title: yFR083_sas3delta_Spt16vsinput_repl2_20131119

description:
Biological replicate 2 of 2. FACT (Spt16) occupancy by ChIP-chip in sas3Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR083_sas3delta_Spt16vsinput_rep1-2_20131119_S.cerevisiaeApr11_720064.bed

data_processing:
BED description:  A genome browser-ready file for Spt16 occupancy by ChIP-chip (IP/Input) in sas3Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Spt16 (a gift from T. Formosa, 1 μL). 50 μL of Dynabeads coated with Protein G (Thermo Fisher Scientific, 10004D) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0, sas3{delta}kanMX


title: cell22

status: Public on Jul 26 2021

type: SRA

city: Beijing

first: Zeyuan

last: Liu

address: 15 Datun Road, Chaoyang District, Beijing, 100101, China

country: China

institute: Institute of Biophysics,Chinese Academy of Sciences

description:
rep3-OP_lp13
smart-seq-raw-counts-for-geo.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling
Reads were aligned to GRCm38 mouse genome and mm10 mouse genome by STAR(v2.5.3a) and Cellranger(v3.0.2)
Filtered count matrix was merged by Seurat Package
Genome_build: GRCm38, mm10
Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx and txt file, and barcode and gene information was with tsv format

molecule: total RNA

organism: Mus musculus

source_name: mouse brain

extract_protocol:
Mouse brain samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single nuclei were extracted by lysis buffer
Chromium™ Single Cell 3’ Reagent Kits v3

tag: age

value: 3 months

tag: tissue

value: brain

tag: region

value: superior colliculus

tag: sequencing stragery


title: cell21

description:
rep3-OP_lp12
smart-seq-raw-counts-for-geo.txt


title: polysome_4_snoRA37

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

description: Mouse liver polysome profiling by Illumina NovaSeq 6000

data_processing:
Reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) by using fastp and aligned to mouse rRNA by using bowtie2.
Unmapped reads were extracted by using samtools.
Reads were aligned to the mouse transcriptome (Ensembl version 102) using kallisto and transcript counts were converted to gene counts using tximport.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Liver

extract_protocol:
Input RNA for transcriptome studies was recovered from liver tissue lysed in polysome buffer using Trizol LS and RNeasy mini kit (Qiagen) including on column DNase digestion. For translatome studies, RNA was recovered from corresponding polysome fractions by Trizol-LS extraction, followed by chloroform-isopropanol-ethanol precipitation, heparinase treatment (New England Biolabs, 15 minutes, 37°C), and RNA cleanup step using RNA Clean & Concentrator (Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: type

value: polysome

tag: mouse

tag: group


title: polysome_12_snoRA37


title: polysome_6_snoRA37


title: G6E11_b2_2mo

city: New York

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Digital expression was carried out using Drop-Seq tools
STAR v2.5.2a was used for read alignments
HTO antibodies were counted using CITE-Seq Count (v1.4.2) and demultiplexed using Seurat v3.0
Cells with <200 detectable genes, <500 reads and >20% mitochondrial rate were removed using Seurat v3.0(dev)
Data were integrated using SCTransform (Seurat v3.0 (dev)) and annotated using SingleR with custom reference libraries built from Polioudakis et al. Neuron, 2019 and Zhang et al. Neuron, 2016
Genome_build: Hg19
Supplementary_files_format_and_content: Gene read counts per cell

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC-derived cerebral organoid

growth_protocol: Cerebral organoids were generated as per previously published protocol - see Yoon et al. Nature Methods, 2019.

extract_protocol:
Organoids were dissociated into single cell suspensions using Papain (Worthington). Resulting cells were labelled with hash-tag oligonucleotide antibodies as described in Stoeckius et al. Genome Biology, 2018.
Libraries were prepared and sequenced using either the 10x Genomics Single Cell v2 or v3 platforms. Libraries were sequenced with either a 26x90bp or 28x90bp read length
Single-cell RNA sequencing

treatment_protocol: No treatment

tag: cell line

value: 2 months

tag: batch

tag: genotype


title: FT194_NMNAT-2_Input rep2.fastq.gz

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Replicates merged

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

source_name: FT194 Cells

growth_protocol: OVCAR3 cells were cultured in RPMI media containing 10% FBS, 1% Pencillin-streptavidin, 1% Glutamax and 250 µg/mL G418 . FT194 cells were cutured in DMEM-F12 media containing 10% FBS and 150 µg/mL G418

extract_protocol:
Input RNA and polysome associated RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions from 2 individual 15 cm plates per replicate per treatment.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate RNA-seq libraries. The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina Nextseq 500.

treatment_protocol: OVCAR3 cells were transfected with lentiviral particles encoding for GFP or NMNAT-2 and positive clones were selected using 500 µg/mL G418 The cells were maintained in 250  µg/mL G418 after selection. FT194 cells were transfected with lentiviral particles encoding for vector or NMNAT-2 and positive clones were selected and maintained in 250  µg/mL G418.

tag: genotype/variation

tag: rna isolated from

value: inputs

tag: molecule subtype

value: cDNA from reverse transcribed RNA


title: cell20

description:
rep2-InG_ZI19
smart-seq-raw-counts-for-geo.txt


title: yFR083_sas3delta_Spt16vsinput_repl1_20131119

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 1 of 2. FACT (Spt16) occupancy by ChIP-chip in sas3Δ cells. Spt16 ChIP sample (Cy5-labeled) was performed using a rabbit polyclonal antibody against Spt16 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR083_sas3delta_Spt16vsinput_rep1-2_20131119_S.cerevisiaeApr11_720064.bed

hyb_protocol: ChIP and control samples were combined and dried by SpeedVac. Combined samples were resuspended in 110 µL of fresh hybridization mix (5 µL 10 mg/mL Salmon Sperm DNA (Thermo Fisher Scientific, 15632011), 5 µL 8 mg/mL Yeast tRNA (Thermo Fisher Scientific, 15401011) and 100 µL DIG Easy Hyb (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 45˚C. Samples were hybridized to Agilent microarrays in SureHyb enabled chambers (Agilent, G2534A) with rotation at 42˚C for at least 18 hr. Microarrays were washed on an orbital shaker for 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-Lauroylsarcosine), followed by a second wash with pre-warmed (31˚C) Wash II buffer (0.06X SSPE) for 5 min at room temperature. The microarrays used were described before (Jeronimo and Robert, 2014) and were custom designed by Agilent Technologies and contain a total of about 180,000 Tm-adjusted 60-mer probes covering the entire yeast genome with virtually no gaps between probes.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: The ChIP and Input samples were blunted as follow. 40 µL of ChIP DNA or about 400 ng of Input DNA were added to 70 µL of blunting¬¬ mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples Input DNA or no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: 50 mL of YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

tag: strain

tag: chip antibody

value: anti-Spt16 (a gift from T. Formosa, 1 uL)

extract_protocol:
IP protocol:  none
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


title: cell19

description:
rep2-InG_ZI18
smart-seq-raw-counts-for-geo.txt


title: G7A01_b3_2mo_NDB06_b3_2mo_NDB09_b3_2mo


title: FT194_NMNAT-2_Input rep1.fastq.gz

description: Replicates merged


title: polysome_10_snoRA37


title: cell23

description:
rep3-OP_lp15
smart-seq-raw-counts-for-geo.txt


title: yFR083_sas3delta_Rpb3vsinput_repl2_20131119

description:
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in sas3Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR083_sas3delta_Rpb3vsinput_rep1-2_20131119_S.cerevisiaeApr11_806971.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in sas3Δ cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

extract_protocol:
IP protocol:  Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (Neoclone W0012, 3 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup protocol:  Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: anti-Rpb3 (Neoclone W0012, 3 uL)


title: G7F02_b3_2mo_G6A02_b3_2mo


title: cell18

description:
rep2-InG_ZI17
smart-seq-raw-counts-for-geo.txt


title: FT194_Vec_Polysome rep2.fastq.gz

description: Replicates merged

value: vector

value: polysome fractions


title: yFR083_sas3delta_Rpb3vsinput_repl1_20131119

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in sas3Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR083_sas3delta_Rpb3vsinput_rep1-2_20131119_S.cerevisiaeApr11_806971.bed


title: polysome_9_GFP

value: GFP


title: polysome_11_snoRA37


title: yFR117_WT_Rpb3vsInput_repl2_20130731

description:
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
SmthBED_yFR117_WT_Rpb3vsInput_Rep1-2_20130731_S.cerevisiaeApr11_292139.bed

data_processing:
BED description:  A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells.
BED method:  The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalization = limma loess (subgrid)

value: MATa, his3{delta}1, leu2{delta}0, met15{delta}0, ura3{delta}0


title: cell17

description:
rep2-InG_ZI16
smart-seq-raw-counts-for-geo.txt


title: polysome_8_GFP


title: NDB06_b3_2mo_NDB09_b3_2mo


title: polysome_3_GFP


title: cell16

description:
rep2-InG_ZI14
smart-seq-raw-counts-for-geo.txt


title: cell15

description:
rep2-InG_ZI13
smart-seq-raw-counts-for-geo.txt


title: polysome_2_GFP


title: G7B12_b2_2mo_G7F02_b2_2mo


title: NDB06_b2_2mo_NDB09_b2_2mo_G7A01_b1_2mo (BOW_14_2)


title: G6A02_b2_2mo_G7A01_b2_2mo


title: G6E11_b3_2mo_G7B12_b3_2mo


title: cell14

description:
rep2-InG_ZI12
smart-seq-raw-counts-for-geo.txt


title: OVCAR3_siNMNAT-2_mNMNAT2 Polysome-rep2.fastq.gz

description: Replicates merged

source_name: OVCAR3 cells

value: OVCAR3 transfected with siNMNAT-2 and mNMNAT


title: FT194_Vec_Input rep1.fastq.gz

description: Replicates merged


title: FT194_Vec_Polysome rep1.fastq.gz

description: Replicates merged


title: OVCAR3_siNMNAT-2_mNMNAT2 Input-rep2.fastq.gz

description: Replicates merged


title: cell13

description:
rep2-InG_ZI11
smart-seq-raw-counts-for-geo.txt


title: input_4_snoRA37

value: input


title: FT194_Vec_Input rep2.fastq.gz

description: Replicates merged


title: OVCAR3_siNMNAT-2_mNMNAT2 Polysome-rep1.fastq.gz

description: Replicates merged


title: NDB06_b2_2mo_NDB09_b2_2mo_G7A01_b1_2mo (BOW_14_1)


title: OVCAR3_siNMNAT-2_mNMNAT2 Input-rep1.fastq.gz

description: Replicates merged


title: input_12_snoRA37


title: input_6_snoRA37


title: G6E11_b1_2mo_G6A02_b1_2mo


title: G7B12_b1_2mo_G7F02_b1_2mo


title: cell10

description:
rep2-InG_ZI3
smart-seq-raw-counts-for-geo.txt


title: polysome_1_GFP


title: OVCAR3_siNMNAT-2_GFP Polysome-rep2.fastq.gz

description: Replicates merged

value: OVCAR3 transfected with siNMNAT-2 and GFP


title: OVCAR3_siNMNAT-2_GFP Polysome-rep1.fastq.gz

description: Replicates merged


title: NDB06_b1_4mo

value: 4 months


title: input_10_snoRA37


title: cell12

description:
rep2-InG_ZI5
smart-seq-raw-counts-for-geo.txt

value: 3 months


title: OVCAR3_siNMNAT-2_GFP Input-rep2.fastq.gz

description: Replicates merged


title: input_9_GFP


title: cell08

description:
rep1-OP_lp10
smart-seq-raw-counts-for-geo.txt

value: brain


title: NDB06_b1_2mo_NDB09_b1_2mo (BOW13770_2)


title: input_3_GFP

description: Mouse liver polysome profiling by Illumina NovaSeq 6000


title: cell07

description:
rep1-OP_lp9
smart-seq-raw-counts-for-geo.txt

value: superior colliculus


title: NDB06_b1_2mo_NDB09_b1_2mo (BOW13770_1)


title: input_8_GFP


title: 11_16PCW Retina [scATAC-seq]

