title: RNA-seq of wt embryonic stem cells, replicate 1


title: HEK_a12eCBS_dCas9-VPR_ChIPSeq

status: Public on Apr 15 2019

type: SRA

city: San Francisco

first: Daniele

last: Canzio

state: CA

address: 555 Mission Bay Boulevard South

department: Neurology

country: USA

institute: University of California San Francisco

description: ChIP-Seq, Single End

library_source: genomic

data_processing:
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.
For ChiP-Seq experiments, raw FASTQ files were aligned using Bowtie2 using hg19 reference genome upon adapter sequences removal using CutAdapt. Uniquely aligning reads were selected using Samtools and reads with alignment quality below 30 (-q 30) were removed. The HOMER software package was used to generate signal tracks.
For in situ Hi-C experiments, raw FASTQ files were processed through use of the Juicer Tools Version 1.76 pipeline (Durand et al., 2016)  with one modification. Reads were aligned to hg38 using BWA 0.7.17 mem algorithm and specifying the -5 option implemented specifically for in situ Hi-C data.
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha12

growth_protocol: SK-N-SH cells were purchased from ATCC and cultured in RPMI-1640 supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

extract_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

tag: tissue

value: HEK293T cells

value: genomic DNA

tag: chip antibody

value: Flag (Sigma F1804)


title: MEFs  D2_AGHMT_H3K27ac

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
The raw reads were aligned to the mouse reference genome (GRCh38/mm10) using default parameters in BWA v0.7.12 (Li and Durbin, 2009).
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 (Li et al., 2009) and Sambamba version 0.6.6 (Tarasov et al., 2015).
Library complexity was measured using BEDTools version 2.26.0 (Quinlan and Hall, 2010) and meets ENCODE data quality standards (Landt et al., 2012).
Relaxed peaks were called using MACS version 2.1.0 (Feng et al., 2012) with a p-value of 1x10-2 for H2K27ac and SPP version 1.4 (Kharchenko et al., 2008) with an IDR = 0.01 for each replicate and pseudoreplicates. For H3K27ac peak calls that are either observed in both pseudoreplicates were used for subsequent analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: ChIP-seq BigWig files were generated using MACS version 2.1.0; Scores represent the ChIP-seq fold change over control

organism: Mus musculus

source_name: MEFs  D2_AGHMT_H3K27ac

growth_protocol: MEFs from E13.5-14.5 C57BL/6 mice were prepared as preciously described (Nam et al., 2014) and cultured in fibroblast growth medium (DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin) until experiments were performed. MEFs infected were induced using DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin-selenium-transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). The induction medium was replaced every other two or three days until experiments were performed.

extract_protocol:
MEFs two or seven days after retroviral transduction were crosslinked with 1% formaldehyde in PBS for 30 min and neutralized by the addition of glycine to a final concentration of 0.125M for 5min. MEFs were then harvested and washed with cold PBS for ChIP. For mouse heart sample preparation, ChIP was performed as previously described (Huang et al., 2016; Xu et al., 2012), or by using ChIP-IT Express ChIP kits (Active Motif) following the vender’s protocol.
ChIP-seq libraries were generated using KAPA Hyper Prep Kit following the manufacturer’s protocol (Kapa Biosystems).

treatment_protocol: MEFs were transduced with indicated retroviruses cocktail twice for 24 hours period followed by induction media. Cells were then harvested for at indicated timepoints post-induction for experiments.

tag: background strain

value: Mouse embryonic fibroblast (MEF)

tag: treatment

value: AGHMT

tag: induction time

value: 2 days

tag: development stage

tag: antibody

value: H3K27ac (Diagenode, C15410196)


title: RNA-seq of wt embryonic stem cells, replicate 3

city: Edinburgh

first: Magdalena

middle: Maria

last: Maslon

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
Base calling was performed with Illumina cassava and bcl2fastq2-v2.17.1.14
RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 1.0 (Tapial et al., Genome Res. 2017), which is available on github (https://github.com/vastgroup/vast-tools).
Alternative splicing analysis: From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Significantly differential AS was assessed with the diff module of vast-tools under development and were additionally required to have a PSI difference >10.
Expression analysis: Expression differences were calculated based on vast-tools raw read counts per gene using the GLM stream in the R package edgeR (McCarthy JD et al., NAR 2012) with a one-column design matrix describing genotype and time point.
Genome_build: mm9
Supplementary_files_format_and_content: vast-tools.altSplicing.tab.gz: Primary vast-tools output for alternative splicing
Supplementary_files_format_and_content: AltSplicing.tab.gz: Filtered PSI values and differential alternative splicing annotation
Supplementary_files_format_and_content: Expression.tab.gz: Raw read counts per gene, normalized expression and fold-change (edgeR analysis)

molecule: polyA RNA

source_name: Embryonic stem cells (ESCs)

growth_protocol: ESCs were cultured in 2i medium (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.05% BSA, 1uM 0325901, 3uM CHIR99021, 2mM L-glutamine, 0.15mM monothioglycerol, 100U/ml LIF) on gelatin coated-plates

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy kit
1ug of total RNA was used for poly-A selection, TruSeq stranded mRNA-seq library kit was used to prepare libraries

value: Embryonic stem cells (ESCs)

tag: genotype

value: wt/wt


title: (p)ppGpp0 48 °C noPP [ppGpp_Null_48C_III_NoPP]

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: Bacillus subtils 168 genome with insertion of rrnJp1-lacZ in the amyE site (amyE::rrnJp1-lacZ Cm). For reference sequence/annotation see files: B.subtilis_168_BHS220_modified_chr_spike.fna and B.subtilis_168_BHS220_modified_chr_spike.gff
Supplementary_files_format_and_content: htseqcounts*.tab files:  raw read counts per gene; htseqcounts*.rpkm files: RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes; Fasta and GFF files with genomic reference and annotation

molecule: total RNA

organism: Bacillus subtilis

source_name: (p)ppGpp0 48 °C noPP

growth_protocol: Cells were grown in LB medium to the mid-exponential phase (OD 0.4) in a water bath with orbital shaking at 200 rpm.

extract_protocol:
Total RNA was isolated from flash-frozen cells using phenol/TRIzol extraction as described in Lamy et al. (2004) Molecular Microbiology, 54: 1250-1268 and treated with DAase using the TURBO DNA-free kit (Ambion). RNA integrity was checked on a Bioanalyzer 2100
rRNA was depleted using the MICROBExpress Kit (Invitrogen). mRNA was supplemented with ERCC ExFold RNA Spike-In Mixes, treated with 5'RNA-polyphosphatase, sonicated and treated with PNK. The library was generated using the NEB Next Small RNA Kit as described by Manufacturer. In addition, one replicate without ERCC was not treated with polypphosphatase

treatment_protocol: The culture was divided and treated either with 48 °C or left untreated for 15 min. Then, both cultures were transferred to a 53 °C water bath for another 15 min. Samples of 25 mL were harvested by centrifugation for 3 min and flash-frozen in luqid nitrogen.

tag: genotype/variation

value: amyE::rrnJp1 lacZ cm relA::mls ywaC E154V yjbM E139V

value: 48 °C 15 min

tag: replicate

value: III

tag: polyphosphatase treatment

value: no


title: HEK_a12pCBS_dCas9-VPR_ChIPSeq

description: ChIP-Seq, Single End

source_name: HEK293T cells transfected with dCas9 targeting the pCBS of Pcdha12


title: (p)ppGpp0 37 °C noPP [ppGpp_Null_37C_III_NoPP]

source_name: (p)ppGpp0 37 °C noPP

value: 37 °C (control)


title: HEK_a4eCBS_dCas9-VPR_ChIPSeq

description: ChIP-Seq, Single End

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha4


title: ΔrelA 48 °C noPP [F_48C_delta_relA_III_NoPP]

source_name: ΔrelA 48 °C noPP

value: amyE::rrnJp1 lacZ cm relA::mls


title: SKNSH_CTCF_ChIPSeq

description: ChIP-Seq, Single End

source_name: HEK293T cells

value: CTCF (Pugacheva et al, 2015)


title: HEK_a4pCBS_dCas9-VPR_ChIPSeq

description: ChIP-Seq, Single End

source_name: HEK293T cells transfected with dCas9 targeting the pCBS of Pcdha4


title: RNA-seq of slow/slow NPCs, replicate 1

source_name: Neuronal progenitor cells (NPCs)

growth_protocol: One day prior to induction of differentiation, ESCs were seeded at high density in 2i medium. The following day, cells were detached using accutase, resuspended in N2B27 media (1:1 Neurobasal and DMEM/F12, supplemented with 0.5X N2, 0.5x B27, 0.1 mM β-mercaptoethanol, 0.2 mM L-glutamine), counted and plated at the appropriated density onto either 15 cm plates or 6-well plates that have been coated with a 0.1% gelatin solution. The initial plating density varied between WT and slow/slow ESCs, and was established to be 1x10e4 and 3x10e4 per cm2, respectively. Culture medium was changed every second day. Cells were considered NPCs at day 7 of this culture

value: Neuronal progenitor cells (NPCs)


title: wild type 48/53 °C noPP [D_48-53C_III_NoPP]

source_name: wild type 48/53 °C noPP

value: amyE::rrnJp1 lacZ cm

value: 48 °C 15 min, then 53 °C 15 min


title: SKNSHadel1_H3K4me3_ChIPSeq

description: ChIP-Seq, Single End

source_name: SK-N-SH heterozygous for the Pcdha cluster

value: SK-N-SH neuroblastoma cells

value: genomic DNA

value: H3K4me (ThermoFisher PA5-27029)


title: ΔrelA 37 °C noPP [E_37C_delta_relA_III_NoPP]

source_name: ΔrelA 37 °C noPP


title: wild type 48 °C noPP [B_48C_III_NoPP]

source_name: wild type 48 °C noPP


title: wild type 53 °C noPP [C_37-53C_III_NoPP]

source_name: wild type 53 °C noPP

value: 53 °C 15 min


title: HEK_a12pCBS_dCas9-VPR_sorted_HiC_rep2

description:
captureHiC-Seq, Paired End
Processed data file includes data for rep1, 2 and 3. File is available on GSM3514558

