animal 4

city: Berlin

first: Stefanie

last: Hessel-Pras

address: Max-Dohrn-Str. 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

description:
mRNA, liver after 28 days oral treatment
gene expression data of livers of PA treated rats

hyb_protocol: hybridization to GeneChip cartridge, staining and washing on a GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing: microarray data was normalized using the package limma in R, then,  the dataset was filtered and only transcripts were kept for which annotations were available. The reduced dataset comprising 26480 probe sets was analyzed further using Qlucore Omics Explorer (version 3.3, Qlucore, Lund, Sweden). After a correction for batch-dependent differences of microarray chips, a comparison of all high-dose groups of single PA was performed using one-way analysis of variance

source_name: PA treated rats

label_protocol: biotin-labeling with GeneChipWT plus reagent kit

extract_protocol: small pieces of the deep-frozen liver lobe 1 were homogenized under liquid nitrogen and transferred to RLT buffer (Qiagen, Hilden, Germany) containing 1 % β-mercaptoethanol  RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) in combination with QiaShredder (Qiagen, Hilden, Germany)

treatment_protocol: rats were orally exposed to 4 different doses pf 6 structurally different pyrrolizidine alkaloids daily, after 28 d liver samples were gained, snap frozen and stored at 80°C prior isoation of RNA

tag: gender

value: male

value: liver

value: Platyphylline 3.3 mg/kg/bw


title: Platyphylline 3.3 mg/kg/bw_animal 5


title: Pat_33_PLE

description: miRNA expression data from PLE Fontan patient

value: Fontan

value: PLE


title: Platyphylline 3.3 mg/kg/bw_animal 3


title: 110cell-8

source_name: 110-cell embryo

value: embryo

value: 110-cell embryo


title: LS_+glc_2

city: Clemson

first: Rooksana

middle: Elizabeth

last: Noorai

state: South Carolina

address: 105 Collings St, BRC 157

department: Clemson University Genomics and Bioinformatics Facility

institute: Clemson University

description:
Long slender parasites in RPMI media with 5mM glucose
SL_pGlc_2
This BioSample is also included in PRJNA438967
The raw data for this sample is in SRP142743

data_processing:
Basecalls performed by bcl2fastq version 2.20.0
Sequenced reads were trimmed for low quality bases and adaptor sequence using trimmomatic version 0.36 with recommended parameters.
Gsnap was used to align reads to the reference genome.
Subread's featureCounts was used to call features using TriTrypDB-28_TbruceiTREU927.gff
BioConductor's edgeR was used to filter and normalize the data and complete the differential gene expression analyses.
Genome_build: Modified_TriTrypDB-28_TbruceiTREU927_Genome_no_Tb927_11_bin_v5.1
Supplementary_files_format_and_content: tab-delimited text file including raw counts per sample for each gene in reference.

organism: Trypanosoma brucei brucei

source_name: Whole Trypanosoma brucei brucei

extract_protocol:
Total RNA was isolated using an Aurum Total RNA Mini Kit (Bio-Rad).
Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA USA) and input RNA normalized to 200 ng per sample.

tag: life stage

value: bloodstream long slender form

tag: replicate


title: Pat_29_non-PLE

value: non-PLE


title: LS_+glc_3

description:
Long slender parasites in RPMI media with 5mM glucose
SL_pGlc_3
This BioSample is also included in PRJNA438967
The raw data for this sample is in SRP142743


title: WT_Bmdms_untreated_rep2

value: untreated


title: LS_+glc_1

description:
Long slender parasites in RPMI media with 5mM glucose
SL_pGlc_1
This BioSample is also included in PRJNA438967
The raw data for this sample is in SRP142743


title: WT_120_03

city: Baltimore

first: Mark

middle: R.

last: Marten

state: MD

address: 1000 Hilltop Circle

department: Chemical, Biochemical, and Environmental Engineering

institute: University of Maryland Baltimore County

data_processing:
Samples were checked for base quality, aligned to reference genome of Aspergillus nidulans (www.ensemblfungi.com) using Hisat2, read counts were generated using HT-Seq-Counts, and Normalized and Differential expression analysis was done using DESeq2
Genome_build: Aspergillus nidulans
Supplementary_files_format_and_content: Tab-delimited test files including Raw counts, Normlized Counts, log2fold values

organism: Aspergillus nidulans

source_name: Parental Strain

growth_protocol: 1E7 fresh spores of A. nidulans (FGSC A1405) grown in 50mL of low pH YGV media at 250rpm and 28C for 12h. This flask was then used to seed 1.2L of YGV media in a 2.8L Fernbach flask at 250rpm and 28C. Fungi were allowed to grow for approximately 20hours.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 20hours growth 20ng micafungin/mL culture per 1g/kg biomass was added to shake flasks. Samples were removed and flash frozen at 0, 5, 10, 15, 20, 25, 30, 40, 50, 60, 75, 90, and 120 minutes.

tag: replicate number

tag: genotype

value: Parental Strain

tag: time (minutes)


title: Platyphylline 3.3 mg/kg/bw_animal 2

tag: strain


title: Pat_26_tga

description: miRNA expression data from TGA patient

tag: surgery type

value: TGA

tag: condition

value: tga


title: BPSM_a-BvgA_CHIPSEQ-RUN1_sample1

value: BPSM

value: anti-BvgA

tag: culture conditions

value: strain were cultivated in SS media to OD600 nm = 2.

value: Loic Coutte


title: WT_90_03


title: Orc1 IP2 array1

type: genomic

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

description: Biological replicate 2 of Orc1 chip-chip

hyb_protocol: Labeled DNA was hybridized to a custom ChIP-on-Chip 2x105K microarray (Agilent G4498A), designed with 102,839 60-nucleotide probes tiled across the K. lactis genome spaced approximately every 100 bp (AMADID 018357)

scan_protocol: see Agilent website

data_processing: data were processed using MA2C software, the normalization method is: Robust, FDR cutoff for detecting ChIP-enriched regions is: 0.05, bandwidth is set to 500, min_probes is: 5 and max_gap is: 250.

organism: Kluyveromyces lactis

source_name: IP performed with anti-HA antibody in wildtype Kluyveromyces lactis strain LRY2022

label_protocol: 500 ng of input DNA or an entire immuno-precipitated DNA sample was dried in a speed-vac and resuspended in 15 µL of primer mix (1X NEB buffer 2, 5 µg of random nonamer).  Once the DNA was dissolved, 2 nmole of labeled dUTP was added in 2 µl. The samples were placed in a thermocycler and denatured for 5 minutes at 95°C, and then cooled to 4°C.  The samples were combined with 3 µL of Klenow reaction mix, resulting in a final concentration of 1X NEB buffer 2, 0.25 mM dATP, 0.25 mM dCTP, 0.25 mM dGTP, 0.1 mM dTTP and 12.5 U of Klenow. The sample was ramped to 37°C at 0.1°/sec and then incubated for 30 minutes. Following incubation, the sample was heat-denatured and cooled to 4°C, and fresh Klenow (4 U) was added for a second round of labeling. Finally, unincorporated nucleotides, oligonucleotides, and dye were removed using Microcon YM-30 filters (Millipore).The immunoprecipitated DNA was labeled with either Cy5- or Cy3-conjugated dUTP (Perkin Elmer NEL578001EA or NEL579001EA), using Klenow DNA polymerase (NEB M0212M) and random nonamer oligonucleotides (IDT). For LRY2021, the IP sample was labeled with Cy5 and the input was labeled with Cy3.  For LRY2022, the dyes were swapped.