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

library_source: genomic

data_processing:
Peaks were detected using Cellranger ATAC software (version 1.2) in each of the samples. A set of shared peaks was then defined using the Cellranger ATAC aggregate function.
Genome_build: GRCh38
Supplementary_files_format_and_content: The peak files, peak annotation and cell metadata files are provided

source_name: Retina

extract_protocol:
Retinal tissue was excised from donated eyes and dissociated to single cells using a multi tissue dissociation kit (Miltenyi Biotec). Dissociation time varied from 15 to 45 minutes depending on the age of the tissue and a gentleMACS Dissociator (Miltenyi Biotec) was used to aid dissociation of the adult tissue.
For scATAC-Seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit, version 1 (10x Genomics).

tag: developmental stage

value: Retina


title: Polysome for PARP16 KD2 Replicate2

source_name: OVCAR3_Polysome for PARP16 KD2

growth_protocol: OVCAR3 cells were cultured in RPMI media containing 10% FBS, 1% Pencillin-streptavidin, 1% Glutamax and 0.5 µg/mL puromycin

treatment_protocol: OVCAR3 cells were transfected with lentiviral particles encoding for Control or NMNAT-2 or PARP-16 shRNAs and positive clones were selected using 1  µg/mL puromycin. The cells were maintained in 0.5  µg/mL puromycin after selection

value: PARP16 knockdown with shRNA #2


title: cell06

description:
rep1-OP_lp7
smart-seq-raw-counts-for-geo.txt


title: cell05

description:
rep1-OP_lp5
smart-seq-raw-counts-for-geo.txt


title: cell11

description:
rep2-InG_ZI4
smart-seq-raw-counts-for-geo.txt


title: input_2_GFP


title: 10_16PCW Retina [scATAC-seq]


title: input_1_GFP


title: cell04

description:
rep1-OP_lp4
smart-seq-raw-counts-for-geo.txt


title: input_11_SnoRA37


title: 9_10PCW Retina [scATAC-seq]


title: cell09

description:
rep2-InG_ZI2
smart-seq-raw-counts-for-geo.txt


title: NDB09_b1_4mo


title: Polysome for PARP16 KD1 Replicate1

source_name: OVCAR3_Polysome for PARP16 KD1

value: PARP16 knockdown with shRNA #1


title: cell03

description:
rep1-OP_lp3
smart-seq-raw-counts-for-geo.txt


title: Polysome for PARP16 KD1 Replicate2

value: cDNA from reverse transcribed RNA


title: Polysome for Control KD for PARP-16 Replicate2

source_name: OVCAR3_Polysome for Control KD for PARP-16

value: Control shRNA knockdown


title: OVCAR3_siNMNAT-2_GFP Input-rep1.fastq.gz

description: Replicates merged

value: inputs


title: Polysome for PARP16 KD2 Replicate1


title: cell02

description:
rep1-OP_lp2
smart-seq-raw-counts-for-geo.txt


title: splenic T cells, SV.Spike+aOX40 4 RNA-seq

city: NYC

first: Silvana

last: Opp

address: 550 1st Avenue

department: Pathology

institute: NYU School of Medicine

description: replicate 4

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the STAR pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: splenic T cells

growth_protocol: T cells were freshly isolated from the mice spleens

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit including DNASE1 treatment. Quality control was performed with Agilent Bioanalyser.
30 Automated stranded RNA-seq library prep, polyA selection, per sample, minimum 16 samples

treatment_protocol: Prime vaccine doses administered on day 0, T cells isolated at day 7

tag: cell type

value: splenic T cells

tag: treatment group


title: 8_Retinoblastoma_2_years [scATAC-seq]

source_name: Retinoblastoma

tag: tissue

value: Retinoblastoma


title: cell01

description:
rep1-OP_lp1
smart-seq-raw-counts-for-geo.txt

tag: age

tag: region


title: 6_20PCW Retina [scATAC-seq]


title: splenic T cells, SV.Spike+aOX40 2 RNA-seq

description: replicate 2


title: splenic T cells, SV.Spike+aOX40 5 RNA-seq

description: replicate 5


title: Input for PARP16 KD2 Replicate2

source_name: OVCAR3_Input for PARP16 KD2


title: 5_12PCW Retina [scATAC-seq]


title: splenic T cells, SV.Spike+aOX40 1 RNA-seq

description: replicate 1


title: ML3

city: Lanzhou

first: wei

middle: shang

last: Li

address: No. 335, Qilihe District

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Science

data_processing:
clean reads  were used for assembly and subsequent analysis. Then De Novo assembly was performed on the reads after quality control using Trinity software.
Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set
Genome_build: de novo
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Alternaria oxytropis

source_name: mycelia

extract_protocol:
Mycelias were flash frozen on dry ice, and RNA was harvested using Trizol reagent. the library preparations were sequenced on an Illumina Hiseq 2000 platform and paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

tag: treatment

value: supplement with L- lysine


title: 4_16PCW Retina [scATAC-seq]


title: 7_21PCW Retina [scATAC-seq]


title: ML2


title: Polysome for Control KD for PARP-16 Replicate1

value: polysome fractions


title: splenic T cells, SV.Spike+aOX40 3 RNA-seq

description: replicate 3


title: ML1


title: 3_12PCW Retina [scATAC-seq]


title: MC3

value: non-supplement with L- lysine


title: splenic T cells, aOX40 4 RNA-seq

description: replicate 4


title: 2_Retinoblastoma_4months [scATAC-seq]


title: 1_20PCW Retina [scATAC-seq]


title: Input for PARP16 KD2 Replicate1


title: MC1


title: 12_16PCW_Retina [scRNA-seq]

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: The filtered count, barcode matrix from cellranger are provided

extract_protocol:
Retinal tissue was excised from donated eyes and dissociated to single cells using a multi tissue dissociation kit (Miltenyi Biotec). Dissociation time varied from 15 to 45 minutes depending on the age of the tissue and a gentleMACS Dissociator (Miltenyi Biotec) was used to aid dissociation of the adult tissue.
For scRNA-Seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics)


title: splenic T cells, aOX40 2 RNA-seq

description: replicate 2


title: 13_16PCW_Retina [scRNA-seq]


title: splenic T cells, aOX40 1 RNA-seq

description: replicate 1


title: splenic T cells, SV.Spike 4 RNA-seq

description: replicate 4


title: 11_2years_Retinoblastoma [scRNA-seq]


title: splenic T cells, SV.Spike 5 RNA-seq

description: replicate 5


title: 10_2years_Normal_Tissue [scRNA-seq]


title: splenic T cells, aOX40 5 RNA-seq

description: replicate 5


title: splenic T cells, SV.Spike 3 RNA-seq

description: replicate 3


title: 9_4months_Retinoblastoma [scRNA-seq]


title: MC2


title: splenic T cells, SV.Spike 2 RNA-seq

description: replicate 2


title: Polysome for Control KD for NMNAT-2 Replicate2

source_name: OVCAR3_Polysome for Control KD for NMNAT-2


title: Input for PARP16 KD1 Replicate2

source_name: OVCAR3_Input for PARP16 KD1


title: Polysome for NMNAT2 KD2 Replicate2

source_name: OVCAR3_Polysome for NMNAT2 KD2

value: NMNAT2 knockdown with shRNA #2


title: Polysome for NMNAT2 KD1 Replicate2

source_name: OVCAR3_Polysome for NMNAT2 KD1

value: NMNAT2 knockdown with shRNA #1


title: Input for Control KD for PARP-16 Replicate2

source_name: OVCAR3_Input for Control KD for PARP-16


title: Polysome for NMNAT2 KD1 Replicate1


title: Input for Control KD for PARP-16 Replicate1


title: Polysome for Control KD for NMNAT-2 Replicate1


title: Input for PARP16 KD1 Replicate1


title: Polysome for NMNAT2 KD2 Replicate1


title: splenic T cells, SV.Spike 1 RNA-seq

description: replicate 1


title: splenic T cells, aOX40 3 RNA-seq

description: replicate 3


title: 7_20PCW_Retina [scRNA-seq]


title: Input for NMNAT2 KD2 Replicate2

source_name: OVCAR3_Input for NMNAT2 KD2


title: splenic T cells, naïve 5 RNA-seq

description: replicate 5

value: naive


title: splenic T cells, naïve 4 RNA-seq

description: replicate 4


title: Input for NMNAT2 KD2 Replicate1


title: 6_16PCW_Retina [scRNA-seq]


title: 5_12PCW_Retina [scRNA-seq]


title: Input for NMNAT2 KD1 Replicate2

source_name: OVCAR3_Input for NMNAT2 KD1


title: splenic T cells, naïve 3 RNA-seq

description: replicate 3


title: 4_15PCW_Retina [scRNA-seq]


title: Input for NMNAT2 KD1 Replicate1


title: Input for Control KD for NMNAT-2 Replicate2

source_name: OVCAR3_Input for Control KD for NMNAT-2


title: 2_21PCW_Retina [scRNA-seq]


title: 3_20PCW_Retina [scRNA-seq]


title: 1_10PCW_Retina [scRNA-seq]


title: Input for Control KD for NMNAT-2 Replicate1


title: splenic T cells, naïve 2 RNA-seq

description: replicate 2


title: splenic T cells, naïve 1 RNA-seq

description: replicate 1


title: Pancreatic islets cells from MIP-GFP; Ppy-Cre; Rosa26-tdTomato mouse

city: Maebashi

first: Yoshio

last: Fujitani

state: Gunma

address: 3-39-15 Showa-machi,

department: Developmental Biology and Metabolism

country: Japan

institute: Institute for Molecular and Cellular Regulation

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq2 (ver2.20).
Sequence data was processed using Cell Ranger 4.0.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rawUMI_matrix.txt: raw UMI count matrix data (tsv).