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All mouse samples were aligned to mm10, human samples aligned to hg19. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

growth_protocol: HEK293T cells were purchased from ATCC and cultured in DMEM supplemented with 10% (vol/vol) FBS, 1X GlutaMax, 1mM sodium pyruvate, 1X non-essential amino acids, 1% penicillin-streptomycin. Cells were maintained at 37°C in a 5% (vol/vol) CO2 incubator.

tag: cell type

value: HEK293T cells

value: HEK293T cells positively transfected with dCas9-VPR targeting the pCBS of Pcdha12


title: SKNSHadel1_Rad21_ChIPSeq

description: ChIP-Seq, Single End

value: Rad21 (Abcam ab992)


title: wild type 37 °C (control) noPP [A_37C_III_NoPP]

source_name: wild type 37 °C (control) noPP


title: SKNSHadel1_CTCF_ChIPSeq

description: ChIP-Seq, Single End


title: RNA-seq of slow/slow embryonic stem cells, replicate 2

value: Embryonic stem cells (ESCs)


title: SKNSHadel1_TotRNASeq

description: RNA-Seq, Paired End

value: total RNA


title: (p)ppGpp0 48 °C [ppGpp_Null_37C_II]

source_name: (p)ppGpp0 48 °C

value: amyE::rrnJp1 lacZ cm relA::mls ywaC E154V yjbM E139V

value: 48 °C 15 min

value: II

value: yes


title: (p)ppGpp0 37 °C [ppGpp_Null_37C_I]

source_name: (p)ppGpp0 37 °C

value: 37 °C (control)

value: I


title: hneurons_TotRNASeq

description: captureRNA-Seq, Single End

source_name: human brain neurons

value: human brain neurons


title: hneurons_PolyARNASeq

description: captureRNA-Seq, Single End

value: PolyA


title: (p)ppGpp0 48 °C [ppGpp_Null_48C_I]


title: (p)ppGpp0 37 °C [ppGpp_Null_48C_II]


title: SKNSHadel1_H3K27ac_ChIPSeq

description: ChIP-Seq, Single End

value: SK-N-SH neuroblastoma cells

value: H3K27ac (Abcam ab4729)


title: (p)ppGpp0 37 °C [ppGpp_Null_37C_III]

value: III


title: HEK_a12eCBS_TotRNASeq_rep1

description: captureRNA-Seq, Paired End

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha12


title: HEK_a9eCBS_TotRNASeq_rep2

description: captureRNA-Seq, Paired End

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha9


title: HEK_a12eCBS_TotRNASeq_rep2

description: captureRNA-Seq, Paired End


title: ΔrelA 48 °C [F_48C_delta_relA_III]

source_name: ΔrelA 48 °C

value: amyE::rrnJp1 lacZ cm relA::mls


title: ΔrelA 48 °C [F_48C_delta_relA_II]


title: HEK_a9eCBS_TotRNASeq_rep1

description: captureRNA-Seq, Paired End

value: HEK293T cells


title: HEK_a6eCBS_TotRNASeq_rep2

description: captureRNA-Seq, Paired End

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha6


title: ΔrelA 48 °C [F_48C_delta_relA_I]


title: (p)ppGpp0 48 °C [ppGpp_Null_48C_III]


title: HEK_a6eCBS_TotRNASeq_rep1

description: captureRNA-Seq, Paired End


title: HEK_a4pCBS_TotRNASeq

description: RNA-Seq, Paired End


title: HEK_a4eCBS_TotRNASeq

description: RNA-Seq, Paired End

source_name: HEK293T cells transfected with dCas9 targeting the eCBS of Pcdha4


title: ΔrelA 37 °C [E_37C_delta_relA_I]

source_name: ΔrelA 37 °C


title: HEK_TotRNA_rep2

description: captureRNA-Seq, Paired End

source_name: HEK293T cells


title: ΔrelA 37 °C [E_37C_delta_relA_III]


title: wild type 48/53 °C [D_48-53C_III]

source_name: wild type 48/53 °C

value: amyE::rrnJp1 lacZ cm

value: 48 °C 15 min, then 53 °C 15 min


title: ΔrelA 37 °C [E_37C_delta_relA_II]


title: wild type 48/53 °C [D_48-53C_I]


title: wild type 48/53 °C [D_48-53C_II]


title: SKNSH_S4U_t20_rep4

description: capture s4UDRB-Seq, Paired End

source_name: SK-N-SH WT neuroblastoma cells treated with DRB for 3hrs

value: Nascent RNA, +S4U, time = 20min after DRB release


title: wild type 53 °C [C_37-53C_III]

source_name: wild type 53 °C

value: 53 °C 15 min


title: SKNSH_S4U_t20_rep3

description: capture s4UDRB-Seq, Paired End


title: wild type 53 °C [C_37-53C_I]


title: HEK_TotRNA

description: RNA-Seq, Paired End

value: total RNA


title: SKNSH_S4U_t20_rep2

description: capture s4UDRB-Seq, Paired End


title: wild type 53 °C [C_37-53C_II]


title: wild type 48 °C [B_48C_III]

source_name: wild type 48 °C

value: 48 °C 15 min


title: SKNSH_S4U_t8_rep4

description: capture s4UDRB-Seq, Paired End

value: Nascent RNA, +S4U, time = 8min after DRB release


title: HEK_TotRNA_rep1

description: captureRNA-Seq, Paired End


title: wild type 48 °C [B_48C_II]

value: II

value: yes


title: SKNSH_S4U_t8_rep3

description: capture s4UDRB-Seq, Paired End


title: CD133+CD15+ U-CH2

type: RNA

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

description: miRNA expression data from CD133+CD15+ chordoma cells

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

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

label: biotin

source_name: CD133+CD15+ chordoma cells

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

growth_protocol: Chordoma cells were cultured in IMDM: RPMI (4/1) supplemented with %10 FBS  %1 PS

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

treatment_protocol: Not Applicable

tag: cell markers

value: chordoma


title: CD133-CD15-MUG-CHOR1(2)

description: miRNA expression data from CD133-CD15- chordoma cells

source_name: CD133-CD15- chordoma cells


title: CD133+CD15+ U-CH2(2)


title: CD133-CD15- MUG-CHOR1


title: CD133-CD15- U-CH2


title: CD133-CD15-U1 (2)


title: CD133+CD15+ MUG-CHOR1


title: CD133+CD15+ MUG-CHOR1(2)


title: CD133-CD15-U-CH2(2)


title: CD133-CD15- U1


title: CD133+CD15+ U1(2)


title: SKNSH_S4U_t8_rep1

description: capture s4UDRB-Seq, Paired End


title: CD133+CD15+ U1


title: wild type 48 °C [B_48C_I]

value: I


title: SKNSH_S4U_t20_rep1

description: capture s4UDRB-Seq, Paired End


title: CD133-CD15- JHC7


title: CD133-CD15- JHC7 (2)


title: SKNSH_S4U_t0

description: s4UDRB-Seq, Single End

value: Nascent RNA, time = 0min after DRB release


title: SKNSH_S4U_t8_rep2

description: capture s4UDRB-Seq, Paired End

value: SK-N-SH neuroblastoma cells

value: Nascent RNA,+S4U, time = 8min after DRB release


title: wild type 37 °C control [A_37C_III]

source_name: wild type 37 °C control

value: 37 °C (control)

value: III


title: wild type 37 °C control [A_37C_II]


title: SKNSH_S4U_t0_DMSO

description: s4UDRB-Seq, Single End

source_name: SK-N-SH WT neuroblastoma cells treated with DMSO for 3hrs

value: Nascent RNA, time = 0min, no DRB control


title: W3

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

country: China

institute: JunLin Song

data_processing:
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: tab-delimited text files include gene expression count for each Sample

organism: Argopecten irradians irradians x Argopecten purpuratus

source_name: adductor muscle

extract_protocol:
Adductor muscle tissues were dissected and stored in liquid nitrogen individually.Total RNA from each tank was isolated by TRIzol reagent (Invitrogen, UK).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adductor muscle

tag: synonym

value: Bohai Red Scallop

tag: variant

value: white color variant of adductor muscle

tag: age

value: one year old


title: SSTL-F_LpM

city: Taipei

first: Yue-ie

middle: Caroline

last: Hsing

address: Sinica  Address：128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica,Taiwan

data_processing:
CLC Genomics Workbench 11 software were used for basecalling and sequenced reads were trimmed for low-quality sequence.
RPKM, TPM and CPM were calculated using CLC Genomics Workbench 11 software.
Genome_build: Oryza sativa Japonica Group (assembly Build 4.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM, TPM, and CPM values for each sample

organism: Oryza sativa Japonica Group

source_name: Rice anther

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) were grown in a growth chamber under day 28°C/night 25°C, 16 h of light and 80% humidity at Academia Sinica, Taipei.

extract_protocol:
Anther was extracted with TRIzol reagent for total RNA.
RNA single-end libraries were prepared for sequencing using standard Illumina protocols and sequenced on a Illumina HiSeq2000 system.