extract_protocol: Cells were crosslinked for one hour each in 10 mM DMA and then 1% formaldehyde.  After cell lysis, chromatin was sonicated four times for 15 seconds.  160 µl of lysate (derived from 10 OD equivalents of cells) was brought to a final volume of 400 µl in lysis buffer and incubated overnight with 7 µl anti-HA antibody (Upstate).

tag: chip antibody

value: anti-HA

source_name: Input DNA


title: WT_75_03


title: Orc1 IP1 array1

description: Biological replicate 1 of Orc1 chip-chip

source_name: IP performed with anti-HA antibody in wildtype Kluyveromyces lactis strain LRY2021


title: Hfq CLASH replicate 2 OD600=4.0 Sample

description: CLASH sample

data_processing:
Library strategy: CRAC (CLIP-Seq derivative)
Raw sequencing reads in fastq files were processed using a pipeline developed by Sander Granneman, which uses tools from the pyCRAC package (Webb et al., 2014a). The entire pipeline is available at https://bitbucket.org/sgrann/). The CRAC_pipeline_PE.py pipeline first demultiplexes the data using pyBarcodeFilter.py and the in-read barcode sequences found in the L5 5’ adapters. Flexbar then trims the reads to remove 3’-adapter sequences and poor quality nucleotides (Phred score <23). Using the random nucleotide information present in the L5 5’-adaptor sequences, the reads were collapsed to remove potential PCR duplicates. The reads were then mapped to the Escherichia coli MG1655 genome with Novoalign (www.novocraft.com). To determine which genes the reads overlapped with we generated an annotation file in the Gene Transfer Format (GTF). This file contains the start and end positions of each gene on the chromosome as well as what genomic features (i.e. sRNA, protein- coding, tRNA) it belongs to. To generate this file, we used the Rockhopper software (Tjaden, 2015) on E. coli  rRNA-depleted total RNA-seq data (generated by Christel Sirocchi), a minimal GTF file obtained from ENSEMBL (without UTR information). The resulting GTF file contained information not only on the coding sequences, but also complete 5’ and 3’ UTR coordinates. PyReadCounters then used the novoalign output file and the GTF file to count the total number of unique cDNAs that mapped to each gene.
To demultiplex the CLASH datasets, the following command lines were used: pyBarcodeFilter.py -f Hfq_CRAC_1_1.fastq -r Hfq_CRAC_1_2.fastq -k -m 1 -b barcodes_CLASH1.txt &  pyBarcodeFilter.py -f Hfq_CRAC_2_1.fastq -r Hfq_CRAC_2_2.fastq -k -m 1 -b barcodes_CLASH2.txt &. NOTE!! The -k flag in these command lines instructs pyBarcodeFilter NOT to remove the 5' in-read barcodes. Therefore, before analyzing the data, the user still needs to trim these sequences from the Forward read CLASH fastq files.
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.22
Supplementary_files_format_and_content: text files with raw counts or TPM. GTF and FASTA files are available on the SuperSeries record.

growth_protocol: Cells were grown in standard LB medium to the desired optical density (OD600).