source_name: mouse pancreatic islets cells

extract_protocol:
Islet isolation was performed by collagenase (Sigma Aldrich) digestion of the adult pancreas. For the single-cell suspension of islets, mouse islets were handpicked in a 200 µL WATSON tube, pelleted (1,000 rpm, 1 min), washed with PBS, and digested with 0.05% trypsin EDTA (Nacalai Tesque) at 37 °C for 3 min with some mechanical digestion. A single cell suspension was obtained by filtering with a 40 µm cell strainer.
Library preparation were performed with the Single Cell 3' Library & Gel Bead Kit v3.1 according to the 10X Genomics' standard protocol.

value: MIP-GFP; Ppy-Cre; Rosa26-tdTomato mice with a mixed background of C57BL/6J and CD-1

value: 8 weeks

tag: Sex

value: male

value: pancreatic islets cells


title: 20

status: Public on Jul 25 2021

city: Northridge

first: Yoshie

last: Hanzawa

state: California

address: 18111 Nordhoff Street, CR 5217

department: Biology

institute: California State University, Northridge

data_processing:
Trimmomatic v0.36 was used to trim the low-quality base calls and the adapter content in single end mode with the adapter in TruSeq3-SE.fa, a leading and trailing base call threshold of 28 and a minimum read length of 30.
STAR v2.5.2b was used to align the reads with the --quantMode GeneCounts option to the reference genome file and the gene annotation file obtained from Phytozome.
the (relative) abundance of the mRNAs in transcripts per million (TPM) was quantitated using the relative mapping efficiency model.
Genome_build: Glycine max Wm82.a2.v1 (Soybean), release date: 6/10/2015, BioProject: PRJNA19861, Accession ID: ACUP02000000.
Supplementary_files_format_and_content: csv files include raw counts and normalized expression levels.

organism: Glycine max

source_name: The whole shoot above cotelydon

growth_protocol: soybeans were grown in either long day (14-hour) or short day (10-hour) conditions at 25C for 3 weeks.

extract_protocol:
RNA samples were prepared using the GeneJET Plant RNA Purification Kit following the manufacturer's protocol (ThermoFisher GeneJET #K0802)
RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq® Stranded mRNA Sample Preparation Guide)

treatment_protocol: 3 weeks after germination, soybeans were moved to long day (14-hour) or short day (10-hour) conditions at 16C, 25C or 32C.

value: The whole shoot above cotelydon

tag: temperature (celsius)

tag: photoperiod

value: LD

tag: sample time


title: 21

value: SD

tag: genotype


title: 23


title: Gene electrotransfer GET condition, biological rep 2

type: RNA

city: Toulouse

first: Laure

last: Gibot

address: 118 route de Narbonne

department: University Paul Sabatier

country: France

institute: CNRS

description: Gene expression data from one human dermal substitute exposed to pulsed electric field of GET type (x10, 5ms, 600V/cm, 1Hz) only, no addition of external molecules

hyb_protocol: Following fragmentation, 5 µg of ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Human Clariom S. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing:
CEL files data were analyzed using Transcriptome Analysis Control (TAC) software. Expression analysis settings were as follow: Gene-Level Fold Change < -2 or > 2; Gene-Level FDR < 0,05; Anova Method: ebayes; A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.; DABG < 0,05
affymetrix-algorithm-name = gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

source_name: Dermal substitute exposed to pulsed electric field of GET type (x10, 5ms, 600V/cm, 1Hz)

label_protocol: Biotinylated ss-cDNA were prepared according to the Affymetrix GeneChip Pico Reagent protocol from 5 ng total RNA (Manual Target Preparation for GeneChip, Expression Arrays, UserGuide, P/N 703308 REV 4, Affymetrix).

growth_protocol: 30,000 cells/cm² primary human dermal fibroblasts were seeded in 24-well plates. Cells were cultivated for 4 weeks in DMEM cell culture medium supplemented with 50 µg/ml of ascorbic acid. On the day of treatment, after 4 weeks of culture, substitutes are made up of 108,000 ± 6630 cells

extract_protocol: RNAs were extracted 4 hours after dermal substitutes electrostimulation using RNeasy Mini kit (Qiagen #74104) according to the manufacturer's recommendations. Extraction was facilitated using TissueLyser II (Qiagen) and 5 mm diameter stainless steel balls

treatment_protocol: Four-weeks old dermal substitutes were exposed to pulsed electric field using stainless plate electrodes and replaced in cell culture medium in the incubator for 4hours

tag: gender

value: Male

value: Foreskin dermis


title: Gene electrotransfer GET condition, biological rep 4

value: exposed to pulsed electric field of GET type (x10, 5ms, 600V/cm, 1Hz)


title: 19


title: 6H08


title: LA04


title: 6F04


title: Gene electrotransfer GET condition, biological rep 1


title: Electrochemotherapy ECT condition, biological rep 3

description: Gene expression data from one human dermal substitute exposed to pulsed electric field of ECT type (x8, 100µs, 1000V/cm, 1Hz) only, no addition of external molecules

source_name: Dermal substitute exposed to pulsed electric field of ECT type (x8, 100µs, 1000V/cm, 1Hz)


title: 8_4months_Normal_Tissue [scRNA-seq]

value: Retinoblastoma


title: 6C03


title: 3G09


title: Electrochemotherapy ECT condition, biological rep 1

value: exposed to pulsed electric field of ECT type (x8, 100µs, 1000V/cm, 1Hz)


title: 3G08


title: Electrochemotherapy ECT condition, biological rep 4


title: 1C05


title: 3F03


title: 3C01


title: Control condition, biological rep 3

description: Gene expression data from one human dermal substitute not treated (control condition)