tag: variety

value: Tainung 67

value: control

tag: developmental stage

value: LpM:Late pollen mitosis stage

tag: phenotype

value: Fertile panicles

value: Rice anther


title: sstl-s_LpM

value: semi-sterile mutant (sstl)

value: Sterile panicles

tag: tissue


title: sstl-s_YM

value: YM:Young microspore stage


title: SSTL-F_YM


title: W2


title: SKNSH_PolyAcRNASeq

description: captureRNA-Seq, Single End

source_name: SK-N-SH WT neuroblastoma cells

value: SK-N-SH neuroblastoma cells

value: PolyA


title: O3

value: Orange color variant of adductor muscle


title: SKNSH_StartSeq_rep2

description: StartSeq

value: Short 5'capped RNAs associated with paused RNAPII


title: ModA10 ON, rep3

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

description:
ModA10 ON
processed data file: modA10_gene_counts.txt
processed data file: modA10_ON.VS.OFF-all_genes.txt

data_processing:
Illumina bcl2fastq 2.20.0.422 pipeline.
Bowtie aligner (2.3.2) was used to map reads to the R2866 genomic DNA sequence; accession number CP002277.
edgeR version 3.18.1 was used to perform differential expression analysis.
Genome_build: Haemophilus influenzae strain R2866 genomic DNA sequence (CP002277.1).
Supplementary_files_format_and_content: modA10_gene_counts.txt: Tab-delimited text file includes abundance measurements.
Supplementary_files_format_and_content: modA10_ON.VS.OFF-all_genes.txt: Tab-delimited text file includes abundance measurements and expression differences modA10 ON vs. modA10 LOCK OFF.

organism: Haemophilus influenzae R2866

source_name: Non-typeable Haemophilus influenzae strain R2866

growth_protocol: Mid-log cultures in supplemented BHI (sBHI; containing haemin and NAD).

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols.

tag: presence or absence of methyltransferase

value: Present


title: ModA10 OFF, rep1

description:
ModA10 OFF
processed data file: modA10_gene_counts.txt
processed data file: modA10_ON.VS.OFF-all_genes.txt

value: Absent


title: ModA10 OFF, rep2


title: SKNSH_StartSeq_rep1

description: StartSeq


title: CD133+CD15+ JHC7

value: chordoma


title: O2

value: adductor muscle

value: Bohai Red Scallop


title: SKNSH_TotcRNASeq

description: captureRNA-Seq, Single End

value: total RNA


title: ModA10 ON, rep2


title: wild type 37 °C control [A_37C_I]

value: amyE::rrnJp1 lacZ cm

tag: treatment

value: 37 °C (control)

value: I

value: yes


title: ModA10 ON, rep1


title: SKNSH_TotRNASeq

description: RNA-Seq, Single End


title: O1

value: one year old


title: Zikv-Aag2 (small RNA)

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

data_processing:
The sequencing reads were mapped to the human genome (release hg19) or mosquito genome (AaeGL5.0) by using Bowite 2.2.5 and the cellular miRNA expression level was determined on the
basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot be mapped to human genome were then mapped to ZIKV genome with 100% identity. The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary
22-nt vsRNAs in each library in different distance categories were computed using principles as previously described(Li et al., 2016; Li et al., 2013).
Genome_build: hg19, AaeGL5.0
Supplementary_files_format_and_content: txt files generated by bowtie2

organism: Aedes aegypti

source_name: Aedes aegypti Aag-2 cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina)

tag: infection

value: Zika virus


title: CD133+CD15+ JHC7 (2)


title: Neff/Pam+Lpn_96hpi_3

status: Public on Apr 14 2019

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

description:
Acanthamoeba castellanii/Protochlamydia amoebophila/Legionella pneumophila
Legionella_pneumophila_Paris.txt
Protochlamydia_amoebophila_UWE25.txt

data_processing:
PRINSEQ-lite was used trimming and quality filtering of the raw reads: first 13 based were removed (-trim_left 13), reads were trimmed when the base calling quality decreased below a phred score of 20 within a window of 5 bases (-trim_qual_right 20, -trim_qual_window 5), reads containing more than two ambiguous bases (Ns) were removed (-ns_max_n 2), poly-A/T tails were trimmed (-trim_tail_left 5, -trim_tail_right 5), and all reads shorter than 25 bases were removed (-min_len 25).
Trimmed reads were mapped to the P. amoebophila and L. pneumophila genomes, respectively, using BWA (default settings). Using samtools, only uniquely mapped reads were kept (-q 10, -F 4).
Strand-specific reads per predicted gene were counted via HTSeq (union mode).
Differential gene expression (logFC >1, FDR < 0.05) was determined using edgeR.
Genome_build: NC_005861.1
Genome_build: NC_002942.5
Supplementary_files_format_and_content: raw read counts as output by HTSeq for each gene locus tag (rows) and sample (columns); one file for each organism

organism:
Acanthamoeba castellanii
Candidatus Protochlamydia amoebophila

source_name: amoebae cells containing the endosymbiont and infected with L. pneumophila

growth_protocol: Amoebae with and without the endosymbiont were maintained at 20°C in PYG (20 g/l proteose peptone, 100 mM glucose, 2 g/l yeast extract, 1 g/l sodium citrate dihydrate, 4 mM MgSO4*7H2O, 1.32 mM Na2HPO4*2H2O, 2.5 mM KH2PO4, 0.05 mM Fe(NH4)2(SO4)2*6H2O; pH 6.5). Before infection with L. pneumophila, amoebae with and without endosymbionts were seeded (9x10^6 cells per flask) and allowed to grow for 3 days at 20°C. Infectious L. pneumophila were prepared as follows: ACES-buffered yeast extract (AYE) medium supplemented with 0.4 g/l L-cysteine and 0.135 g/l ferric nitrate was inoculated with L. pneumophila Paris, grown overnight at 37°C on a roller drum (Eppendorf, Hamburg, Germany), diluted with fresh medium to OD600 = 0.2-0.3, and grown to post-exponential phase (OD600 ≥ 3.5). Only cultures exhibiting a high proportion of motile cells were used for infection.  Motility was assessed qualitatively as described previously (Byrne & Swanson, 1998). The number of viable L. pneumophila added to amoebae was determined by diluting the cultures in infection buffer (Moffat & Tompkins, 1992) and subsequent plating of dilutions on ACES-buffered charcoal yeast extract (CYE) plates in triplicate.

extract_protocol:
Total RNA from extracellular bacteria (with and without symbionts) and intracellular bacteria enriched from co-cultures at 24 and 96 hpi (with and without symbionts) was extracted using TRIzol Reagent (Thermo Fisher Scientific), and residual DNA was digested using the Turbo DNA-free Kit (Thermo Fisher Scientific), both as described before (König et al., 2016). rRNA depletion using the Ribo-Zero Gold rRNA Removal Kit (Illumina) was performed by the Vienna Biocenter Core Facilities (VBCF) Next-Generation Sequencing (NGS) Unit (http://www.vbcf.ac.at).
Library preparation using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) as well as sequencing on an Illumina HiSeq 2500 with 100 bp read length was performed by the Vienna Biocenter Core Facilities (VBCF) Next-Generation Sequencing (NGS) Unit (http://www.vbcf.ac.at).

treatment_protocol: Cultures were infected by adding L. pneumophila directly to the flasks. Symbiont-free and symbiont-containing cultures, as well as uninfected symbiont-containing cultures were then incubated for 2 hours before amoebae were washed four times with infection buffer (Moffat & Tompkins, 1992). PYG medium was added, cultures were sampled at 2 hours post infection (hpi) to monitor initial infection efficiency by FISH, and were further incubated at 20°C for 24 and 96 h, respectively. Released, extracellular L. pneumophila were collected at 96 hpi by centrifuging the supernatant of infected cultures at 150 x g for 2 min to roughly separate amoebae from bacterial cells, then filtering the supernatant through 5 µm syringe filters (Sartorius) to remove residual amoebae, and finally pelleting the bacterial cells at 12,850 x g for 2 min. L. pneumophila infected amoebae as well as uninfected amoebae were harvested and bacteria were roughly enriched as previously described (König et al., 2016), but to optimize yield of intracellular bacteria, cell suspensions were additionally vortexed for 1 min together with smaller glass beads (diameter 0.25-0.5 mm, Carl Roth) after vortexing with larger beads (diameter 0.75 - 1 mm, Carl Roth).

tag: a. castellanii strain

value: Neff

tag: p. amoebophila strain

tag: l. pneumophila strain

value: Paris

tag: condition

value: L. pneumophila

tag: time point

value: 96 hours post infection

tag: l. pneumophila multiplicity of infection (moi)


title: ModA10 OFF, rep3

tag: genotype/variation


title: Neff/Pam+Lpn_96hpi_2


title: W1

tag: synonym

value: white color variant of adductor muscle


title: DNA from FLAG-RocS pulldown, replicate 2

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

data_processing:
Reads were mapped using bowtie2 v. 2.2.6.
Per-base coverage was determined with a custom script.
Peak calling for identification of RocS-bound segments of the genome was performed with SeqMonk 1.45.0
Genome_build: NC_003098.1
Supplementary_files_format_and_content: Processed data files contain strand-specific per-base coverage information for each position in the NC_003098.1 genome.

organism: Streptococcus pneumoniae

source_name: Bacterial culture

growth_protocol: Cells were pre-cultured in acid C+Y (pH 6.8) and grown until OD600 0.40. Cells were then diluted 1:50 in acid C+Y, to a final volume of 30 mL and grown until OD600 0.20.