extract_protocol:
Total RNA was extracted using the Guanidium thiocyanate phenol method. RNA integrity was assessed with the Prokaryote Total RNA Nano assay on a 2100 Bioanalyzer (Agilent). Genomic DNA was removed by incubating 10 μg of total RNA with 2U Turbo DNase (Ambion) in a 50 μl final volume for 30 minutes at 37°C in the presence of 10 U SuperaseIn RNase Inhibitor (Ambion). RNA was subsequently phenol-chloroform extracted and purified by ethanol-precipitation.
For CLASH: CLASH was performed essentially as described (Waters et al., 2017), with a number of modifications including changes in incubation steps, cDNA library preparation, reaction volumes and UV cross-linking. E. coli expressing the chromosomal Hfq-HTF were grown overnight in LB at 37°C with shaking (200 rpm), diluted to starter OD600 0.05 in fresh LB, and re-grown with shaking at 37°C in 750 ml LB. A volume of culture equivalent to 80 OD600 per ml was removed at the following cell-densities (OD600): 0.4, 0.8, 1.2, 1.8, 2.4, 3.0 and 4.0, and immediately subjected to UV (254 nm) irradiation for 22 seconds (~500 mJ/cm2) in the Vari-X-linker (Van Nues et al., 2017a). Cells were harvested using a rapid filtration device (Van Nues et al., 2017a) onto 0.45 μM nitrocellulose filters (Merck Millipore) and flash-frozen on the membrane in liquid nitrogen. The following day, the membranes were washed with ~15 ml ice-cold phosphate-buffered saline (PBS), and cells were harvested by centrifugation. Cell pellets were lysed by bead-beating in 1 volume per weight TN150 buffer (50mM Tris pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM β-mercaptoethanol) in the presence of protease inhibitors (Roche), and 3 volumes 0.1 mm Zirconia beads (Thistle Scientific), by performing 5 cycles of 1 minute vortexing followed by 1-minute incubation on ice. One additional volume of TN150 buffer was added. To reduce the viscosity of the lysate and remove contaminating DNA the lysate was incubated with RQ1 DNase I (10U/ml Promega) for 30 minutes on ice. Two-additional volumes of TN150 were added and mixed with the lysates by vortexing. The lysates were centrifuged for 20 minutes at 4000 rpm at 4°C and subsequently clarified by a second centrifugation step at 13.4 krpm, for 20 min at 4°C. Purification of the UV cross-linked Hfq-HTF-RNA complexes and cDNA library preparation was performed as described (Granneman et al., 2009b). Cell lysates were incubated with 50 μl of pre-equilibrated M2 anti-FLAG beads (Sigma) for 1-2 hours at 4°C. The anti-FLAG beads were washed three times 10 minutes with 2 ml TN1000 (50 mM Tris pH 7.5, 0.1% NP-40, 1M NaCl) and three times 10 minutes with TN150 without protease inhibitors (50 mM Tris pH 7.5, 0.1% NP-40, 150mM NaCl). For TEV cleavage, the beads were resuspended in 250 μl of TN150 buffer (without protease inhibitors) and incubated with home-made GST-TEV protease at room temperature for 1.5 hours. The TEV eluates were then incubated with a fresh 1:100 dilution preparation of RNaceIt (RNase A and T1 mixture; Agilent) for exactly 5 minutes at 37ºC, after which they were mixed with 0.4g GuHCl (Sigma), NaCl and Imidazole to final concentrations of 6M, 300 mM and 10 mM, respectively. Note this needs to be carefully optimized to obtain high-quality cDNA libraries. The samples were then transferred to 50 μl Nickel-NTA agarose beads (Qiagen), equilibrated with wash buffer 1 (6 M GuHcl, 0.1% NP-40, 300 mM NaCl, 50 mM Tris pH 7.8, 10 mM Imidazole, 5 mM beta-mercaptoethanol). Binding was performed at 4ºC overnight with rotation. The following day, the beads were transferred to Pierce SnapCap spin columns (Thermo Fisher), washed 3 times with wash buffer 1 and 3 times with 1xPNK buffer (10 mM MgCl2, 50mM Tris pH 7.8, 0.1% NP-40, 5 mM beta-mercaptoethanol). The washes were followed by on-column TSAP incubation (Thermosensitive alkaline phosphatase, Promega) treatment for  1h at 37ºC with 8 U of phosphatase in 60 μl of 1xPNK, in the presence of 80U RNasin (Promega). The beads were washed once with 500 μl wash buffer 1 and three times with 500 μl 1xPNK buffer. To add 3’-linkers (App-PE - Table S7), the Nickel-NTA beads were incubated in 80 μl 3’-linker ligation mix with (1 X PNK buffer, 1 mM 3’-adapter, 10% PEG8000, 30U Truncated T4 RNA ligase 2 K227Q (NEB), 60U RNasin). The samples were incubated for 4 hours at 25ºC. The 5’-ends of bound RNAs were radiolabeled with 30U T4 PNK (NEB) and 3μl 32P-γATP (Perkin Elmer) in 1xPNK buffer for 40 min at 37ºC, after which 100 mM cold ATP (Roche) was added to a final concentration of 1mM, and the incubation prolonged for another 20 min to complete 5’-end phosphorylation. The resin was washed three times with 500 μl wash buffer 1 and three times with equal volume of 1xPNK buffer. For on-bead 5’-linker ligation, the beads were incubated 16h at 16ºC in 1xPNK buffer with 40U T4 RNA ligase I (NEB), and 1 μl 100 μM L5 adapter (Table S7), in the presence of 1mM ATP and 60U RNasin (Promega). The Nickel-NTA beads were washed three times with wash buffer 1 and three times with buffer 2 (50 mM Tris–HCl pH 7.8, 50 mM NaCl, 10 mM imidazole, 0.1% NP-40, 5 mM β-mercaptoethanol). The protein-RNA complexes were eluted in two steps in new tubes with 200 μl of elution buffer (wash buffer 2 with 250 mM imidazole). The protein-RNA complexes were precipitated on ice by adding TCA to a final concentration of 20%, followed by a 20-minute centrifugation at 4ºC at 13.4 krpm. Pellets were washed with 800 μl acetone, and air dried for a few minutes in the hood. The protein pellet was resuspended and incubated at 65ºC in 20 μl 1x NuPage loading buffer (Novex), resolved on 4–12% NuPAGE gels, and visualised by autoradiography. The cross-linked proteins-RNA were cut directly from the gel and incubated with 160 μg of Proteinase K (Roche) in 600 μl wash buffer 2 supplemented with 1% SDS and 5 mM EDTA at 55ºC for 2-3 hours with mixing. The RNA was subsequently extracted by phenol-chloroform extraction and ethanol precipitated. The RNA pellet was directly resuspended in RT buffer and was transcribed in a single reaction with the SuperScript IV system (Invitrogen) according to manufacturer’s instructions using the PE_reverse oligo as primer. The cDNA was purified with the DNA Clean and Concentrator 5 kit (Zymo Research) and eluted in 11 μl DEPC water. Half of the cDNA (5 μl) was amplified by PCR using Pfu Polymerase (Promega) with the cycling conditions (95°C for 2 min; 20-24 cycles: 95°C for 20s, 52°C for 30s and 72°C for 1 min; final extension of 72°C for 5 min). The PCR primers are listed in Table S7. PCR products were treated with 40U Exonuclease 1 (NEB) for 1 h at 37ºC to remove free oligonucleotide and purified by ethanol precipitation/ or the DNA Clean and Concentrator 5 kit (Zymo Research). Libraries were resolved on a 2% MetaPhor agarose (Lonza) gel and 175-300bp fragments were gel-extracted with the MinElute kit (Qiagen) according to manufacturer’s instructions. All libraries were quantified on a 2100 Bionalyzer using the High-Sensitivity DNA assay. Individual libraries were pooled based on concentration and barcode sequence identity. Paired-end sequencing (75 bp) was performed by Edinburgh Genomics on an Illumina HiSeq 4000 platform.

treatment_protocol: Once cells reached the desired density they were either cross-linked in the Vari-X-linker (22 seconds; ~500mJ/cm2) or harvested by rapid filtration.

