title: IBC_H3K27me3_Std_PAT-ChIP

city: Fano (PU)

first: Stefano

last: Amatori

state: PU

address: Via Arco d'Augusto, 2

department: Biomolecular Sciences

institute: University of Urbino

description: H3K4me3 bedgraph files for BA processed with standard PAT-ChIP

data_processing:
Reads were aligned to hg19 using 'bowtie’ (version 0.6.2-r126).
Unmapped reads, reads with a MAPQ smaller than 1 and duplicate reads were removed using samtools (version 0.1.18).
Mapped sequence reads were extended to 200 bp using deepTools (version 2.5.4).
Peaks were called using MACS2 software from Galaxy browser (http://usegalaxy.com - bdgpeakcall function to call narrow peaks from H3K4me3 and H3K27ac tracks and MACS2 bdgbroadcall function for broad peaks from H3K27me3).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files containing tracks and bedgraph files containing called peaks

source_name: FFPE tissue

extract_protocol:
Chromatin was extracted from FFPE sections of 10 µm thickness using the standard PAT-ChIP protocol
ChIP DNA was blunt-ended and phosphorylated, and a single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to adapters that have a single-base 'T' overhang using enzymes and reagents from NEB (New England Biolabs). The ligation products were purified and size-selected by Agencourt AMPure XP beads (Beckman Coulter). Purified DNA was PCR-amplified with PfuUltra II Fusion HS DNA Polymerase (Agilent Technologies) to enrich for fragments that have adapters on both ends. The final purified product was then quantitatively and qualitatively checked on Bioanalyzer 2100 (Agilent Technologies). Libraries with distinct adapter indexes were multiplexed (1/5 libraries per lane) and after cluster generation on FlowCell were sequenced for 50 bases in the single read mode on a HiSeq 2000 sequencer (Illumina Inc.).

value: Invasive breast carcinoma

tag: antibody


title: HT1912011248_MCF712h_COL18

status: Public on Nov 20 2018

type: SRA

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

country: China

institute: University of Macau

library_source: transcriptomic

data_processing:
For processing the HT samples, demultiplexing was performed using Fluidigm’s HT Demultiplexer Perl script (available on series record).
cell barcode is included in the R1 reads.
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: MCF7_HT_fpkm.txt: tab-delimited text files include FPKM values for each single cell
Supplementary_files_format_and_content: HT_barcodes.txt: tab-delimited text files include cell barcodes
Supplementary_files_format_and_content: demultiplex_perl_script.tar: tar archive contains perl script files include Fluidigm’s HT Demultiplexer Perl script

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MCF-7 ERα-positive human breast cancer cell lines were obtained from ATCC and maintained in DMEM and RPMI 1640 media (Gibco), respectively. Both media were supplemented with 5 % fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: Nextera XT Index Kit v2 (96 Indices, 384 Samples) is used for C1-HT.

treatment_protocol: Three days prior to E2 stimulation, MCF-7 cells were transferred into phenol-red free DMEM/F12 and RPMI media (Gibco), respectively. Both media were supplemented with 5 % charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or E2 at 2 time points (0 and 12 h), before being dissociated and triturated into single-cell suspensions for single-cell analyses.

tag: tissue

value: breast

tag: time

tag: cell line


title: HT1912011248_MCF712h_COL11


title: HT1912011248_MCF712h_COL16


title: HT1912011248_MCF712h_COL15


title: HT1912011248_MCF712h_COL14


title: wt-CNS-ChP-5

type: RNA

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

description: growth protocol: ND

hyb_protocol: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

molecule: total RNA

organism: Mus musculus

source_name: Central nervous system

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 24h IVT

growth_protocol: Maintained under normal mouse chow (ND)

extract_protocol: Qiagen RNEasy Lipid Tissue Mini kit, standard protocol

treatment_protocol: Fresh-frozen nervous system tissues were isolated by laser capture microdissection and taken up in Trizol

tag: strain

value: Choroid plexus

tag: genotype

value: wild-type

tag: gender

value: male

tag: age

value: 78 weeks


title: HT1912011248_MCF712h_COL12


title: wt-CNS-ChP-2

description: growth protocol: ND


title: wt-CNS-ChP-1

description: growth protocol: ND


title: HT1912011248_MCF712h_COL13


title: IBC_H3K27ac_Std_PAT-ChIP

country: Italy

library_source: genomic

molecule: genomic DNA


title: HT1912011248_MCF712h_COL10


title: apoE-CNS-ChP-3

description: growth protocol: ND

value: apoE-/-


title: wt-CNS-ChP-4

description: growth protocol: ND


title: apoE-CNS-ChP-4

description: growth protocol: ND


title: apoE-CNS-ChP-1

description: growth protocol: ND


title: HT1912011248_MCF712h_COL09


title: HT1912011248_MCF712h_COL03


title: HT1912011248_MCF712h_COL07


title: HT1912011248_MCF712h_COL04


title: HT1912011248_MCF712h_COL08


title: HT1912011248_MCF712h_COL17


title: HT1912011248_MCF712h_COL06


title: HT1912011248_MCF712h_COL05


title: HT1912011248_MCF712h_COL02


title: HT1912011246_MCF70h_COL19


title: apoE-CNS-ChP-2

description: growth protocol: ND


title: HT1912011248_MCF712h_COL01


title: wt-CNS-ChP-3

description: growth protocol: ND


title: HT1912011246_MCF70h_COL17


title: HT1912011246_MCF70h_COL16


title: HT1912011246_MCF70h_COL15


title: HT1912011246_MCF70h_COL18


title: HT1912011246_MCF70h_COL13


title: HT1912011246_MCF70h_COL14


title: HT1912011246_MCF70h_COL10


title: HT1912011246_MCF70h_COL11


title: HT1912011246_MCF70h_COL09


title: HT1912011246_MCF70h_COL03


title: HT1912011246_MCF70h_COL20


title: HT1912011246_MCF70h_COL07


title: HT1912011246_MCF70h_COL06


title: HT1912011246_MCF70h_COL08


title: HT1912011246_MCF70h_COL05


title: HT1912011246_MCF70h_COL02


title: HT1912011246_MCF70h_COL01


title: C2-rFVIII

city: Waltham

first: Katalin

last: Kis-Toth

state: MA

address: 225 Second Avenue

country: USA

institute: Bioverativ

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were aligned with STAR (version 2.4.0c) and genes annotated in Gencode v18 were quantified with featureCounts (v1.4.3-p1).
Normalization and differential expression was done with the Bioconductor package DESeq2.
Genome_build: GRCh37.p12
Supplementary_files_format_and_content: Text files include RPKM values for each Sample.

source_name: macrophage_recombinant FVIII

growth_protocol: Human monocytes were isolated from PBMC and differentiated to macrophages by adherence for 24h prior treatment.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy kit and rRNA was removed using Epicentre Ribo-Zero kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Macrophages were treated with 200 nM of IgG1, rFVIII or rFVIIIFc for 6h prior to RNA isolation.

tag: donor id

tag: cell type

value: monocyte-derived macrophage

tag: treatment

value: recombinant FVIII


title: C2-rFVIIIFc

source_name: macrophage_recombinant FVIIIFc

value: recombinant FVIIIFc


title: C2-IgG

value: IgG


title: C3-IgG


title: C3-rFVIIIFc


title: C3-rFVIII


title: C1-rFVIIIFc


title: HT1912011246_MCF70h_COL12


title: IBC_H3K27me3_ePAT-ChIP

description: H3K27me3 bedgraph files for BA processed with ePAT-ChIP

extract_protocol:
Chromatin was extracted from FFPE sections of 10 µm thickness using the ePAT-ChIP protocol
ChIP DNA was blunt-ended and phosphorylated, and a single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to adapters that have a single-base 'T' overhang using enzymes and reagents from NEB (New England Biolabs). The ligation products were purified and size-selected by Agencourt AMPure XP beads (Beckman Coulter). Purified DNA was PCR-amplified with PfuUltra II Fusion HS DNA Polymerase (Agilent Technologies) to enrich for fragments that have adapters on both ends. The final purified product was then quantitatively and qualitatively checked on Bioanalyzer 2100 (Agilent Technologies). Libraries with distinct adapter indexes were multiplexed (1/5 libraries per lane) and after cluster generation on FlowCell were sequenced for 50 bases in the single read mode on a HiSeq 2000 sequencer (Illumina Inc.).


title: IBC_H3K27ac_ePAT-ChIP

description: H3K27ac bedgraph files for BA processed with ePAT-ChIP


title: IBC_H3K4me3_Std_PAT-ChIP


title: IBC_H3K4me3_ePAT-ChIP

description: H3K4me3 bedgraph files for BA processed with ePAT-ChIP


title: C1-IgG


title: Fitness_in vivo_-Dox_rep2

type: genomic

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

description:
Sample 10
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.

hyb_protocol: The Cy3- and Cy5-labeled DNAs were mixed in 50 µl of DIG Easy Hyb solution (Roche) and hybridized overnight at 24°C to a barcode microarray.

scan_protocol: Images of Cy5 and Cy3 fluorescence intensities were generated by scanning the barcode arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were subsequently analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into Arraypipe 2.0 (http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl). Following background subtraction, spot filtering and bad-spot flagging, global signal intensities were normalized using Loess normalization. Replicate slides were combined and Z-scores and P-values (standard Student’s t-test) were calculated.

organism: Candida albicans

source_name: Inoculum made of Candida albicans pooled strains at a concentration of 5x10E7 cell/200 µl

label_protocol: A modified base [5-(3-aminoallyl)-dUTP] was included during PCR at a ratio of two 5-(3-aminoallyl)-dUTP molecules to three dTTP molecules. The PCR products were purified, and the DNA was labeled with either Cy3 (for the in vitro experiments, untreated control; for the in vivo experiments, inoculum) or Cy5 (for the in vitro experiment, Dox-treated samples; for the in vivo experiments, stools from dox-treated or dox-untreated mice) monoreactive NHS esters.

growth_protocol:
In vitro conditions: An aliquot (1.6 µl) from the frozen 50 OD600-unit strain-pool was used to inoculate 2 ml of YPD medium (starting OD600 = 0.0625) and grown at 30ºC with agitation (200 rpm) for 20 generations, in the absence or presence of 40 μg/ml doxycycline.
In vivo conditions: See treatment protocol.

extract_protocol:
In vitro fitness experiments: Genomic DNA was extracted using the MasterPure Yeast DNA Purification Kit (Epicentre) as per the manufacturer's instructions.
In vivo fitness experiments: Total genomic DNA from stools was extracted using FastDNA SPIN Kit for Feces according to the manufacturer’s instructions (MP Biomedicals, cat.# 6570). Barcodes were amplified from genomic DNA by PCR using common primers flanking each barcode sequence.