source_name: Dermal substitute no treatment

value: no treatment


title: Control condition, biological rep 4


title: Control condition, biological rep 2


title: 1G05


title: Control condition, biological rep 1


title: 1A06


title: 1A07


title: 1A05


title: 1A08


title: 7_E11

value: Sh


title: 8H06


title: 6C02


title: Gene electrotransfer GET condition, biological rep 3


title: 6G07


title: 1A03


title: 7B08


title: 6G05


title: 6A05


title: 2A12


title: 1C04


title: 4F03


title: 3F01


title: 1B06


title: 2C01


title: 3D04


title: 4F02


title: 4F12


title: 2F09


title: 3G10


title: 2A08


title: 1D12


title: 1A04


title: 1_E05


title: 1D02


title: 1C03


title: 7H09


title: 1_E04


title: 5F08


title: 7D12


title: 7C07


title: 7_00E_04


title: 3H04


title: 7C04


title: 3G05


title: 3F12


title: Electrochemotherapy ECT condition, biological rep 2


title: 3C03


title: 3F02


title: 2G06


title: 2_00E_12


title: 1H05


title: 1_00E_10


title: 1F04


title: 1_00E_06


title: YH40_9C4


title: YH40_9F3


title: YH40_7A2


title: YH40_6E3


title: YH40_6D8


title: YH40_7A5


title: YH40_6B7


title: YH40_5B1


title: YH40_4B6


title: YH40_3E1


title: YH40_2G2


title: YH40_3H3


title: YH40_5B8


title: YH40_1E5


title: YH39_9E1


title: YH39_9D2


title: YH39_8F3


title: YH39_9A5


title: YH40_3D6


title: YH39_6B12


title: YH39_8B6


title: YH40_9C7


title: YH39_4F10


title: YH39_7F7


title: YH40_2E2


title: YH39_5G10


title: YH39_4D7


title: YH39_2D12


title: YH39_1D8


title: YH39_5E5


title: YH39_1G5


title: YH39_1E3


title: YH39_1A6


title: YH38_9B3


title: YH38_6C1


title: YH38_9F12


title: YH38_6A6


title: YH38_5G1


title: YH38_5E4


title: YH38_3G2


title: YH38_4G11


title: YH38_5D3


title: YH39_5F9


title: YH38_4C5


title: YH40_5C6


title: YH39_3C10


title: YH39_2B8


title: YH38_1H4


title: YH38_2F10


title: YH38_1H9


title: YH38_1C2


title: YH38_0B1


title: YH38_0A5


title: YH38_2A11


title: 1G11


title: YH37_8C5


title: YH37_9C1


title: YH37_7G11


title: YH37_7B5


title: YH37_6G8


title: YH37_6H5


title: YH37_6A4


title: YH37_5G7


title: YH37_5A5


title: YH38_1E9


title: YH37_3C7


title: YH37_3A3


title: YH37_4E9


title: YH37_2F4


title: YH37_2F11


title: YH37_1G1


title: YH36_9C9


title: YH36_8A6


title: YH36_7F11


title: YH36_9A1


title: YH37_1G2


title: YH37_8D11


title: YH36_6E1


title: YH37_7C6


title: YH36_6D6


title: YH36_6A11


title: YH37_7A11


title: YH36_5H4


title: YH36_6A2


title: YH36_5H10


title: YH36_3A12


title: YH37_5F10


title: YH36_2D5


title: YH36_2C1


title: YH36_1D2


title: YH35_9G2


title: YH35_9A11


title: YH36_8H5


title: YH37_5D2


title: YH35_8F7


title: YH35_8B3


title: YH35_7C10


title: YH35_5G12


title: YH35_3F4


title: YH35_4C7


title: YH35_3C2


title: YH35_2G5


title: YH35_2E4


title: YH35_2C6


title: YH35_2B12


title: YH35_2A6


title: YH35_1D3


title: YH36_2D8


title: YH34_8G10


title: YH36_2G9


title: YH34_9E4


title: YH34_7B1


title: YH35_9A3


title: YH34_6G2


title: YH34_4F11


title: YH35_6F11


title: YH34_5F12


title: YH35_6E10


title: YH34_4B3


title: YH34_5H5


title: YH34_4E6


title: YH34_1H8


title: YH33_9H8


title: YH34_2E11


title: YH34_9H6


title: YH34_1B8


title: YH34_1F10


title: YH33_8D6


title: YH34_0E1


title: YH33_8D2


title: YH33_7F9


title: YH33_8E2


title: YH33_7D1


title: YH33_6F10


title: YH33_8B4


title: YH33_3H6


title: YH34_7A4


title: YH33_4A2


title: YH33_3C5


title: YH33_2F3


title: YH34_5D1


title: YH33_4G12


title: YH33_2C4


title: YH33_1F1


title: YH33_1D7


title: YH32_9F2


title: YH33_2B5


title: YH32_6C6


title: YH32_4A1


title: YH32_7H3


title: YH32_1F3


title: YH32_7F12


title: YH32_7F10


title: YH32_1A11


title: YH32_1B4


title: YH32_4F8


title: YH31_6D12


title: YH32_3B11


title: YH31_6C9


title: YH32_6G12


title: YH31_7G12


title: YH32_9D5


title: YH32_6B2


title: YH31_5G9


title: YH31_5E2


title: YH31_4C2


title: YH31_4H10


title: YH31_4B7


title: YH31_3B6


title: YH31_5B2


title: YH31_8F10


title: YH32_4A6


title: YH31_7C1


title: YH31_1A4


title: YH30_7D5


title: YH31_1H3


title: YH30_9A8


title: YH30_8H3


title: YH31_6D7


title: YH30_5F7


title: YH30_7D4


title: YH30_9G6


title: YH30_4E11


title: YH30_4D11


title: YH30_3H9


title: YH30_6B5


title: YH30_5A4


title: YH30_5B6


title: YH30_2A2


title: YH31_5A11


title: YH31_5A1


title: YH30_2F12


title: YH30_1H5


title: YH30_1D1


title: YH30_0D2


title: YH30_4D12


title: YH30_1F11


title: YH29_6E6


title: YH29_5F11


title: YH29_5C10


title: YH29_6B4


title: YH30_7E6


title: YH29_5A7


title: YH29_4F1


title: YH29_4E1


title: YH29_3G6


title: YH29_4B12


title: YH29_3H7


title: YH29_3D5


title: YH29_3G12


title: YH29_3D2


title: YH29_2D7


title: YH29_4C6


title: YH29_4B11


title: YH29_1F9


title: YH28_8B11


title: YH29_1B1


title: YH29_1G7


title: YH28_6E5


title: YH28_5B12


title: YH28_9E2


title: YH29_2B3


title: YH28_6H4


title: YH28_4H8


title: YH28_8A3


title: YH28_4H5


title: YH28_4E12


title: YH28_3D8


title: YH29_2H3


title: YH28_8C3


title: YH28_2G1


title: YH28_1F4


title: YH28_1C6


title: YH28_0H3


title: YH28_0G3


title: YH27_9G9


title: YH27_9F7


title: YH27_9D6


title: YH27_8C4


title: YH27_9D11


title: YH28_0C2


title: YH27_3E12


title: YH27_3E3


title: YH27_2E10


title: YH27_2F2


title: YH27_1F8


title: YH27_4D5


title: YH27_5A12


title: YH27_3E2


title: YH27_2C9


title: YH26_9H9


title: YH27_1A8


title: YH27_1A2


title: YH26_9A6


title: YH26_8E9


title: YH26_7A12


title: YH26_9G11


title: YH26_8E10


title: YH26_6B1


title: YH26_6E4


title: YH26_5G5


title: 6D03


title: YH26_3C9


title: YH26_2G8


title: YH26_1E12


title: YH26_0F2


title: YH25_8E12


title: YH26_4G9


title: YH25_7E9


title: YH25_7A6


title: YH25_5H9


title: YH25_6C8


title: YH25_4G6


title: YH25_5C7


title: YH25_5C2


title: YH25_5B11


title: YH25_2H7


title: YH25_4A5


title: YH25_1D5


title: YH25_0H1


title: YH25_1G12


title: YH24_9H3


title: YH26_5H8


title: YH25_2C5


title: YH24_9F4


title: YH27_6B11


title: YH24_9G10


title: YH24_8D5


title: YH24_9C5


title: YH24_8D3


title: YH24_4H6


title: YH24_7H7


title: YH24_6H9


title: YH24_4E5


title: YH24_7G7


title: YH24_4B8


title: YH24_4B2


title: YH25_4G7


title: YH24_8C7


title: YH24_1C8


title: YH25_9G5


title: YH24_1E11


title: YH23_9A2


title: YH24_2A12


title: YH23_9E9


title: YH23_9B1


title: YH23_8B7


title: YH23_7A1


title: YH24_3B3


title: YH24_2G6


title: YH23_8G1


title: YH23_6H8


title: YH23_7F2


title: YH23_5F3


title: YH23_4A3


title: YH23_4D4


title: YH23_6G5


title: YH23_3C8


title: YH23_3H10


title: YH23_2C3


title: YH23_1G10


title: YH23_2A7


title: YH23_1E4


title: YH23_2B2


title: YH23_1C5


title: YH22_7B2


title: YH22_8D4


title: YH22_7G2


title: YH22_7E4


title: YH22_6D2


title: YH22_7E10


title: YH22_5B4


title: YH22_4D8


title: YH22_7E2


title: YH22_3G1


title: YH22_3H5


title: YH22_1H10


title: YH22_1C1


title: YH21_8B12


title: YH22_2A5


title: YH22_1B5


title: YH22_2B11


title: YH21_8A12


title: YH22_1C10


title: YH21_6G1


title: YH21_6B6


title: YH22_8F4


title: YH21_5G8


title: YH21_5E1


title: YH22_8D7


title: YH21_5A2


title: YH21_4H4


title: YH21_4B4


title: YH21_2A1


title: YH21_2E3


title: YH21_2H5


title: YH20_9E6


title: YH21_1C3


title: YH20_8H6


title: YH20_8E1


title: YH20_9G7


title: YH21_3H8


title: YH21_4A11


title: YH20_6H10


title: YH21_5H6


title: YH20_3D3


title: YH20_6A8


title: YH20_7C7


title: YH20_6F8


title: YH20_7H4


title: YH20_7F4


title: YH20_3C3


title: YH20_3B8


title: YH21_5E6


title: YH20_1E2


title: YH20_2E5


title: YH20_0B3


title: YH19_9B8


title: YH19_7E1


title: YH19_7D12


title: YH19_7C2


title: YH20_6C2


title: YH19_6A3


title: YH20_4C9


title: YH19_2H6


title: YH19_3E6


title: YH19_2D4


title: YH19_1B12


title: YH19_0C4


title: YH19_4G1


title: YH18_9E11


title: YH19_2C8


title: YH19_2B6


title: YH19_1B11


title: YH19_1A7


title: YH18_9A4


title: YH18_8H9


title: YH20_0B4


title: YH19_9C3


title: YH18_8C6


title: YH18_8C8


title: YH18_8B2


title: YH18_7H6


title: YH19_6G9


title: YH19_5G2


title: YH19_8B1


title: YH18_6H3


title: YH18_4D6


title: YH18_5D12


title: YH18_6B8


title: YH18_4C3


title: YH19_0B5


title: YH18_4A8


title: YH18_1F2


title: YH18_3A5


title: YH17_8H7


title: YH17_7D6


title: YH18_0G1


title: YH17_6H6


title: YH17_9B6


title: YH17_7D8


title: YH17_5D7


title: YH17_5D5


title: YH17_5E12


title: YH17_6A7


title: YH17_6D4


title: YH17_4G2


title: YH18_6C4


title: YH17_2D1


title: YH17_3A8


title: YH18_5A6


title: YH17_2B7


title: YH17_1A12


title: YH18_3G10


title: YH18_2G11


title: YH17_0C1


title: YH18_7H10


title: YH17_8B8


title: YH16_9E3


title: YH16_8D12


title: YH16_8F11


title: YH16_7F3


title: YH16_5D8


title: YH16_4H9


title: YH16_4G10


title: YH16_3C1


title: YH16_4H7


title: YH16_4D1


title: YH16_2E9


title: YH16_2C10


title: YH16_2D6


title: YH16_1H6


title: YH16_3B1


title: YH16_1C4


title: YH16_0C3


title: YH15_9F10


title: YH15_8G8


title: YH15_9C10


title: YH16_9C8


title: YH15_8G12


title: YH15_8G5


title: YH15_8C2


title: YH15_7H8


title: YH15_7G6


title: YH16_4G8


title: YH15_5E9


title: YH16_4A7


title: YH15_8A1


title: YH15_7B6


title: YH15_4F7


title: YH15_4C8


title: YH15_9E5


title: YH14_9H10


title: YH14_9F11


title: YH15_1C9


title: YH14_8H4


title: YH14_8F2


title: YH14_8H8


title: YH14_8E3


title: YH14_8D8


title: YH15_3C6


title: YH14_8A4


title: YH14_6G11


title: YH14_6F9


title: YH14_8A11


title: YH14_6C10


title: YH14_7A8


title: YH15_2G10


title: YH14_6A12


title: zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days [pollen CuSO4]

city: Parma

first: Luca

last: Pagano

address: Parco Area delle Scienze 11/A

department: Chemistry Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days.
POLLEN CuSO4

data_processing:
Base calling and demultiplexing.
Trimming (removing lower quality bases and adapters) using ERNE and Cutadapt softwares.
Alignments with STAR.
Transcripts count with Stringtie.
Quality control by using RSeqQC pack.
Genome_build: PRJNA386743 (ASM280686v2); http://cucurbitgenomics.org/
Supplementary_files_format_and_content: Normalized_data.txt: Tab-delimited text file includes FPKM values.

organism: Cucurbita pepo

source_name: plant tissue

growth_protocol: Cucurbita pepo L. (cv. Costata Romanesco) seeds were pre-germinated in vermiculite for 10 days prior to transplanting to soil.

extract_protocol:
Total RNA was extracted from 0.1 g of fresh plant material using a Sigma-Aldrich Spectrum Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
TruSeq Stranded mRNA kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions. RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent Technologies, Santa Clara, CA). Final libraries were checked Agilent Bioanalyzer DNA assay (Agilent Technologies, Santa Clara, CA).
Libraries were prepared for sequencing and sequenced on single-end 75 bp mode on NextSeq 500 (Illumina, San Diego, CA).

treatment_protocol: CuO NPs, CuO (bulk) or (copper sulfate) CuSO4 stock dispersions were slowly added to 500g of soil. The final concentration of CuO NPs and bulk in pots was 100 mg kg-1 while for CuSO4·5H2O (copper sulfate pentahydrate) was 320 mg kg-1, representing a total concentration of Cu about 80 mg kg-1 for all the treatments. Zucchini seedlings were planted (one each pot) and grown indoor under supplemental fluorescent lighting (60 μE m2 sec) under a photoperiod of 16h light, at approximately 22−28 °C until complete flowering. The plants were top watered for 60d growth period.

