title: Rep2

city: Wuhan

first: Jun

last: Xiong

state: Hubei

department: Chemistry

institute: Wuhan university

description:
2_BKDL202603957-1a
Bisulfite-free, single-base resolution mapping of 4mC

data_processing:
Raw reads were first trimmed to remove low-quality bases and adaptor sequences with FastQC (v0.11.8), Trim Galore (v0.6.7) and Cutadapt (v3.5 with Python 3.9.7).
Trimmed reads were mapped to the reference genome of D. radiodurans (NCBI accession: ASM832978v1) by Bisamrk (v0.23.1).
Bismark (v0.23.1) was used to remove PCR duplication and extract methylation sites.
For each site, the number of ‘‘C’’ bases were counted as 4mC sites (denoted NC) and the number of ‘‘T’’ bases were counted as not 4mC sites (denoted NT).The sequencing depth (defined as N = NC + NT) and coverage of samples were calculated using samtools (v1.9) software.
For screening of 4mC sites, parameters of the sequencing depth ≥ 100 and methylation level (defined as methylation level = NC/(NC + NT)) ≥ 0.1 were used based on CX report generated from Bismark methylation extractor. The 6 bp contexts of upstream and downstream of 4mC sites were extracted and used for the motif searching and identification with STREME (v5.4.1).
Genome_build: Deinococcus radiodurans R1 NCBI genome build 4
Supplementary_files_format_and_content: number of reads csv files

organism: Deinococcus radiodurans

source_name: Deinococcus radiodurans cells

growth_protocol: D. radiodurans cells were grown in tryptone glucose yeast extract (TGY) liquid media or on agar plates (0.5% tryptone, 0.1% glucose, and 0.3% yeast extract) at 30°C.

extract_protocol:
D. radiodurans DNA was isolated using Ezup Column Bacteria Genomic DNA Purification kit (Sangon, Shanghai, China) according to the manufacturer's instruction.
D. radiodurans DNA (100 ng in 400 μL of water) was fragmented to an average size of 300–400 bp using an ultrasonic homogenizer. The sheared DNA was lyophilized to dryness and then reconstituted in water. The resulting DNA was end-repaired and adenylated at 30°C for 20 min and immediately at 72°C for 20 min using Hieff NGS® Ultima Endprep Mix (Yeasen Biotechnology Co., Ltd., Shanghai). Adaptor-OH and Adaptor-P (Table S4 in Supporting Information) were mixed at a final concentration of 20 μM each in 1× annealing buffer and then incubated in 95°C for 5 min followed by cooling gradually to 25°C. Adaptor ligation was performed at 20°C for 15 min using Hieff NGS® Ultima DNA Ligation Module (Yeasen) followed by DNA purification using KAPA Pure beads (Roche). The adaptor ligation was confirmed by 20% native PAGE. The resulting DNA (16 μL) was added with 2 μL of DMSO and then denatured at 95°C for 10 min and immediately chilled at 0oC. The deamination reaction by A3A protein was carried out at 37°C for 2 h in a final concentration of 20 mM MES (pH 6.5), 0.1% Triton X-100 and 6 μM A3A protein. The resulting A3A-deaminated DNA was amplified by PCR with 10 cycles using pre-P5 primer, pre-P7 primer, and Q5U® Hot Start High-Fidelity DNA polymerase (New England Biolabs). After purification by KAPA Pure beads, the DNA products were amplified by PCR with 5 cycles using P5-universal primer, P7-index primer, and Q5® Hot Start High-Fidelity 2× Master Mix (New England Biolabs). The final PCR products were purified with KAPA Pure beads and 1.5% agarose gel electrophoresis and examined by Agilent 2100 before sequencing on the Illumina NovaSeq 6000 platform (Novogene Co., Ltd., China).

treatment_protocol: D. radiodurans cells were collected after culturing for 12 h and then DNA was extracted.


title: Rep3

status: Public on Dec 15 2021

type: SRA

country: China

description:
3_BKDL202603958-1a
Bisulfite-free, single-base resolution mapping of 4mC

library_source: genomic

molecule: genomic DNA

tag: strain


title: Rep1

description:
1_BKDL202603956-1a
Bisulfite-free, single-base resolution mapping of 4mC


title: T72_LZD_4.2_B

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

library_source: transcriptomic

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: bacterial culture

growth_protocol: Samples grown in 7H9-rich media  at 37 degrees C with shaking

extract_protocol:
In three biological replicates, M. tuberculosis cultures with or without drug treatment were harvested at 4, 24  or 72 h. Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment with no drug or linezolid at 0.84 or 4.2 μg/mL for 4, 24 or 72 h

tag: drug treatment

value: 4.2 ug/mL

tag: treatment time

value: 72 hour


title: round_spermatids3(RS3)

city: Yangling

first: Lingkai

last: zhang

address: No. 3, Taicheng Road, Yangling District,  Xianyang 712100，Shaanxi Province，China.

institute: Northwest A&F University

data_processing:
RNA-seq: After raw data process, high qualities clean reads were aligned to the reference genome (Sscrofa11.1) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization. The differentially expressed mRNAs were identified by p-value and fold change.
scRNA-seq: Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Sample demultiplexing, barcode processing and single-cell 3’ gene counting by using the Cell Ranger pipeline and scRNA-seq data were aligned to Ensembl genome Sscrofa11.1, a total of 16,966 single cell captured from 150-day-old porcine testis were processed using 10X Genomics Chromium Single Cell 3’ Solution. The Cell Ranger output was loaded into Seurat (version 3.2.0) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: RNA-seq: mRNA_Expression_Profiling.xlsx file includes raw counts and counts normalized by edgeR.
Supplementary_files_format_and_content: scRNA-seq: barcodes.tsv (cell barcode file), genes.tsv (gene file), matrix.mtx (gene-barcode counts).

organism: Sus scrofa

source_name: germ cells

extract_protocol:
Testis cell suspensions were loaded into Chromium microfluidic chips with 3’ v3 chemistry and used to generate single-cell gel bead emulsions (GEMs) using the Chromium controller (10X Genomics), GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations. Fractions with high purity of spermatogonia, pachytene spermatocytes and round spermatids were resuspended with Trizol (Invitrogen, USA) and total RNA was extracted for bulk RNA-seq.
RNA seq: The rRNAs were removed from total RNA by using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer’s instruction. NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) was used to construct RNA libraries. Library quality was confirmed by BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Hiseq 4000 with 150 bp paired end reads.
scRNA-seq: Single-cell suspensions were loaded to 10x Chromium to capture 16,966 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology co. ltd., (HangZhou, China) at a minimum depth of 25,000 reads per cell.

tag: tissue

value: round spermatids


title: ANW9

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: monocyte.results.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the human (GRCh38) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

organism: Homo sapiens

source_name: Monocyte

growth_protocol: Two independent single centers (Arthritis Northwest, ANW, Spokane, WA, USA and Dx Biosamples, LLC in San Diego, California, USA) performed the prospective and open clinical study. The participant approval and informed consent was obtained from all participants prior to the clinical sample collection. The study was approved by the Quorum Review Institutional Review Board (IRB) for the ANW Clinic, Spokane, WA with code # AE010831, and Investigational Review Board (www.dxirb.com) of Dx Biosamples, LLC, San Diego, CA, USA, with code IORG # 0006584, and IRB # 00007904. All research was performed in accordance with relevant guidelines/regulations.