treatment_protocol:
In vitro: Absence or presence of 40 μg/ml doxycycline in culture medium (see growth protocol).
In vivo: Nine- to twelve-week-old female BALB/c mice (Charles River, L'Arbresle, France) were given drinking water containing 5% sucrose, 0.1 mg/ml gentamycin and 2 mg/mL streptomycin and was supplemented or not with 2 mg/ml doxycycline, during the course of the whole experiment (14 days). Mice were housed by groups of 3 individuals per cage and were inoculated by gavage with 5x10^7 C. albicans cells (in 200 µl 1X phosphate-buffered saline (PBS) solution) from 579-strain pools at day 4 post-antibiotic treatment. The remaining inoculum was directly used for genomic DNA extraction using the MasterPure Yeast DNA Purification Kit (Epicentre). Stool samples were collected at days 4 and 10 post-gavage, weighed and either i) homogenized then serially diluted in 1 ml 1X PBS (2 stool pellets) for CFU counting on YPD plates supplemented with 1 g/l chloramphenicol and 50 mg/l gentamycin or ii) directly processed (up to 500 mg of stool pellets) for genomic DNA extraction using FastDNA SPIN Kit for Feces according the manufacturer's instructions (MP Biomedicals, cat.# 6570).

tag: strain/background

tag: experiment type

value: in vivo

source_name: Stools produced from dox-untreated mice at day 10 post-gavage with an inoculum of Candida albicans pooled strains at a concentration of 5x10E7 cells/200 µl


title: Fitness_in vivo_-Dox_rep1

description:
Sample 9
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_-Dox_rep3

description:
Sample 11
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_-Dox_rep4

description:
Sample 12
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: C1-rFVIII


title: Fitness_in vitro_rep1

description:
Sample 1
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.

source_name: Candida albicans pooled strains, untreated, 20 generations, growth in YPD medium at 30ºC

value: in vitro

source_name: Candida albicans pooled strains, inducing conditions (+doxycycline), 20 generations, growth in YPD medium at 30ºC

value: doxycycline


title: Fitness_in vivo_+Dox_rep1

description:
Sample 4
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.

source_name: Stools produced from dox-treated mice at day 10 post-gavage with an inoculum of Candida albicans pooled strains at a concentration of 5x10E7 cells/200 µl


title: Fitness_in vitro_rep2

description:
Sample 2
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vitro_rep3

description:
Sample 3
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_+Dox_rep3

description:
Sample 6
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_+Dox_rep2

description:
Sample 5
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_+Dox_rep5

description:
Sample 8
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: Fitness_in vivo_+Dox_rep4

description:
Sample 7
Background strain is BWP17 (ura3-/-, arg4-/-, his1-/-) complemented for arg- and his- auxotrophies (his1-delta::hisG/HIS1, arg4-delta::hisG/ARG4) and carrying the pNIMX plasmid (ADH1/adh1::PTDH3-carTA::SAT1). The resulting strain is CEC2908, isogenic to CEC2907 described in Chauvel et al. 2012 PLOS ONE 7(9): e45912.


title: HT-144-ASO-SREBF1-S4-Rep-4

city: Charlestown

first: Su

last: Wu

address: Building 149 7-330, 13th Street

department: Cancer Center

institute: Mass General Hospital

description: polyadenylated mRNA

data_processing:
For RNA-Seq, Illumina sequencing reads (FASTQ files) were checked with FASTQC for quality control and then aligned to the human genome (GRCh38.94).
Genome index generation and sequence alignment were performed using STAR software (2.6.1a).
Sequence alignment were performed using STAR software (2.6.1a) with arguments including “--quantMode TranscriptomeSAM GeneCounts --twopassMode Basic”.
Genome_build: GRCh38.94
Supplementary_files_format_and_content: Tab-delimited files (*ReadsPerGene.out.tab) include gene counts generated by STAR from individual samples.

source_name: melanoma cell line HT-144

growth_protocol: Transfected HT-144 cells were cultured in 1% ITS medium. That is composed of RPMI-1640 medium with 1 x Insulin-Transferrin-Selenium (ITS-G, Thermo Fisher Scientific), 2 mM L-glutamine (Gibco) and 50 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
RNA samples were harvested and treated with RNase-free DNase (Qiagen). RNA quality was verified with the RNA ScreenTape (Agilent) on Agilent 2200 TapeStation (Agilent). mRNAs were isolated from total RNA for RNA library preparation using NEBNext® Poly(A) mRNA magnetic isolation module (NEB).
100 ng of purified mRNA was used for RNA-Seq library synthesis with NEBNext® Ultra™ directional RNA library prep kit for Illumina® (NEB). The final RNA-Seq libraries were quantified with KAPA Library Quantification Kit (KAPABiosystem). Adaptor indexed strand-specific RNA-Seq libraries were pooled and sequenced using the pair-end 75-bp per read setting for NextSeq® 500 High Output v2 Kit (150 cycles) on the NextSeq® 500 sequencer (Illumina).

treatment_protocol: HT-144 cells were transfected with ASOs (5 nM) or pooled siRNAs (50 nM) in 1% ITS medium for three days using Lipofectamine RNAiMAX transfection reagent (Thermo Fisher Scientific) and the reverse transfection protocol suggested by the manufacture.

value: Malignant Melanoma; Derived From Metastatic Site

value: ASO-4 for SREBF1


title: HT-144-ASO-Neg-Rep-4

description: polyadenylated mRNA

value: negative control ASO


title: HT-144-ASO-Neg-Rep-1

description: polyadenylated mRNA


title: HT-144-siNegative-Rep-4

description: polyadenylated mRNA

value: scramble siRNA


title: HT-144-ASO-SREBF1-S1-Rep-1

description: polyadenylated mRNA

value: ASO-1 for SREBF1


title: HT-144-ASO-SREBF1-S1-Rep-2

description: polyadenylated mRNA


title: HT-144-ASO-SREBF1-S4-Rep-3

description: polyadenylated mRNA


title: HT-144-siSREBF1-Rep-2

description: polyadenylated mRNA

value: pooled siRNA for SREBF1


title: HT-144-siSREBF1-Rep-3

description: polyadenylated mRNA


title: HT-144-ASO-SREBF1-S4-Rep-2

description: polyadenylated mRNA


title: HT-144-ASO-Neg-Rep-2

description: polyadenylated mRNA


title: HT-144-ASO-Neg-Rep-3

description: polyadenylated mRNA


title: HT-144-siSREBF1-Rep-1

description: polyadenylated mRNA


title: HT-144-ASO-SREBF1-S4-Rep-1

description: polyadenylated mRNA


title: HT-144-siNegative-Rep-1

description: polyadenylated mRNA


title: HT-144-siNegative-Rep-3

description: polyadenylated mRNA


title: HT-144-siNegative-Rep-2

description: polyadenylated mRNA


title: HT-144-ASO-SREBF1-S1-Rep-3

description: polyadenylated mRNA


title: HT-144-siSREBF1-Rep-4

description: polyadenylated mRNA


title: WT_rep2

city: Frankfurt am Main

first: Denise

last: Haslinger

address: Theodor-Stern-Kai 7

institute: University Hospital Frankfurt

description:
wtb
Protocol: MACE-seq

data_processing:
Sequencing on Illumina NextSeq 500, basecalling pipeline: bcl2fastq2 Conversion Software v2.19
Sequences were cleaned from duplicates (TrueQuant/UMI), bases with low sequencing quality and sequencing adapters were removed
The trimmed reads were mapped to ENSEMBL genome version Homo_sapiens.GRCh38.89 using Bowtie 2 version 2.2.4 with standard parameters
Expression analysis was performed by in-house scripts and DESeq2 (R package)
Genome_build: Homo_sapiens.GRCh38.89
Supplementary_files_format_and_content: csv with raw read counts

growth_protocol: WT, del268T, ins395A and eCtrl were seeded with a density of 2x10^4 cells/cm2 and harvested after 3 days of differentiation without media changes.

extract_protocol:
RNA of three biological replicates was extracted using the GeneJet RNA Purification Kit (Thermo Fisher Scientific) including DNase treatment. RNA integrity number (RIN) was analyzed using the LabChip GX system and only samples with RINs above 9.7 underwent further analysis.
MACE-Seq libraries were prepared by GenXPro GmbH Frankfurt am Main, Germany, using the “MACE-Seq Kit” and the provided software tool (http://tools.genxpro.net). Briefly, mRNA was captured by modified poly-T primers, cDNA was generated and fragmented to an average size of 350 bps. Adapters were ligated and the 3’ Ends amplified by PCR.

treatment_protocol: Differentiation medium: Neurobasal®-A medium supplemented with 1x GlutaMAX, 1x B-27 supplement (all Life Technologies), 10µM RA, 2mM cAMP (both Sigma Aldrich), 50ng/ml hBDNF (Immunotools), 1% Penicillin/Streptomycin (PAA) and 20mM KCl.

value: female

value: neuroblastoma

value: wild type

tag: differentiation day

value: 3day differentiation


title: WT_rep3

description:
wtc
Protocol: MACE-seq


title: HT-144-Mock-Rep-1

description: polyadenylated mRNA

value: mock


title: WT_rep1

description:
wta
Protocol: MACE-seq


title: HT-144-Mock-Rep-3

description: polyadenylated mRNA


title: eCtrl_rep2

description:
leer_2b
Protocol: MACE-seq

value: empty control vector


title: eCtrl_rep1

description:
leer_2a
Protocol: MACE-seq


title: HT-144-Mock-Rep-4

description: polyadenylated mRNA


title: HT-144-Mock-Rep-2

description: polyadenylated mRNA


title: ins395A_rep3

description:
a3_6c
Protocol: MACE-seq

value: QPRT-knockout


title: ins395A_rep2

description:
a3_6b
Protocol: MACE-seq


title: del268T_rep3

description:
a1_1c
Protocol: MACE-seq


title: ins395A_rep1

description:
a3_6a
Protocol: MACE-seq


title: del268T_rep1

description:
a1_1a
Protocol: MACE-seq


title: del268T_rep2

description:
a1_1b
Protocol: MACE-seq


title: WT_ATACseq_Treg1_thymus

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

description: naïve/unstimulated

data_processing:
Library strategy: ATAC-seq
After trimming adapter sequences with trim_galore (ver0.3.7), the sequences mapped using bwa mem (ver0.7.13).
Filtering out non-uniquely mapped reads by samtools (ver0.1.19) view -q 30
ChrM mapped reads and duplicated reads were eliminated by the picard-tools (ver1.92) MarkDuplicates function and samtool (ver0.1.19) rmdup functions.
Peak was called with macs2 (ver2.1.0)
Peaks below the IDR cutoff of 0.05 were selected
Genome_build: mm10
Supplementary_files_format_and_content: BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. (MACS2 narrowPeak file)

source_name: Thymus

extract_protocol:
Briefly, nuclei were isolated from 50,000 FACS sorted RFP+ Treg cells from reporter mice using a solution of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630.
Immediately following nuclei isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 45 min at 37o C. Transposed DNA fragments were purified using Qiagen MinElute Kit and PCR amplified using NEBNext High Fidelity 2x PCR master mix (New England Labs) with dual indexes primers (Illumina Nextera). The size distribution and molarity of the sequencing library were determined by using an Bioanalyzer analysis (High Sensitivity DNA chip, Agilent).