tag: cultivar

value: Costata Romanesco

value: Pollen


title: zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days [pollen CuO bulk]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days.
POLLEN CuO bulk

value: CuO bulk


title: YH15_3D7


title: zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days [pollen CuO NPs]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days.
POLLEN CuO NPs

value: CuO nanoparticles


title: YH14_6A1


title: YH14_5C5


title: YH15_1E10


title: YH14_6F3


title: zucchini grown in pot soil, for 60 days [pollen Cnt untreated]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, for 60 days.
POLLEN Cnt untreated

value: Untreated control


title: YH14_4D2


title: zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days [leaf CuO NPs]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days.
LEAF CuO NPs

value: Leaf


title: YH14_1H7


title: YH14_0G4


title: YH13_9H5


title: zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days [root CuSO4]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days.
ROOT CuSO4

value: Root


title: zucchini grown in pot soil, for 60 days [leaf Cnt untreated]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, for 60 days.
LEAF Cnt untreated


title: YH13_8E11

value: The whole shoot above cotelydon


title: YH13_8D1


title: zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days [root CuO bulk]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days.
ROOT CuO bulk


title: YH13_8A7


title: zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days [root CuO NPs]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO NPs (100 mg kg-1), for 60 days.
ROOT CuO NPs


title: YH13_7G9


title: zucchini grown in pot soil, for 60 days [root Cnt untreated]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, for 60 days.
ROOT Cnt untreated


title: YH14_6D1


title: YH13_7E5


title: YH13_7D11


title: zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days [leaf CuSO4]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuSO4 5H2O (320 mg kg-1), for 60 days.
LEAF CuSO4


title: YH13_7D2


title: YH13_6C7


title: YH13_6F12


title: YH13_7C9


title: zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days [leaf CuO bulk]

description:
Cucurbita pepo L. (cv. Costata Romanesco)
Zucchini grown in pot soil, with addition of CuO raw material (100 mg kg-1), for 60 days.
LEAF CuO bulk


title: YH13_5F2


title: YH13_3G7

value: LD


title: YH13_5C1

value: SD


title: YH13_4A4


title: ZfpKOTP-3

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua University

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTP-3

data_processing:
Raw reads were processed by trim_galore to get clean reads
The clean reads were mapped to the mouse genome (mm10) through STAR v2.2.0 with default settings.
FeatureCounts software was used to collect reads located in the coding sequence (CDS) of each gene.
CDS counts normalized to mappable reads were used for measuring gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing the raw and normalized CDS counts analyzed from RNA-seq

source_name: spleen

extract_protocol:
Approximately 1000 cells of desired type were lysed in 6 μl lysis buffer (0.2% Triton X-100 and 2 U/μl of RNase inhibitor). Lysates were mixed with 3 μl of anchored oligo-dT primer (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 μl of dNTP mix (10 mM, Fermentas), denatured at 72 °C for 3 min and immediately placed on ice afterwards. The first-strand reaction mix containing 1 μl SuperScript II reverse transcriptase (Invitrogen), 0.5 μl RNAse inhibitor (Clontech), 4 μl Superscript II First-Strand Buffer (Invitrogen), 1 μl DTT (100 mM, Invitrogen), 4 μl betaine (5 M, Sigma), 0.12 μl MgCl2 (1 M, Sigma), 0.2 μl TSO (100 μM) and 0.58 μl nuclease-free water, were added to each sample. Reverse transcription reaction was carried out by incubating at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). Finally, the reverse transcriptase was inactivated by incubation at 70 °C for 15 min. PCR mix containing 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl IS PCR primers (10 μM) and 1.1 μl nuclease-free water were added to each sample. The reaction was incubated at 98 °C for 3 min, then cycled 17 times (98 °C 20 s, 67 °C 15 s, 72 °C 6 min), with a final extension at 72 °C for 5 min. cDNAs were purified by Vazyme DNA clean beads following manufacturer's instructions. 1 ng of cDNA were used for the tagmentation reaction using Tn5 (Vazyme). The tagmentation reaction (20 μl) was incubated at 55 °C for 10 min and stopped by addition of 2 μl 0.2%SDS and incubated at 70 °C for 20 min. A second amplification was performed using Q5 polymerase (NEB) as follows: 72 °C 3 min, 98 °C 30 s, then 12 cycles of (98 °C 15 s, 60 °C 30 s, 72 °C 3 min), final extension at 72 °C 5 min. Libraries were purified using Vazyme DNA clean beads.
smart-seq2

value: B220+CD138-GL7-FAS-CD38+IgD-NIP-binding tdTomato+ B cells

value: Zfp318ZSDAT/ZSDAT AID-Cre B1-8hi GFP

tag: immunization

value: NP-OVA/LPS/Alum 7dpi


title: ZfpKOTP-2

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTP-2

tag: strain


title: ZfpKOTP-1

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTP-1


title: ZfpKOTN-4

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTN-4

value: B220+CD138-GL7-FAS-CD38+IgD-NIP-binding tdTomato- B cells


title: YH13_0C5


title: ZfpKOTN-3

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTN-3


title: YH13_1D6


title: YH13_3B5


title: MIAPaCa2_miR-766-5p_rep1

city: Tokyo

first: Yasuyuki

last: Gen

address: 1-5-45 Yushima, Bunkyo-ku, Tokyo

institute: Tokyo Medical and Dental University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained with Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after TURBO DNA-free™ Kit (Ambion, Austin, TX) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: mir-NC or miR-766-5p were transfected into cells using RNAiMax

tag: cell line

value: Pancreatic cancer

tag: transfection


title: HCT116-/-_miR-766-5p_rep1

value: Colon cancer


title: MIAPaCa2_miR-766-5p_rep2


title: HCT116-/-_miR-NC_rep1

value: miR-NC


title: MIAPaCa2_miR-NC_rep1


title: HCT116-/-_miR-766-5p_rep2


title: YH12_9F8

value: Sh


title: ZfpKOTN-2

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTN-2

tag: cell type


title: MIAPaCa2_miR-NC_rep2


title: ZfpKOTN-1

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTN-1


title: YH12_9B2


title: YH12_9B11


title: YH12_8G6


title: ZfpHetTP-3

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTP-3

value: Zfp318ZSDAT/+ AID-Cre B1-8hi GFP


title: ZfpHetTP-4

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTP-4


title: ZfpKOTP-4

description:
ZfpKOTPvsTN_CDS_counts.txt.gz
ZfpKOTP-4


title: YH12_8E5


title: ZfpHetTP-2

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTP-2


title: YH12_7D3


title: YH12_7E11


title: ZfpHetTP-1

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTP-1


title: YH12_6C3


title: ZfpHetTN-3

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTN-3


title: ZfpHetTN-4

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTN-4


title: HCT116-/-_miR-NC_rep2


title: ZfpHetTN-2

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTN-2


title: ZfpHetTN-1

description:
ZfpHetTPvsTN_CDS_counts.txt.gz
ZfpHetTN-1


title: YH12_5E3


title: YH12_4E4


title: YH12_3F2


title: S16_Young_adults_12_w

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: RNA-Seq of livers from aged mice not exposed to antibiotics

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2
Aligned to genome using HISAT2 version 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts per gene counts

source_name: Liver

extract_protocol:
Liver portions were snap frozen and 500 mg sections were resuspended in trizol as described. RNA was extracted according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 12 weeks

tag: antibiotics


title: YH12_2G7

tag: tissue


title: S15_Young_adults_12_w

tag: age


title: S14_Young_adults_12_w


title: YH12_3F11


title: S13_Young_adults_12_w


title: YH12_3G8


title: YH12_2F9


title: S12_Aged_ABX_II

description: RNA-Seq of livers from aged mice exposed to antibiotics

value: 102 weeks

value: ABX


title: YH12_2G12


title: S11_Aged_ABX_II


title: YH12_2E6


title: S10_Aged_ABX_II


title: YH12_2C2


title: S9_Aged_ABX_II


title: S7_Aged_ABX_I


title: S8_Aged_ABX_I


title: YH12_0H5


title: YH11_9H4


title: S6_Aged_ABX_I


title: YH11_8G9


title: S5_Aged_ABX_I


title: YH11_9D12


title: YH11_8F8


title: S4_Aged_no_ABX


title: S3_Aged_no_ABX


title: YH11_7G1


title: S2_Aged_no_ABX


title: YH11_7A3


title: S1_Aged_no_ABX


title: YH11_7E3


title: YH11_4D3


title: Monkey2_vCp1521_48hr

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

institute: RPM Bioinfo Solutions

description:
CREB1 immunoprecipitation
NHP_48hr_ALVAC_empty_vs_media_optimal.narrowPeak.gz
-

data_processing:
FASTQ files with qood quality reads were aligned using BWA against the Mmul_10 genome with the unstimulated media as a control
Unmapped and duplicated reads were filtered out using SAMtools, bedtools and Picard as described in the ENCODE Chip-seq pipeline.
Replicates were cross-correlated with Pearson for QC
Peaks were called using MACS2.
Consistent peaks across replicates were selected usig bedtools.
Genome_build: Mmul_10 (rheMac10)
Supplementary_files_format_and_content: Narrowpeaks (peaks)

organism: Macaca mulatta

source_name: PBMC

growth_protocol: Not applicable

extract_protocol:
Cells were harvested and cross-linked in 10% Formaldehyde for 30 minutes. Cells were pelleted and stored dry at -20C for future work. Thawed pellets were sonicated using Bioruptor (Diagenode) to a fragment size of 300-500bp and then incubated O/N with CREB1 Ab. Antibody was pulled down, DNA:protein de-crosslinked and DNA purified/eluted using the commerical True MicroChIP kit (Diagenode)
Libraries were prepared and indexed using the MicroPlex kit (Diagenode).
100 bp single end read sequencing was performed on the NovaSeq platform

treatment_protocol: PBMC were infected infected in vitro with an MOI 10:1 of ALVAC-HIV or empty ALVAC, with media cultured cells as a control

tag: stimulation

value: Empty ALVAC

tag: timepoint

value: 48 hours

tag: animal id


title: Monkey3_vCp1521_48hr


title: Monkey3_vCppp_48hr

description:
CREB1 immunoprecipitation
-
NHP_48hr_ALVAC_full_vs_media_optimal.narrowPeak.gz

value: HIV-ALVAC


title: Monkey2_vCppp_48hr


title: YH11_3G5

value: The whole shoot above cotelydon

tag: temperature (celsius)

value: LD


title: Monkey2_media_48hr

description:
CREB1 immunoprecipitation
NHP_48hr_ALVAC_empty_vs_media_optimal.narrowPeak.gz
NHP_48hr_ALVAC_full_vs_media_optimal.narrowPeak.gz