extract_protocol:
Buccal samples were frozen and stored (-20 °C) for the subsequent epigenetic analysis. Blood was collected into BD Vacutainer CPT tubes (Becton, Dickinson and Company, Franklin Lakes, NJ) by ANW Spokane, WA and shipped overnight on ice for immediate processing. Monocytes were isolated using antibody-linked magnetic beads (Dynabeads CD14, Life Technologies # 11149D). Human buccal samples were kept frozen and thawed for analysis. Blood samples were kept refrigerated before monocyte isolation. For monocyte isolation the blood was diluted 1:2 in Isolation Buffer (1X PBS, 0.1% BSA, 2mM EDTA) then centrifuged at 600 x g for 10 min at room temperature in a swinging bucket rotor. The plasma upper layer was discarded, and the blood resuspended to the original volume in Isolation Buffer. Magnetic beads (Dynabeads CD14, Life Technologies # 11149D) were added to the blood samples (25 µL of pre-washed beads for 1 ml of blood sample). The mixture (beads-cells) was incubated for 20 min between 2 °C and 8 °C with gentle tilting and rotation. The mixture was then placed on a magnet for 2 minutes and the supernatant carefully removed. One ml of Isolation Buffer was added to the beads-cells mixture then homogenized and incubated 2 minutes on the magnet. This step was repeated at least 3 times. The bead-bound cells were resuspended in 100 µl 1X PBS pH 7.4 and genomic DNA isolation was performed.  Genomic DNA from buccal swabs or monocytes was prepared as follows: The buccal swabs were incubated with 750 µl of cell lysis solution (100 mM NaCl, 10 mM Tris, 25 mM EDTA, 0.5% SDS) and 3.5 µl of Proteinase K (20 mg/ml) for 3 hours in a heating block at 55 °C. The lysis solution was transferred to a new tube and spun for 2 min at full speed. For the monocytes, 820 μl of DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl Proteinase K (20 mg/ml) were added to the bead-bound monocytes and the sample incubated at 55 °C for 2 hours under constant rotation. The samples were placed on a magnet where the magnetic beads were discarded and the supernatants containing the DNA kept. Then for both the buccal swabs and the monocytes, 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A, Madison, WI) was added, the sample was mixed and incubated on ice for 15 min, then spun at 4 °C at 13,500 x g for 20 min. The supernatant was transferred to a fresh tube, then precipitated over night at -20 °C with 1 mL of cold 100% isopropanol and 2 μl glycoblue. The sample was then centrifuged at 4 °C, 13,500 x g for 20 min. The supernatant was discarded and the pellet washed with 70% cold ethanol then returned to freezer for 20-30 min. The sample was then centrifuged at 4 °C, 13,500 x g for 10 min. The supernatant was discarded, and the pellet air-dried for 5 min then resuspended in 100 μl nuclease free water. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual genomic DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1X Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was measured. The sonicated DNA was then diluted with TE buffer (10 mM Tris HCl, pH 7.5; 1 mM EDTA) to 400 μl, heat-denatured for 10 min at 95 °C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 °C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml 1X PBS with 0.1% BSA and 2 mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1X IP buffer (50 mM sodium phosphate pH 7.0, 700 mM NaCl, 0.25% Triton X-100) as the initial volume of beads. Beads (50 μl) were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2 hours on a rotator at 4 °C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1X IP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20 mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 °C, then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000 x g for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 13,500 x g for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2 μl of glycoblue (20 mg/ml), 20 μl of 5M NaCl and 500 μl ethanol were added and mixed well, then precipitated in -20 °C freezer for 1 hour to overnight. The precipitate was centrifuged at 13,500 x g for 20 min at 4 °C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 μl cold 70% ethanol in -20 °C freezer for 15 min then centrifuged again at 13,500 x g for 5 min at 4 °C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20 μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each sample received a separate index primer.

treatment_protocol: The arthritis severity was assessed for the Caucasian population with diagnostic rheumatoid factor autoantibody (RF) positive assay and cyclic citrullinated peptide autoantibody (CCP) positive assay. The arthritis severity was also assessed for both the Caucasian and African American populations with a more qualitative Clinical Disease Activity Index (CDAI) analysis with a high activity score of >22.1-76.0 and moderate activity score of 10.1-22.0. The CDAI was also supported with DAS28 and RAPID3 assays for the Caucasian population.

tag: sample group

value: Rheumatoid arthritis

tag: subject

value: ANW T13

tag: age


title: T72_LZD_4.2_C


title: round_spermatids2(RS2)


title: T72_LZD_4.2_A


title: ANW8

description: monocyte.results.csv.gz

value: ANW T12


title: T24_LZD_4.2_C

value: 24 hour


title: ANW7

description: monocyte.results.csv.gz

value: ANW T10


title: round_spermatids1(RS1)


title: T24_LZD_4.2_B


title: ANW6

description: monocyte.results.csv.gz

value: ANW T09


title: pachytene_spermatocytes3(PS3)

value: pachytene spermatocytes


title: T24_LZD_4.2_A


title: pachytene_spermatocytes1(PS1)


title: ANW34

description: anw.buccal.results.csv.gz, comb.buccal.results.csv.gz

source_name: Buccal

value: Control

value: ANW C07


title: ANW23

value: ANW T06


title: spermatogonia3(SPG3)

value: spermatogonia


title: ANW4

description: monocyte.results.csv.gz

value: ANW T05


title: ANW5

description: monocyte.results.csv.gz


title: T4_LZD_4.2_B

value: 4 hour


title: ANW3

description: monocyte.results.csv.gz

value: ANW T04


title: T4_LZD_4.2_A

value: 4.2 ug/mL


title: spermatogonia2(SPG2)


title: ANW2

description: monocyte.results.csv.gz

value: ANW T03


title: MPAF palbociclib

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 20.0.4, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Genome_build: Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
Supplementary_files_format_and_content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resulting p-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. A p-value of ≤0.05 was considered significant.

source_name: fibroblast

growth_protocol: 2102EP, JAR, and JEG-3 cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM); TCam-2 and NCCIT were cultivated in RMPI medium  (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM); MPAF cells were  cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM, 1% MEM non-essential amino acids 100x) at 37°C and 7.5% CO2.

extract_protocol:
RNA was isolated using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturer’s protocol (‘VAHTS Stranded mRNA-Seq Library Prep Kit’). 300 ng total RNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.
RNA sequencing performed on the HiSeq 3000/4000 system (Illumina Inc., San Diego, USA) with a read setup of 1x150 basepairs (bp).

treatment_protocol: cells were treated with 10 μM palbociclib for 16 h

value: fibroblast

tag: cell line

value: MPAF

tag: treatment

value: palbociclib treatment


title: MPAF ctrl.

value: solvent control


title: spermatogonia1(SPG1)


title: ANW1

description: monocyte.results.csv.gz

value: Rheumatoid arthritis

value: ANW T01


title: T72_LZD_0.84_C

value: 72 hour


title: T24_LZD_0.84_C

value: 24 hour


title: T72_LZD_0.84_A


title: JEG-3 palbociclib

source_name: non-seminoma germ cell tumor, choriocarcinoma


title: JEG-3 ctrl.

value: non-seminoma germ cell tumor, choriocarcinoma


title: T4_LZD_4.2_C


title: T24_LZD_0.84_B


title: PCW-1001-10uM-24h-2

type: RNA

city: Seoul

first: Minsung

last: Kang

address: 75 Nowon-ro

country: South Korea

institute: Korea institute of radiological and medical sciences

data_processing: Quantitative changes in mRNA levels were analyzed and clustered using the nSolver software (NanoString Technologies).