treatment_protocol: Naïve steady state mice of 20 weeks old bred in our SPF facility and thymuses were used as a source of donor Treg cells.

value: Foxp3+ CD4+ Treg cell

value: Il2ra WT


title: WT_ATACseq_Treg2_thymus

description: naïve/unstimulated


title: eCtrl_rep3

description:
leer_2c
Protocol: MACE-seq


title: Il2ramut/mut_ATACseq_Treg3_thymus

description: naïve/unstimulated

value: Il2ra mut/mut


title: Il2ramut/mut_ATACseq_Treg4_thymus

description: naïve/unstimulated


title: mouse_mef_7day_dox_RRBS_r1

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: Please note that r1 and r2 sample raw data bams were merged for CpG calling to create the mouse_mef_dox_noshRNA_RRBS.bed.

data_processing:
Raw sequencing reads were aligned to the mm9 build of the mouse genome using MAQ (H. Li, Ruan, & Durbin, 2008). We used custom Python scripts to call methylation at each CpG, computed as the ratio of methylated reads to total reads at that genomic position.
Genome_build: mm9
Supplementary_files_format_and_content: RRBS processed data column headers are: chromosome, start, end, (methylated reads / total reads), methylation score (0 - 1000), strand.

source_name: mouse embryonic fibroblasts (E13.5)

growth_protocol: MEFs were cultured in knockout Dulbecco's modified Eagle's medium (KD DMEM, Life Technologies) supplemented with 10% fetal bovine serum (Seradigm).

extract_protocol:
DNA was either harvested from mouse tissues, or from cultured MEFs.
Flash-frozen mouse tissues and cell pellets were lysed in 300-600µl DNA lysis buffer (10 mM Tris-HCl pD 8.0, 10mM EDTA, 10mM NaCl and 0.5% wt/vol SDS) supplemented with 50 ng/µl Dnase-free Rnase (Roche) and 1 ng/µl proteinase K (NEB) at 55°C overnight. After phenol:chloroform extraction and ethanol precipitation, DNA was resuspended in elution buffer (10 mM Tris-HCl pH 8.0, 1mM EDTA)
100 ng genomic DNA was used to make RRBS libraries as previously described (Boyle et al., 2012).

treatment_protocol: "Treatment time" refers to length of time that mice were treated for - either control (no doxycycline) or with doxycycline supplied in the drinking water. This was either from birth (0 months: 0M) to 1.5M, 0-3M or 3-6M, described in the sample name.

tag: strain background

tag: tissue/cell type

value: embryonic fibroblasts (E13.5)

tag: dnmt3b oe

value: yes

tag: treatment time

value: 7 days

tag: molecule subtype

value: Bisulfite-converted genomic DNA


title: mouse_cd4_0-3M_control_RRBS

source_name: mouse cd4+ blood cells

value: cd4+ blood cells

value: no

value: 3 months


title: mouse_cd8_0-3M_dox_RRBS

source_name: mouse cd8+ blood cells

value: cd8+ blood cells


title: mouse_mef_control_Eed_shRNA4_RRBS


title: mouse_mef_dox_Eed_shRNA5_RRBS


title: mouse_cd4_0-3M_dox_RRBS


title: mouse_mef_7day_dox_RRBS_r2


title: mouse_mef_control_Eed_shRNA5_RRBS


title: mouse_clp_0-3M_dox_RRBS

source_name: mouse CLP cells

value: CLP cells


title: mouse_cd8_0-3M_control_RRBS


title: mouse_mef_1day_dox_RRBS

value: 1 day


title: IL17SA10PL

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression data from PBMC samples obtained from Severe asthma

hyb_protocol: hybridized to Affymetrix HG U133+ PM GeneChips following standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw microarray gene expression data was normalized using RMA in R and subjected to several quality control procedures. Differentially expressed genes were identified using a linear modelling approach in the limma package in R and only genes with FDR corrected p-values < 0.05 for multiple testing (using the Benjamini-Hochberg method) were considered significant.

label: biotin

source_name: PBMC

label_protocol: standard Affymetrix protocol; RNA was isolated and reverse transcribed into cDNA using a High Capacity cDNA Reverse Transcription Kit with random hexamers. RT-qPCR was performed for each gene target in duplicate using Taqman Universal PCR Master Mix, No AmpErase UNG on 7900HT Fast Real-Time PCR System. GAPDH was used as a normalizer to obtain fold changes and t-tests were performed to determine significance. Thermal cycling conditions were 95˚C for 10 minutes followed by 40 cycles of 95˚C for 15 seconds and 60˚C for 1 minute.

growth_protocol: sample collection: Lung samples were obtained by hypertonic-saline sputum induction, bronchoscopy, bronchoalveolar lavage and endobronchial epithelial brushing as previously described (Hinks et al., 2015).

extract_protocol: RNA was isolated from the samples using the Absolutely RNA Nanoprep Kit. RNA quality was assessed using a Bioanalyzer 2100 and samples were hybridized to Affymetrix HG U133+ PM GeneChips

tag: disease state

value: Severe asthma

tag: tissue

value: PBMC

value: Male


title: WT_ATACseq_Treg3_thymus

description: naïve/unstimulated

tag: strain


title: Il2ramut/mut_ATACseq_Treg2_thymus

description: naïve/unstimulated

tag: genotype


title: mouse_mef_dox_Eed_shRNA4_RRBS


title: mouse_mpp_0-3M_control_RRBS

source_name: mouse MPP cells

value: MPP cells


title: mouse_hsc_0-3M_control_RRBS

source_name: mouse HSCs

value: HSCs


title: mouse_mpp_0-3M_dox_RRBS


title: mouse_hsc_0-3M_dox_RRBS


title: mouse_liver_3-6M_dox_RRBS_r3

source_name: mouse liver

value: liver


title: mouse_liver_3-6M_dox_RRBS_r4


title: mouse_liver_3-6M_control_RRBS_r4


title: mouse_liver_3-6M_dox_RRBS_r1


title: mouse_mef_7day_control_RRBS_r1

description: Please note that r1 and r2 sample raw data bams were merged for CpG calling to create the mouse_mef_control_noshRNA_RRBS.bed.


title: mouse_liver_3-6M_control_RRBS_r3


title: mouse_mef_7day_control_RRBS_r2


title: WT_ATACseq_Treg4_thymus

description: naïve/unstimulated

value: Foxp3+ CD4+ Treg cell

value: Il2ra WT


title: mouse_liver_3-6M_control_RRBS_r1


title: mouse_intestine_3-6M_dox_RRBS_r3

source_name: mouse intestine

value: intestine

value: yes


title: mouse_intestine_3-6M_control_RRBS_r3

value: Bisulfite-converted genomic DNA


title: mouse_intestine_3-6M_dox_RRBS_r2


title: mouse_intestine_3-6M_control_RRBS_r1


title: mouse_intestine_3-6M_dox_RRBS_r1


title: mouse_intestine_3-6M_control_RRBS_r2


title: mouse_kidney_3-6M_dox_RRBS_r2

source_name: mouse kidney

value: kidney


title: mouse_kidney_3-6M_dox_RRBS_r3


title: mouse_kidney_3-6M_dox_RRBS_r1


title: mouse_kidney_3-6M_control_RRBS_r4

value: no


title: mouse_liver_3-6M_control_RRBS_r2

value: 3 months


title: mouse_kidney_3-6M_control_RRBS_r3


title: mouse_kidney_3-6M_dox_RRBS_r4


title: mouse_kidney_3-6M_control_RRBS_r2


title: mouse_muscle_0-1.5M_dox_RRBS

source_name: mouse muscle

value: muscle

value: 1.5 months


title: mouse_lung_0-1.5M_dox_RRBS

source_name: mouse lung

value: lung


title: mouse_muscle_0-1.5M_control_RRBS


title: mouse_lung_0-1.5M_control_RRBS


title: mouse_liver_0-1.5M_control_RRBS


title: mouse_kidney_0-1.5M_dox_RRBS


title: mouse_intestine_0-1.5M_dox_RRBS


title: mouse_intestine_0-1.5M_control_RRBS


title: mouse_kidney_0-1.5M_control_RRBS


title: mouse_heart_0-1.5M_dox_RRBS

source_name: mouse heart

value: heart


title: mouse_monocytes_0-1.5M_dox_RRBS

source_name: mouse monocytes

value: monocytes


title: mouse_granulocytes_0-1.5M_control_RRBS

source_name: mouse granulocytes

value: granulocytes


title: mouse_granulocytes_0-1.5M_dox_RRBS


title: mouse_cd8_0-1.5M_dox_RRBS

value: cd8+ blood cells


title: mouse_cd8_0-1.5M_control_RRBS


title: Il2ramut/mut_SPCD4+thym_input_thymus

description:
SATB1 bound genomic DNA
naïve/unstimulated

data_processing:
Library strategy: ChIP-seq
After trimming adapter sequences with trim_galore (ver0.3.7), the sequences mapped using bwa mem (ver0.7.13).
Filtering out non-uniquely mapped reads by samtools (ver0.1.19) view -q 30
ChrM mapped reads and duplicated reads were eliminated by the picard-tools (ver1.92) MarkDuplicates function and samtool (ver0.1.19) rmdup functions.
Peak was called with macs2 (ver2.1.0) on read-1 sequences with merged (WT and MUT) input read 1 sequences.
Peaks below the IDR cutoff of 0.05 were selected
Genome_build: mm10
Supplementary_files_format_and_content: BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. (MACS2 narrowPeak file)

extract_protocol:
Cross-linked DNA was lysed in Farnham lysis buffer (5mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40), fragmented in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS in 1xPBS) using Bioruptor (Diagenode), and incubated overnight at 4_ with 100 µl of DynaBeads M-280 Sheep anti-Rabbit IgG magnet beads (Invitrogen) preincubated with 20 µg of anti-SATB1 antibody (Abcam, ab70004).  Beads were washed 5 times with LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40 and 1% sodium deoxycholate) and one time with 10mM Tris/0.1M EDTA. SATB1-bound DNA was then eluted from the beads and reverse cross-linked by incubating the beads pellet in 200 µl of IP elution buffer (1% SDS and 0.1 M NaHCO3) at 65_ overnight and further purified with MinElute PCR Purification Kit (QIAGEN)
The library was prepared using Accel-NGS 2S Plus DNA library kit according to the manufacturer's instructions

treatment_protocol: Naïve steady state mice of 6- 8 weeks old were bred in our SPF facility and lymph nodes used as a source of donor T cells.