value: Media


title: Monkey1_vCppp_48hr


title: YH11_5A8

tag: photoperiod

value: SD


title: YH11_3E9

tag: sample time


title: YH11_3G11

tag: genotype


title: YH11_2F7


title: YH11_3F9


title: YH11_3E4


title: Monkey3_vCp1521_24hr

description:
CREB1 immunoprecipitation
NHP_24hr_ALVAC_empty_vs_media_optimal.narrowPeak.gz
-

value: 24 hours


title: Monkey3_vCppp_24hr

description:
CREB1 immunoprecipitation
-
NHP_24hr_ALVAC_full_vs_media_optimal.narrowPeak.gz


title: Monkey1_media_48hr


title: YH11_2A4


title: Monkey2_vCp1521_24hr


title: YH11_1G6


title: Monkey2_vCppp_24hr


title: YH11_1C7


title: YH10_8E4


title: Monkey3_media_24hr

description:
CREB1 immunoprecipitation
NHP_24hr_ALVAC_empty_vs_media_optimal.narrowPeak.gz
NHP_24hr_ALVAC_full_vs_media_optimal.narrowPeak.gz


title: YH10_8A8


title: Monkey2_media_24hr


title: YH10_7F1


title: Monkey1_vCp1521_24hr


title: YH13_5C8


title: Monkey1_media_24hr


title: YH10_7C8


title: YH10_6C5


title: 9

organism: Glycine soja


title: YH10_6D5


title: 6


title: 8


title: YH10_5G6


title: 7


title: YH10_5C9


title: YH10_4B1


title: YH10_5G11


title: YH10_4C10


title: 2


title: YH10_3A6


title: YH10_3D11


title: 22


title: YH10_3A7


title: 3


title: YH11_7G10


title: 5


title: 18


title: YH10_2D3


title: 17


title: 16


title: YH10_0D4


title: YH10_1B6


title: 15


title: 14


title: YH09_9G1


title: YH09_9D4


title: 12


title: 13


title: YH09_9C2


title: YH09_8G7


title: YH10_3A4


title: YH09_8G11


title: 1


title: 11


title: 10


title: YH09_8F1


title: 7H11


title: YH09_7C3


title: 6B10


title: YH09_8C9


title: YH09_7B8


title: YH09_7B7


title: YH09_7B11


title: 4


title: 6C11


title: 3G03


title: YH09_6G6


title: YH09_6E9


title: 3A09


title: Lu134A_siNC

city: Bunkyo-ku

first: NAOYA

last: MIYASHITA

state: Tokyo

department: Respiratory Medicine

institute: The University of Tokyo

hyb_protocol: Samples were prepared for Affymetrix GeneChip miRNA 4.0 Array according to the GeneChipTM miRNA Array Procedure (P/N 900720).

scan_protocol: GeneChip miRNA 4.0 Arrays were scanned with the Affymetrix GeneChipTM Scanner 3000.

data_processing: Affymetrix Transcriptome Analysis Console Software 3.0 was used to analyze the resulting array data.

label: biotin

label_protocol: microRNA was labelled with the FlashTag Biotin HSR RNA labeling kit from Affymetrix.

growth_protocol: Lu134A cells were cultured in RPMI-1640 Medium with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol: microRNA was isolated from cells using a miRNeasy miRNA isolation kit from Qiagen.

treatment_protocol: Lu134A cells were transfected with 20 nM siRNA.

tag: treatment

value: transfected with ASCL1 siRNAs


title: 5G04


title: 2G03


title: 6G03


title: YH09_3B4


title: 1A10


title: 2B09


title: YH09_4E3


title: YH09_2D11


title: YH09_1F12


title: YH09_2C7


title: 1H12


title: 3D09


title: 3C12


title: 3D10


title: 7G04


title: 3B09


title: YH40_9E8


title: YH08_8F12


title: YH08_9D8


title: Lu134A_siASCL1#1

value: transfected with control siRNAs


title: YH08_8B5


title: YH09_0A4


title: YH08_9B7


title: 3G04


title: YH40_5H12


title: YH09_1E1


title: YH08_7H9


title: YH40_4E7


title: YH09_1A3


title: YH08_7E12


title: YH40_2B10


title: YH08_7A7


title: YH08_6G7


title: YH39_4H12


title: YH08_5F8


title: YH08_2H4


title: YH38_2G4


title: YH39_1E8


title: YH38_1G3


title: YH08_1D4


title: YH08_2D2


title: YH36_8G3


title: YH37_7C11


title: YH08_1B2


title: YH08_1D11


title: YH08_1B3


title: YH07_9F9


title: YH36_6B9


title: YH36_6C12


title: YH08_2F1


title: YH08_1A1


title: YH07_9D7


title: YH36_4D10


title: YH35_5E8


title: YH07_9B4


title: YH35_8B10


title: YH39_7H2


title: YH08_6F4


title: YH38_7D10


title: YH38_9C12


title: YH07_8G2


title: YH35_2H12


title: YH07_7F8


title: YH34_9G3


title: YH07_6G10


title: YH07_8A5


title: YH34_4C11


title: YH34_3A10


title: YH07_5D4


title: YH07_6F7


title: YH36_3H12


title: YH34_2H1


title: YH07_5C4


title: YH07_5C3


title: YH33_8C11


title: YH07_4G5


title: YH07_2E12


title: YH07_1D12


title: YH32_8F6


title: YH35_4H11


title: YH07_0H4


title: YH32_6F5


title: YH32_7B9


title: YH07_0F3


title: YH07_0F1


title: YH06_8C1


title: YH32_6E8


title: YH32_6A9


title: YH34_1H12


title: YH32_3B10


title: YH07_4F2


title: YH31_7G3


title: YH06_6F2


title: YH06_7B4


title: YH33_7H12


title: YH06_7C4


title: YH07_3F12


title: YH31_8E8


title: YH33_2F6


title: YH06_6D3


title: YH06_9F1


title: YH33_1C12


title: YH06_6A5


title: YH33_5G3


title: YH31_6H2


title: YH31_2F5


title: YH32_3C11


title: YH06_5H7


title: YH06_5A3


title: YH31_0A2


title: YH30_6D10


title: YH30_2E8


title: YH06_3G9


title: YH29_3F6


title: YH28_6F6


title: YH28_5B10


title: YH06_0G2


title: YH06_1B7


title: YH06_0A1


title: YH27_9D10


title: YH28_4C12


title: YH27_9A10


title: YH28_1D9


title: YH27_8E7


title: YH05_9C6


title: YH05_5B7


title: YH05_9D3


title: YH27_3H1


title: YH05_5F1


title: YH27_8C12


title: YH26_7A9


title: YH05_4F9


title: YH06_4H3


title: YH26_6H12


title: YH05_4E2


title: YH05_4E10


title: YH26_4H2


title: YH06_2H10


title: YH26_4G3


title: YH06_2A8


title: YH06_1E6


title: YH28_9F5


title: YH26_4A10


title: YH05_4A12


title: YH05_5B5


title: YH05_3D1


title: YH25_5F5


title: YH26_3H11


title: YH25_4B10


title: YH26_1H1


title: YH05_3B12


title: YH05_2F8


title: YH25_1H2


title: YH05_2B1


title: YH05_3C4


title: YH25_1G4


title: YH05_0H2


title: YH05_0G5


title: YH24_8H12


title: YH25_1A9


title: YH24_5H1


title: YH24_4F5


title: YH05_4C1


title: YH04_9D1


title: YH04_9B12


title: YH04_9A12


title: YH24_4D9


title: YH04_6D11


title: YH23_9H12


title: YH23_9H1


title: YH04_6B3


title: YH23_6G3


title: YH04_6F1


title: YH04_5H3


title: YH22_8F5


title: YH04_5F4


title: YH22_7H1


title: YH22_7B10


title: YH22_5F6


title: YH04_3F3


title: YH04_2H8


title: YH21_9F6


title: YH04_3E5


title: YH21_9A9


title: YH04_1G8


title: YH21_8G4


title: YH21_3H2


title: YH21_8H1


title: YH04_1F7


title: YH20_8A10


title: YH04_0D3


title: YH04_0F5


title: YH03_9G12


title: YH03_9G8


title: YH20_6H1


title: YH20_7H11


title: YH03_9A7


title: YH20_2D9


title: YH19_8B9


title: YH03_8H10


title: YH04_3H4


title: YH04_5D6


title: YH03_8E6


title: YH21_9H11


title: YH03_7D7


title: YH19_6D9


title: YH03_6H7


title: YH03_6E2


title: YH19_2A10


title: YH03_5E11


title: YH03_5D11


title: YH03_4F3


title: YH03_3F8


title: YH18_3D9


title: YH18_5C12


title: KDM5B ChIP

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

institute: Yale University

description: Skin Melanoma Cell line

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using bowtie2  with default parameters
Reads Per Gene were calculated using FeatureCount of subread package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene expression values normalized with DESeq2 variance stabilizing transformation (VST) for each Sample

source_name: Melanoma cancer cell line

growth_protocol: Cells were grown in monolay in DMEM/F12+5%FBS+1% Penicillin-streptomycin at 37°C, 5% CO2

extract_protocol:
Chromatin was prepared and immunoprecipiated following previously described protocol ( Greer et al, Cell Rep 2015, 13(7):1444-1455). Anti-KDM5B (Abcam # ab50958) was used for KDM5B ChIP experiment.
ChIP libraries were prepared for sequencing using Illumina DNA Library Preparation protocol

treatment_protocol: Cells were fixed in 1% formaldehyde DMEM/F12 for 10 min.

value: 1445 (Cdkn2a and Pten inactivated with beta-catenin stabilization)

value: Skin Melanoma Cell line

value: Wild type cell

tag: antibody

value: KDM5B ChIP


title: Input

description: Skin Melanoma Cell line

value: Input


title: YH03_3E10


title: Ventral prostate GLLP3 pnd540 [miRNA]

city: Botucatu

first: Sérgio

middle: Alexandre Alcantara

last: Santos

state: São Paulo

address: Rua Professor Doutor Antonio 250 Celso Wagner Zanin

department: department of structural and functional biology

country: Brazil

institute: UNESP

data_processing:
For data analysis we used the Oasis tool (http://oasis.dzne.de/), which provided us with the processed files.
Supplementary_files_format_and_content: Tab-delimited text files include counts.

organism: Rattus norvegicus

source_name: ventral prostate

extract_protocol:
Ventral prostate were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. The total RNA was sent to Macrogen company to the sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dams were submitted to gestational and lactational normal diet (17% protein) or gestational and lactational low protein diet (6% protein), and the ventral prostate was collected from offspring on postnatal day 21 and 540.