growth_protocol: MCF7 cells were maintained in Dulbecco’s modified Eagle medium (DMEM; Corning, NY, USA) supplemented with 10% fetal bovine serum (Corning) and 1% penicillin/streptomycin (GenDEPOT, USA) or 1% ZellShieldTM (Minerva Biolabs, Berlin, Germany). The cells maintained under standard conditions, at humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted by standard protocol

treatment_protocol: MCF7 cells were treated with DMSO and 10 μM PCW-1001 for 24 h


title: CTRL-2

source_name: MCF7, DMSO, 24h

value: DMSO


title: JAR palbociclib

value: JAR


title: T24_LZD_0.84_A


title: Testis_RNA

description:
One sample from 150-day-old porcine testicular tissue.
scRNA-seq

source_name: testis cells

value: testis

value: 150 days


title: ANW12

description: monocyte.results.csv.gz

value: Control

value: ANW C03


title: CTRL-1


title: T72_LZD_0.84_B


title: activated_lactate_4

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-sequencing: Nextseq 550, 50-cycle v2.5, generating 71 bp single-end reads
Base calling and demultiplexing was performed using Illumina bcl2fastq (v2.20.0.422).
Reads were aligned to the mm10 reference genome (mm10/GRCm38) with STAR 2.7.5b
Read summarization to gene counts was performed using featureCounts.
Normalization of raw counts and differential gene expression were performed using EdgeR.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: CD8+ T cells were isolated from mouse splenocytes and either immediately snap-frozen for RNA extraction (naïve cells), or activated for 72h with anti-CD3/CD28 dynabeads and 10 U/ml recombinant human IL-2, in either plain media or in media supplemented with 40 mM sodium lactate, before RNA extraction.

extract_protocol:
Total RNA was extracted with the Qiagen’s RNeasy kit
To construct libraries suitable for Illumina sequencing, the Illumina TruSeq Stranded mRNA Sample preparation protocol which includes cDNA synthesis, ligation of adapters, and amplification of indexed libraries was used. The yield and quality of the amplified libraries were analysed using Qubit by Thermo Fisher and the Agilent Tapestation.

treatment_protocol: For naive (non-activated) samples, purified mouse CD8+ T cells were snap-frozen in RLT Plus lysis buffer immediately after isolation, untreated. For activation, mouse CD8+ T cells were incubated for 72h with anti-CD3/CD28 dynabeads and 10 U/ml IL-2, in either plain media or 40 mM sodium lactate.

tag: cell type

value: CD8+ T cells

tag: activation

value: 72h with aCD3/CD8 dynabeads

value: 40 mM sodium lactate


title: T4_LZD_0.84_B

value: 4 hour


title: T4_LZD_0.84_C


title: activated_lactate_3


title: NCCIT palbociclib

source_name: non-seminoma germ cell tumor, embryonal carcinoma

value: NCCIT

value: palbociclib treatment


title: PCW-1001-10uM-24h-1


title: activated_lactate_2


title: NCCIT ctrl.

value: non-seminoma germ cell tumor, embryonal carcinoma

value: solvent control


title: 2102EP palbociclib


title: activated_lactate_1


title: T72_LZD_0x_C

value: no drug

value: 72 hour


title: 2102EP ctrl.


title: T72_LZD_0x_B


title: TCam-2 palbociclib

source_name: germ cell tumor, seminoma

value: germ cell tumor, seminoma


title: activated_vehicle_3

value: vehicle


title: 28F_Malignant melanoma of the skin

type: genomic

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

description: Hybridized to CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the recent laboratory protocol of UD GenoMed Medical Genomic Technologies Ltd. (Clinical Genomic Center, University of Debrecen, Debrecen, Hungary).

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations FS450, and scanned using the Gene Chip Scanner 3000.

data_processing: Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US). CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v4.2.0.80 Software. CNV data were analyzed with the Nexus Copy Number software (BioDiscovery, CA, ver. 8).

label: Biotin

source_name: Malignant melanoma tissue, cryopreserved, autopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from frozen autopsy or FFPE archived diagnostic melanoma tissue samples using the QIAamp DNA Mini and QIAamp DNA FFPE Tissue Kits, respectively. DNA quality and quantity was assessed using a NanoDrop ND-1000 UV–visible spectrophotometer and Qubit dsDNA HS Assay on a Qubit 1.0 fluorometer. Fragment analysis of DNA was carried out applying 1% agarose gel electrophoresis as well as BioAnalyzer 2100 using High Sensitivity DNA Kit.

value: malignant melanoma


title: TCam-2 ctrl.


title: T24_LZD_0x_C

value: 24 hour


title: T72_LZD_0x_A


title: H37Rv_T72_MXF_0x_B

treatment_protocol: Treatment with no drug or Moxifloxacin at 0.12 or 0.3 μg/mL for 4, 24 or 72 h


title: activated_vehicle_2


title: JAR ctrl.

value: non-seminoma germ cell tumor, choriocarcinoma

value: JAR


title: T24_LZD_0x_B


title: activated_vehicle_1


title: T24_LZD_0x_A


title: naïve_4

value: non-activated

value: no treatment


title: TB9_CVB1_CDC7_S9

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6 A

country: Finland

institute: Turku Bioscience Centre, University of Turku

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 10796 strain - rep3

data_processing:
The quality of the raw RNA-seq reads was evaluated using the high throughput quality control tool FastQC. The raw reads were observed to be of high quality with no need for additional trimming.
The raw RNA-seq reads were mapped to the University of California, Santa Cruz (UCSC) human reference genome Genome Reference Consortium Human Build 38 (GRCh38) using the STAR aligner version 2.5.2b.
The featureCounts tool version 1.5.1 included in the Subread software package was applied to generate the read counts using the uniquely mapped reads.
Genome_build: University of California, Santa Cruz (UCSC) human reference genome Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary_files_format_and_content: Processed data file is tab delimited text file containing the genewise read counts for each sample.

growth_protocol: Pancreatic ductal cells (PANC-1) were obtained from American type culture collection (ATCC) and cultured in Dulbecco’s modified eagle media (DMEM) supplemented with 10% v/v of FBS and 0.5 % penicillin-streptomycin (Pen-Strep, Gibco). PANC-1 were infected with Coxsackievirus B1 (CVB1) prototype strain obtained from ATCC (American type culture collection, strain Conn-5) and a wild type CVB1 strain (strain 10796) (Hämäläinen et al., 2014), purchased from Centers for Disease Control and Prevention (CDC).

extract_protocol:
Total RNA was purified using the Allprep DNA/RNA/miRNA Universal kit (Qiagen) and treated in-column with DNase for 15 min according to the manufacturer's instructions. The quality of the total RNA was ensured with Advanced Analytical Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany).
Libraries were prepared according to Illumina TruSeq® Stranded mRNA sample protocol. The high quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantification kit (Life Technologies).

treatment_protocol: Persistent infection was established as described by Sane et al (Sane et al., 2013) and as in our previous studies (Honkimaa et al., 2020; Lietzén et al., 2019). Briefly, PANC-1 cells were infected using a low titer of the virus which led to a strong cytopathic effect and cell death. Cells were washed regularly with Hank’s balanced salt solution (Sigma-Aldrich) and passaged by scraping using Grainer-Bio cell scraper. After the initial infection, cells started to grow and the virus propagated in the cell culture for over 300 days (Lietzén et al., 2019) before sample collection. Persistent CVB1 (ATCC and 10796) infection samples were collected by scraping and dry cell pellets were quick frozen in liquid nitrogen and stored at -80°C for further analysis.