value: Thymus

value: SP CD4 thymocytes

value: Il2ra mut/mut

tag: antibody

value: input

tag: gender

value: female

value: 6-8 weeks


title: mouse_b220_0-1.5M_dox_RRBS

source_name: mouse b220 blood cells

value: b220 blood cells

value: yes

value: Bisulfite-converted genomic DNA


title: mouse_b220_0-1.5M_control_RRBS

value: no


title: mouse_cd4_0-1.5M_dox_RRBS

value: cd4+ blood cells


title: Il2ramut/mut_SATB1 ChIPseq_SPCD4+thym2_thymus

source_name: Thymus

value: anti-SATB1 antibody (Abcam, ab70004)

tag: age


title: mouse_kidney_3-6M_control_RRBS_r1

value: kidney

value: 3 months


title: mouse_liver_0-1.5M_dox_RRBS

value: liver

value: 1.5 months


title: WT_SPCD4+thym_input_thymus

tag: cell type

value: Il2ra WT


title: WT_SATB1_ChIPseq_SPCD4+thym1_thymus

value: Thymus


title: day2_DM2_rep2

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

description:
Sample_R14
cDNA
C2C12_myodiff.rsem_gene.counts.tsv

data_processing:
Raw sequencing reads were aligned to full mouse genome and transcriptome using STAR v2.5.1b splice-aware alignment software. Primary part of GRCm38.p5 mouse genome assembly and Gencode vM12 annotation were used to generate the genomic and transcriptomic reference index.
The resulting transcriptome-aligned sequences were used for expression quantification with RSEM v1.2.31.
Genome_build: Primary GRCm38.p5
Supplementary_files_format_and_content: C2C12_myodiff.rsem_gene.counts.tsv: Tab-delimited text file; expression table of raw read counts per gene, with additional gene annotation (Ensembl, symbol, type of a gene).

source_name: C2C12 myoblasts

growth_protocol: C2C12 cell line was provided by Prof. Thomas Sejersen laboratory (Karolinska Institutet, Stockholm, Sweden). Cells were cultured in proliferation media III (DMEM supplemented with 4.5 g/L D-glucose, L-glutamine, penicillin-streptomycin, and 20% FCS). Cells were passaged at 60% of confluence. To induce differentiation, the proliferation media was removed, and replaced with differentiation media, that was renewed afterwards every other day. In this project, we used three types of differentiation media, which we shall hereafter call DM1, DM2 and DM3 media. The DM1 differentiation media was the “classical” media that induces myogenic differentiation in skeletal muscle progenitor cells: DMEM media supplemented with 2% HS (1, 2). DM2 was one of widely used media that induces fat differentiation in mesenchymal and adipose tissue progenitor cells (2): DMEM supplemented with 10% FCS and pro-adipogenic cocktail (1mkg/ml insulin (# I9278, Sigma USA), 0.5 mM 3-Isobutyl-1-methylxanthine (I587, Sigma USA), 0.5 microM Dexamethasone ( D1756, Sigma, USA) and 2 microM rosiglitazone (#R2408, Sigma, USA)). DM3 media we used to induce mixed pro-myogenic/pro-adipogenic stimulation and that was DMEM media supplemented with 2% HS and pro-adipogenic cocktail.

extract_protocol:
RNA was isolated with ExtractRNA reagent (#BC032, Evrogen, Moscow, Russia), quantified with Bioanalyser 2100 instrument (Agilent Technologies, Palo Alto, CA) using BA RNA nano kit; concentration was determined on Nanodrop 1000 (Thermo Scientific, Wilmington, DE, USA). Full-length poly(A) mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
RNA fragmentation, first and second strand synthesis, end repair, adaptors ligation, and PCR enrichment with Indexed primers (NEBNext® Multiplex Oligos for Illumina, NEB E7335S) were performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420), according to manufacturer manual. For first strand synthesis, Actinomycin D (Sigma A1410) was used to inhibit DNA-dependent DNA synthesis. After enrichment, PCR amplification with 11 cycles on Veriti Thermal Cycler was performed (Applied Biosystems, Foster City, CA, USA), followed by purification with Agencourt AMPure XP Beads (Beckman Coulter, Inc.). Libraries were quantified with Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA) instrument using BA High sensitivity kit, accurate molarity quantification was obtained with qPCR according to Illumina Sequencing Library qPCR Quantification Guide using standard qPCR primers 1.1 and 1.2, and qPCRmix-HS SYBR+LowROX kit (#PK156L, Evrogen , Moscow, Russia), using 7500 real-time PCR system (Applied Biosystems, Foster City, CA).

tag: cell line

value: immortalized murine myoblast cell line

tag: medium

tag: time point

value: day 2


title: Il2ramut/mut_SATB1 ChIPseq_SPCD4+thym1_thymus

value: SP CD4 thymocytes

value: Il2ra mut/mut


title: WT_SATB1 ChIPseq_SPCD4+thym2_thymus

value: female

value: 6-8 weeks


title: day7_DM2_rep2

description:
Sample_R12
cDNA
C2C12_myodiff.rsem_gene.counts.tsv

value: day 7


title: day7_DM1_rep2

description:
Sample_R08
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day7_DM2_rep1

description:
Sample_R11
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day7_DM3_rep2

description:
Sample_R10
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day7_DM3_rep1

description:
Sample_R09
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: mouse_heart_0-1.5M_control_RRBS

value: heart

value: Bisulfite-converted genomic DNA


title: mouse_monocytes_0-1.5M_control_RRBS

value: monocytes

value: no


title: mouse_cd4_0-1.5M_control_RRBS

source_name: mouse cd4+ blood cells

value: cd4+ blood cells


title: day7_DM1_rep1

description:
Sample_R07
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day2_DM3_rep2

description:
Sample_R06
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day2_DM3_rep1

description:
Sample_R05
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day2_DM1_rep2

description:
Sample_R04
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day0_Control_rep2

description:
Sample_R02
cDNA
C2C12_myodiff.rsem_gene.counts.tsv

value: Control

value: day 0


title: day0_Control_rep1

description:
Sample_R01
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day2_DM2_rep1

description:
Sample_R13
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: day2_DM1_rep1

description:
Sample_R03
cDNA
C2C12_myodiff.rsem_gene.counts.tsv


title: d10_Tet

city: Boston

first: Kevin

last: Bi

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v2.2.0)
Single cell signatures scoring was performed using the FastProject software (v1.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples

source_name: CD8+ TIL

growth_protocol: 3 x 10^5 B16-OVA tumor cells were injected subcutaneously into C57BL/6 mice. On day 10 or 20 after implantation, tumors were extracted and processed as noted below

extract_protocol:
Tumors were dissected from the surrounding fascia, mechanically minced and treated with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched using Optiprep (Sigma) density gradient followed by CD8+ MACS positive selection (Miltenyi) and FACS isolation. Cells were counted and loaded onto the 10x device (10x Genomics).
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B)
10X single-cell 3' RNA-seq v2

treatment_protocol: Mice were not treated

value: SIINFEKL Tetramer+ CD8+ T cells isolated from B16-OVA melanoma tumors day 10 after implantation

tag: isolation of cd45+ cells from tumors

value: CD8+ MACS positive selection (Miltenyi) followed by FACS


title: d28_Clone13_1

source_name: CD8+ T-cells

growth_protocol: C57BL/6 mice were infected with 2 x 10^6 pfu LCMV Clone 13 via IV injection. On day 28 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation

extract_protocol:
CD8+ MACS negative selection was performed on single-cell suspensions of splenocytes from chronically infected mice, followed by FACS. Purifed cells were loaded onto the 10x device (10x Genomics)
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B)
10X single-cell 3' RNA-seq v2

value: GP33-Tetramer+ CD44+PD-1+ CD8+ T cells isolated from spleens

tag: agent

value: LCMV Cl13

value: 28 days post-infection

tag: isolation of cd8+ t cells

value: CD8+ MACS negative selection (Miltenyi) followed by FACS


title: d28_Clone13_2


title: d20_Tet_2

value: SIINFEKL Tetramer+ CD8+ T cells isolated from B16-OVA melanoma tumors day 20 after implantation


title: d20_Tet_1


title: Islet1Cre;Ebf1fl/- 2

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

data_processing:
The analyses were performed using the Eoulsan pipeline [1], including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus Musculus  genome from Ensembl version mm10 using STAR(2.4.0k) [2]
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools[3]
To compute gene expression, Mus musculus GFF3 genome annotation version 81 from Ensembl database was used.
All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3 [4]
The sample counts were normalized using DESeq (1.8.3)
Statistical treatments and differential analyses were also performed using DESeq (1.8.3)
1.Laurent Jourdren, Maria Bernard, Marie-Agnès Dillies and Stéphane Le Crom. Bioinformatics (2012) 28 (11): 1542-1543; http://dx.doi.org/10.1093/bioinformatics/bts165
2.Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras: STAR: ultrafast universal RNA-seq aligner Bioinformatics (2013) 29 (1): 15-21 first published online October 25, 2012 doi:10.1093/bioinformatics/bts635
3.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
4.S Anders, T P Pyl, W Huber: HTSeq — A Python framework to work with high-throughput sequencing data. Bioinformatics (2014); http://dx.doi.org/10.1093/bioinformatics/btu638
5.Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106. http://dx.doi.org/10.1186/gb-2010-11-10-r106
Genome_build: mm10 from Ensembl81
Supplementary_files_format_and_content: tsv file containing raw counts

extract_protocol:
Embryos for each genotype were obtained by crossing either Ebf1+/-;Dlx5/6::Cre or Ebf1+/-;Islet1Cre/+ males with Ebf1fl/fl females. Embryonic tissue from individual dissected embryos was collected in RNAse free-conditions and stored in RNAlater solution. The genotype of each embryo was attested by PCR.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA  Kit (Part# 20020594), with 400ng of total RNA

tag: strain background

tag: genotype/variation

tag: developmental stage

value: striatum


title: Islet1Cre;Ebf1fl/- 3


title: Dlx5/6::Cre;Ebf1fl/- 3


title: d10_All

value: CD44+PD-1+CD8+ T cells isolated from B16-OVA melanoma tumors day 10 after implantation


title: Control 2


title: Control 1


title: Islet1Cre;Ebf1fl/- 1


title: Dlx5/6::Cre;Ebf1fl/- 2


title: ULK_DKO_IFNg_4

city: Chicago

first: Diana

last: Saleiro

state: Illinois

address: 303 E. Superior St.

department: Hematology-Oncology

institute: Robert H. Lurie Comprehensive Cancer Center

description: IFNgamma treated

data_processing:
Base calls were performed using bcl2fastq v2.17.1.14 for NextSeq output.
RNA-Seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
RNA-Seq reads were aligned to UCSC mm9 using Tophat version 2.1.0.  Only uniquely mapping reads with at most two mismatches were retained.
To create RNA-Seq coverage plots, the mapped RNA-Seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA fragments at a given genomic coordinate.