extract_protocol:
Cells were then diluted 1:50 in acid C+Y, to a final volume of 30 mL and grown until OD600 0.20. Then, 3 mL of fixation buffer (11% formaldehyde; 5 mM NaOH; 50 mM Tris, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA) was added, the culture was mixed by inversion and incubated at RT for 15 min . Formaldehyde was quenched by the addition of 11 mL of 1M tris and 10 min incubation at RT. First, cells were spun down at 5,000g for 12 min at 4°C and washed in 20 mL ice-cold PBS. Secondly, cells were spun down at 5,000g for 12 min at 4°C and washed in 10 mL ice-cold PBS. Thirdly, cells were spun down at 5,000g for 12 min at 4°C and washed in 1 mL ice-cold PBS. Finally, cells were spun down at 11,000g for 2 min at 4°C, supernatant was removed and the pellet was snap-frozen in liquid nitrogen and stored at -80°C. DynabeadsTM Protein G (Invitrogen) were prepared according to the manufacturers instructions and loaded with 10 ug of anti-FLAG antibody. Cell pellets were resuspended in 2 mL ice-cold lysis buffer and transferred to a 5 ml round-bottom tube. Samples were sonicated on ice for 5-10x 30 sec on a Sonics Vibracell VCX130 with 65% amplitude. Samples were then split into 200 uL whole-cell extract (WCE, stored at -20C) and 800 uL for immunoprecipitation. The latter fractions were incubated for 2-4 hours at 4°C on a rotating wheel. Supernatant was removed on a magnet. The beads were washed three times 5 min, shaking at 800 rpm at RT. The first wash was performed with 1 mL lysis buffer, the second wash with 1 mL lysis buffer with extra NaCl (500 mM final concentration), and the third wash with 1 mL wash buffer (10 mM Tris, pH 8.0; 250 mM LiCl; 1 mM EDTA; 0.5% NP-40; 0.5% sodium deoxycholate; 1 mM PMSF). Supernatant was removed and beads were resuspended in 520 μL TES buffer. WCE samples were thawed and combined with 300 μL TES buffer and 20 μL of 10% SDS. To elute DNA, both WCEs and immunoprecipitates (IPs) were incubated overnight on a shaker at 65°C. On a magnet, the DNA-containing supernatant was transferred to a fresh tube. To the DNA samples, 1 μL phenol per μL of sample was added, followed by vortexing and centrifugation at 11,000g for 5 min. The DNA-containing layer was then added to 1 μL chloroform per 1 μL of sample, followed by vortexing and centrifugation at 11,000g for 5 min. The DNA-containing layer was transferred to a fresh tube and 1 μL of glycogen (Roche) and 40 μL of 3M NaOAc (pH 5.3) were added. After mixing, 1 mL of pure ethanol was added and tubes were incubated for 20 min. at -20°C, followed by centrifugation for 15 min at 4°C. The pellets were resuspended in 100 μL TE (pH 8.0) and incubated for 15 min at 65°C.
GATC Biotech performed further library preparation and sequencing on an Illumina HiSeq with 50 nt single-end reads (HSHOv4 SR50)

tag: strain

value: R6; rocS:flag-rocS

tag: chip antibody

value: Monoclonal ANTI-FLAG M2 F3165


title: DNA from FLAG-RocS whole-cell extract, replicate 2


title: DNA from FLAG-RocS whole-cell extract, replicate 1


title: Neff/Pam+Lpn_24hpi_3

value: 24 hours post infection


title: Neff/Pam+Lpn_24hpi_1


title: Neff/Pam_96hpi_2

description:
Acanthamoeba castellanii/Protochlamydia amoebophila
Protochlamydia_amoebophila_UWE25.txt

source_name: amoebae cells containing the endosymbiont

value: continuous culture, 96 hours after the other cultures were infected with L. pneumophila


title: Neff+Lpn_extracellular_2

description:
this sample stems from sample 9; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Legionella pneumophila
Legionella_pneumophila_Paris.txt

organism: Legionella pneumophila

source_name: extracellular L. pneumophila

value: extracellular L. pneumophila


title: Neff+Lpn_extracellular_3

description:
this sample stems from sample 10; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Legionella pneumophila
Legionella_pneumophila_Paris.txt


title: Neff/Pam_24hpi_2

value: continuous culture, 24 hours after the other cultures were infected with L. pneumophila


title: Neff/Pam+Lpn_24hpi_2


title: Neff/Pam_24hpi_1

value: 24 hours after the other cultures were infected


title: Neff+Lpn_extracellular_1

description:
this sample stems from sample 8; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Legionella pneumophila
Legionella_pneumophila_Paris.txt


title: Neff+Lpn_96hpi_3

description:
Acanthamoeba castellanii/Legionella pneumophila
Legionella_pneumophila_Paris.txt

organism: Acanthamoeba castellanii

source_name: amoebae cells infected with L. pneumophila

value: L. pneumophila infection


title: Neff/Pam+Lpn_96hpi_1


title: Neff+Lpn_96hpi_1


title: Neff/Pam+Lpn_extracellular_3

description:
this sample stems from sample 19; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Protochlamydia amoebophila/Legionella pneumophila
Legionella_pneumophila_Paris.txt

organism:
Legionella pneumophila
Candidatus Protochlamydia amoebophila

source_name: extracellular L. pneumophila and endosymbionts

value: extracellular L. pneumophila and P. amoebophila


title: Neff+Lpn_96hpi_2


title: Neff/Pam_96hpi_1

value: 96 hours after the other cultures were infected


title: Neff/Pam+Lpn_extracellular_2

description:
this sample stems from sample 18; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Protochlamydia amoebophila/Legionella pneumophila
Legionella_pneumophila_Paris.txt


title: Neff+Lpn_24hpi_3


title: Neff+Lpn_24hpi_2


title: bmlA

city: Shanghai

first: Zhuanghui

last: Feng

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.10.1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: subcutaneous white adipose tissue

tag: age


title: Neff/Pam+Lpn_extracellular_1

description:
this sample stems from sample 17; extracellular bacteria were harvested from the culture supernatant before infected amoebae cells were harvested
Protochlamydia amoebophila/Legionella pneumophila
Legionella_pneumophila_Paris.txt


title: ctrlB

value: DMSO


title: bmlB


title: ctrlA


title: Neff+Lpn_24hpi_1

value: Neff


title: RMS398

status: Public on Apr 13 2019

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)

data_processing:
Transcripts Per Million (TPM) were calculated using RSEM (Bo Li and Colin N Dewey, BMC Bioinformatics, 2011).
Genome_build: mm4
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM values for each Sample.

source_name: Skin

extract_protocol: Cells were loaded onto C1 integrated fluidic circuits IFC (5- to 10-μm chip) for cell lysis, reverse transcription with oligo (dT) primers and amplification of cDNA on a C1 Single Cell Auto Prep System according to the mRNA-seq protocol of the manufacturer (Fluidigm). Only cells with high-quality cDNA were processed for subsequent library preparation. A Nextera_XT Kit (PN FC-131-1096; Illumina) with dual indices (PN FC-131-1002; Illumina) was used for the preparation of single-cell multiplexed libraries, which were sequenced as 101-bp single-end reads on the Illumina HiSeq 2000 platform (96 samples/lane).

value: Propionibacterium acnes infection

tag: cell type

value: Skin CD103+DC


title: RMS407

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS405

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS399

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: MT170DAF, biological rep2

first: Feng

last: Zhu

address: No.1,Shizishan Street

department: College of Horticulture & Forestry Sciences

institute: Huazhong Agricultural University

description: Gene expression data from the flavode of the stay-green mutant citrus  at 170 days after flowering

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Citrus reticulata

source_name: The flavode of the citrus were collected at 170 days after flowering

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The  RNA samples were isolated according to the method described by Liu et al. (2009)

value: The flavode of the citrus  at 170 days after flowering

tag: cultivar

value: Citrus. reticulata cv. Suavissima


title: MT170DAF, biological rep1

tag: tissue


title: RMS394

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS392

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: WT170DAF, biological rep1

description: Gene expression data from the flavode of the wild type citrus  at 170 days after flowering


title: RMS389

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: Pulmonary endothelial cells_CLP_Rep 3

city: Aurora

first: Kaori

last: Oshima

state: CO

address: 12700 E 19th Ave Research Complex 2 Room 9480A

institute: University of Colorado

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45C on Mouse Clariom D Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing:
CEL Files were generated using GeneChip Command Console Software.  The data were analyzed with Expression Console Analysis Software using RMA Gene expression Tools with the default analysis setting and global scaling as normalization method.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

source_name: Pulmonary endothelial cells from cecal ligation and puncture-operated mouse, 48 hrs post surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng Total RNA (Expression Analysis Technical Manual. 2001 Affymetrix).

growth_protocol: Adult male mice (8-10 weeks) were purchased from the Jackson Laboratory and kept in the University animal facility for at least a week for acclimation.

extract_protocol: Total RNA was performed according to the manufacturer's instructions (RNeasy Mini kit, Qiagen).

treatment_protocol: Animals were subjected to either sham or cecal ligation and puncture surgeries. Forty-eight hours later, the whole lung was harvested, minced, and digested with collagenase type II (Worthington Biochemical Corporation) , Dispase I (Sigma-Aldrich) and DNase I (Qiagen). Red blood cells in the samples were lysed with ACK lysing buffer (Gibco) and cells were washed with PBS+ 4% FBS and stained with  anti-mouse CD31-APC antibody (Clone:390, eBioscience) and anti-mouse CD144-PE antibody (Clone: 11D4.1, BD Biosciences). Live (DAPI-), CD31+ CD144+ cells were sorted with FAC sorting and  immediately lysed with lysis buffer provided in RNeasy Mini kit (Qiagen).