title: TB7_CVB1_CDC7_S7

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 10796 strain - rep1


title: TB8_CVB1_CDC7_S8

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 10796 strain - rep2


title: T4_LZD_0x_C


title: naïve_3

value: CD8+ T cells


title: T4_LZD_0x_B


title: activated_vehicle_4

value: 72h with aCD3/CD8 dynabeads


title: naïve_2


title: TB6_CVB1_ATCC_EXP2_S6

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 ATCC strain - rep3


title: TB5_CVB1_ATCC_EXP2_S5

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 ATCC strain - rep2


title: naïve_1


title: TB4_CVB1_ATCC_EXP2_S4

description: pancreatic ductal-like cell line PANC-1 cells - persistent carrier state infection CVB1 ATCC strain - rep1


title: T72_CFZ_3.65_C

treatment_protocol: Treatment with no drug or Clofazamine at 0.73 or 3.65 μg/mL for 4, 24 or 72 h

value: 3.65 microg/mL


title: T4_LZD_0.84_A

value: 4 hour


title: T72_CFZ_3.65_B


title: TB3_CNTRL_ATCC_levy_S3

description: pancreatic ductal-like cell line PANC-1 cells - non infected control - rep3

value: non-infected control


title: TB2_CNTRL_ATCC_levy_S2

description: pancreatic ductal-like cell line PANC-1 cells - non infected control - rep2


title: T72_CFZ_3.65_A


title: TB1_CNTRL_ATCC_levy_S1

description: pancreatic ductal-like cell line PANC-1 cells - non infected control - rep1


title: SCH300_2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling.
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene.
Gene count measurements were obtained using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count.

source_name: Rhabdomyosarcoma cell line RD

growth_protocol: RD cells were grown in RPMI medium supplemented with 10% FBS.

extract_protocol:
RNA was isolated using RNeasy mini kit (Qiagen) as per manufacturer instructions.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide.

treatment_protocol: siRNA (10nM) transfection experiments were performed using Lipofectamine RNAi MAX (Life Technologies) following manufacturer instructions. Cells were harvested after 48 hours. For drug treatment, the cells were treated with 300 nM SCH772984 or DMSO for 24 hours.

value: RD

tag: harvest time


title: SCH300_1


title: 12-986418J

city: Edinburgh

first: Luke

last: Boulter

address: IGC

institute: MRC Human Genetics Unit

description: Exome capture and DNA sequencing of KrasG12D screen

data_processing:
Library strategy: exome-seq
Data aligned to the FVB_NJ_v1.86 genome using Burrows-Wheeler  Aligner
Indels identified using Vardict
Identification of CRISPR induced indels using Integrative  Genomics Viewer
Indels with  start or end sites out-with sgRNA targets were removed
To determine if editing had induced structural rearrangements, structural variants (SVs) were called using Delly2304 (v0.7.9) as follows: all reads which had a minimum mapping quality of 20 were used to call germline and somatic SVs, SVs with a PASS flag for somatic status, had a minimum variant allele fraction of 0.15, had zero read support in the normal, and had precisely mapped breakpoints were then visually analysed on IGV to determine if they overlapped with sgRNA target sites.
Genome_build: FVB_NJ_v1.86
Supplementary_files_format_and_content: .txt files contain identified CRISPR induced INDELS

source_name: Mouse Intrahepatic Cholangiocarcinoma

extract_protocol:
DNA was extracted using Phenol/Chloroform precipitation and a Qiagen Blood and Tissue clean up kit
DNA libraries were constructed according to standard Illumina protocols

value: FVB/N

value: Liver cancer

tag: genetic background

value: wild-type


title: 14-986418D


title: DMSO control replicate 2

value: DMSO


title: 13-986418I


title: 15-986418K


title: H37Rv_T24_MXF_0.3_A

value: 0.3 ug/mL


title: DMSO control replicate 1


title: T4_LZD_0x_A

value: no drug


title: T24_CFZ_3.65_A

value: 24 hour


title: T4_CFZ_3.65_C


title: T4_CFZ_3.65_B


title: 16-986418F


title: 10-986423T4


title: NRAS siRNA-2 replicate 2

value: NRAS siRNA 2

value: 48 hours


title: 9-986423T3


title: NRAS siRNA-2 replicate 1


title: T72_CFZ_0.73_C

value: 0.73 microg/mL

value: 72 hour


title: 8-986424E


title: NRAS siRNA-1 replicate 2

value: NRAS siRNA 1


title: T72_CFZ_0.73_B


title: NRAS siRNA-1 replicate 1


title: T24_CFZ_3.65_C


title: 6-986420C


title: T24_CFZ_3.65_B


title: T4_CFZ_3.65_A


title: 5-986420D


title: 11-986419


title: nonspecific siRNA, replicate 2

value: scrambled-siRNA control


title: 4-986420A


title: nonspecific siRNA, replicate 1


title: T24_CFZ_0.73_A


title: 2-986418Panc

source_name: Mouse Intrahepatic Cholangiocarcinoma pancreatic lesion

value: Cancer in pancreas


title: T24_CFZ_0.73_C


title: T4_CFZ_0.73_C

value: 4 hour


title: T24_CFZ_0.73_B


title: 3-986420Panc


title: 939811N

description: Exome capture and DNA sequencing of NrasG12V screen

source_name: Mouse normal liver

value: Normal liver


title: T4_CFZ_0.73_B


title: 872720A


title: Differentiation_CTRL_rep2

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

description: Treated by EtOH(vehicle) for 7 days in differentiation medium

data_processing:
Raw fastq files were assessed by FastQC (v0.11.5).
The adapters and low-quality sequence were trimmed by cutadapt (v-1.13).
RSEM (v1.3.0), coupled with Bowtie2(v2.2.9), were used to quantify the expression of genes and transcripts based on the reference genome mm10 (GRCm38) with gene annotation from GENCODE (release vM17).
The raw counts of reads mapped to each gene were extracted and used for subsequent analysis.
Genome_build: GRCm38, mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and raw counts values for each Sample

source_name: Hippocampus-derived NSCs

growth_protocol: The Hippocampus-derived primary NSCs were cultured under two conditions: proliferation(DMEM/F12 containing 20 ng/ml EGF, 20 ng/ml bFGF, 1% glutaMAX , 1% B27 and 1% penicillin/streptomycin and differentiation(DMEM/F12 containing 1% glutaMAX , 2% B27 and 1% penicillin/streptomycin).

extract_protocol:
Total RNA were extracted from these cells using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In each condition, the cells were treated by either 1 μM 4-Hydroxybenzoic acid(4HBP) or EtOH for 7 days, as the treatment group and control group respectively.

value: Primary NSCs

tag: culture condition

value: Differentiation

value: EtOH (vehicle)


title: 872718B

value: FVB/N

value: Liver cancer

value: wild-type


title: T72_CFZ_0x_C

source_name: bacterial culture

value: no drug


title: T72_CFZ_0.73_A


title: Differentiation_CTRL_rep1


title: 7-986423T5


title: 872718A


title: 1-986420


title: 872714A


title: T72_CFZ_0x_A


title: T72_CFZ_0x_B


title: T24_CFZ_0x_C

value: 24 hour


title: 818602A


title: Differentiation_4HBP_rep1

description: Treated by 4-Hydroxybenzoic acid for 7 days in differentiation medium

value: 4-Hydroxybenzoic acid


title: Differentiation_4HBP_rep2


title: T24_CFZ_0x_A


title: 818601B


title: T24_CFZ_0x_B


title: T4_CFZ_0.73_A


title: 3T3-L1_Day 4 pos-tinduction

city: Dongguan

first: Changqing

last: Zuo

state: Guangdong

address: 1 Xincheng Avenue, Songshan Lake Industrial and Technology Park

department: Department of Pharmacology

institute: Guangdong Medical University

description: Gene expression after induced adipocyte differentiation for 4 day in 3T3-L1 cells