tag: 5' in-read barcode

value: NNNGACTTAGC

tag: optical density


title: Pat_28_tga

description: miRNA expression data from TGA patient

value: whole blood


title: Senkirkine 3.3 mg/kg/bw_animal 5

value: male

value: liver

tag: treatment

value: Senkirkine 3.3 mg/kg/bw


title: Pat_27_non-PLE

value: Fontan


title: Senkirkine 3.3 mg/kg/bw_animal 4


title: Platyphylline 3.3 mg/kg/bw_animal 1

value: Platyphylline 3.3 mg/kg/bw


title: Hfq CLASH replicate 2 OD600=3.0 Sample

description: CLASH sample

value: NNNACTCAGC


title: Pat_25_non-PLE

value: non-PLE


title: Pat_24_non-PLE


title: Pat_22_non-PLE


title: Senkirkine 3.3 mg/kg/bw_animal 3


title: Pat_23_non-PLE


title: Senkirkine 3.3 mg/kg/bw_animal 2


title: Hfq CLASH replicate 2 OD600=2.4 Sample

description: CLASH sample

value: NNNTGGAGC


title: WT_60_03

value: Parental Strain


title: Senkirkine 3.3 mg/kg/bw_animal 1


title: Sir2 IP1 array1

description: Biological replicate 1 of Sir2 chip-chip


title: Sir2 IP2 array1

description: Biological replicate 2 of Sir2 chip-chip


title: WT_50_03


title: Hfq CLASH replicate 2 OD600=1.8 Sample

description: CLASH sample

value: NNNCTAGC


title: WT_30_03


title: Senkirkine 1 mg/kg/bw_animal 5

value: Senkirkine 1 mg/kg/bw


title: Hfq CLASH replicate 2 OD600=1.2 Sample

description: CLASH sample

value: NNNTCTCTAGC


title: WT_40_03


title: WT_25_03


title: Hfq CLASH replicate 2 OD600=0.8 Sample

description: CLASH sample

value: NNNCACTAGC


title: Hfq CLASH replicate 2 OD600=0.4 Sample

description: CLASH sample

value: NNNGTGAGC


title: WT_20_03


title: WT_15_03


title: Hfq CLASH replicate 2 Negative Control Sample

description: CLASH sample

value: NNNAGAGC


title: Hfq CLASH replicate 1 OD600=4.0 Sample

description: CLASH sample

value: NNNACAGTG


title: WT_10_03


title: Hfq CLASH replicate 1 OD600=3.0 Sample

description: CLASH sample

value: NNNTGTCAC


title: WT_05_03


title: Pat_20_non-PLE

value: whole blood


title: Pat_19_PLE

value: PLE


title: Pat_21_non-PLE


title: Pat_17_PLE


title: Pat_18_non-PLE


title: Hfq CLASH replicate 1 OD600=2.4 Sample

description: CLASH sample

value: NNNGTGACA


title: Senkirkine 1 mg/kg/bw_animal 3

value: male

value: liver


title: Senkirkine 1 mg/kg/bw_animal 4


title: Pat_16_non-PLE

value: Fontan


title: Senkirkine 1 mg/kg/bw_animal 2


title: WT_00_03


title: Pat_15_non-PLE

value: non-PLE


title: Hfq CLASH replicate 1 OD600=1.8 Sample

description: CLASH sample

value: NNNCACTGT


title: Senkirkine 1 mg/kg/bw_animal 1


title: Senkirkine 0.33 mg/kg/bw_animal 3

value: Senkirkine 0.33 mg/kg/bw


title: Senkirkine 0.33 mg/kg/bw_animal 4


title: Pat_14_PLE


title: WT_120_02

value: Parental Strain


title: WT_90_02


title: Hfq CLASH replicate 1 OD600=1.2 Sample

description: CLASH sample

value: NNNATCACG


title: Pat_13_PLE


title: Hfq CLASH replicate 1 OD600=0.8 Sample

description: CLASH sample

value: NNNTAGTGC


title: WT_75_02


title: Hfq CLASH replicate 1 OD600=0.4 Sample

description: CLASH sample

value: NNNGCACTA


title: WT_60_02


title: Senkirkine 0.33 mg/kg/bw_animal 2


title: Senkirkine 0.33 mg/kg/bw_animal 5


title: Hfq CLASH replicate 1 Negative Control Sample

description: CLASH sample

value: NNNCGTGAT


title: WT_50_02


title: Pat_12_non-PLE


title: BF_0mM_Glc_12hr_3

description:
Bloodstream form parasites in RPMI media at 12hr
BF_0mM_Glc_12hr_3
The raw data for this sample is in SRP145483

value: Lister 427

value: bloodstream form


title: Pat_9_non-PLE


title: Senkirkine 0.33 mg/kg/bw_animal 1


title: BF_0mM_Glc_12hr_2

description:
Bloodstream form parasites in RPMI media at 12hr
BF_0mM_Glc_12hr_2
The raw data for this sample is in SRP145483


title: WT_40_02


title: Pat_10_PLE


title: Senkirkine 0.1 mg/kg/bw_animal 3

value: Senkirkine 0.1 mg/kg/bw


title: Pat_11_PLE

value: whole blood


title: Senkirkine 0.1 mg/kg/bw_animal 2


title: Senkirkine 0.1 mg/kg/bw_animal 4


title: Senkirkine 0.1 mg/kg/bw_animal 5


title: Pat_7_non-PLE


title: Senkirkine 0.1 mg/kg/bw_animal 1


title: WT_30_02


title: WT_25_02


title: BF_1mM_Glc_12hr_3

description:
Bloodstream form parasites in RPMI media with 1mM glucose at 12hr
BF_1mM_Glc_12hr_3
The raw data for this sample is in SRP145483


title: Pat_6_non-PLE


title: BF_1mM_Glc_12hr_2

description:
Bloodstream form parasites in RPMI media with 1mM glucose at 12hr
BF_1mM_Glc_12hr_2
The raw data for this sample is in SRP145483


title: WT_10_02


title: BF_1mM_Glc_12hr_1

description:
Bloodstream form parasites in RPMI media with 1mM glucose at 12hr
BF_1mM_Glc_12hr_1
The raw data for this sample is in SRP145483


title: Lasiocarpine 3.3 mg/kg/bw_animal 5

value: Lasiocarpine 3.3 mg/kg/bw


title: Pat_8_PLE

value: PLE


title: Pat_4_PLE


title: Pat_5_PLE


title: Pat_3_non-PLE


title: ∆NtrYX Rep D

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
For RNA-seq analysis, the paired-end FASTQ files were split into R1 and R2 files and R1 files were retained for further analysis as previous data contained only single-end reads. Reads were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3,  SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the R. sphaeroides 2.4.1 genome sequence (GenBank accession GCA_000012905.2) using Bowtie2 version 2.2.2 with default settings except the number of mismatches was set to 1. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings except for the “reverse” strandedness argument was used. edgeR version 3.26.8 was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Genome_build: GCA_000012905.2
Supplementary_files_format_and_content: Normalized RPKM read counts for RNA-seq. WIG files for ChIP-seq

organism: Cereibacter sphaeroides 2.4.1

source_name: Bacterial culture

growth_protocol: R. sphaeroides 2.4.1 cultures were grown in Sistrom’s minimal medium (SMM), with 4 g/L succinate.  500 ml cultures were grown in Roux bottles bubbled with 30% O2, 1% CO2, and 69% N2.

extract_protocol:
R. sphaeroides cultures were grown aerobically in 500 ml cultures. At OD600 = 0.3-0.4, 44 ml of harvested culture was combined with 6 ml of ice-cold stop solution (95% ethanol, 5% water-saturated phenol). These mixtures were centrifuged at 4 °C for 10 min at 5,000 x g. Cell pellets were resuspended into 2 ml of lysis solution (2% SDS, 16 mM EDTA in RNase-free water) and then incubated at 65 °C for 5 min. Nucleic acid was extracted by adding equal volume of acid-phenol:chloroform (5:1, pH4.5), mixing, incubating at 65 °C for 5 min, mixing, and centrifuging at 16,000 x g. The aqueous phase was removed, and extracted 2 more times, before adding an equal volume chloroform, and centrifuging at 16,000 x g for 5 min. 1/10 volume of 3M sodium acetate and 1 ml isopropanol was added to the aqueous phase, followed by incubation at -20°C for 30 min, and then centrifugation at 16,000 x g for 30 min at 4°C to precipitate the nucleic acids. The pellet was washed with 75% ethanol and resuspended in RNase-free water. Samples were treated with RNase-free DNase and then purified with an RNeasy kit (Qiagen).
RNA-seq library preparation and sequencing was performed at the Joint Genome Institute. Libraries for sequencing were created using the Illumina TruSeq Stranded Total RNA kit (Illumina) following the standard protocol. RNA-seq libraries were sequenced on an Illumina NextSeq in 2x151 reads using the standard protocol.