value: adult; 8-10 weeks

tag: gender

value: male

value: cecal ligation and puncture-operated

value: lung

value: Pulmonary endothelial cells

tag: cell subtype


title: Pulmonary endothelial cells_CLP_Rep 2

tag: treatment


title: Pulmonary endothelial cells_Sham_Rep 3

source_name: Pulmonary endothelial cells from sham-operated mouse, 48 hrs post surgery

value: sham-operated


title: Pulmonary endothelial cells_Sham_Rep 2


title: Pulmonary endothelial cells_CLP_Rep 1


title: RMS386

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS387

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: WT170DAF, biological rep2


title: RMS385

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: Pulmonary endothelial cells_CLP_Rep 4


title: Pulmonary endothelial cells_Sham_Rep 1


title: RMS383

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS376

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS375

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS379

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS382

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS381

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS378

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS377

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS369

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS371

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS374

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS370

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS380

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS362

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS365

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS354

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS353

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS350

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS346

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS349

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS345

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS348

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS343

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS339

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS341

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS337

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS332

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS325

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS335

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS321

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS323

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS318

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS309

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS312

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS307

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS295

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS291

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS282

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS278

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS296

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS284

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS330

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS276

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS275

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS268

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS271

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS266

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS267

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS263

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS256

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS326

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS253

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS260

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS255

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS244

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS248

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS241

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS297

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS226

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS223

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS225

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS221

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS214

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS209

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS205

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS211

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS199

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS198

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS212

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS201

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS192

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS194

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS196

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS193

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS179

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS174

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS175

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS229

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS178

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS182

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS159

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS231

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS165

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS158

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS157

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS302

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS154

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS155

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS219

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS153

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS152

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS150

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS183

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS148

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS149

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: KO_siEri1_5.8S

city: Boston

first: Aref

last: Ebrahimi

state: MA

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

data_processing:
Grep read files by adapter and the gene-specific primer used for amplification.
Using the method published by Pirouz et al. (DOI 10.1016/j.ymeth.2018.10.024) the regions of interest were quantified.

source_name: 5.8S rRNA in siEri1_treated Dis3l2 KO mESCs

growth_protocol: mouse embryonic stem cells (mESCs) were cultured on gelatin-coated dishes and fed by LIF/serum medium.

extract_protocol:
input and Dis3l2-bound RNAs after immunoprecipitation of FLAG-tagged mutant Dis3l2 protein (RIP) were extracted using Trizol/chloroform and precipitated by isopropanol.
Using the method published by Pirouz et al. (DOI 10.1016/j.ymeth.2018.10.024) the regions of interest were amplified by PCR and cloned for MiSeq.

treatment_protocol: gene manipulations (by CRISPR/Cas9 or specific siRNAs) are indicated for each samples.

value: TC1 mESCs


title: RMS147

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: KO_siCTRL_5.8S

source_name: 5.8S rRNA in siCTRL_treated Dis3l2 KO mESCs


title: WT_siCTRL_5.8S

source_name: 5.8S rRNA in siCTRL_treated Dis3l2 WT mESCs


title: KO_siExosc10

source_name: 5.8S-ITS2 rRNA in siExosc10_treated Dis3l2 KO mESCs


title: RMS146

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS156

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: WT_siExosc10

source_name: 5.8S-ITS2 rRNA in siExosc10_treated Dis3l2 WT mESCs


title: RMS144

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: WT_siExosc3

source_name: 5.8S-ITS2 rRNA in siExosc3_treated Dis3l2 WT mESCs


title: RMS143

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: KO_siExosc3

source_name: 5.8S-ITS2 rRNA in siExosc3_treated Dis3l2 KO mESCs


title: 28S_IP

source_name: 28S rRNA in FLAG-mutant Dis3l2 RIP sample from Dis3l2 KO mESCs


title: RMS142

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: KO_siCTRL

source_name: 5.8S-ITS2 rRNA in siCTRL_treated Dis3l2 KO mESCs


title: 28S_input

source_name: 28S rRNA in input sample from Dis3l2 KO mESCs


title: 5S_IP

source_name: 5S rRNA in FLAG-mutant Dis3l2 RIP sample from Dis3l2 KO mESCs


title: RMS145

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS139

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS138

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS151

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: RMS140

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: WT_siEri1_5.8S

source_name: 5.8S rRNA in siEri1_treated Dis3l2 WT mESCs


title: RMS141

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)


title: 5.8S_IP

source_name: 5.8S rRNA in FLAG-mutant Dis3l2 RIP sample from Dis3l2 KO mESCs


title: RMS136

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)

source_name: Skin


title: 5.8S_input

source_name: 5.8S rRNA in input sample from Dis3l2 KO mESCs


title: RMN063

description:
SMARTSeq2
mRNA

data_processing:
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) were calculated using edgeR.
Genome_build: mm7
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values for each Sample.

source_name: Neutrophils

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation kit according to manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bioanalyser for quality assessment.
cDNA libraries were prepared using 2ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol described in Picelli et al., 2014 (Nature Protocols, volume 9, pages 171-181) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit.

value: Neutrophils


title: RMN062

description:
SMARTSeq2
mRNA


title: WT_siCTRL

source_name: 5.8S-ITS2 rRNA in siCTRL_treated Dis3l2 WT mESCs


title: RMN060

description:
SMARTSeq2
mRNA


title: RMN061

description:
SMARTSeq2
mRNA


title: genomic DNA from CB-317

type: genomic

city: Kaohsiung

first: Jen-Chieh

last: Chang

address: 123 Ta-Pei Road, Niaosong

department: Department of Medical Research

institute: Kaohsiung Chang Gung Memorial Hospital

description:
With PTS sample
1842787055_R004_C012

hyb_protocol: Bisulfite conversion of DNA samples was done using the EZ DNA methylation kit (Zymo Research Co., Orange, CA), then amplified, fragmented and hybridized to the Illumina GoldenGate Methylation Cancer Panel I array using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting in Illumina BeadScan software (version 3.5.49)

data_processing: Average normailization in Illumina BeadStudio software (version 3.1.3.0) with Methylation Analysis Module (version 3.2.0)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Umbilical cord blood leukocytes were subjected to DNA extraction using the Gentra Purgene kit (Qiagen Inc., Valencia, CA) according to standard instructions

value: Umbilical cord blood

value: Female

tag: group

value: paternal tobacco smoke


title: genomic DNA from CB-134

description:
With PTS sample
1842787055_R004_C003


title: genomic DNA from CB-49

description:
With PTS sample
1842787055_R004_C011

value: Male


title: RMN058

description:
SMARTSeq2
mRNA


title: RMN059

description:
SMARTSeq2
mRNA


title: 5S_input

source_name: 5S rRNA in input sample from Dis3l2 KO mESCs


title: genomic DNA from CB-105

description:
Without PTS sample
1842787055_R005_C005

value: Without paternal tobacco smoke


title: genomic DNA from CB-118

description:
With PTS sample
1842787055_R004_C002


title: genomic DNA from CB-65

description:
Without PTS sample
1842787055_R005_C002


title: genomic DNA from CB-210

description:
With PTS sample
1842787055_R005_C007


title: genomic DNA from CB-275

description:
With PTS sample
1842787055_R005_C006


title: genomic DNA from CB-74

description:
Without PTS sample
1842787055_R005_C004


title: RMS137

description:
mRNA
Single Cell RNA-Seq (Fluidigm C1)

value: Propionibacterium acnes infection


title: RMN056

description:
SMARTSeq2
mRNA


title: RMN055

description:
SMARTSeq2
mRNA


title: genomic DNA from CB-234

description:
Without PTS sample
1842787055_R005_C001


title: genomic DNA from CB-71

description:
Without PTS sample
1842787055_R005_C003


title: genomic DNA from CB-647

description:
Without PTS sample
1842787055_R004_C009


title: genomic DNA from CB-92

description:
Without PTS sample
1842787055_R004_C007


title: genomic DNA from CB-456

description:
Without PTS sample
1842787055_R004_C008


title: genomic DNA from CB-874

description:
Without PTS sample
1842787055_R004_C006


title: RMN054

description:
SMARTSeq2
mRNA


title: genomic DNA from CB-446

description:
Without PTS sample
1842787055_R004_C004


title: genomic DNA from CB-384

description:
Without PTS sample
1842787055_R004_C005


title: RMN057

description:
SMARTSeq2
mRNA


title: genomic DNA from CB-245

description:
Without PTS sample
1842787055_R004_C001


title: RMN053

description:
SMARTSeq2
mRNA


title: RMN052

description:
SMARTSeq2
mRNA


title: genomic DNA from CB-230

description:
Without PTS sample
1842787055_R004_C010


title: Cre-BMAL KO_M_3

city: Bern

first: Emanuele

last: Pignatti

address: Freiburgstrasse 15

country: Switzerland

institute: University of bern

data_processing:
RNA sequencing was performed on an Illumina NextSeq 500 sequencing platform with single-end 75-bp reads.
All samples were processed using an RNA-Seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org).
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Adapter sequences, other contaminant sequences such as polyA tails, and low-quality sequences with PHRED quality scores <5 were trimmed from reads using atropos (Didion, Martin, and Collins 2017).
Trimmed reads were aligned to UCSC build mm10 of the Mus musculus genome, augmented with transcript information from Ensembl release GRCm38 using star (Pertea et al. 2016).
Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (e.g., alignments in known transcripts and introns), complexity, and other quality checks using a combination of FastQC and Qualimap(García-Alcalde et al. 2012), MultiQC(Ewels et al. 2016) and custom code within the bcbio-nextgen pipeline.
Counts of reads aligning to known genes were generated by featureCounts(Liao, Smyth, and Shi 2014).
In parallel, Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon (Patro et al. 2017).
Normalization at the gene level was called with DESeq2(Liao, Smyth, and Shi 2014; Patro et al. 2017; Love, Huber, and Anders 2014), preferring to use counts per gene estimated from the Salmon quasialignments by tximport (Liao, Smyth, and Shi 2014; Patro et al. 2017; Love, Huber, and Anders 2014; Soneson, Love, and Robinson 2015).
The bcbioRNASeq package was used to load all the data from the bcbio-nextgen pipeline and QC (https://doi.org/10.12688/f1000research.12093.1), and the DEGreport Bioconductor package was used for clustering analysis (10.18129/B9.bioc.DEGreport).
DESeq2 was used for differentially expression analysis.
Significantly differentially expressed genes were determined using the following cutoff criteria: Fold change > 1.5 or < 0.6, adjusted p-value > 0.05, base mean > 50. P values were multiple test corrected using the Benjamini-Hochberg method.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include Ensembl Gene ID, gene name, normalized expression values