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: 3T3-L1, Day 4 pos-tinduction

label_protocol: according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted using Trizol reagent according to the manufacture's protocol

tag: cell

value: cell


title: 3T3-L1_Day 0 pos-tinduction

description: Gene expression after induced adipocyte differentiation for 0 day in 3T3-L1 cells

source_name: 3T3-L1, Day 0 pos-tinduction


title: 818600B


title: Proliferation_CTRL_rep2

description: Treated by EtOH(vehicle) for 7 days in proliferation medium

value: Proliferation


title: C3H10T1/2_Day 0 pos-tinduction

description: Gene expression after induced adipocyte differentiation for 0 day in C3H10T1/2 cells

source_name: C3H10T1/2, Day 0 pos-tinduction


title: Proliferation_CTRL_rep3


title: 818600A


title: T4_CFZ_0x_C


title: Differentiation_4HBP_rep3


title: Proliferation_CTRL_rep1


title: T4_CFZ_0x_B


title: Proliferation_4HBP_rep3

description: Treated by 4-Hydroxybenzoic acid for 7 days in proliferation medium


title: T4_CFZ_0x_A


title: Proliferation_4HBP_rep2


title: KrasNf2-856

description: Ribosome depleted total RNA

data_processing:
The primary RNA-Seq processing, quality control to transcript-level quantitation, was carried out using nf-core/rnaseq v1.4.3dev (https://github.com/ameynert/rnaseq)
Reads were mapped to the mouse FVB_NJ_v1 decoy-aware transcriptome using the salmon aligner
RNA-Seq analysis was performed in R (4.0.2)
Reads were summarized to gene-level and differential expression analysis was performed using the bioconductor packages tximport (1.16.1) and DESeq2 (1.28.1). A pre-filtering was applied to keep only genes that have at least 10 reads in a group and 15 reads in total.
The Wald test was used for hypothesis testing for pairwise group analysis. A shrunken log2 fold changes (LFC) was also computed for each comparison using the adaptive shrinkage estimator from the 'ashr' package
Genome_build: FVB_NJ_v1
Supplementary_files_format_and_content: Raw gene counts for every sample and every gene

source_name: Mouse intrahepatic cholangiocarcinoma generated through in vivo CRISPR-SpCas9 editing of Nf2 and expression of KRasG12D cDNA

extract_protocol:
Trizol and chloroform extraction with Qiagen miniprep clean up
Standard Illumina library preparation


title: 818599A


title: T72_PA824_3.5_C

treatment_protocol: Treatment with no drug or Pretomanid at 0.7 or 3.5 μg/mL for 4, 24 or 72 h

value: Pretomanid, 3.5 μg/mL

value: 72 hour


title: Proliferation_4HBP_rep1


title: KrasNf2-855

description: Ribosome depleted total RNA


title: T72_PA824_3.5_B


title: T72_PA824_3.5_A


title: C3H10T1/2_Day 4 pos-tinduction

description: Gene expression after induced adipocyte differentiation for 4 day in C3H10T1/2 cells

source_name: C3H10T1/2, Day 4 pos-tinduction


title: KrasNf2-854

description: Ribosome depleted total RNA


title: 986418-I

description: Ribosome depleted total RNA

source_name: Mouse intrahepatic cholangiocarcinoma generated through in vivo CRISPR-SpCas9 screening


title: T4_PA824_3.5_C


title: T24_PA824_3.5_B


title: 986418-D

description: Ribosome depleted total RNA


title: 986418-F

description: Ribosome depleted total RNA


title: T4_PA824_3.5_B


title: T24_PA824_3.5_A


title: T4_PA824_3.5_A


title: 986418-K

description: Ribosome depleted total RNA


title: 986419-A

description: Ribosome depleted total RNA


title: T72_PA824_0.7_B

value: Pretomanid, 0.7 μg/mL


title: 818599B


title: 986420-B

description: Ribosome depleted total RNA


title: 986418-J

description: Ribosome depleted total RNA


title: 986420-A

description: Ribosome depleted total RNA


title: T72_PA824_0.7_A


title: 986420-C

description: Ribosome depleted total RNA


title: 986420-D

description: Ribosome depleted total RNA


title: T24_PA824_0.7_C


title: 986423T3

description: Ribosome depleted total RNA


title: T24_PA824_0.7_B


title: 986423T4

description: Ribosome depleted total RNA


title: T4_PA824_0.7_C


title: T4_PA824_0.7_B


title: T24_PA824_3.5_C


title: 986424-E

description: Ribosome depleted total RNA


title: T4_PA824_0.7_A


title: T72_PA824_0.7_C


title: KRAS-Tp53-848

description: Ribosome depleted total RNA

source_name: Mouse intrahepatic cholangiocarcinoma generated through in vivo CRISPR-SpCas9 editing of Trp53 and expression of KRasG12D cDNA


title: T72_PA824_0x_B


title: KRAS-Tp53-850

description: Ribosome depleted total RNA


title: T72_PA824_0x_C


title: S2_polysome_porthos_dsRNA_3

city: Klosterneuburg

first: Daria

last: Siekhaus

address: Am Campus 1

department: Bertalanffy Building

country: Austria

institute: IST Austria

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6)
To calculate Translation efficiency (TE), TPMs (transcripts per million) values for polysome-libraries were calculated (Flora et al., 2018). All transcripts with zero reads were discarded from libraries for further analysis. The log2 ratio of TPMs between the polysome fraction and total mRNA was measured. This ratio represents TE. The TE value of each replicate was averaged and delta TE (ΔTE) was calculated as (porthos RNAi TE)/(GFP RNAi TE). Targets were defined as transcripts falling greater or less than two standard deviations (SD) from the median of ΔTE.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: tab-delimited text files include raw read values

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2 Cells

growth_protocol: S2 cells were cultured Schneider's media supplemented with 10% BSA according to standard methods. Samples were treated either with control, GFP dsRNA or dsRNA targeting porthos using 1 µg of dsRNA as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465107/). 0.5-1.0 x 106 cells were seeded 30 minutes prior to transfection to adhere. Prior to transfection, the media was changed for 500 µl of fresh media. The seeded cells were treated with 500 µl of transfection complexes per well of a 6-well plate. After 48 hours post transfection, cells were passaged to 10 cm dishes. Following more 3 days cells were harvested for polysome sequencing.