tag: media

value: SIS medum

tag: oxygen

value: 30% Oxygen

value: Bacterial culture


title: BF_5mM_Glc_12hr_3

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 12hr
BF_5mM_Glc_12hr_3
The raw data for this sample is in SRP145483


title: Lasiocarpine 3.3 mg/kg/bw_animal 4

value: male

tag: tissue

value: liver


title: WT_05_02


title: WT_00_02


title: BF_5mM_Glc_12hr_2

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 12hr
BF_5mM_Glc_12hr_2
The raw data for this sample is in SRP145483


title: WT_20_02


title: WT_120_01


title: BF_5mM_Glc_12hr_1

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 12hr
BF_5mM_Glc_12hr_1
The raw data for this sample is in SRP145483


title: WT_90_01


title: Pat_2_tga

description: miRNA expression data from TGA patient

value: TGA

value: tga


title: BF_5mM_Glc_0hr_3

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 0hr
BF_5mM_Glc_0hr_3
The raw data for this sample is in SRP145483


title: Lasiocarpine 3.3 mg/kg/bw_animal 3

description:
mRNA, liver after 28 days oral treatment
gene expression data of livers of PA treated rats

tag: gender


title: Lasiocarpine 1 mg/kg/bw_animal 5

value: Lasiocarpine 1 mg/kg/bw


title: ∆NtrYX Rep A


title: Lasiocarpine 3.3 mg/kg/bw_animal 1


title: Lasiocarpine 3.3 mg/kg/bw_animal 2


title: WT_75_01

value: Parental Strain


title: ∆NtrYX Rep C


title: Parent Bep C


title: ∆NtrYX Rep B


title: Parent Rep B


title: WT_60_01


title: BF_5mM_Glc_0hr_2

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 0hr
BF_5mM_Glc_0hr_2
The raw data for this sample is in SRP145483

tag: life stage


title: WT_50_01


title: BF_5mM_Glc_0hr_1

description:
Bloodstream form parasites in RPMI media with 5mM glucose at 0hr
BF_5mM_Glc_0hr_1
The raw data for this sample is in SRP145483

tag: replicate


title: Lasiocarpine 1 mg/kg/bw_animal 2


title: Lasiocarpine 1 mg/kg/bw_animal 1


title: Lasiocarpine 1 mg/kg/bw_animal 3


title: LS_-glc_3

description:
Long slender parasites in RPMI media
SL_nGlc_3
The raw data for this sample is in SRP145483

value: bloodstream long slender form


title: WT_40_01

tag: replicate number


title: CLN6_RNAseq

city: wuxi

first: denghua

last: yin

state: jiangsu

address: shanshui east road 9

institute: Freshwater Fisheries Research Center

data_processing:
We performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences, USA) following the vendor’s recommended protocol.
After removing adaptor sequences, poly-N contained reads (N% > 10%), and low-quality sequences (quality score ≤ 20), the remaining clean reads were assembled using Trinity 2.4.0 as described for de novo transcriptome assembly without a reference genome.
All assembled Unigenes were aligned against the non-redundant (Nr) protein databases, Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggnog databases using DIAMOND with a threshold of Evalue<0.00001.
The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR
We determined the p value threshold using a false discovery rate (FDR), An FDR value < 0.001 indicates significant expression abundance
Genome_build: without a reference genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Coilia nasus

source_name: liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A mRNASeq sample preparation kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: status

value: fasting

tag: source

value: field


title: LS_-glc_2

description:
Long slender parasites in RPMI media
SL_nGlc_2
The raw data for this sample is in SRP145483

tag: strain


title: Parent Rep A


title: CLN5_RNAseq


title: WT_30_01

tag: genotype

tag: time (minutes)


title: S626_CD8

city: Toulouse

first: Clara-Maria

last: Scarlata

state: toulouse

address: 2 avenue Hubert Curien

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v3.0.2).
Fastq files were then run with count application (Cell Ranger v3.0.2) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Head and Neck Tumor infiltrating lymphocytes

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

treatment_protocol: CD45+ TIL magnetically sorted

tag: cell type

value: lymphocytes


title: WT_25_01


title: CLN4_RNAseq


title: Lasiocarpine 1 mg/kg/bw_animal 4


title: Lasiocarpine 0.33 mg/kg/bw_animal 5

value: Lasiocarpine 0.33 mg/kg/bw


title: S624_CD8


title: Lasiocarpine 0.33 mg/kg/bw_animal 4


title: Lasiocarpine 0.33 mg/kg/bw_animal 3


title: WT_20_01


title: Lasiocarpine 0.33 mg/kg/bw_animal 2


title: CLN3_RNAseq


title: CLN2_RNAseq


title: S533_CD8


title: WT_10_01


title: S526_CD8


title: WT_05_01


title: CLI6_RNAseq

value: feeding


title: CLN1_RNAseq


title: WT_00_01


title: CLI5_RNAseq


title: 333-JF-24_G2152F

city: Ann Arbor

first: Jaime

middle: Joel

last: Fuentes

state: MI

address: 1150 West Medical Center Drive, 6751 Medical Science BLDG II

department: Microbiology and Immunology

institute: University of Michigan

description:
rRNA-depleted, mRNA
Bt Acaps ARB25 in vivo.xlsx

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in ribose was compared to gene expression in heat-killed phage treated reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1%
Genome_build: NC_004663.1
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Bacteroides thetaiotaomicron VPI-5482

growth_protocol: For in vitro samples: Bacteroides thetaiotaomicron cells were grown overnight in Bacteroides phage recovery media (BPRM) then diluted 1:100 in fresh BPRM, and 5x10^6 PFU/mL of heat-killed (HK) or live phage was added to 100ul of culture in a 96 well plate. Cells were then grown until mid-log phase (absorbance between 0.4-0.5); For in vivo samples: Germ-Free swiss webster mice were monocolonized with either WT (tdk) or acapsular (cps) and gavaged with ARB25 phage 7 days later.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit buffers (Qiagen) and purified on RNA-binding spin columns (Epoch), treated with DNase I (NEB) after elution and purified again using a second RNeasy mini kit isolation column. Total RNA was then rRNA depleted using the Ribo-Zero Bacterial rRNA Removal Kit (Illumina Inc.) and concentrated with the RNA Clean and Concentrator-5 kit (Zymo Research Corp, Irvine, CA).
Samples were multiplexed for sequencing on the Illumina NextSeq 500 platform at the University of Michigan Sequencing Core.

treatment_protocol: Two volumes of RNA Protect (Qiagen) were added to cells and frozen at -80C until RNA was extracted

value: Bt acapsular

tag: culture method

value: in vivo, mus musculus cecal content

tag: growth phase

value: 80 day cecal content

value: ARB25 phage treated


title: CLI4_RNAseq


title: Lasiocarpine 0.1 mg/kg/bw_animal 5

value: Lasiocarpine 0.1 mg/kg/bw


title: Lasiocarpine 0.33 mg/kg/bw_animal 1

value: male


title: 333-JF-23_G2166F


title: 9_PM: Patient 43 NON cancer

city: Shatin

first: Katie

last: Meehan

state: Northern Territories

address: Rooms 84026 - 31, 6th Floor, Lui Che Woo Clinical Sciences Building

country: Hong Kong

institute: Chinese University of Hong Kong

hyb_protocol: Input RNA was hybridized to target sequence-specific capture probes and fluorescent-labelled reporter probes for 15-19 hours at 65°C. The mRNA-probe complexes were washed, and immobilized, and quantified by the nCounter Digital Analyzer as described by the manufacturer.

data_processing: Reporter probe counts for samples were subjected to sequential data-processing steps, starting with quality control (QC) metrics using the NSolver software v4.0 (NanoString Technologies). Samples that failed QC metrics were excluded. Remaining samples were normalised and differential expression analyzes was performed using three different software packages (NanoStringDiff, R v3.3.3, http://www.r-project.org; Degust v3.1, https://degust.erc.monash.edu/; NSolver Advanced Analysis module v2.0.115).