source_name: Mouse embryonic fibroblasts

growth_protocol: The immortalized Ulk1/2+/+ and Ulk1/2-/- MEFs were cultured in DMEM supplemented with 10% FBS and antibiotics and incubated at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
Sequencing libraries were prepared from 1μg of high-quality RNA samples using Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina) as per the manufacturer’s instructions

treatment_protocol: Ulk1/2+/+ and Ulk1/2-/- MEFs were plated in triplicate and were left untreated or were treated for 6 hours with 2.5x103 IU/ml of mouse IFNg

value: embryonic fibroblasts

value: Ulk 1/2 double KO + IFNg


title: Control 3


title: ULK_DKO_IFNg_1

description: IFNgamma treated


title: ULK_DKO_IFNg_2

description: IFNgamma treated


title: ULK_DKO_UT_4

description: Untreated

value: Ulk 1/2 double KO


title: ULK_DKO_IFNg_3

description: IFNgamma treated


title: ULK_DKO_UT_3

description: Untreated


title: ULK_DKO_UT_2

description: Untreated


title: ULK_DKO_UT_1

description: Untreated


title: Dlx5/6::Cre;Ebf1fl/- 1


title: ULK_WT_IFNg_2

description: IFNgamma treated

value: Wildtype/WT + IFNg


title: Il2ramut/mut_ATACseq_Treg1_thymus

description: naïve/unstimulated

value: Foxp3+ CD4+ Treg cell

value: Il2ra mut/mut


title: ULK_WT_UT_2

description: Untreated

value: Wildtype/WT


title: ULK_WT_UT_4

description: Untreated


title: ULK_WT_UT_3

description: Untreated


title: WTMEF_LPS_Bmal1

first: Heekyung

last: Hong

state: IL

address: 303 E Superior Street

institute: Northwestern University

data_processing:
FASTQ files are generated using the FASTQ Generation App v1.0.0 in BaseSpace Sequence Hub, Illumina, Inc.
Reads were aligned to the mm10 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings.
For visualization on the UCSC genome browser, bedGraph files for peaks were generated using MACS2/2.1.0 with --SPMR setting to view signal per million reads.  For H3K27Ac ChIP-seq,  peaks were called using the --nomodel and --broad settings.  For each ChIP-seq sample, input was used as control (-c).
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser

source_name: p65 KO MEF treated with LPS

growth_protocol: MEF cells – were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 1-% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Preparation kits (NEB) according to the manufacturer's instructions.  Quality of the library and concentration were determined by Bioanlayzer using the High Sensitivity chip (Agilent) and qPCR-based quantification (NEBNext Library Quant Kit), respectively.

treatment_protocol:
MEF cells – cells were treated with LPS (100 ng/ml) or saline for 1 hour prior to ChIP assays.
Liver cells -- WT mice were injected with either LPS (20 mg/kg body weight) or saline at ZT6 and livers were collected at ZT8 for ChIP-seq analyses.  Livers from mouse fed on high-fat diet or regular chow were harvested at ZT8 for ChIP-seq analysis.

value: p65 KO

value: MEF

value: LPS

tag: chip-antibody

value: BMAL1 Perelis et al., 2015

tag: protocol

value: Barish and Tangirala, 2013


title: RC72_input

source_name: Liver from regular chow fed mice

tag: tissue

value: Liver

tag: diet

value: regular chow

tag: strain

value: adult

tag: Sex

value: male

value: input


title: p65KOMEF_input


title: WTMEF_LPS_input


title: RC99_input

tag: age


title: WTMEF_Saline_Bmal1

source_name: p65 WT MEF treated with LPS

value: p65 WT

tag: cell type


title: WTMEF_Saline_input


title: p65KOMEF_LPS_Bmal1

source_name: p65 WT MEF treated with saline

value: saline


title: RC52_input


title: SFD91_input


title: ULK_WT_IFNg_3

description: IFNgamma treated

value: embryonic fibroblasts


title: SFD61_input

source_name: Liver from high-fat diet fed mice

value: high-fat diet


title: RC98_input


title: RC69_input


title: Saline21_input

source_name: LPS-treated Liver


title: SFD71_input


title: ULK_WT_IFNg_4

description: IFNgamma treated

value: Wildtype/WT + IFNg


title: Saline12_input

source_name: saline-treated Liver


title: Saline11_input


title: ULK_WT_IFNg_1

description: IFNgamma treated


title: ULK_WT_UT_1

description: Untreated


title: SFD74_input


title: SFD62_input


title: LPS12_input


title: LPS11_input


title: SFD91_Bmal1


title: SFD68_input


title: SFD74_Clock

value: CLOCK Perelis et al., 2015


title: SFD61_Clock


title: RC69_Clock


title: SFD62_Bmal1


title: RC69_Bmal1


title: Saline12_PolII

value: RNA polimerase II Santa Cruz SC-899


title: RC52_Clock


title: RC99_p65

value: p65, Santa Cruz sc-372


title: Saline12_Clock


title: LPS12_PolII


title: Saline11_H3K27

value: H3K27ac Active Motif 39133


title: RC98_p65


title: SFD68_p65

source_name: Liver from saturated fat diet fed mice

value: saturated fat diet


title: LPS11_Clock

value: LPS


title: Saline21_Bmal1

value: BMAL1 Perelis et al., 2015

value: Barish and Tangirala, 2013


title: Saline12_Bmal1

value: Liver


title: SFD71_p65

value: adult


title: LPS12_H3K27

value: male


title: LPS11_H3K27


title: LPS11_Bmal1


title: Saline11_Clock


title: LPS12_Clock


title: Saline12_p65

value: p65 Abcam  Ab7970


title: Saline11_p65


title: LPS11_p65


title: RC72_Bmal1

value: regular chow


title: Saline12_H3K27

value: saline


title: Skin_ABT5

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm10 -d <List of tag dir> -count 3utr -condenseGenes -strand + -raw
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
Tissues were harvested following perfusion and submersed whole in Invitrogen RNAlater Solutions (Invitrogen). Samples were flash frozen in -80o C until further processing. mRNA from all tissues was purified using RNeasy mini kit (Qiagen) according to manufacturer’s guidelines. RNA quality was assessed by TapeStation (Agilent). Libraries were prepared using a derivation of MARS-seq as described previously 85, optimized for bulk RNA-seq. Briefly, 50 ng of RNA from each sample were reverse transcribed into cDNA, pooled and linearly amplified by in vitro transcription. Following fragmentation and addition of Illumina sequences, successful final libraries were sequenced using the Illumina NextSeq-500 platform.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: We administrated ABT-737 (25mg/kg) or a vehicle solution to 18 months old Prf1-/- mice, for two consecutive days monthly for a period of two months

tag: genotype

value: Skin

tag: age at sacrifice [months]

tag: treatment


title: Skin_ABT3


title: LPS12_Bmal1


title: Skin_DM5

value: Vehicle


title: Skin_Y3


title: mouse_clp_0-3M_control_RRBS

source_name: mouse CLP cells

tag: tissue/cell type

value: CLP cells

tag: dnmt3b oe

value: no

tag: treatment time

value: 3 months

tag: molecule subtype

value: Bisulfite-converted genomic DNA


title: Skin_DM3


title: mouse_liver_3-6M_dox_RRBS_r2

source_name: mouse liver

tag: strain background

value: liver

value: yes


title: Skin_Y1


title: Lung_ABT4

description: processed_data_kidney_liver_lung_RefSeq.csv

value: Lung


title: Lung_ABT5


title: Skin_Y2


title: Lung_ABT3


title: Lung_DM5


title: Skin_DM4


title: LPS12_p65

tag: agent

value: LPS


title: Skin_ABT4


title: Lung_DM4


title: Lung_DM3


title: Lung_Y4


title: Lung_Y3


title: Lung_Y1


title: Liver_DM5


title: DFCI-5268-mse-sf3b1atmold-01

first: Catherine

address: 450 Brookline Avenue

data_processing:
Raw data were aligned to mm10 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
TPM (Transcripts Per Kilobase Million) value was used to measure gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was extracted using the PrepEase RNA Spin Kit
NEBNext Ultra Library Preparation Kit

tag: genotype/variation

value: DM

value: B cell


title: DFCI-5268-mse-sf3b1atmold-05

value: DM-CLL


title: DFCI-5268-mse-sf3b1atmold-04


title: Liver_ABT5

value: Liver


title: CLH5-S, biological rep1

city: Taipei

first: CHIH-AN

last: LIN

address: 7F, No. 2, Xuzhou Road

department: Clinical Laboratory Science and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CLH5-S cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The expression data were analyzed by GeneSpring GX 13.0 (Silicon Genetics, Redwood City, CA). The Affymetrix CEL files were transformed by RMA algorithm, and each probe set was summarized using the median of the corresponding probes.

source_name: lung cancer cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: The human lung cancer cell line, CLH-A, CLH-S, CLH5-A and CLH5-S were grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

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

tag: tumor type

value: Small cell lung cancer

tag: ethnicity

value: Asian

value: 45 years

tag: gender

value: male


title: Liver_ABT4

tag: strain

tag: tissue


title: DFCI-5268-mse-sf3b1atmold-06


title: CLH5-S, biological rep2

description: Gene expression data from CLH5-S cells

tag: age


title: CLH-A, biological rep2

description: Gene expression data from CLH-A cells

value: 51 years

value: female

tag: cell type

value: CLH-A


title: Liver_ABT3

tag: genotype


title: DFCI-5268-mse-sf3b1atmold-03


title: Lung_Y2

tag: age at sacrifice [months]


title: Liver_DM4

tag: treatment

value: Vehicle


title: DFCI-5268-mse-atmMTold-05

value: Atm MT


title: CLH-A, biological rep3

description: Gene expression data from CLH-A cells


title: PPP2R2A-depleted cells by using siPPP2R2A_2B

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

state: CA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

hyb_protocol: Hybridize at 45C for 16 hours with rotation at 60rpm (GeneChip Hybridization Oven 645)

scan_protocol: Affymetrix GeneChip Scanner 7G with default settings

data_processing: Affymetrix Expression Console

label_protocol: Ambion MessageAmp Premier protocol

extract_protocol: RNA was isolated using  TRIzol (Invitrogen product name) and subsequently the Qiagen  RNeasy mini Kit (cat 74104).  Column based.

treatment_protocol: RT-112 cells were trypsinized and transfected with 50nΜ siRNA (#1 or #2) for PPP2R2A or scramble siRNA. Lipofectamine ® RNAiMAX was used as transfection reagent. RNA-Lipofectamine complexes were made in Opti-MEM (serum free). Cells were plated at a 50% confluence in serum and antibiotic-containing media. 24h later double transfection was performed with the same amounts of siRNAs and cells were incubated for 24h before RNA isolation.