extract_protocol:
RNA was isolated using TRIzol for input samples(Invitrogen, 15596026) or phenol-chloroform treatment for polysome samples, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: For samples with prefixes  "polysome_" samples were loaded onto polysome gradients and fractionated prior to RNA isolation as follows: Polysome sequencing was performed as described by (Flora et al., 2018) with minor modifications. Cells were incubated with fresh medium 2-4 hours before harvesting. Cycloheximide (100 μg/ml) was first added to the medium for 3 min at RT, and the cells were subsequently centrifuged at 800 xg for 3 min. The cell pellet was afterwards washed two times with ice-cold phosphate-buffered saline (1X PBS, pH 7.4). The supernatant was discarded and the pellet was gently resuspended in 300 µl of lysis buffer A (300 mM NaCl, 15 mM Tris-HCl, pH 7.5, 15 mM EDTA, 1 mg/ml heparin, 1% Triton-X100, and 100 μg/ml cycloheximide) and lysed for 15 min on ice. The lysate was clarified by centrifugation at 8500 xg for 5 min at 4°C. 20% of the lysate was kept aside as an input. The clarified lysate was loaded onto 10%-50% sucrose gradient in Buffer B (300 mM NaCl, 15 mM Tris-HCl, pH 7.5, 15 mM MgCl2, supplemented with 100 μg/ml cycloheximide) and centrifuged for 3 hours at 35,000 rpm in an SW41 rotor in a Beckman L7 ultracentrifuge (Beckman Coulter, Krefeld, Germany). The gradients were simultaneously fractionated on a Density Gradient Fractionation System (#621140007) at 0.75 ml/min. We added 20 μl of 20% SDS, 8 μl of 0.5 M pH 8 EDTA, and 16 μl of proteinase K (#P8107S) to each polysome fraction and incubated them for 30 min at 37°C. The RNA from each fraction was extracted by standard acid phenol: chloroform purification followed by 80% ethanol precipitation. The polysome fractions were then measured for RNA content and RNAseq libraries were prepared.

tag: source

value: polysome fractions

value: porthos dsRNA

value: S2 Cells


title: KRAS-Tp53-Nf2-852

description: Ribosome depleted total RNA

source_name: Mouse intrahepatic cholangiocarcinoma generated through in vivo CRISPR-SpCas9 editing of Trp53;Nf2 and expression of KRasG12D cDNA


title: KRAS-Tp53-Nf2-872

description: Ribosome depleted total RNA


title: KRAS-Tp53-Nf2-851

description: Ribosome depleted total RNA


title: S2_polysome_porthos_dsRNA_2


title: WT_BileDuct_1

description: Ribosome depleted total RNA

source_name: Uninjured bile ducts

value: Bile ducts


title: T24_PA824_0.7_A


title: T24_PA824_0x_A


title: T72_PA824_0x_A


title: T24_PA824_0x_C


title: S2_polysome_GFP_dsRNA_3

value: GFP dsRNA


title: S2_polysome_porthos_dsRNA_1


title: 986423T5

description: Ribosome depleted total RNA


title: T4_PA824_0x_C

value: 4 hour


title: S2_polysome_GFP_dsRNA_2


title: S2_polysome_GFP_dsRNA_1


title: T24_PA824_0x_B


title: WT_BileDuct_3

description: Ribosome depleted total RNA

value: FVB/N


title: T4_PA824_0x_B


title: T4_PA824_0x_A


title: WT_BileDuct_2

description: Ribosome depleted total RNA


title: S2_input_porthos_dsRNA_3

value: input


title: WT 2

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

data_processing:
The quality of RNA-Seq raw reads were evaluated using FastQC quality control tool, filtered using the TrimGalore software (version 0.4.1 with the parameter-illumina), Afterwards, a reference genome index was established using Bowtie2 software.
Sequence reads were trimmed off adaptor sequences and independently aligned using TrimGalore software (version 0.4.1 with the parameter-illumina) with default setting against mRNA  accounting for a maximum of two gaps or mismatches in each sequence
Differential expression, p-value and fold changes for each gene were determined using linear model in R with the package Cuffdiff  (version 2.2.1) according to a design with a single factor comprising all different experimental groups with default parameters.
Genome_build: PlasmoDB Release 33
Supplementary_files_format_and_content: FPKM

organism: Plasmodium berghei

source_name: RNA-seq

growth_protocol: All strains were collected from infected RBCs of mice

extract_protocol:
The infected blood was collected from mice and passed though Plasmodipure (Euro Proxima, Netherlands, cat# 8011) to remove WBCs. The purified RBCs were lysed in 0.2% saponin and the parasite pellet was washed thrice with PBS to obtain pellet devoid of any RBC contamination. The parasite RNA was isolated using Trizol and confirm RINs value above 8.0. Alternatively, the quality of the ribosomal 28 S and 18 S on an agarose gel was used as a measure of integrity and the absorbance at 260/280 nm was used to determine quantity.
The sequencing library is prepared by random fragmentation of the cDNA sample preparation kit (TruSeq RNA Sample Preparation v2 Guide, Part #15026495 Rev. F.) according to the manufacturer’s instructions. Briefly the total RNA (5µg) were ligated 5’ and 3' adapter using T4 RNA ligase 2 truncated (NEB)and a 5' and 3’ adapter using  T4 RNA ligase 2. The ligation products were reverse transcribed using Superscript II Reverse Transcriptase (Life Technologies) and amplified with  PCR (12 Cycle). The PCR products were purified with electrophoresis of 6% Novex TBE PAGE Gel. The purified cDNA library for each sample was analyzed on Agilent 2100 Bioanalyzer using Agilent DNA high sensitivity kit.

tag: genotype

value: WT

tag: Stage

value: Blood stage


title: S2_input_porthos_dsRNA_2


title: KRAS-Tp53-849

description: Ribosome depleted total RNA

tag: strain

value: Liver cancer

value: wild-type


title: T72_INH_1.8_C

treatment_protocol: Treatment with no drug or Isoniazid at 0.18 or 1.8 μg/mL for 4, 24 or 72 h

tag: drug treatment

value: 1.8 μg/mL

tag: treatment time


title: T72_INH_1.8_B


title: ΔHspJ62 line 2

value: deltaHspJ62 line


title: T24_INH_1.8_B

value: 24 hour


title: S2_input_GFP_dsRNA_1


title: WT 1


title: S2_input_porthos_dsRNA_1


title: S2_input_GFP_dsRNA_3


title: T72_INH_1.8_A

value: 72 hour


title: ΔHspJ62 line 1


title: T4_INH_1.8_C


title: Piglet_overfed_metformin_sample43

city: Salt

first: Abel

last: López-Bermejo

state: Girona

address: Dr. Castany s/n

department: Pediatrics

country: Spain

institute: IDIBGI

data_processing:
Quality control of sequencing reads was performed using FastQC.
Adapter removal was carried out using Trim Galore! version 0.4.1.
Reads were then aligned to the reference genome using bismark v0.16.1, followed by methylation calling using the corresponding bismark functionality.
Differentially methylated cytosines in CpG sites were obtained after retrieval with Bioconductor Methylkit package v1.1.8. and filtering out Single Nucleotide Polymporphisms in CpG sites together with non-CpG cytosines.
Genome_build: susScr3
Supplementary_files_format_and_content: cov files with headers: <chromosome>,<position>,<strand>,<count methylated>,  <count unmethylated>, <C-context>, <trinucleotide context>

source_name: Piglet_adipose tissue

extract_protocol:
High quality genomic DNA (400ng) was isolated from adipose tissue samples with Gentra PureGene tissue kit (Qiagen) according to manufacturer's instructions. DNA was bisulfited with the EZ DNA Methylation-Gold Kit (Zymo Research), according to manufacturer's instructions. Bisulfite conversion rate was over 99%.
Libraries were were prepared for sequencing using standard Illumina protocols and Sequencing was performed on a HiSeq 3000 (Illumina).

treatment_protocol: All piglets were sacrified at weaning (28 days) and visceral adipose tissue samples were collected and stored at -80ºC until processed.