value: Ventral prostate

value: Postnatal day 540

value: Maternal low protein diet


title: Ventral prostate GLLP4 pnd540 [miRNA]


title: YH17_8D9

value: Sh


title: YH03_3F1


title: YH03_2H9


title: YH03_1A5


title: YH17_7A10


title: YH03_3D4


title: Ventral prostate GLLP1 pnd540 [miRNA]


title: Ventral prostate GLLP2 pnd540 [miRNA]


title: YH03_0D5


title: YH17_3F5


title: Ventral prostate CTR5 pnd540 [miRNA]

value: Control


title: YH03_0A3

value: The whole shoot above cotelydon


title: YH17_3E7

value: LD


title: YH02_9H7


title: YH02_9E12


title: Ventral prostate CTR4 pnd540 [miRNA]


title: Ventral prostate CTR3 pnd540 [miRNA]


title: YH02_8F9


title: YH17_2C12


title: YH02_8C10


title: YH17_1H11


title: YH16_7E8


title: YH02_7C5


title: YH02_8A2


title: Ventral prostate GLLP4 pnd21 [miRNA]

value: Postnatal day 21


title: YH02_7B12


title: YH02_7G5


title: YH16_5D10

value: SD


title: YH02_5E10


title: YH02_6E11


title: Ventral prostate GLLP3 pnd21 [miRNA]


title: Ventral prostate CTR2 pnd540 [miRNA]


title: YH02_4B5


title: YH02_5B3


title: YH16_1A10


title: Ventral prostate CTR1 pnd540 [miRNA]


title: Ventral prostate GLLP2 pnd21 [miRNA]


title: YH02_3A11


title: YH02_3B2


title: Ventral prostate GLLP1 pnd21 [miRNA]


title: YH15_9G4


title: YH02_2B4


title: YH15_2C11


title: YH02_2A3


title: YH02_0E3


title: Ventral prostate CTR4 pnd21 [miRNA]


title: YH15_3D10


title: Ventral prostate CTR3 pnd21 [miRNA]


title: YH02_0D1


title: YH15_0F4


title: YH01_9E10


title: YH01_9B5


title: Ventral prostate CTR2 pnd21 [miRNA]


title: YH01_7H5


title: YH14_5E7


title: Ventral prostate CTR1 pnd21 [miRNA]


title: YH14_1B10


title: YH01_7B3


title: YH01_7G8


title: YH01_6E12


title: Ventral Prostate GLLP4 PND 540 [mRNA]

description:
GLLP 8 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 12

data_processing:
Basecalls performed using STAR version.
mRNA-seq reads were aligned to the Rnor_6.0 genome assembly using GTF file from Annotation provider Ensembl.
Counts were called using edgeR version 3.34.0 with the following setting: mRNA threshold (0.05), Enrichment Fold (0.66).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files include counts.

source_name: Ventral Prostate

treatment_protocol: Dams were submitted to gestational normal diet (17% protein) or gestational and lactational low protein diet (6% protein), and the ventral prostate was collected from offspring on postnatal day 21 and 540.


title: YH13_7E7


title: Ventral Prostate GLLP3 PND 540 [mRNA]

description:
GLLP 7 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 11


title: YH01_4F12


title: YH01_4F4


title: Ventral Prostate GLLP2 PND 540 [mRNA]

description:
GLLP 6 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 7


title: YH02_0E2


title: YH13_2H2


title: YH01_3F7


title: YH13_2G3


title: YH01_4C4


title: YH01_3E11


title: YH01_3F10


title: Ventral Prostate CTR5 PND 540 [mRNA]

description:
CTR 5 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 10


title: YH01_3B7


title: Ventral Prostate GLLP1 PND 540 [mRNA]

description:
GLLP 5 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 6


title: YH13_1D10


title: YH12_6B10


title: Ventral Prostate CTR4 PND 540 [mRNA]

description:
CTR 4 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 9


title: YH01_3A1


title: Ventral Prostate CTR3 PND 540 [mRNA]

description:
CTR 3 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 5


title: YH12_5G4


title: YH01_2E1


title: YH01_1G9


title: YH01_1G11


title: Ventral Prostate CTR1 PND 540 [mRNA]

description:
CTR 1 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 3


title: YH11_8H11


title: YH01_0E5


title: Ventral Prostate GLLP4 PND 21 [mRNA]

description:
GLLP 8 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 8


title: Ventral Prostate CTR2 PND 540 [mRNA]

description:
CTR 2 PND 540
processed data file: results_540_mRNA.counts.txt
column header: 4


title: H358 KRAS-WT + dox rep 2

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Reads were mapped to amplicon sequence using bwa (v.0.7.15)
Extracted mismatched reads and pielup was generated using samtools
Computed the perbase composition from pileup using pileup2base
Calculated per base error rate
Supplementary_files_format_and_content: tab-separated file & perbase composition from mismatched reads

source_name: Results of LentiMutate using KRAS-WT cDNA and AMG 510 in the H358 cell line

growth_protocol: For parental cell lines, cells were grown to approximately 70% confluency and genomic DNA was isolated using the Qiagen DNeasy Blood and Tissue kit. For cells that survived LentiMutate, all colonies from a 15 cm dish or T175 were harvested and DNA was isolated using the Qiagen DNeasy Blood and Tissue kit.

extract_protocol:
Qiagen Dneasy Blood and Tissue kit
For EGFR the entire open reading frame, for BCR-ABL two large amplicons, for RUVBL1 three short barcoded amplicons, and for KRASwt/KRASG12C two short barcoded amplicons were then PCR amplified, purified (Qiagen QIAquick PCR purification kit catalog # 28104), ran on a D5000 HS ScreenTape on the Agilent Tapestation 4200 and DNA concentrations determined by Qubit. For EGFR and BCR-ABL the PCR products were sheared on the Covaris S2 for 40 seconds and libraries are prepared with the KAPA Hyper Prep Kit. Samples were end repaired, 3' ends were adenylated and then barcoded with multiplex adapters. Samples are size selected prior to PCR to remove small fragments. The short RUVBL1 and KRASwt/KRASG12C PCR products were directly (i.e. without sonication) ligated with the adapters. Four cycles of PCR were used to amplify the libraries, which were then purified with AmpureXP beads and validated on the Agilent Tapestation 4200. Before being normalized and pooled, samples were quantified by Qubit then ran using the Nextseq500 V2.5 150PE or MiSeq V2.5 250/300PE chemistry. Reads obtained from pooled samples were separated into sample specific readIDs based on the barcode information. For each read in the pooled sample fastq file, the barcode and primer sequences were trimmed from the 5’ end. Using the trimmed fastq file and readIDs obtained in the first step, sample specific fastq files were generated using BBMap (v 38.11). These reads were mapped to the reference cDNA sequence using BWA (v. 0.7.15). For identification of point mutations, read pileup information was obtained from mapped reads using the samtools (v.0.1.19) mpileup command. From the read pileup information, per base mismatch/indel information was obtained using pileup2base tool. Per base error ratios were computed using an in-house Perl script, and the frequency of mutations at positions was compared between the parental (no doxycycline, no drug) and +doxycycline/drug surviving cells. For identification of deletions, the trimmed reads were mapped to the reference cDNA sequences using speedseq, which in turn uses BWA-mem algorithm to map the reads. In addition to the alignment, speedseq tool marks duplicates and identifies split and discordant read pairs. The speedseq mapped files were used to call structural variations (SVs) using Lumpy SV caller. Lumpy SV calls were further filtered using number of split and discordant supporting reads.

value: Cancer cell line from a patient with non-small cell lung cancer


title: H358 KRAS-WT

source_name: H358 cells infected with KRAS-WT cDNA before AMG 510 treatment (parental population)


title: YH12_1E7


title: YH12_2H11


title: Ventral Prostate GLLP3 PND 21 [mRNA]

description:
GLLP 7 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 7


title: YH01_3A2


title: H358 KRAS-G12C

source_name: H358 cells infected with KRAS-G12C cDNA before AMG 510 treatment (parental population)


title: Ventral Prostate CTR4 PND 21 [mRNA]

description:
CTR 4 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 4


title: Ventral Prostate GLLP2 PND 21 [mRNA]

description:
GLLP 6 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 6


title: H358 KRAS-WT + dox rep 1


title: H358 KRAS-G12C + dox rep 1

source_name: Results of LentiMutate using KRAS-G12C cDNA and AMG 510 in the H358 cell line


title: H358 KRAS-G12C + dox rep 2


title: H1993-RUVBL1-WT - dox

source_name: H1993 cells infected with RUVBL1-WT cDNA before compound B treatment (parental population)


title: YH10_7C12


title: YH01_3D12


title: YH11_8D10


title: H1993-RUVBL1-WT + dox rep 3

source_name: Results of LentiMutate using RUVBL1-WT cDNA and compound B in the H1993 cell line


title: Ventral Prostate CTR3 PND 21 [mRNA]

description:
CTR 3 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 3


title: YH10_6H11

source_name: The whole shoot above cotelydon


title: H1993-RUVBL1-WT + dox rep 2


title: H1993-RUVBL1-WT + dox rep 1


title: Ventral Prostate CTR2 PND 21 [mRNA]

description:
CTR 2 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 2


title: H1993-RUVBL1-PCR-mut - dox

source_name: H1993 cells infected with RUVBL1-PCR-Mutated cDNA before compound B treatment (parental population)


title: YH10_5D9


title: YH10_4B9


title: YH11_6E7


title: YH11_7G4


title: H1993-RUVBL1-PCR-mut + dox rep 3

source_name: Results of LentiMutate using RUVBL1-PCR-mutated cDNA and compound B in the H1993 cell line


title: H1993-RUVBL1-PCR-mut + dox rep 2


title: WT IFNG treat ATAC Rep1

description:
Skin Melanoma Cell line
YRtreatIFNG-ATAC_merge.msd.redup.cutsite.bw
allYRandall4H3-ATAC_merge.bed
atac.counts.txt

data_processing:
Illumina Casava software used for basecalling.
Reads were trimmed of adapters using Trimmomatic
Trimmed reads were aligned using Bowtie2 using standard parameters and a maximum fragment length of 2000
Bam files were filtered using samtools -F 1804
Reads were then processed where only the most 5' base pair for each read was kept and forward strand reads were shifted +4bp, and reverse strand reads were shifted -5bp.
Peak calling was performed using MACS3 with parameters --nomodel --keep-dup all -s 1 --shift -75 --extsize 150.
For a consensus peak set, all bam files were merged using samtools and used for peak calling
featureCounts was used to count reads from replicates that fall within the consensus peak set using default parameters
Bigwig files were generated using deeptools
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (merged rep1, rep2), bed (all ATAC peaks), txt (raw counts)

extract_protocol:
50,000 cells were treated with Transposase. Protocol as previously described in Corces et al (Nat.Methods 2017).
DNA libraries were prepared as previously described in Corces et al (Nat.Methods 2017).