tag: cell line

value: bladder cancer


title: CLH-S, biological rep3

description: Gene expression data from CLH-S cells

value: CLH-S


title: CLH5-A, biological rep3

description: Gene expression data from CLH5-A cells


title: DFCI-5268-mse-atmMTold-03


title: CLH5-S, biological rep3

description: Gene expression data from CLH5-S cells


title: Cells transfected with siRNA scramble_1B


title: CLH5-A, biological rep1

description: Gene expression data from CLH5-A cells


title: DFCI-5268-mse-atmMTold-06


title: PPP2R2A-depleted cells by using siPPP2R2A_1B


title: Cells transfected with siRNA scramble_1A


title: PPP2R2A-depleted cells by using siPPP2R2A_2A


title: CLH-A, biological rep1

description: Gene expression data from CLH-A cells


title: CLH-S, biological rep1

description: Gene expression data from CLH-S cells


title: CLH5-A, biological rep2

description: Gene expression data from CLH5-A cells


title: Liver_Y4


title: PPP2ARA-depleted cells by using siPPP2R2A_1A


title: Liver_Y1


title: DFCI-5268-mse-atmMTold-01


title: Liver_Y3


title: Kidney_ABT5

value: Kidney


title: DFCI-5268-mse-sf3b1MTold-03

value: Sf3b1 MT


title: Liver_Y2


title: DFCI-5268-mse-atmMTold-02


title: Kidney_ABT4


title: Kidney_DM5


title: Kidney_ABT3


title: Liver_DM3


title: CLH-S, biological rep2

description: Gene expression data from CLH-S cells


title: Kidney_DM3


title: DFCI-5268-mse-sf3b1WTold-03

value: WT


title: DFCI-5268-mse-sf3b1MTold-01

value: B cell


title: Kidney_DM4


title: Kidney_Y2


title: DFCI-5268-mse-sf3b1MTold-02


title: DFCI-5268-mse-sf3b1WTold-01


title: Kidney_Y4


title: Kidney_Y3


title: Kidney_Y1

description:
processed_data_kidney_liver_lung_RefSeq.csv
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: ansc_ko_rna_rep4

city: Worcester

first: Botao

last: Liu

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Cytoplamic mRNA
ansc.ribo.rna.rsem.gene.summary.counts.txt
ansc.ribo.rna.rsem.gene.summary.tpm.txt
ansc.deg.anota2seq.sva.gene.summary.txt

data_processing:
Basecallling and fastq file generation were performed by Illumina Basespace.
For ribosome profiling data, individual samples were separated from the raw fastq files based on the barcode sequences. Barcode and UMI sequences were trimmed and moved to the read names. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1).
Trimmed reads were quality filtered and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9).
PCR duplicates were marked based on the UMI sequences and only uniquely mapped reads without duplicates were retained with samtools (0.0.19) for the downstream analysis.
Cleaned bam files of ribosome footprints were converted to fastq files with bedtools (2.22.0). Cleaned fastq files without rRNA or tRNA were used for RNA-seq quantification. For both ribosome profiling and RNA-seq, gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks.
Genes were filtered with minimum 10 reads across all replicates and then the read counts were batch-corrected with the Combat function in sva (3.24.4) using a full model matrix.
Batch-corrected counts were normalized with trimmed mean of M values (TMM) method and used to identify differential expressed genes (DEGs) with anota2seq (1.0.0). Relaxed cut-offs (absolute fold changes > 1.2 and adjusted p-value < 0.2) were used to obtained sufficient DEGs for the downstream analysis. Instead of using the default setting, the priorities of translation and buffering groups were determined by the adjusted p-values and were set to be higher than the priority of mRNA only groups.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TPM values from RSEM, as well as batch-corrected counts, TPM, and anota2seq (differential translation analysis) output values for each sample

source_name: Dentate gyrus

growth_protocol: Adult-derived NSCs were isolated from the dentate gyrus (DG) of 8- to 10-week-old male Fmr1 KO mice and wild-type (WT) littermate controls based on our published method (Guo et al., 2012). Briefly, DG were dissected using forceps and 27gauge needle (BD, #305109) and placed in Hank’s balanced salt solution (HBSS, Invitrogen, # 14025-126) on ice. Tissue was spun down and digested using MACS Neural Tissue Dissociation kit (Miltenyi Biotech, #130-090-753). After dissociation with a fire-polished glass pipette, cells were filtered through a 70-μm cell strainer (BD Falcon, #252350) and washed with HBSS, the single-cell suspension from each sample was collected and cultured in proliferation medium [Neurobasal medium containing B27 serum-free supplement (Invitrogen, #17504-044), 20 ng/ml basic fibroblast growth factor (FGF-2, PeproTech, #K1606), 20 ng/ml epidermal growth factor (EGF, PeproTech, #A2306), 1% Antibiotic-Antimycotic, and 2 mM L-glutamine], in a 5% CO2 incubator at 37°C. Half of the medium was replaced every two days. Independently isolated cells serve as biological replicates.

extract_protocol:
Frozen cell pellets were thawed in ice-cold polysome lysis buffer [20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide, 25U/ml Turbo DNaseI (Ambion, #AM2238), 1% TritonX-100 in nuclease-free water] and lysed by trituration through a 25-G need for 10 times. After 10-min incubation on ice, lysates were clarified by centrifugation at 14,000g 4 °C for 10min. The supernatants were collected and the amounts of nucleic acids (A260 units) were measured with Nanodrop (Thermo Fisher Scientific). For each sample, cytoplasmic RNA for RNA-seq was purified from one fourth of the lysate with TRIzol LS reagent (Invitrogen, #10296028). The other three fourths of the lysate was digested with 100ng/A260 RNase A (Ambion, #AM2270) and 60U/A260 RNAse T1 (Thermo Fisher Scientific, #EN0542) at 25°C for 30min. The digestion was stopped by adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694) and chilling on ice. Digested lysates were loaded on 10%-50% sucrose gradients prepared in 1Xpolysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection interval through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS.
Ovation RNA‑Seq System V2 (NuGEN)
For the cytoplasmic RNA-seq, 500ng total RNA per sample was used for the library preparation with the Ovation RNA‑Seq System V2 (NuGEN, #0304) following manufacturer’s instructions. HL-dsDNase (ArcticZymes, #70800-201) method was used to eliminate DNA contamination and cDNA was fragmented with M220 Covaris Focused-ultrasonicator for a target median fragment size of 300bp (peak power: 50.0, duty factor 20.0, cycles/burst: 200, treatment time: 75sec). qPCR test was performed with EvaGreen Dye (Biotium, #31000-T) to determine the optimal PCR cycles. For the ribosome profiling samples, libraries were prepared following the published protocols (Heyer et al., 2015; Ingolia et al., 2012). Briefly, rRNA was depleted from the purified monosomal RNA samples with RiboZero (Illumina, #MRZG12324). Remaining RNA samples were separated on a 15% TBU gel (National Diagnostics, #EC-833) and the ribosome footprints were size-selected based on the 26 and 34nt markers. RNA was eluted from the crushed gel pieces in RNA elution buffer (300mM NaOAc pH5.5, 1mM EDTA, 0.25% SDS) at RT overnight, filtered with Spin-X Centrifuge Tube Filters (Corning, #8162) and precipitated with equal volume of isopropanol. Recovered RNA was dephosphorylated with T4 Polynucleotide Kinase (NEB, #M0201S) and ligated with preadenylated adaptor in miRCat®-33 Conversion Oligos Pack (IDT) using T4RNL2Tr.K227Q ligase (NEB, #M0351L). Reverse transcription was performed with RT primers with 5nt-barcode and 5nt or 8nt unique molecular identifier (UMI) and SuperScript III (Invitrogen, #18080-044) in 1X first-strand buffer without MgCl2 (50 mM Tris-HCl, pH 8.3, 75 mM KCl). RT products were separated on a 10% TBU gel and the 130-140nt region was selected. cDNA was eluted in DNA elution buffer (10mM Tris pH 8.0, 300mM NaCl, 1mM EDTA) at RT overnight, filtered, and precipitated with isopropanol. Purified cDNA was circularized with CircLigase (Epicentre, #CL4115K). cDNA derived from remaining rRNA was hybridized to biotin-labelled antisense probes (IDT) and further depleted with Dynabeads MyOne Streptavidin C1 (Inivtrogen, #65001). Optimal PCR cycle was determined empirically by test PCR reactions with titrated cycle numbers. Final PCR amplification was performed with KAPA Library Amplification Kit (Kapa Biosystems, #KK2611) and 180-190bp products were size-selected on an 8% TBE gel. DNA was eluted in DNA elution buffer and precipitated with isopropanol. The final library DNA was purified with AMPure XP beads (Beckman Coulter, #A63880)

treatment_protocol: Cycloheximide (CHX, Sigma-Aldrich, #C7698) was added into cultured aNSCs to a final concentration of 100μg/ml, and let cells incubate at 37 °C for 10 min in order to stabilize ribosomes. Then, cells were transported to cold room and spun down gently at 1000g for 3 min and the supernatant was carefully discarded. Cells were washed twice with ice-cold PBS containing 100μg/ml CHX and were spun down at 1000g for 3 minutes. The supernatant was carefully removed to collect the cell pellet. The cell pellet was immediately stored and kept in -80 °C freezer for later analysis.

value: Dentate gyrus

value: Adult neural stem cells

value: FVB/N

tag: Sex

value: 8-10 weeks


title: DFCI-5268-mse-sf3b1WTold-02


title: ansc_ko_rna_rep2


title: ansc_ko_rna_rep1


title: jazD_rep1

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
Illumina Casava1.8.2 software used to convert and demultiplex basecall files to FASTQ.
Reads assessed for quality and filtered with Illumina quality control tools filters and FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.25 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data (jazD_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary_files_format_and_content: count data (jazD_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

organism: Arabidopsis thaliana

source_name: whole rosette

growth_protocol: Trays of soil-grown plants were covered with a transparent plastic dome for 10 days after seed sowing. Plants were maintained under a 16-h light (100 μE m-2 s-1) and 8-h dark photoperiod at 20 ºC

extract_protocol:
For each replicate sample, approximately 20 plants (whole rosette, excluding roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80 ºC until processing. Wild-type Col-0 and mutant plants were grown in the same tray to minimize tray-to-tray variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Qiagen RNeasy kit with Qiagen on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 7.0.
Barcoded sequencing libraries were prepared using the Illumina RNAseq kit according to the manufacturer's instructions. Normalized libraries were sequenced on the Ilumina HiSeq 2000 platform with multiplexing of nine libraries per lane.