source_name: Adrenal Gland

extract_protocol:
Total RNA was extracted from whole adrenals using a Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA) following the manufacturer’s instructions.
Libraries were prepared using a TrueSeq RNA Library Prep Kit (Illumina Inc., San Diego, CA).

value: Adrenal Gland

value: 2.9 months

tag: genotype

value: SCC::Cre_BMAL1 KO

tag: Sex

value: M


title: Cre-BMAL KO_M_2

value: 3.3 months


title: genomic DNA from CB-21

description:
Without PTS sample
1842787055_R003_C012


title: Cre-CTRL_M_5


title: Cre-CTRL_M_6


title: RMN050

description:
SMARTSeq2
mRNA


title: Cre-CTRL_M_4

value: 3.1 months


title: Cre-CTRL_M_2

value: 4.6 months


title: RMN049

description:
SMARTSeq2
mRNA


title: 136_RSJ_replicate4

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description:
Gene expression in RSJ of 136
136_R4

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Quantile normalization and log2 transformation was performed for all raw microarray data using the R package “Agi4x44PreProcess”. All probes with signal within 95% confidence interval of the signal of negative control probes were discared from down-stream analysis.  All replicated probes were averaged.

organism: Nicotiana attenuata

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata EV and ir-max2 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: In the early flowering stage, pith of root-shoot-junction was harvested from each line.

value: root-shoot-junction

tag: line


title: 136_RSJ_replicate2

description:
Gene expression in RSJ of 136
136_R2


title: 136_RSJ_replicate3

description:
Gene expression in RSJ of 136
136_R3


title: Cre-CTRL_M_1

value: 4.7 months


title: RMN048

description:
SMARTSeq2
mRNA


title: Cre-BMAL KO_F_5

value: 2.4 months

value: F


title: 107_RSJ_replicate4

description:
Gene expression in RSJ of 107
107_R4


title: 107_RSJ_replicate3

description:
Gene expression in RSJ of 107
107_R3


title: 136_RSJ_replicate1

description:
Gene expression in RSJ of 136
136_R1


title: Cre-BMAL KO_F_4


title: 107_RSJ_replicate2

description:
Gene expression in RSJ of 107
107_R2


title: Cre-BMAL KO_F_1

value: 3.4 months


title: Cre-BMAL KO_M_1

value: 3.7 months


title: Cre-BMAL KO_M_4


title: RMN051

description:
SMARTSeq2
mRNA

value: Neutrophils


title: Cre-CTRL_F_4

value: 1.5 months


title: Cre-CTRL_M_3


title: RMN047

description:
SMARTSeq2
mRNA


title: EV_RSJ_replicate4

description:
Gene expression in RSJ of EV
EV_R4

value: wild type


title: Cre-CTRL_F_5


title: Cre-BMAL KO_F_3

value: 2.6 months


title: RMN046

description:
SMARTSeq2
mRNA

value: Propionibacterium acnes infection


title: Cre-BMAL KO_F_2

value: Adrenal Gland

value: 2.7 months


title: M1T1DTK6

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

description: Rnase-free Dnase treatment

data_processing:
Primary sequencing data that produced by Illumina Hiseq 4000, called as raw reads, were subjected to quality control to determine if resequencing step is needed. After QC, raw readere were filtered into clean reads which were then aligned to reference sequence Streptococcus pyogenes  GenBank file: NC_007297.2:Various software analysis were applied. Sequence mapping to a reference sequence was done using the software Bowtie2 (ver 2.2.3).Differential gene expression analysis of samples with bioreplicates, without replicates and treated with special condition (deletion of gene) were anlyzed using  DEseq (ver 1.10.1), DEGSeq (ver 1.12.0) and EdgeR (ver 30.8) softwares respectively (Anders, S. et al [2015] HTSeq--a Python framework to work with high-throughput sequencing data.Bioinformatics, 31:166-169; Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data.(DEseq) Genome Biol.11:R106;   Anders, S. and Huber, W. (2012). Differential expression of RNA-Seq data at the gene level-the DESeq package.(DESeq);   and Wang, L.Feng, Z .Wang, X.Z hang, X. (2010). DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics.(DEGseq), Bioinformatics 26:138-138.
Genome_build: Streptococcus_pyogenes.NC_007297.2
Supplementary_files_format_and_content: *xls…..DEGS and RPKM, Pvalue and Padj (qval), start/stop codon, protein name geneID/locus tag etc.

organism: Streptococcus pyogenes

source_name: Late-log phase culture

growth_protocol: All S. pyogenes cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.4) i.e. till late log phase. The cultures were then centrifuges at 4oC  and washed once with sterile autoclaved PBS. The cells were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
Total RNA was extracted using  Norgen RNA isolation kit (canada).The high quality total RNA samples were obtained by RNase-free DNase treatment.
The samples were then sent to Novogene Co. The RNA purity, integrity and quantification were measured using Nanodrop, Qbit and agilent 2100.  After total RNA sample QC, Ribo-zero kits were used to remove rRNAs, then fragmentation buffer were added to fragment the mRNAs. Using random hexamers as primers, the mRNA fragments were reverse-transcribed to single stranded cDNAs. After the systhesis of single stranded cDNAs, buffer, dNTPs (in which dTTP were replaced by dUTP), DNA polymerase I and RNase H were applied to systhesis the complementary cDNA strands. The double stranded cDNAs were purified using AMPure XP beads. The double stranded cDNAs were end-repaired, polyadenylated, ligated with adapter squences and size-selected using AMPure XP beads. Then the uracil containing strands were degraded by USER Enzyme, and the remained strands were amplified using PCR and purified using AMPure XP beadsd. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM)..Library were sequenced using IlluminaHiseq 4000 HWI_ST1276 as instrument identifier and C1162ACXX as flow cell ID.

treatment_protocol: Using pFW6 vector, S. pyogenes mutants lacking SP-TyK were derived. The washed concentrated bacterial pellet suspension was treated with phage-lysin to lyse the bacterial cells.

value: <delta>TyK mutant

tag: sample type

value: M1T15448 strain lacking-SP-TyK


title: input DNA

city: Beijing

first: Bo

last: Huang

address: #5 Dong Dan San Tiao

department: Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

data_processing:
Quality inspection:Fastqc version 0.11.8; trimmomatic version 0.39
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.3.5
peaks were called using macs2 version 2.1.2 with a FDR cutoff of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: bed files

source_name: CD8+ memory T cell

growth_protocol: OT-I splenocytes were activated with OVA257–264 peptides (200 ng ml-1) and IL-2 (10 ng ml-1) for 3 days. Subsequently, the cells were harvested, washed three times with RPMI1640, and further cultured in the presence of either IL-15 (10 ng ml-1) for an additional 4 days to program  CD8+ Tm cells.

extract_protocol:
ChIP-seq experiments for histone marks were carried out according to the instructions from the ChIP-IT High Sensitivity kit (Active Motif) using 4 ug H3K9bhb antibody.
All ChIP-seq datasets were sequenced with 2*150 bp paired-end reads. The total number of reads for each experiments is 70M.