value: YUMMER1.7(Braf V600E, Pten -/- and Cdkn2 -/- with high frequency of stable UV-induced somatic mutations

value: IFNG

value: Control knockout


title: YH10_2A9


title: H1993-RUVBL1-PCR-mut + dox rep 1


title: WT ATAC Rep2

description:
Skin Melanoma Cell line
YR-ATAC_merge.msd.redup.cutsite.bw
allYRandall4H3-ATAC_merge.bed
atac.counts.txt

value: Skin Melanoma Cell line


title: HCC827 EGFR M-RT

data_processing:
Primer and UMI information is extracted
UMI combination from plus and minus reads were quantified
Reads were mapped using BOWTIE2 (v.2.3.5)
Identifies mismatches/indels using samtools calmd command
Supplementary_files_format_and_content: tab-separated file & perbase composition from mismatched reads

source_name: HCC827 EGFR M-RT

growth_protocol: Cells were infected with EGFRdel746-750 lentiviral particles that were packaged using either the WT-RT or M-RT

extract_protocol:
DNA was extracted using the Qiagen Dneasy kit
Genomic DNA was isolated (Qiagen DNeasy Blood & Tissue Kit, catalog # 69504) from HCC827 cells transduced at an MOI of approximately .3 with EGFRdel746-750 cDNA that was packaged using either the WT-RT or M-RT and otherwise identical conditions. Two microgram of this DNA was used for two PCR cycles (using New England Biolabs Q5 Hot Start Polymerase, catalog # M0494S) of a 243 bp amplicon of the EGFR open reading frame using the primers TTGCGGTGTCAATCTTACCANNNNNNNNCAGCGCTACCTTGTCATTCA and ATGAATCCAAACCGGATGAANNNNNNNNTTGCAGCCCATTTCTATCAA to label both ends of individual amplicon molecules with unique molecular identifiers (UMIs) of 8 nucleotides. After removal of the UMI-containing primers by Exonuclease I (NEB) digestion and column purification (Qiagen QIAquick PCR purification kit catalog # 28104), the UMI-tagged amplicons were then further amplified using the primers TTGCGGTGTCAATCTTACCA and ATGAATCCAAACCGGATGAA and purified (Qiagen QIAquick PCR purification kit catalog # 28104) to generate 299 bp products. For these, barcoded Illumina libraries were prepared with the KAPA HyperPrep Kit (Roche) for sequencing on the NextSeq500 (Illumina) with V2.5 150PE chemistry. PE reads were demultiplexed and from each read in the fastq file, 20bp primer was trimmed from the 5’ end and 8bp was extracted which contained the UMI information. We used UMIs in which all basepairs had a sequence quality value of >=30 for further analysis. The UMI combinations from plus and minus reads were quantified and assigned a UMI combination and its count to each readID. After preprocessing (including further trimming of the UMI and the sequences of the second primers), singletons from preprocessed fastq files were separated using fastq-pair tool. Resulting fastq files were mapped to the EGFR cDNA sequence using BOWTIE2 (v.2.3.5). To identify mismatches in each mapped sequence we used samtools calmd command and custom in-house python and perl scripts. First, for each read we identified mismatches in each position and combined this information with UMI counts. Then, for each base pair mismatch, we calculated the ratio between the total number of reads that show a given mismatch/ and the total number of reads sequenced (given by total number of UMIs). Events with greater than .9 mismatch rate were used for further analysis.

treatment_protocol: Cells were not treated

value: Cancer cell line derived from a non-small cell lung cancer patient


title: HCC827 EGFR WT-RT

source_name: HCC827 EGFR WT-RT


title: YH09_0B2


title: IF5

city: Shanghai

first: Yizhen

address: 320 Yue Yang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Illumina 1.5 software used for basecalling.
The reads that contain adapters were trimmed and mapped to the genome with mapper.pl script in miRDeep2
The miRNAs were annotated with WormBase genome build WS255, quantified to reads per million isomiR reads(RPMs) and log-transformed normalized.
Genome_build: WS255
Supplementary_files_format_and_content: csv files include RPM values

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
We precipitated the total RNA by pure ethylacohol, run a 6% PAGE gel to select and purify the 18-30 nt small RNA from total RNA and add adapter, amplify these small RNAs.
RNA library construction process followed Illumina Small RNA library construction kit V1.5 .

tag: agent

value: IF

tag: strian

value: adult day 10


title: HCC827 EGFR M-RT.

source_name: HCC827 cells infected with EGFRdel746-750 lentivirus using M-RT before osimertinib treatment (parental population)


title: YH09_3B9


title: HCC827 EGFR osi+dox M-RT rep2

source_name: Results of LentiMutate using M-RT, EGFRdel746-750 and osimertinib in the HCC827 cell line


title: WT ATAC Rep1

source_name: Melanoma cancer cell line

tag: strain


title: IF4

value: adult day 8


title: YH08_6G4


title: IF3

value: adult day 6


title: Kdm5b KO IFNG treat ATAC Rep2

description:
Skin Melanoma Cell line
4H3treatIFNG-ATAC_merge.msd.redup.cutsite.bw
allYRandall4H3-ATAC_merge.bed
atac.counts.txt

value: Kdm5b deletion 2


title: HCC827 EGFR osi+dox M-RT rep1


title: Kdm5b KO IFNG treat ATAC Rep1

value: Kdm5b deletion 1


title: IF2

value: adult day 4


title: WT IFNG treat ATAC Rep2


title: Kdm5b KO ATAC Rep2

description:
Skin Melanoma Cell line
4H3-ATAC_merge.msd.redup.cutsite.bw
allYRandall4H3-ATAC_merge.bed
atac.counts.txt


title: Ventral Prostate CTR1 PND 21 [mRNA]

description:
CTR 1 PND 21
processed data file: results_21_mRNA.counts.txt
column header: 1

value: Ventral prostate

value: Control


title: Kdm5b KO ATAC Rep1


title: HCC827 EGFR gef+dox WT-RT rep2

source_name: Results of LentiMutate using WT-RT, EGFRdel746-750 and gefitinib in the HCC827 cell line


title: YH08_3A9

value: The whole shoot above cotelydon

value: LD


title: CR5

value: CR


title: YH08_1B9


title: YH08_7F5

value: Sh


title: HCC827 EGFR gef+dox WT-RT rep1

value: Cancer cell line from a patient with non-small cell lung cancer


title: YH07_9B10


title: CR3


title: Ctrl5

value: Al


title: CR2


title: K562 BCR-ABL + dox rep 1

source_name: Results of LentiMutate using BCR-ABL and imatinib in the K562 cell line

value: Cancer cell line from a patient with chronic myelogenous leukemia


title: YH07_8H2


title: YH07_7F6


title: K562 BCR-ABL + dox rep 2


title: HCC827 EGFR WT-RT.

source_name: HCC827 cells infected with EGFRdel746-750 lentivirus before gefitinib treatment (parental population)


title: shRNF5_HL_60_rep2

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standstard illumina base calling pipeline and stored in illumina cloud service BaseSpace. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned with the STASR aligner
FeatureCounts implemented in Subread will be used to count the sequencing reads from mapped BAM files. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR)10 implemented using SARTools R Package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each annoted gene.

source_name: AML cell line HL_60

extract_protocol:
RNA was prepared 7 days following RNF5 knockdown, and triplicates were used for RNAseq analysis. Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: AML cell line

tag: knockdown


title: YH07_2B9

value: SD


title: YH06_9D9


title: Ctrl4


title: YH08_3C12


title: shRNF5_HL_60_rep1


title: Ctrl3


title: Ctrl2


title: YH06_9B9


title: Ctrl1

value: adult day 2


title: pLKO_HL_60_rep3

value: vector only control


title: YH06_6A10


title: K562 BCR-ABL

city: Dallas

source_name: K562 cells infected with BCR-ABL lentivirus before imatinib treatment (parental population)

tag: cell type


title: Donor3_vCppp_24hr

description:
CREB1 immunoprecipitation
HSapiens_24hr_ALVAC_full_vs_media_optimal.narrowPeak.gz

data_processing:
FASTQ files with qood quality reads were aligned using BWA against the Homo sapiens genome with the unstimulated media as a control
Unmapped and duplicated reads were filtered out using SAMtools, bedtools and Picard as described in the ENCODE Chip-seq pipeline.
Replicates were cross-correlated with Pearson for QC
Peaks were called using MACS2.
Consistent peaks across replicates were selected usig bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Narrowpeaks (peaks)

source_name: PBMC

treatment_protocol: PBMC were infected infected in vitro with an MOI 10:1 of ALVAC-HIV, with media cultured cells as a control

value: HIV-ALVAC

value: 24 hours

tag: donor


title: CR4

tag: age

value: adult day 8


title: pLKO_HL_60_rep2

tag: tissue


title: YH06_5H2

data_processing:
Trimmomatic v0.36 was used to trim the low-quality base calls and the adapter content in single end mode with the adapter in TruSeq3-SE.fa, a leading and trailing base call threshold of 28 and a minimum read length of 30.
STAR v2.5.2b was used to align the reads with the --quantMode GeneCounts option to the reference genome file and the gene annotation file obtained from Phytozome.
the (relative) abundance of the mRNAs in transcripts per million (TPM) was quantitated using the relative mapping efficiency model.
Genome_build: Glycine max Wm82.a2.v1 (Soybean), release date: 6/10/2015, BioProject: PRJNA19861, Accession ID: ACUP02000000.
Supplementary_files_format_and_content: csv files include raw counts and normalized expression levels.


title: shRNF5_HL_60_rep3


title: shRNF5_U937_rep3

source_name: AML cell line U937


title: YH06_4A9


title: Donor3_media_24hr

tag: stimulation

value: Media

tag: timepoint


title: shRNF5_U937_rep1


title: Donor2_vCppp_24hr


title: Donor2_media_24hr


title: Donor1_vCppp_24hr


title: YH05_5H11

tag: temperature (celsius)


title: pLKO_U937_rep2


title: Donor1_media_24hr


title: YH05_7D9

tag: photoperiod


title: shRNF5_MOLM_13_rep1

source_name: AML cell line MOLM_13


title: pLKO_MOLM_13_rep3


title: YH05_5A9

source_name: The whole shoot above cotelydon

tag: sample time


title: YH05_3G4

tag: genotype


title: pLKO_HL_60_rep1


title: YH05_1C11