tag: accession

value: jazD

tag: replicate


title: Col-0_rep1

value: wildtype


title: ansc_wt_rna_rep4

value: male


title: jazQ_rep3

value: jazQ


title: jazQ_rep2


title: Col-0_rep3


title: jazD_rep3


title: jazD_rep2


title: ansc_wt_rna_rep3


title: Col-0_rep2


title: ansc_wt_rna_rep2


title: jazQ_rep1


title: ansc_wt_rna_rep1


title: ansc_ko_ribo_rep4

description:
Ribosome protected footprints
8nt UMI sequences
ansc.ribo.rna.rsem.gene.summary.counts.txt
ansc.ribo.rna.rsem.gene.summary.tpm.txt
ansc.deg.anota2seq.sva.gene.summary.txt

data_processing:
Library strategy: Ribosome profiling
Basecallling and fastq file generation were performed by Illumina Basespace.
For ribosome profiling data, individual samples were separated from the raw fastq files based on the barcode sequences. Barcode and UMI sequences were trimmed and moved to the read names. Adaptor sequences (TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG) were removed with cutadapt (1.7.1).
Trimmed reads were quality filtered and mapped to the mouse rRNA and then tRNA references with Bowtie2 (2.1.0). Unmapped reads were next mapped to the mm10 mouse genome with Tophat2 (2.0.9).
PCR duplicates were marked based on the UMI sequences and only uniquely mapped reads without duplicates were retained with samtools (0.0.19) for the downstream analysis.
Cleaned bam files of ribosome footprints were converted to fastq files with bedtools (2.22.0). Cleaned fastq files without rRNA or tRNA were used for RNA-seq quantification. For both ribosome profiling and RNA-seq, gene expression was quantified with RSEM (1.2.11) using the cleaned fastq files and Refseq (V69) mouse CDS without the first and last 30nt to avoid the translation initiation and termination peaks.
Genes were filtered with minimum 10 reads across all replicates and then the read counts were batch-corrected with the Combat function in sva (3.24.4) using a full model matrix.
Batch-corrected counts were normalized with trimmed mean of M values (TMM) method and used to identify differential expressed genes (DEGs) with anota2seq (1.0.0). Relaxed cut-offs (absolute fold changes > 1.2 and adjusted p-value < 0.2) were used to obtained sufficient DEGs for the downstream analysis. Instead of using the default setting, the priorities of translation and buffering groups were determined by the adjusted p-values and were set to be higher than the priority of mRNA only groups.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TPM values from RSEM, as well as batch-corrected counts, TPM, and anota2seq (differential translation analysis) output values for each sample

extract_protocol:
Frozen cell pellets were thawed in ice-cold polysome lysis buffer [20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide, 25U/ml Turbo DNaseI (Ambion, #AM2238), 1% TritonX-100 in nuclease-free water] and lysed by trituration through a 25-G need for 10 times. After 10-min incubation on ice, lysates were clarified by centrifugation at 14,000g 4 °C for 10min. The supernatants were collected and the amounts of nucleic acids (A260 units) were measured with Nanodrop (Thermo Fisher Scientific). For each sample, cytoplasmic RNA for RNA-seq was purified from one fourth of the lysate with TRIzol LS reagent (Invitrogen, #10296028). The other three fourths of the lysate was digested with 100ng/A260 RNase A (Ambion, #AM2270) and 60U/A260 RNAse T1 (Thermo Fisher Scientific, #EN0542) at 25°C for 30min. The digestion was stopped by adding 50U SUPERase In RNase inhibitor (Ambion, #AM2694) and chilling on ice. Digested lysates were loaded on 10%-50% sucrose gradients prepared in 1Xpolysome buffer (20mM Tris-HCl pH7.4, 5mM MgCl2, 100mM KCl, 1mM DTT, 100ug/ml cycloheximide in nuclease-free water). After the ultracentrifugation in a SW41Ti rotor (Beckman Coulter) at 35,000 rpm 4°C for 2.5 hours, gradients were fractionated at 1.5 ml/min and 12 sec collection interval through a fractionation system (Brandel) that continually monitored A260 values. Monosome fractions were identified, pooled, and extracted with TRIzol LS.
Homemade
3' ligation based library construction, which is similar to miRNA-seq. Ribosome protected mRNA fragments were ligated to 3' adapters. RT was then performed and cDNA was circularized. PCR was performed to add adapters for Illumina sequencing.


title: ansc_ko_ribo_rep2

description:
Ribosome protected footprints
5nt UMI sequences
ansc.ribo.rna.rsem.gene.summary.counts.txt
ansc.ribo.rna.rsem.gene.summary.tpm.txt
ansc.deg.anota2seq.sva.gene.summary.txt


title: ansc_ko_ribo_rep3


title: 914 A

city: Atlanta

first: Renee

last: Read

state: Georgia

address: 1510 Clifton Rd

department: Pharmacology

institute: Emory University School of Medicine

description: paired end RNAseq, experimental replicate A

data_processing:
Sequence quality assessed by Phred quality per sample over the forward and reverse read, as calcultaed by FastQC
Sequence mapping was performed on the human genome reference sequence GRCh38, using Tophat version 2.0.9 in conjunction with Bowtie version 1.0.0.
Cufflinks version 2.1.1 was used to detect genes and transcripts that are expressed by comparing the Tophat2 read mapping with the Ensembl gene models for the grch37 release of the human genome.
Cufflinks and Cuffdiff version 2.1.1 was used to collect FPKM expression values across all samples, both at the gene, transcript, and isoform level.
Genome_build: GRCCh38, grch37
Supplementary_files_format_and_content: excel file, cufflinks processed data, statisitical comparison of normalized gene expression levels between neurosphere cultures of normal human progenitor cells and glioblastoma tumor cells for all identified transcripts

source_name: GBM 914 tumor neurospheres

growth_protocol: bulk neurospheres prepared from glioblastoma surgical specimens, grown in seru-free DMEM:F12 with EGF and bFGF supplmentation

extract_protocol:
total RNA was prepared from bulk cultured cells using Trizol and phenol-choloform extraction; RNA quality was examined on a Bioanalyzer, and smaples with a RIN score of 8 or greater were selected for prolfing.
Automated Illumina TruSeq total stranded RNA-seq library construction, with Ribo-Zero ribosomal RNA reduction chemistry

value: GBM 914 tumor neurospheres

tag: culture conditions

value: neurosphere culture, low passage (<15)

tag: initial preparation

value: bulk total RNA, Trizol purification

tag: library preparation

value: rRNA depleted


title: 56 A

source_name: GBM 56 tumor neurospheres

value: GBM 56 tumor neurospheres


title: 1219 C

description: paired end RNAseq, experimental replicate C

source_name: GBM 1219 tumor neurospheres

value: GBM 1219 tumor neurospheres


title: 730 B

description: paired end RNAseq, experimental replicate B

source_name: GBM 730 tumor neurospheres

value: GBM 730 tumor neurospheres


title: 914 B


title: 56 B


title: 730 A

description: paired end RNAseq experimental replicate A


title: ansc_ko_ribo_rep1


title: ansc_wt_ribo_rep3

value: WT


title: HK2R

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description: Ribominus RNA

data_processing:
Illumina RTA 1.18.64 software used for demultiplexing.
Illumina Bcl2fastq 1.8.4 software used for barcode demultiplexing by allowing 1 mismatch.
Paired-end reads were aligned to a modified reference human genome of GRCh37, which included the complete genome sequence of KSHV, NC009333, using two-pass alignment with chimeric alignment detection.
CIRCexplorer version 1.1.1 was used to detect circular RNA
Genome_build: GRCh37 plus KSHV genome sequence (NC009333)
Supplementary_files_format_and_content: tab-delimited text files include each circular RNA specification for each sample

source_name: Primary cells, HUVEC

growth_protocol: MC116 cells were grown in RPMI media. HUVEC cells were grown in EGM2 media.

extract_protocol:
Total RNA (20 µg) was purified using miRNeasy System (Qiagen).
Total RNA samples were depleted of ribosomal RNA using RiboMinus Eukaryote System v2 (ThermoFisher). Ribo-depleted RNA was treated with 6 U of RNase R (Epicenter Biotechnologies) at 37° for 15 min. Libraries were generated using TruSeq Stranded Total RNA System (Illumina). Paired-end 150bp RNA-Seq sequencing reads (35.3 million reads per sample in average) were aligned with STAR version 2.4.2a (31) to a modified reference human genome of GRCh37, which included the complete genome sequence of KSHV, NC009333.

treatment_protocol: Some conditions included KSHV infection. Some conditions included RNase R treatment of the purified RNA.

value: HUVEC

tag: infection status

value: infected with KSHV

tag: rnase treatment

value: yes

tag: infection type

value: 7 days post infection


title: 1219 D

description: paired end RNAseq, experimental replicate D


title: ansc_wt_ribo_rep2

value: Dentate gyrus

value: Adult neural stem cells

tag: strain

value: FVB/N

value: 8-10 weeks


title: ansc_wt_ribo_rep1

tag: tissue

value: male


title: H1R

description: Ribominus RNA

value: uninfected


title: H2R

description: Ribominus RNA


title: HNPC A

source_name: human neural progenitor cells

value: human neural progenitor cells

value: neurosphere culture, low passage (<15)


title: HK1R

description: Ribominus RNA


title: HNPC B

value: bulk total RNA, Trizol purification

value: rRNA depleted


title: MK3R

description: Ribominus RNA

source_name: Cell line, MC116

value: stable infection


title: HK2M

description: Ribominus RNA

value: no


title: HK1

description: gene expression with and without KSHV infection

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Axon GenePix 4000B microarray scanner (Molecular Devices, Inc.).

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 12 samples have flag expressed (greater than 2 times background standard deviation) were retained for further analyses.

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was purified using miRNeasy System (Qiagen).

tag: kshv-infection type


title: HK2

tag: cell type


title: H1M

description: Ribominus RNA


title: HK3


title: M3R

description: Ribominus RNA


title: ansc_wt_ribo_rep4

tag: genotype

value: WT

tag: age


title: MCK1


title: MCK2


title: H2M

description: Ribominus RNA

value: HUVEC


title: HK1M

description: Ribominus RNA

value: infected with KSHV


title: M1R

description: Ribominus RNA

value: yes


title: H3


title: MK2R

description: Ribominus RNA


title: MC1


title: MCK3


title: H1


title: MK1R

description: Ribominus RNA


title: H2


title: M2M

description: Ribominus RNA


title: MC2


title: CNV_MSC_KO_rep2

city: Beijing

first: Zunpeng

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Library strategy: WGS
Reads were trimmed to remove the adapter sequences and low quality bases.
Trimmed reads then mapped to UCSC hg19 human genome using hisat2 (RNA-seq) or bowtie2 (WGS).
Reads were counted by Htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include the reads count information of each RNA-Seq samples.
Supplementary_files_format_and_content: wig files include the copy number normalized by HMMcopy in each 500-kb windows.

source_name: ES-derived mesenchymal stem cell

growth_protocol: hMSCs were cultured in culture plates or dishes (Corning) coated by gelatin (Sigma) in hMSC culture medium (MEMα (Invitrogen) and 10% fetal bovine serum (FBS, Gemcell, Cat. No. 100-500, lot. No. A77E01F), with additional 2 mM GlutaMAX, 0.1 mM NEAA, 1% penicillin/streptomycin and 1 ng/mL FGF-β).

extract_protocol:
Genomic DNA of early passage (P2) hMSCs was extracted by DNeasy Blood and Tissue Kit (Qiagen)
Library construction and sequencing were carried out by GENEWIZ Company.