label: biotin and fluorescent probe

source_name: oral tongue

label_protocol: A minimum of 200ng of RNA was used to measure the expression of 730 immune-related genes and 40 housekeeping genes using the nCounter® platform (NanoString Technologies) and the PanCancer Immune Profiling Panel according to the manufacturer instructions.

extract_protocol: A FFPE section stained with hematoxylin and eosin (H&E) was examined by a head and neck pathologist to confirm the presence of invasive tumor. For RNA purification (High Pure RNA Isolation Kit, Roche Diagnostic), either 2-4 x 10μm scrolls were obtained or if the tumor percentage was <70%, macro-dissection was performed on multiple air-dried sections

tag: disease state

value: non-cancer

value: oral tongue


title: WT_15_01


title: Lasiocarpine 0.1 mg/kg/bw_animal 4

value: liver

tag: treatment


title: 75P_R: Patient 36 recurrent cancer_TUMOUR

scan_protocol: The mRNA-probe complexes were washed, and immobilized, and quantified by the nCounter Digital Analyzer as described by the manufacturer.

value: recurrent oral tongue squamous cell carcinoma


title: 76A_R: Patient 37 recurrent cancer_TUMOUR


title: CLI2_RNAseq


title: 659-JF-2_G1768M

description:
rRNA-depleted, mRNA
Bt WT in vivo ARB25 .xlsx

value: Bt Wild-type


title: 8_PM: Patient 42 NON cancer


title: Lasiocarpine 0.1 mg/kg/bw_animal 2


title: CLI1_RNAseq


title: Lasiocarpine 0.1 mg/kg/bw_animal 3


title: Lasiocarpine 0.1 mg/kg/bw_animal 1


title: 75LN_R: Patient 36 recurrent cancer_LYMPH NODE

source_name: involved lymph node

value: involved lymph node


title: 74B_R: Patient 35 recurrent cancer_RECURRENCE


title: Senecionine 3.3 mg/kg/bw_animal 4

value: Senecionine 3.3 mg/kg/bw


title: 74A_R: Patient 35 recurrent cancer_TUMOUR


title: Senecionine 3.3 mg/kg/bw_animal 3


title: 659-JF-1_G1NTF(6379)


title: LUNG3886

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

description: WGS; 150bp paired-end

data_processing:
Library strategy: DNA-seq
NGSQCToolkit v2.3.3 was used to trimmed adapter sequences and low quality reads.
All the clean reads were mapped on the reference genome (ARS-UCD1.2) using BWA v0.7.12 software. We only used the reliable mapped reads for SNP calling.
The SNP positions within the aligned reads compared to the reference genome were detected using the pileup function in SAMtools v.1.7 utilities. SNPs were predicted with a minimum mapping quality (-Q) of 20 and with the minimum and maximum read depths of 3 and 100, respectively.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data file contain the SNP information in vcf format.

organism: Bos taurus

source_name: Lung

extract_protocol:
Genomic DNA for lung tissue was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The lung DNA samples of the two Holstein cows were sequenced using the Illumina NextSeq550 platform, with the Nextera library preparation and sequence generation according to the manufacturer's protocols.

value: Lung

tag: Sex

value: F

tag: breed

value: Holstein


title: H3K18ub-ChIP-seq-ko

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

institute: Capital Medical University

data_processing:
ChIP-seq and hMeDIP reads quality control performed using FastQC v0.11.5 and  cutadapt v1.8.3
ChIP-seq and hMeDIP reads were aligned to the mm10 genome assembly using Bowtie2 v2.2.5
ChIP-seq and hMeDIP peaks were called using macs2 v2.1.1.20160309
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq and hMeDIP bw files were generated using bamCoverage

source_name: pituitary tissues of Foxk2 knockout mice

extract_protocol:
Approximately 5X10^7 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by polyclonal antibodies against Foxk2, Sin3a, Tet1 and Uhrf1. The DNA samples were purified with the Qiagen PCR purification kit before in-depth whole genome DNA sequencing was performed by BGI (Wu Han, China).
The raw sequencing image data were examined by the BGISEQ-500 analysis pipeline, aligned to the unmasked mouse reference genome (mm10) using Bowtie2, and further analyzed by MACS (Model-based Analysis for ChIP-seq).

tag: tissue

value: pituitary

tag: age

value: female

value: Foxk2 Knockout

tag: antibodies

value: H3K18ub prepared by PTM Biolabs


title: CLI3_RNAseq

value: feeding

value: field


title: 333-JF-22_G2767M

value: Bt acapsular

value: in vivo, mus musculus cecal content

value: 80 day cecal content

value: ARB25 phage treated


title: 333-JF-18_acapsular +SJC01

description:
rRNA-depleted, mRNA
Bt acapsular SJC01 in vitro.xlsx

source_name: acapsular +SJC01

value: in vitro, BPRM culture

value: Mid-Log, exponential growth

value: SJC01 phage treated


title: 333-JF-17_acapsular +SJC01


title: Input DNA-ChIP-seq-pituitary-ko

tag: gender


title: H3K18ub-ChIP-seq-wt

source_name: pituitary tissues of wild-type mice

value: Wild-type


title: 71B_R: Patient 33 recurrent cancer_RECURRENCE

value: recurrent oral tongue squamous cell carcinoma

value: involved lymph node


title: Senecionine 3.3 mg/kg/bw_animal 5

value: male

value: liver

value: Senecionine 3.3 mg/kg/bw


title: Input DNA-ChIPseq-pituitary-wt

value: pituitary

value: female


title: 73A_R: Patient 34 recurrent cancer_TUMOUR

value: oral tongue


title: 73B_R: Patient 34 recurrent cancer_RECURRENCE


title: 333-JF-16_acapsular +SJC01


title: 333-JF-15_acapsular +HKSJC01

source_name: acapsular +HKSJC01

value: Heat-killed SJC01 phage treated


title: 71A_R: Patient 33 recurrent cancer_TUMOUR


title: 333-JF-20_G1NTF(6365)

value: Bt Wild-type


title: 333-JF-14_acapsular +HKSJC01

value: Bt acapsular


title: 70C_R: Patient 32 recurrent cancer_RECURRENCE


title: Uhrf1-ChIP-seq

source_name: LbetaT2 cells

growth_protocol: LbetaT2 cells were cultured in 1640 medium supplemented with 10% FBS

value: murine pituitary gonadotrope cell line

tag: cell line

value: Uhrf1 Cell Signaling Technology, cat#12387S


title: LUNG3842

description: WGS; 150bp paired-end

value: Lung

value: F

value: Holstein


title: Tet1-ChIP-seq

value: Tet1  Millipore, cat#09-872


title: 333-JF-13_acapsular +HKSJC01

value: in vitro, BPRM culture

value: Mid-Log, exponential growth


title: BF_0mM_Glc_12hr_1

description:
Bloodstream form parasites in RPMI media at 12hr
BF_0mM_Glc_12hr_1
The raw data for this sample is in SRP145483