treatment_protocol: IL-15-induced CD8+ Tm cells treated with BHB for 3 days

value: Spleen

value: CD8+ memory T cell


title: 107_RSJ_replicate1

description:
Gene expression in RSJ of 107
107_R1

value: root-shoot-junction


title: M1T1DTK5

description: Rnase-free Dnase treatment


title: M1T1DTK4

description: Rnase-free Dnase treatment


title: Cre-CTRL_F_2


title: EV_RSJ_replicate3

description:
Gene expression in RSJ of EV
EV_R3


title: S24hours.8

city: Bron

first: Sally

last: Badawi

address: 59 Bd Pinel

department: Biology

country: France

institute: Université Claude Bernard Lyon1

data_processing:
NCS 2.0.2 and RTA 2.4.11 Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.9.1 software, then mapped to mm10 whole genome using TopHat v2.1.0 software with default parameter (bowtie 2.2.9).
Signals were counted using htseq-count v0.6.0 software with unstranded parameter and tables gathering raw counts and RPK (Read Per Kilobase) were generated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including raw count values matrix for all samples

source_name: Heart

extract_protocol:
Hearts were removed and RNA was extracted using Tripure reagent solution and then purified by Rneasy minikit. NextFlex Rapid Directional mRNA-Seq (Bio-Scientific) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: time post surgery

value: 24 hours


title: H3K9bhb-ChIPseq


title: Cre-CTRL_F_1

value: F


title: EV_RSJ_replicate1

description:
Gene expression in RSJ of EV
EV_R1


title: S24hours.6


title: M1T1_WT-3

description: Rnase-free Dnase treatment

tag: genotype/variation

value: wild-type

value: M1T15448 strain with intact-SP-TyK


title: Cre-CTRL_F_3


title: EV_RSJ_replicate2

description:
Gene expression in RSJ of EV
EV_R2


title: M1T1_WT-1

description: Rnase-free Dnase treatment


title: S24hours.4


title: S24hours.3


title: M1T1_WT-2

description: Rnase-free Dnase treatment


title: AFB1 yeast cells expressing CYP1A2 and NAT2, 3

city: Albany

first: Michael

middle: Thomas

last: Fasullo

state: New York

address: 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description:
PCR amplified barcode tagged DNA
Sample_12
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx

data_processing:
Count barcodes by strain using recharacterized barcodes described in Smith, et al (2009).Quantitative phenotyping via deep barcode sequencing.Genome Research, 19: 1836-1842
Analyze barcode count data using TMM normalization, edger test method and 3 iterations via TCC package for R as described in Sun et al.(2013).TCC:an R package for comparing tag count data with robust normailzation strategies. BMC Bioinformatics,14:219
Genome_build: reads not aligned against a genome build. Barcode counts taken as described above.
Supplementary_files_format_and_content: Sample groupings C969C4AC and B5ULAN each have two MS Excel files: 1) with barcode counts in columns by sample (uptag counts per strain), 2) Separate Analysis output of TCC edger test performed on TMM normalized counts with 3 iterations.

organism: Saccharomyces cerevisiae

source_name: yeast cells expressing CYP1A2 and NAT2

extract_protocol: Equal amounts of PCR amplified barcodes were pooled for DNA sequencing using the illumina platform

tag: agent


title: AFB1 yeast cells expressing CYP1A2 and NAT2, 2

description:
PCR amplified barcode tagged DNA
Sample_11
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx


title: S24hours.2

tag: strain


title: S24hours.5


title: AFB1 yeast cells expressing CYP1A2 and NAT2, 1

description:
PCR amplified barcode tagged DNA
Sample_10
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx


title: DMSO control for AFB1 yeast cells expressing CYP1A2 and NAT2, 2

description:
PCR amplified barcode tagged DNA
Sample_8
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx

value: DMSO


title: Mouse PS3d

first: Lingling

last: Jiang

address: No 19, Xinjiekouwai Street

department: Beijing Key Laboratory of Gene Resource and Molecular Development

institute: Beijing Normal University

description:
processed data file: Mouse_PS3d_vs_PG3d_count.txt
assembled sequences of newGene: Mouse New_gene.fa

data_processing:
The clean reads in the FASTQ format were mapped to the Ensembl mouse genome (ftp://ftp.ensembl.org/pub/release-78/fasta/mus_musculus/) and chicken genome（ftp://ftp.ensembl.org/pub/release-75/fasta/gallus_gallus/） using Tophat2 software respectively.
The aligned results in the BAM/SAM format were further analyzed to trim the potential duplicate molecules and processed with Cufflinks software to evaluate the gene expression level
EBseq was used to estimate the differential gene expression in the comparisons
The differences in the abundance between the samples were analyzed according to the ratios of the FPKM values. Differentially expressed genes (DEGs) were defined as those with a false discovery rate (FDR) of <0.01, which was used to identify the threshold for the p value in multiple tests, along with a fold change of ≥1.5.
Genome_build: Ensembl mouse genome (ftp://ftp.ensembl.org/pub/release-78/fasta/mus_musculus/)
Supplementary_files_format_and_content: Excel files include RPKM values,genes and annotation for each Sample. Fasta files include assembled sequences of newGene.

source_name: Mouse PS3d_cochlea

extract_protocol:
The whole-mount cultured cochleae were pooled, dissolved in TRIzol (GeneCopoeia, America, E01010A) .Total RNA was extracted using a Total RNA Kit (TIANGEN, Beijing, DP419), and the quality was checked. RNA was stored at -80°C for RNA-seq.
Enriched mRNA was obtained from the RNA sample by using an NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Before RNA-seq, cDNA libraries were constructed according to the manufacturer’s instructions for Illumina mRNA-seq. Briefly, the enriched mRNA was fragmented and used to generate first-strand cDNA with random primers. Second-strand synthesis, end repair, poly-A tail addition and adaptor ligation were then conducted.

treatment_protocol: After the cochleae were treated with gentamicin or control media for 2 days, they were allowed to survive for another 1 day. The study included two groups: 3 d post-treatment with gentamicin (PG3d, the first treatment of gentamicin was considered time zero) and control.

value: Kunming

tag: developmental stage

value: post natal day 0-1

value: 3 days after treatment without gentamicin in vitro

value: cochlea


title: MB14: Vismodegib-treated Medulloblastoma

city: Chapel Hill

first: Timothy

last: Gershon

state: NC

address: 6129 NRB, 115 Mason Farm Rd

institute: University of North Carolina

description: Vismodegib Rep 5

data_processing:
bcl2fastq2 (v. 2.18)  software converts the base calls in the per-cycle BCL files to per-read FASTQ format.
Sequenced reads are tagged with cell & molecular barcodes, and trimmed with Drop-Seq Tools 1.13
Reads are aligned to mouse/human reference using STAR 5.4b
Mouse cells are selected, and are aligned only against mm10 using STAR 5.4b
Digital Expression Matrix was generated with Drop-Seq Tools 1.13
Data was filtered in Seurat 2.3.0
Genome_build: mm10, hg19
Supplementary_files_format_and_content: space-delimited files containing both single-cell gene expression counts and metadata.

source_name: Vismodegib-treated Medulloblastoma

extract_protocol:
Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) . Tumors or cerebella were dissected from isofluorane-anesthetized C57BL/6 or M-Smo mice and incubated in papain at 37C for 15 min. The tissue was then triturated, and the cells were spun down, resuspended, and a density gradient was formed with ovomucoid inhibitor. Lastly, cells were resuspended in HBSS with 6g/L glucose and diluted to approximately 100 cells/ul for Drop-seq
Libraries were prepared as described in Drop-seq protocol V3.1, with full details available online (http://mccarrolllab.com/dropseq/).

value: Vismodegib

value: Tumor


title: MB12: Vismodegib-treated Medulloblastoma

description: Vismodegib Rep 4


title: S24hours.7


title: S45minutes.8

value: 45 minutes


title: DMSO control for AFB1 yeast cells expressing CYP1A2 and NAT2, 1

description:
PCR amplified barcode tagged DNA
Sample_7
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx


title: S45minutes.7


title: MB09: Vismodegib-treated Medulloblastoma

description: Vismodegib Rep 3


title: AFB1 yeast cells expressing CYP1A2 , 3

description:
PCR amplified barcode tagged DNA
Sample_6
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx

source_name: yeast cells expressing CYP1A2


title: S45minutes.6


title: MB07: Vismodegib-treated Medulloblastoma

description: Vismodegib Rep 2


title: Citrus+Pp_48hr_Rep2 [GSA7_S16_L004]

city: Apopka

first: Zunaira

last: Afzal

state: FL

address: 2725 S Binion Road

department: Plant pathology

institute: University of Florida

data_processing:
Raw reads were assessed for quality using FastQC (v0.11.5) and the CLC Genomics Workbench 9.0 (Qiagen).
Paired end raw reads were processed for trimming the Illumina sequencing adaptors and low-quality reads with the Trim Galore software (version 0.4.3).
Samples containing Phytophthora parasitica reads were mapped to the P. parasitica INRA-310 genome  using the bowtie2 algorithm of tophat aligner. All pathogen reads were removed before moving further.
De novo assembly was generated  using Trinity to get a pooled  reference assembly for citrus.
RSEM and EdgeR were used for mapping and differential expression anlysis respectively.
Genome_build: Trinity was used for de novo assembly construction.
Supplementary_files_format_and_content: EdgeR results

organism:
Phytophthora nicotianae
Citrus sinensis x Citrus trifoliata

growth_protocol: P. parasitica strain 13-723A was isolated from citrus plants grown in local nursery in Florida. It was grown on 10% solid V8 medium plates at 12:12 hours dark:light cycle at 25 oC for 10 days. Plants were grown under controlled conditions  at 12:12 hours dark:light cycle at76 oF for 60 days.

extract_protocol:
Root samples from pathogen and mock treatments were collected at 24 hours post inoculation (hpi) and 48 hpi. Roots were rinsed in sterile water, immediately frozen in liquid nitrogen and stored at -80 0C until further use. Total RNA was extracted from frozen root tissues by using RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zoospores in P. parasitica were induced by applying dehydration stress on cultures from day 5 to day 7. On 10th day of culture, plates were flooded with sterilized water to induce release of zoospores. Zoospores were filtered through two to four layers of cheesecloth and adjusted to 105 cells/ml. Roots of sixty days old seedlings of Carrizo citrange rootstock grown under controlled conditions in sterilized soil were inoculated with 50 ml zoospore suspension. Mock inoculation was done using 50 ml sterilized water without zoospores.