tag: tissue

value: Visceral adipose tissue

value: 28 days

tag: maternal diet treatment

value: overfed

tag: piglet's intervention

value: metformin


title: Piglet_overfed_metformin_sample45

tag: age


title: Piglet_overfed_vehicle_sample47

value: vehicle


title: Piglet_overfed_vehicle_sample44


title: Piglet_overfed_vehicle_sample48


title: Piglet_overfed_metformin_sample42


title: Piglet_overfed_vehicle_sample46


title: T72_INH_0.18_C


title: T24_INH_1.8_C


title: T4_INH_1.8_A


title: T72_INH_0.18_B


title: S2_input_GFP_dsRNA_2

tag: treatment

value: GFP dsRNA

value: S2 Cells


title: Piglet_overfed_metformin_sample41


title: T24_INH_1.8_A


title: T4_INH_1.8_B

value: 4 hour


title: Piglet_overfed_vehicle_sample40


title: Piglet_overfed_vehicle_sample39


title: Piglet_overfed_metformin_sample37


title: Piglet_overfed_metformin_sample38


title: Piglet_overfed_vehicle_sample36


title: T24_INH_0.18_A


title: T24_INH_0.18_C


title: T24_INH_0.18_B


title: T4_INH_0.18_A


title: T4_INH_0.18_B


title: T72_INH_0.18_A


title: Piglet_overfed_vehicle_sample34


title: Piglet_overfed_metformin_sample33


title: T72_INH_0x_C

value: no drug


title: Piglet_overfed_metformin_sample35


title: T4_INH_0.18_C


title: T72_INH_0x_B


title: Piglet_restricted_vehicle_sample32

value: restricted


title: T72_INH_0x_A


title: T24_INH_0x_C


title: Piglet_restricted_vehicle_sample31


title: Piglet_restricted_metformin_sample30


title: T24_INH_0x_A


title: T24_INH_0x_B


title: Piglet_restricted_metformin_sample29


title: Piglet_restricted_vehicle_sample28


title: T4_INH_0x_C


title: Piglet_restricted_vehicle_sample27


title: T4_INH_0x_B


title: Piglet_restricted_metformin_sample26


title: 513T

city: Heidelberg

first: Mohammed

last: Abba

address: Im Neuenheimer Feld 280

department: Molecular Oncology of Solid Tumors

institute: German Cancer Research Center (DKFZ)

description:
9611518098 R05C02 Grn.idat
9611518098 R05C02 Red.idat
tumor tiisue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: Colorectal cancer tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from resected tumor and corresponding normal samples using the QIAamp DNA mini kit according to the manufacturer’s instructions.

tag: tissue preparation

value: resected tissue

tag: tissue disease state

value: tumor tissue

tag: patient diagnosis

value: Colorectal cancer


title: T4_INH_0x_A

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample

extract_protocol:
In three biological replicates, M. tuberculosis cultures with or without drug treatment were harvested at 4, 24  or 72 h. Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Piglet_restricted_vehicle_sample25


title: 511N

description:
9611518098 R06C01 Grn.idat
9611518098 R06C01 Red.idat
normal tissue

source_name: Colorectal cancer normal

value: normal tissue


title: Piglet_restricted_vehicle_sample24


title: Piglet_restricted_metformin_sample23


title: 519T

description:
9611518098 R05C01 Grn.idat
9611518098 R05C01 Red.idat
tumor tiisue


title: 511T

description:
9611518098 R01C02 Grn.idat
9611518098 R01C02 Red.idat
tumor tiisue


title: 519N

description:
9611518098 R04C01 Grn.idat
9611518098 R04C01 Red.idat
normal tissue


title: Piglet_restricted_vehicle_sample22


title: LEN-Platelets

city: Asahikawa

first: Hiroki

last: Tanaka

state: Hokkaido

address: Midorigaoka-higashi, 2-1-1-1

country: Japan

institute: Asahikawa Medical University

description:
Resident mRNA inherited from megakaryocytes in platelets
LEN-PLT

hyb_protocol: cDNA was hybridized with Clariom™ S Assay, rat (Thermo Fisher Scientific, Waltham, MA, USA)

scan_protocol: GeneChips were scanned by Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The fluorescence intensity was calculated by GeneChip command console (Thermo Fisher Scientific).

label: biotin

organism: Rattus norvegicus

source_name: lenvatinib-encapsulated platelets

label_protocol: cDNA was labeled with PE.

extract_protocol: RNA was extracted using an RNeazy micro kit (Qiagen, Hilden, Germany).

treatment_protocol:
To collect rat citrated blood, an indwelling needle was placed in the tail vein of a rat, and the tail was gently massaged to collect the spontaneously flowing blood into a tube containing acid citrate dextrose solution (ACD: Sigma-Aldrich, St. Louis, MS, USA). In each tube, 1 mL of whole blood was mixed with 0.1 mL of ACD. Then, the citrated blood was diluted 2-fold with platelet suspension solution (calcium-free Hanks? balanced salt solution:ACD = 9:1) and centrifuged at 200 ×g for 7 minutes. The supernatant was collected in a separate tube and used as isolated platelets
Isolated platelets were incubated with 10 µg of sorafenib or lenvatinib at 37°C for 30 minutes with gentle shaking. Extracellular sorafenib or lenvatinib was then washed out after centrifugation at 1000 ×g for 5 minutes.^SAMPLE = GSM5733087
To collect rat citrated blood, an indwelling needle was placed in the tail vein of a rat, and the tail was gently massaged to collect the spontaneously flowing blood into a tube containing acid citrate dextrose solution (ACD: Sigma-Aldrich, St. Louis, MS, USA). In each tube, 1 mL of whole blood was mixed with 0.1 mL of ACD. Then, the citrated blood was diluted 2-fold with platelet suspension solution (calcium-free Hanks? balanced salt solution:ACD = 9:1) and centrifuged at 200 ×g for 7 minutes. The supernatant was collected in a separate tube and used as isolated platelets
Isolated platelets were incubated with 10 µg of sorafenib or lenvatinib at 37°C for 30 minutes with gentle shaking. Extracellular sorafenib or lenvatinib was then washed out after centrifugation at 1000 ×g for 5 minutes.^SAMPLE = GSM5733088
To collect rat citrated blood, an indwelling needle was placed in the tail vein of a rat, and the tail was gently massaged to collect the spontaneously flowing blood into a tube containing acid citrate dextrose solution (ACD: Sigma-Aldrich, St. Louis, MS, USA). In each tube, 1 mL of whole blood was mixed with 0.1 mL of ACD. Then, the citrated blood was diluted 2-fold with platelet suspension solution (calcium-free Hanks? balanced salt solution:ACD = 9:1) and centrifuged at 200 ×g for 7 minutes. The supernatant was collected in a separate tube and used as isolated platelets
Isolated platelets were incubated with 10 µg of sorafenib or lenvatinib at 37°C for 30 minutes with gentle shaking. Extracellular sorafenib or lenvatinib was then washed out after centrifugation at 1000 ×g for 5 minutes.

value: blood

tag: cell type

value: peripheral platelets

value: lenvatinib-encapsulated platelets


title: 513N

description:
9611518098 R04C02 Grn.idat
9611518098 R04C02 Red.idat
normal tissue


title: 504N

description:
9611518098 R02C02 Grn.idat
9611518098 R02C02 Red.idat
normal tissue


title: Piglet_restricted_metformin_sample21

value: Visceral adipose tissue


title: 90T

description:
9611518087 R04C01 Grn.idat
9611518087 R04C01 Red.idat
tumor tiisue


title: SOR-Platelets

description:
Resident mRNA inherited from megakaryocytes in platelets
SOR-PLT

source_name: sorafenib-encapsulated platelets

treatment_protocol: Blood (3 mL) was collected from each of five normal F344 rats. From these samples, three 1 mL volumes from each group of control platelets (PLT), sorafenib-encapsulated platelets (SOR-PLT), and lenvatinib-encapsulated platelets (LEN-PLT) were produced. In these three groups, the prepared platelet suspensions from five rats were pooled.