value: Lister 427

tag: life stage

value: bloodstream form

tag: replicate


title: 6_PM: Patient 41 NON cancer

value: non-cancer


title: 70B_R: Patient 32 recurrent cancer_TUMOUR

value: recurrent oral tongue squamous cell carcinoma


title: 333-JF-12_wild-type +SJC01

description:
rRNA-depleted, mRNA
Bt WT SJC01 in vitro.xlsx

source_name: wild-type +SJC01

tag: strain

value: SJC01 phage treated


title: Sin3a-ChIP-seq

value: Sin3a Santa Cruz Biotechnology, cat#sc-994


title: Senecionine 3.3 mg/kg/bw_animal 2

source_name: PA treated rats

value: male

value: liver

value: Senecionine 3.3 mg/kg/bw


title: Senecionine 3.3 mg/kg/bw_animal 1


title: Senecionine 1 mg/kg/bw_animal 2

value: Senecionine 1 mg/kg/bw


title: Senecionine 0.33 mg/kg/bw_animal 4

value: Senecionine 0.33 mg/kg/bw


title: Senecionine 1 mg/kg/bw_animal 4


title: Senecionine 1 mg/kg/bw_animal 5


title: Senecionine 1 mg/kg/bw_animal 3


title: Senecionine 1 mg/kg/bw_animal 1


title: 333-JF-11_wild-type +SJC01

tag: genotype

value: Bt Wild-type


title: Input DNA

value: murine pituitary gonadotrope cell line


title: 333-JF-10_wild-type +SJC01


title: 333-JF-8_wild-type +HKSJC01

source_name: wild-type +HKSJC01

value: Heat-killed SJC01 phage treated


title: 333-JF-9_wild-type +HKSJC01


title: Foxk2-ChIP-seq

value: Foxk2 LifeSpan Biosciences, cat#LS-C101814


title: 333-JF-7_wild-type +HKSJC01

value: in vitro, BPRM culture


title: Senecionine 0.33 mg/kg/bw_animal 5


title: 68C_R: Patient 31 recurrent cancer_RECURRENCE2

value: involved lymph node


title: 63C_R: Patient 29 recurrent cancer_RECURRENCE2


title: 63D_R: Patient 29 recurrent cancer_RECURRENCE3


title: 65B_R: Patient 30 recurrent cancer_RECURRENCE

value: oral tongue


title: 65A_R: Patient 30 recurrent cancer_TUMOUR


title: 68B_R: Patient 31 recurrent cancer_RECURRENCE1


title: 333-JF-6_CPS1+ARB25

description:
rRNA-depleted, mRNA
Bt CPS1 ARB25 in vitro.xlsx

value: Bt cps1

value: Mid-Log, exponential growth

value: ARB25 phage treated


title: 63B_R: Patient 29 recurrent cancer_RECURRENCE1

value: recurrent oral tongue squamous cell carcinoma


title: 63A_R: Patient 29 recurrent cancer_TUMOUR


title: 333-JF-5_CPS1+ARB25


title: Senecionine 0.33 mg/kg/bw_animal 3


title: Senecionine 0.33 mg/kg/bw_animal 2


title: Senecionine 0.1 mg/kg/bw_animal 5

value: Senecionine 0.1 mg/kg/bw


title: Senecionine 0.33 mg/kg/bw_animal 1

value: male


title: Senecionine 0.1 mg/kg/bw_animal 4

value: liver


title: 333-JF-4_CPS1+ARB25


title: 333-JF-2_CPS1+HKARB25

value: Heat-killed ARB25 phage treated


title: 333-JF-3_CPS1+HKARB25


title: 333-JF-1_CPS1+HKARB25


title: 62LN_N: Patient 28 cancer with nodes_NODE

value: primary oral tongue squamous cell carcinoma


title: HepG2, siNF90 Rep3 (smallRNA-seq)

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

institute: UMR9002 CNRS-UM

data_processing:
Raw data were processed using the Subread package (version 1.6.0). The mapping was performed using the following parameters: -t 1 -n 30 -m 4 -M 4 -I 0 -P 6 --multiMapping -B 10
Mesure gene expression from alignment files with FeatureCounts (version 1.6.3)
Differential expression analysis performed with DESeq2 (2.11.40.2)
Genome_build: GRCh38.96, reference annotation from miRbase (release 22.1)
Supplementary_files_format_and_content: [small-RNA-seq_HepG2.xlsx] tabular file in .xlsx format containing results of differential expression analysis (siNF90 vs siScr).
[.tsv] Counts file

growth_protocol: Human HepG2 cell line was grown in Dulbecco’s Modified Eagle’s medium – high glucose  supplemented with 10% fetal bovine serum , 1% penicillin-streptomicin (v/v) and 1% L-glutamine (v/v). Cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer’s instructions
Libraries were prepared by BGI services, using BGISEQ-500 library type

treatment_protocol: HepG2 cells were transfected with control and NF90 siRNAs (30 nM final concentration) using INTERFERin® transfection reagent according to the manufacturer’s instructions. Two rounds of transfection were performed. Cells were collected for RNA extraction approximately 65 h after the second transfection.

value: Liver

value: Hepatocellular carcinoma


title: 62P_N: Patient 28 cancer with nodes_TUMOUR


title: 59P_N: Patient 27 cancer with nodes_NODE


title: 5_PM: Patient 40 NON cancer

value: non-cancer


title: 55P_N: Patient 26 cancer with nodes_NODE


title: Senecionine 0.1 mg/kg/bw_animal 1


title: 59LN_N: Patient 27 cancer with nodes_TUMOUR


title: 55LN_N: Patient 26 cancer with nodes_TUMOUR


title: Heliotrine 3.3 mg/kg/bw_animal 5

value: Heliotrine 3.3 mg/kg/bw


title: SADRT45

city: Aberdeen

first: Ashish

last: Malik

address: St Machar drive

institute: University of Aberdeen

data_processing:
Resulting sequences from metatranscriptomic analysis were annotated with the Metagenomics Rapid Annotation using Subsystems Technology (MG-RAST) server version 4.0.3.
Functional classification was performed using the SEED Subsystems database and taxonomic annotations up to genus level were performed using the RefSeq database with a maximum e-value cut-off of 10-5, minimum identity cut-off of 60% and minimum length of sequence alignment of 15 nucleotides.
Abundance tables derived from MG-RAST (processed file attached) were imported into R for downstream analyses.
Supplementary_files_format_and_content: Processes data file contains gene adundances under Subsystems heirarchical classification. Sample IDs match the sample titles provided in this file.

organism: leaf litter metagenome

source_name: Leaf litter_Shrub_Reduced_12d after wet-up_microbial community

growth_protocol: In situ

extract_protocol:
We carried out RNA extraction on a coarse-ground litter aliquot of 0.2 g for shrub and 0.5 g for grass using RNeasy PowerSoil Total RNA Kit following manufacturer instructions (Qiagen, Hilden, Germany). Due to a high amount of organic compounds co-extracted from shrub litter, a lower amount of starting material was used in the extraction protocol to increase the RNA yield. After resuspending the RNA pellet in solution SR7 in the final step, purity and concentration of total RNA was assessed using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA), Qubit fluorometer (LifeTechnologies, Carlsbad, CA, USA) and Nanodrop 2000 Spectrophotometer (Thermo Scientific, USA).
Ribosomal RNA was removed using a Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions with a modification that included combining magnetic beads from the yeast and bacteria kit as follows: 0.5x Yeast Removal Solution, 0.25x Gram Negative Bacteria Removal solution, and 0.25x Gram Positive Bacteria Removal Solution. Strand-specific and barcode indexed RNA-seq libraries were then generated using the Kapa RNA-seq Hyper kit (Kapa Biosystems, Cape Town, South Africa) following the instructions of the manufacturer. The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100. The libraries were quantified by fluorometry on a Qubit fluorometer and pooled in equimolar ratios. The pool was quantified by qPCR with a Kapa Library Quant kit (Kapa Biosystems). The pooled library was sequenced on 1 lane of an Illumina HiSeq 4000 (Illumina, San Diego, CA, USA) with single-end 100 bp reads. The sequencing was carried out at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center.