value: infected

tag: tissues

value: roots

tag: time point

value: 48 hour


title: Citrus+Pp_48hr_Rep1 [GSA6_S15_L004]


title: AFB1 yeast cells expressing CYP1A2 , 2

description:
PCR amplified barcode tagged DNA
Sample_5
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx


title: DMSO control for AFB1 yeast cells expressing CYP1A2 and NAT2, 3

description:
PCR amplified barcode tagged DNA
Sample_9
B5ULANXX_Barcode_Counts_AFB1_DMSO.xlsx
B5ULANXX_AFB1_DMSO_Results.xlsx


title: Mouse PG3d

value: 3 days after treatment with gentamicin in vitro


title: MB04: Vismodegib-treated Medulloblastoma

department: Neurology

description: Vismodegib Rep 1


title: AFB1 yeast cells expressing CYP1A2 , 1

description:
PCR amplified barcode tagged DNA
Sample_4
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx


title: S45minutes.4

value: Heart


title: S45minutes.3


title: DMSO control for AFB1 yeast cells expressing CYP1A2, 3

description:
PCR amplified barcode tagged DNA
Sample_3
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx


title: Citrus+Pp_24hr_Rep2 [GSA4_S13_L004]

value: 24 hour


title: S45minutes.5


title: Citrus+Pp_0hr [GSA1_S10_L004]

value: 0 hour


title: MB15: Vehicle-treated Medulloblastoma

description: Vehicle Rep 5

source_name: Vehicle-treated Medulloblastoma

value: Vehicle


title: Citrus+Pp_24hr_Rep1 [GSA3_S12_L004]


title: S45minutes.2


title: DMSO control for AFB1 yeast cells expressing CYP1A2, 2

description:
PCR amplified barcode tagged DNA
Sample_2
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx


title: DMSO control for AFB1 yeast cells expressing CYP1A2, 1

description:
PCR amplified barcode tagged DNA
Sample_1
C69C4ACXX_Barcode_Counts_AFB1_DMSO.xlsx
C69C4ACXX_AFB1_DMSO_Results.xlsx


title: MB10: Vehicle-treated Medulloblastoma

description: Vehicle Rep 3


title: D39STK_3

description: Rnas- Free Dnase -treatment

data_processing:
Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads, were subjected to quality control to determine. if resequencing step is needed. After QC, raw readere were filtered into clean reads which were then aligned to reference sequence Streptococcus  pneumoniae GenBank file: AF026471 (NC_008533.1) with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al  Bioinformatics :Doi:10.1093/bioinformatics/btp336.  259(15)1966-1967]. the alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. gene ontology enrichment analysis were used for pathway enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool such as BOWTIE [Langmead B. et al (2009)genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml] was used as the SOAPaligner/SOAP2 performed better. Hence, the quantification analysis of gene expression was done with SOAPaligner/SOAP2. For significance of differential gene expression profile was determined based on the alogorithms as published [ Audic et al (1997) Gemome Res. 7:986-985]. We used FDR< 0.001 [Benjamini and Yekutieli(2001)Ann Statistics29:1165-1188.] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of differential gene expression. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].
Genome_build: NC_008533
Supplementary_files_format_and_content: *xls…..DEGS and RPKM, Pvalue and FDR etc

growth_protocol: All pneumococcal cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.6) i.e. till late log phase. The cultures were then centrifuges at 4oC  and washed once with sterile autoclaved PBS. The cell were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
Total RNA was extracted using  Norgen RNA isolation kit (canada).
The high quality total RNA samples were obtained by DNase treatment. The samples were then sent to BGI Americas. rRNA was removed from the total RNA samples.cDNA was then made using mRNA as template. Short fragments were made by heat treatment and the they  were purified and resolved  with EB buffer for endrepairation and single nucleotide A ( adenine) addition. Short fragments were then connected to adapters. Subsequently, following agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification. All quality control (QC) steps i.e. for quatification and quality of sample library ABI bioanalyzer and ABI StepOnePlus realtime PCR system were used. Library were sequenced using IlluminaHiseq 2000.

treatment_protocol: Using  Janus cassette [Sung et al (2001) Appl. Environ. Microbiol. 67:5190-5196], S. pneumoniae D39-derived  mutant lacking the ser/thr phosphatase encoding gene phpP (stp) gene was derived as described previously [ Agarwal et al (2012).  Infect. Immun. 80:1361-1372]. The washed concentrated bacterial pellet suspension was treated with mutanolysin (lysozyme 1:10 diluted 20mg/ml) to lyse the bacterial cells.

value: <delta>StkP mutant

value: D39 lacking StkP and intact PhpP


title: S45minutes.1


title: S0minutes.8

value: 0 minutes


title: MB06: Vehicle-treated Medulloblastoma

description: Vehicle Rep 2


title: MB05: Vehicle-treated Medulloblastoma

description: Vehicle Rep 1


title: ModA18 OFF, rep1

city: Gold Coast

first: John

last: Atack

address: Gold Coast Campus

institute: Griffith University

description:
18_OFF_1
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt

data_processing:
Illumina bcl2fastq 2.20.0.422 pipeline.
Bowtie aligner (2.3.2) was used to map reads to the 84P36H1 genomic DNA sequence; accession number CP029621.
edgeR version 3.18.1 was used to perform differential expression analysis.
Genome_build: Haemophilus influenzae strain 84P36H1 genomic DNA sequence (CP029621.1).
Supplementary_files_format_and_content: modA18_gene_counts.txt: Tab-delimited text file includes abundance measurements.
Supplementary_files_format_and_content: modA18_C_ON.VS.OFF-all_genes.txt: Tab-delimited text file includes abundance measurements and expression differences modA18 ON vs. modA18 OFF.
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA18 ON vs. modA18 OFF

organism: Haemophilus influenzae

source_name: Non-typeable Haemophilus influenzae strain 84P36H1

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols.

value: ModA18 OFF

tag: presence or absence of methyltransferase

value: Absent


title: D39STK_2

description: Rnas- Free Dnase -treatment


title: WT05: P7 WT Cerebellum

description: WT Rep 5

organism: Mus musculus

source_name: P7 WT Cerebellum

value: WT

tag: tissue

value: Cerebellum


title: S0minutes.6


title: D39STK_1

description: Rnas- Free Dnase -treatment


title: MB13: Vehicle-treated Medulloblastoma

description: Vehicle Rep 4

value: Tumor


title: D39STP_3

description: Rnas- Free Dnase -treatment

value: <delta>PhpP mutant

value: D39 lacking PhpP and intact STkP


title: S0minutes.5


title: ModA18 OFF, rep3

description:
18_OFF_3
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt


title: D39STP_2

description: Rnas- Free Dnase -treatment


title: WT04: P7 WT Cerebellum

description: WT Rep 4


title: ModA18 ON, rep1

description:
18_ON_1
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt

value: ModA18 ON

value: Present


title: ModA18 ON, rep2

description:
18_ON_2
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt


title: ModA18 OFF, rep2

description:
18_OFF_2
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt


title: ModA15 OFF, rep3

description:
15_OFF_3
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt

data_processing:
Illumina bcl2fastq 2.20.0.422 pipeline.
Bowtie aligner (2.3.2) was used to map reads to the 10P129H1 genomic DNA sequence; accession number CP029620.
edgeR version 3.18.1 was used to perform differential expression analysis.
Genome_build: Haemophilus influenzae strain 10P129H1 genomic DNA sequence (CP029620.1).
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences modA15 ON vs modA15 OFF
Supplementary_files_format_and_content: modA15_gene_counts.txt: Tab-delimited text file includes abundance measurements.
Supplementary_files_format_and_content: modA15_C_ON.VS.OFF-all_genes.txt: Tab-delimited text file includes abundance measurements and expression differences modA15 ON vs. modA15 OFF.

source_name: Non-typeable Haemophilus influenzae strain 10P129H1

value: ModA15 OFF


title: S0minutes.3

value: Heart


title: WT03: P7 WT Cerebellum

description: WT Rep 3


title: WT02: P7 WT Cerebellum

description: WT Rep 2


title: ModA15 OFF, rep2

description:
15_OFF_2
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt


title: WT01: P7 WT Cerebellum

description: WT Rep 1


title: D39STP_1

description: Rnas- Free Dnase -treatment


title: D39WT_3

description: Rnas- Free Dnase -treatment

value: wild-type

value: Intact PhpP and StkP


title: S0minutes.2


title: ModA15 OFF, rep1

description:
15_OFF_1
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt


title: ModA18 ON, rep3

description:
18_ON_3
processed data file: modA18_gene_counts.txt
processed data file: modA18_C_ON.VS.OFF-all_genes.txt


title: S0minutes.7


title: S0minutes.1


title: ModA15 ON, rep3

description:
15_ON_3
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt

value: ModA15 ON


title: D39WT_2

description: Rnas- Free Dnase -treatment


title: S0minutes.4


title: ModA15 ON, rep2

description:
15_ON_2
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt


title: Chicken PG3d

description:
processed data file: Chicken PS3d VS PG3d count.xlsx
assembled sequences of newGene: Chicken.newGene.longest_transcript.fa

organism: Gallus gallus

source_name: Chiken PS3d_cochlea

value: post natal day 6-8

value: 3 days after treatment with gentamicin in vivo

value: cochlea


title: Citrus_NOTinfected_48hr [GSA5_S14_L004]

organism: Citrus sinensis x Citrus trifoliata

value: non infected

value: roots

value: 48 hour


title: D39WT_1

description: Rnas- Free Dnase -treatment


title: Chicken PS3d

value: 3 days after treatment with physiological saline in vivo


title: Citrus_NOTinfected_24hr [GSA2_S11_L004]

value: 24 hour


title: ModA15 ON, rep1

description:
15_ON_1
processed data file: modA15_gene_counts.txt
processed data file: modA15_C_ON.VS.OFF-all_genes.txt