value: Mesenchymal stem cells

value: Rap1 Knockout

tag: passage


title: CNV_MSC_WT_rep2


title: RNA_seq_NSC_WT_rep1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Trimmed reads then mapped to UCSC hg19 human genome using hisat2 (RNA-seq) or bowtie2 (WGS).
Reads were counted by Htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include the reads count information of each RNA-Seq samples.
Supplementary_files_format_and_content: wig files include the copy number normalized by HMMcopy in each 500-kb windows.

source_name: ES-derived neural stem cells

growth_protocol: hNSCs were cultured in plates coated by Matrigel in Neural Stem cell Maintenance Medium (50% Advanced DMEM/F12 (Invitrogen) and 50% Neurobasal (Invitrogen), with additional 1% N2 (Invitrogen), 2% B27 (Invitrogen), 2 mM GlutaMAX, 0.1 mM NEAA, 1% penicillin/streptomycin, 10 ng/mL of human leukemia inhibitory factor (hLIF, Millpore), 3 μM CHIR99021 (Selleck) and 2 μM SB431542 (Selleck)).

extract_protocol:
Total RNAs of early passage  hNSCs (P3) were extracted by TRIzol.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Neural stem cells


title: CNV_MSC_KO_rep1


title: RNA_seq_NSC_WT_rep2


title: MK2M

description: Ribominus RNA

tag: cell line


title: CNV_MSC_WT_rep1


title: RNA_seq_NSC_KO_rep2


title: RNA_seq_MSC_WT_rep2

extract_protocol:
Total RNAs of early passage hMSCs (P2)  were extracted by TRIzol.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.


title: MC3


title: RNA_seq_NSC_KO_rep1


title: MK1M

description: Ribominus RNA


title: M2R

description: Ribominus RNA


title: MK3M

description: Ribominus RNA


title: M3M

description: Ribominus RNA


title: M1M

description: Ribominus RNA


title: RNA_seq_MSC_KO_rep2


title: RNA_seq_MSC_WT_rep1


title: RNA_seq_MSC_KO_rep1


title: DFCI-5268-mse-atmMTold-04

last: Wu

tag: genotype/variation

value: Atm MT

value: B cell


title: PP6fl/fl mKC

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences were trimmed from the raw paired-end reads, and RNA de novo assembly was achieved using the Trinity platform (http://trinityrnaseq.sourceforge.net/).
Unisequences were predicted and annotated using local BLASTX programs against the NCBI nr/nt, SwissProt, STRING and Cluster of Orthologous Groups (COG) databases (10-5-value cutoff).
The read counts were further normalized into FPKM values, and the fold changes were calculated using RSEM software (http://deweylab.biostat.wisc.edu/rsem/).
DEGs were identified using the edgeR software package (http://www.bioconductor.org/packages/elease/bioc/tml/edgeR.html).
Genome_build: mm8
Supplementary_files_format_and_content: The xls file includes FPKM values for each sample.

source_name: keratinocytes

growth_protocol: Keratinocytes derived from mouse tails were cultured in Meidum 154CF for 3 days.

extract_protocol:
Total RNA was extracted with Trizol reagent.
cDNA library was prepared using a TruSeq RNA sample preparation kit (Illumina cat. FC-122-1001) according to the manufacturer’s instructions. Briefly, mRNA was pulled-down with Oligo(dT) magnetic beads, fragmented, and reverse-transcribed with random hexamers. The resulted cDNA was used for second strand synthesis.

tag: strain background

value: 8 weeks

value: keratinocytes


title: Sample 14_Incubation with SiO2

city: Montreal

first: Orcun

last: Hacariz

state: Quebec

address: 1001 Boul Décarie, Site Glen Pavilion E / Block E. E02.2143

country: Canada

institute: Research Institute of the McGill University Health Centre

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 14

data_processing:
Standard Illumina base calling (CASAVA; version 1.8) was performed.
Read quality was checked with FASTQC (version 0.11.3) and adapter related sequences were removed using Trim Galore (version 0.4.5) (https://www.bioinformatics.babraham.ac.uk/projects/).
The genome sequence of C. elegans and GTF file (Caenorhabditis_elegans.WBcel235.91.gtf) were downloaded from ENSEMBL (https://www.ensembl.org/).
Reads were aligned to the C. elegans genome with HISAT2 (version 2.1.0) (doi: 10.1038/nmeth.3317) and sorted alignment files were generated by SAMtools (version 1.7, doi: 10.1093/bioinformatics/btp352).
Raw read counts were extracted using HTSeq (version 0.9.1, doi: 10.1093/bioinformatics/btu638) with the intersection-strict mode. For comparison, we also applied Kallisto - a new ultra-fast RNASeq quantification method based on pseudoalignment (doi: 10.1038/nbt.3519). For this purpose, transcriptome information was obtained from the genome file using gffread (version 0.9.12) (http://ccb.jhu.edu/software/stringtie/gff.shtml) to build the required index and gene level counts were estimated using tximport (doi: 10.12688/f1000research.7563.2).
Genome_build: WBcel235
Supplementary_files_format_and_content: Raw read counts for genes were obtained using HTSeq or Kallisto/Tximport

organism: Caenorhabditis elegans

source_name: Whole tissue

growth_protocol: Around 350 to 400 L1 C. elegans N2 were grown in individual wells of a 12-well plate and supplemented with E. coli OP50, until the worms reached the adult day 1 stage (72 hours at 21˚C).

extract_protocol:
The contents of the wells were centrifuged at 1,000 rpm for 2 minutes, the supernatant was decanted and the worm pellet was washed twice with 1X M9 buffer. 200 µl of Trizol (Ambion, USA) was then added to the worm pellet. The worm pellet then was flash-frozen in liquid nitrogen, followed by a quick thaw. These two steps were repeated once.
RNA libraries were prepared with standard Illumina protocols

treatment_protocol: C. elegans (adult day 1 stage) was incubated in wells containing either 0, 10 µg/ml Ag nanoparticles or 10 µg/ml SiO2 nanoparticles

value: Whole worm

value: adult day 1 stage


title: Sample 12_Incubation with SiO2

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 12


title: Sample 13_Incubation with SiO2

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 13


title: KM3_ATAC

city: PORTLAND

first: Yulong

last: Su

state: OR

address: Oregon Health & Science University CLSB, 4N082, 2730 SW Moody Ave

department: MMG

institute: Oregon Health & Science Univeristy

data_processing:
Base calling - using RTA Version 1.13.48.0.
Conversion to FASTQ using CASAVA 1.8.2.
Reads were aligned using boa men followed by duplicate removal using samtools.
Peaks were called using mac s2 with default parameters.
We then constructed a sites × samples counts matrix that served as the basis for all subsequent analyses using the union peak setWe then constructed a sites × samples counts matrix that served as the basis for all subsequent analyses using the union peak set
Genome_build: mm10
Supplementary_files_format_and_content: File in bed format with merged peak locations from all ATAC-seq samples.

source_name: mouse embryonic fibroblasts

growth_protocol: Cells were maintained and plated in DMEM with 10% FBS and pen/strep

extract_protocol: ATAC-seq was performed using the Omni-ATAC protocol (Corces et al., 2017).

treatment_protocol: Passage 2 primary wildtype or PIN1 knockout MEFs were grown to denstiy arrest. Cells were split to ~50% confluency in 0.2% FBS media and starved for 2 days. ChIPs were done 4 hrs post serum stimulation by 20% FBS media.

value: mouse embryonic fibroblasts

value: PIN1 knockout

tag: starved/stimulated

value: Stimulated


title: cKO mKC


title: Sample 11_Incubation with SiO2

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 11


title: Sample 15_Incubation with SiO2

description:
read_counts_HISAT2_HTSeq.csv; read_counts_Kallisto_Tximport.csv
Sample 15


title: HEC-1A_siControl

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from HEC-1A cells treated with control siRNA

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

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

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: HEC-1A cells treated with siControl

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

growth_protocol: Human endometrial cancer cells, Ishikawa and HEC-1A, were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum.

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

treatment_protocol: Cells were transfected with Efp siRNA or control siRNA.


title: HEC-1A_siEfp

description: Gene expression data from HEC-1A cells treated with siRNA targeting Efp

source_name: HEC-1A cells treated with siEfp


title: scr-shRNA ECs pool 3

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

hyb_protocol: 750 ng of cRNA was hybridized on HumanHT-12_v.4 for 18 h. Array washes were performed using wash buffer

scan_protocol: Hybridized BeadChips were scanned using illumina Array reader

data_processing: Cubic Spline-normalized probe intensity data, togheter with detection p-values, were obtained using the GenomeStudio software v2011.01 (Illumina)

source_name: Human endothelial cells isolated from veins of umbilical cords (HUVEC)  infected with pLKO.1-puro vector (scr-shRNA ECs)

label_protocol: Bioinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit (Life Technologies)

growth_protocol: Human ECs were isolated from veins of umbilical cords and maintained as described (Eremina et al., 2003; Sison et al., 2010). To minimize cell variability, pools of 5 different donors were used.

extract_protocol: Total RNA was extracted from scr-shRNA ECs and sh-TFEB ECs with miRNeasy mini kit (Qiagen)

treatment_protocol: Loss-of-function experiments were carried out with shRNAs against TFEB (TRCN0000013111, NM_007162.2; Sigma) cloned in pLKO.1-puro non-Mammalian vector.   ECs were transduced with specific lentiviral particles (MOI=1) prepared according to (Eremina et al., 2008; Eremina et al., 2003) in the presence of 8 μg/ml polybrene (Sigma). After 24h the medium was replaced, and cells stably expressing the lentivirus were selected by puromycin (1 μg/ml, Sigma) for 24h.


title: KV3_ATAC

value: Starved


title: KV2_ATAC


title: NHF_p62_rep3

city: TORONTO

first: Haiyang

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

hyb_protocol: Agilent Gene Expression Hybridization Kit was using according to the manusfacturer's instructions.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing: Data was extracted using Agilent Feature Extraction software.  Normalization was performed using the normalizeBetweenArrays function from R package limma with method=quantile.

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

growth_protocol: NHFs was cultured in DMEM supplemented with 10% FBS (Gibico). Cells were cultured in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol: Prepare the RNA sample using TRIzol® Reagent. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.

treatment_protocol: We used (normal human fibroblasts) NHFs at passage 62 as replicative senescence model and NHFs at passage 11 as control. To obtain oxidative stress-induced senescent cells, we applied a single dose of 600μM H2O2 to NHFs at passage 11 for five days.

value: Foreskin

value: NHF

value: passage 62


title: sh-TFEB ECs pool 2

source_name: Human endothelial cells isolated from veins of umbilical cords (HUVEC)  infected with specific shRNA against TFEB (sh-TFEB ECs)

value: HUVEC


title: Ishikawa_siControl

description: Gene expression data from Ishikawa cells treated with control siRNA

source_name: Ishikawa cells treated with siControl

value: Ishikawa