treatment_protocol: A subsample of leaf litter was ground in a mixer (a quick whirl for 5 s) and used for RNA and metabolite extraction.

tag: vegetation type

value: Shrub

tag: precipitation treatment

value: Reduced

tag: time point

value: 12d after wet-up


title: HepG2, siNF90 Rep2 (smallRNA-seq)


title: SADRT44


title: HepG2, siNF90 Rep1 (smallRNA-seq)


title: SADRT46


title: SADRT43

source_name: Leaf litter_Shrub_Ambient_12d after wet-up_microbial community

value: Ambient


title: 52P_N: Patient 25 cancer with nodes_NODE

value: oral tongue


title: Senecionine 0.1 mg/kg/bw_animal 2


title: Heliotrine 3.3 mg/kg/bw_animal 4


title: Heliotrine 3.3 mg/kg/bw_animal 1


title: SADRT42


title: HepG2, siScr Rep3 (smallRNA-seq)

value: siScr


title: 52LN_N: Patient 25 cancer with nodes_TUMOUR

value: involved lymph node


title: Heliotrine 3.3 mg/kg/bw_animal 2


title: Heliotrine 1 mg/kg/bw_animal 4

value: Heliotrine 1 mg/kg/bw


title: Heliotrine 1 mg/kg/bw_animal 5


title: SADRT40


title: Heliotrine 3.3 mg/kg/bw_animal 3


title: HepG2, siScr Rep1 (smallRNA-seq)


title: HepG2, siScr Rep2 (smallRNA-seq)


title: 51P_N: Patient 24 cancer with nodes_TUMOUR


title: SADRT38

source_name: Leaf litter_Grass_Reduced_12d after wet-up_microbial community

value: Grass


title: 51LN_N: Patient 24 cancer with nodes_NODE


title: HepG2, siScr Rep2 (RNA-seq)

data_processing:
Quality control with FASTQC (Galaxy Version 0.72)
Alignment with HISAT2 (Galaxy Version 2.1.0). hg38 buid-in reference genome used. Parameters used: strand information "RF"
Mesure gene expression from alignment files with FeatureCounts (Galaxy Version 1.6.3+galaxy2)
Differential expression analysis performed with DESeq2 (Galaxy Version 2.11.40.2)
Genome_build: GRCh38.96
Supplementary_files_format_and_content: [siNF90_paired-end_RNAseq.xlsx]  Tabular file in .xlsx format containing results of differential expression analysis (siNF90 vs siScr).
[.txt]  Counts  file

tag: disease


title: SADRT37


title: SADRT36


title: SADRT39


title: HepG2, siScr Rep1 (RNA-seq)


title: 49LN_N: Patient 23 cancer with nodes_NODE

tag: disease state


title: SADRT35

source_name: Leaf litter_Grass_Ambient_12d after wet-up_microbial community


title: Heliotrine 1 mg/kg/bw_animal 2

value: male

tag: treatment


title: Heliotrine 0.33 mg/kg/bw_animal 5

value: liver

value: Heliotrine 0.33 mg/kg/bw


title: Heliotrine 1 mg/kg/bw_animal 1


title: Heliotrine 0.33 mg/kg/bw_animal 4


title: Heliotrine 1 mg/kg/bw_animal 3


title: Heliotrine 0.33 mg/kg/bw_animal 3


title: 48LN_N: Patient 22 cancer with nodes_NODE

value: primary oral tongue squamous cell carcinoma


title: 4_PM: Patient 39 NON cancer


title: HepG2, siScr Rep3 (RNA-seq)

value: Liver


title: HepG2, siNF90 Rep2 (RNA-seq)

value: Hepatocellular carcinoma


title: HepG2, siNF90 Rep1 (RNA-seq)


title: 49P_N: Patient 23 cancer with nodes_TUMOUR


title: SADRT34


title: HepG2, siNF90 Rep3 (RNA-seq)


title: 48P_N: Patient 22 cancer with nodes_TUMOUR


title: SADRT33


title: 47LN_N: Patient 21 cancer with nodes_NODE


title: SADRT32

source_name: Leaf litter_Grass_Ambient_1d after wet-up_microbial community

value: 1d after wet-up


title: sir2Δ-KO2 rep2

description: Yeast strains generated in Rusche laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Kluyveromyces lactis whole genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: Kluyveromyces lactis
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Sir2 knockout replicate 2

growth_protocol: Strains were grown at 30C in YPD (1% yeast extract, 2% peptone, 2% glucose) to early log phase.

extract_protocol:
Hot phenol treatment was used to harvest total RNA. Turbo Dnase (Life technologies) was used to remove DNA. Samples were concentrated using a Qaigen RNA column.
RNA samples were processed for sequencing using the TruSeq non-stranded RNA Library Prep Kit (Illumina), and 50 bp single end sequencing was performed on an Illumina HiSeq 2000 machine at the Duke IGSP sequencing facility.

treatment_protocol: 10 OD of cells were harvested.

tag: growth phase

value: early log phase yeast cells

value: MATa sir2_delta hmr_delta hml_delta


title: 47P_N: Patient 21 cancer with nodes_TUMOUR

source_name: oral tongue


title: SADRT30

source_name: Leaf litter_Shrub_Reduced_1d after wet-up_microbial community

value: Shrub

value: Reduced


title: 46P_N: Patient 20 cancer with nodes_TUMOUR


title: sir2Δ-KO2 rep1

source_name: Sir2 knockout replicate 1


title: Heliotrine 0.33 mg/kg/bw_animal 2


title: Heliotrine 0.1 mg/kg/bw_animal 5

value: Heliotrine 0.1 mg/kg/bw


title: Heliotrine 0.33 mg/kg/bw_animal 1


title: Heliotrine 0.1 mg/kg/bw_animal 4


title: Heliotrine 0.1 mg/kg/bw_animal 3


title: Heliotrine 0.1 mg/kg/bw_animal 2


title: SADRT28


title: sir2Δ-KO1 rep2


title: SADRT26

source_name: Leaf litter_Shrub_Ambient_1d after wet-up_microbial community

value: Ambient


title: sir2Δ-KO1 rep1


title: SADRT25


title: 46LN_N: Patient 20 cancer with nodes_NODE

source_name: involved lymph node


title: WT_rep1

source_name: Wildtype replicate 1

value: MATa SIR2 hmr_delta hml_delta


title: 45P_N: Patient 19 cancer with nodes_TUMOUR

value: oral tongue


title: WT_rep2

source_name: Wildtype replicate 2