value: sorafenib-encapsulated platelets


title: 102N

description:
9611518077 R01C01 Grn.idat
9611518077 R01C01 Red.idat
normal tissue


title: Control Platelets

description:
Resident mRNA inherited from megakaryocytes in platelets
PLT

source_name: control platelets

value: control platelets


title: 103T

description:
9611518077 R04C01 Grn.idat
9611518077 R04C01 Red.idat
tumor tiisue


title: 90N

description:
9611518087 R03C01 Grn.idat
9611518087 R03C01 Red.idat
normal tissue


title: Truncated ZNF675_F1-F6 construct replicate 1

city: Palo Alto

first: Zheng

state: CA

address: Stanford

department: Genetics

institute: Stanford university

data_processing:
Library strategy: Spec-seq
[Preliminary processing for each sample]  Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
[Data quality check between replicates]  Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
[Specificity and methylation sensitivity analysis]  The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Supplementary_files_format_and_content: Processed data files for each ZFP and analysis workflow for ZNF140
Supplementary_files_format_and_content: For each sample, the associated csv file contains the bound and unbound reads, calculated relative binding energy, library type, and the number of mismatches to some reference site for individual binding site. The data analysis protocol for each ZFP can be accessed through Github https://github.com/zeropin/ZFPCookbook

molecule: other

organism:
Homo sapiens
synthetic construct

source_name: Spec-seq sample to synthetic and genomic DNA library

extract_protocol:
[Recombinant protein expression protocol] We used the NEB PURExpress or E. coli_BL21 system to produce N-terminal HALO tagged ZFP constructs and noticed better success rates than previously used SUMO-tagged constructs.
[EMSA protocol] 20uL binding reactions were loaded onto 10% Tris-glycine gel in cold room and run for 50mins at 200V.
[Sequencing sample prep protocol] The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer _soaking a 55C for more than 30mins. Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles _annealing temperature 52C, extension time 30s. All samples were pooled together for Illumina Nextseq _1X 75bp single end run.

tag: recombinant protein

value: Truncated ZNF675_F1-F6 construct


title: ZNF675_F1-F11 construct replicate 2

value: ZNF675_F1-F11 construct


title: Truncated ZNF675_F1-F6 construct replicate 2


title: 87N

description:
9611518081 R05C02 Grn.idat
9611518081 R05C02 Red.idat
normal tissue


title: Piglet_restricted_metformin_sample18

value: 28 days

value: metformin


title: Piglet_restricted_vehicle_sample19

value: vehicle


title: Chow5

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

description: miRNA

data_processing:
Raw sequence reads were obtained using Illumina Pipeline v1.5 software.
Cutadapt v1.10 was used to remove adapters. Bowtie was used to map sequence reads (21 - 26 bases, Phred scores ≥ Q30) to the vervet transcriptome (ChlSab1.1 Ensembl release 80).
mirDeep2 was used to detect and quantify expression of known miRNAs in mirBase 21.
miRNA expression was normalized by the Transcripts Per Million (TPM) method.
Genome_build: ChlSab1.1 Ensembl release 80 and mirBase21.
Supplementary_files_format_and_content: Matrix table of raw and normalized read counts for known miRNAs in 10 samples.

organism: Chlorocebus sabaeus

source_name: Liver

extract_protocol:
Liver tissue was flash frozen in liquid nitrogen immediately after collection and stored at -80oC. Total RNA was extracted from vervet monkey livers using the Zymo Direct-zol RNA MiniPrep kit.
Small RNA-Seq libraries were prepared using the Illumina TruSeq Small RNA Library Prep Kit.

treatment_protocol: Prior to the study, all animals were maintained on a chow diet. In the study, 5 animals were fed a high fructose diet and 5 animals were fed a chow diet.

tag: diet

value: Chow

tag: gender

value: female

value: liver


title: 504T

description:
9611518098 R03C02 Grn.idat
9611518098 R03C02 Red.idat
tumor tiisue

value: resected tissue

value: tumor tissue


title: 84T

description:
9611518081 R04C02 Grn.idat
9611518081 R04C02 Red.idat
tumor tiisue

value: Colorectal cancer


title: 88N

description:
9611518087 R01C01 Grn.idat
9611518087 R01C01 Red.idat
normal tissue

value: normal tissue


title: 88T

description:
9611518087 R02C01 Grn.idat
9611518087 R02C01 Red.idat
tumor tiisue


title: 87T

description:
9611518081 R06C02 Grn.idat
9611518081 R06C02 Red.idat
tumor tiisue


title: 103N

description:
9611518077 R03C01 Grn.idat
9611518077 R03C01 Red.idat
normal tissue


title: 84N

description:
9611518081 R03C02 Grn.idat
9611518081 R03C02 Red.idat
normal tissue


title: Chow4

description: miRNA


title: Piglet_control_vehicle_sample16

value: control


title: HFr5

description: miRNA

value: High fructose


title: 102T

description:
9611518077 R02C01 Grn.idat
9611518077 R02C01 Red.idat
tumor tiisue


title: Piglet_restricted_metformin_sample20

value: Visceral adipose tissue

value: restricted


title: Chow3

description: miRNA


title: 80T

description:
9611518081 R06C01 Grn.idat
9611518081 R06C01 Red.idat
tumor tiisue


title: Piglet_control_metformin_sample14


title: Chow2

description: miRNA


title: Piglet_control_vehicle_sample13


title: Chow1

description: miRNA


title: Piglet_control_metformin_sample12


title: 82N

description:
9611518087 R01C02 Grn.idat
9611518087 R01C02 Red.idat
normal tissue


title: 70T

description:
9611518081 R02C02 Grn.idat
9611518081 R02C02 Red.idat
tumor tiisue


title: HFr4

description: miRNA


title: 70N

description:
9611518081 R01C02 Grn.idat
9611518081 R01C02 Red.idat
normal tissue


title: 68T

description:
9611518087 R05C02 Grn.idat
9611518087 R05C02 Red.idat
tumor tiisue


title: Piglet_control_vehicle_sample11


title: HFr3

description: miRNA


title: Piglet_control_metformin_sample10


title: HFr2

description: miRNA


title: Piglet_control_vehicle_sample8


title: HFr1

description: miRNA


title: Piglet_control_vehicle_sample9


title: nag5_mutant-complemented-replica-2

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

data_processing:
Sequencing was performed in a MiSeq equipment (Illumina) with single reads of 121 cycles. FASTQ files were generated and purged from low quality reads.
Mapping was carried out with the Bowtie2 software (mode sensitive, local)
SAM files were analyzed using the software SeqMonk v0.31.0 (Babraham Bioinformatics) to which the gff3 annotation file was also incorporated. Duplicate reads were removed. Reads were combined and mapped onto CDS probes extended 50 nucleotides upstream and downstream. Quantification was done for the opposite strand
The outputs were recovered as Annotated Probe Report, which included the coding sequences (overlapping option), and processed in Excel format.
Genome_build: Yarrowia lipolityca strain CLIB122; genome assembly GCA_000002525.1
Supplementary_files_format_and_content: Excel sheet, mapped reads (corrected) on genome, plus EnsemblGenomes transcripts and UniProtKB/TrEMBL protein codes

organism: Yarrowia lipolytica

source_name: whole cell

growth_protocol: cells were grown to exponential phase in minimal medium with glucose as carbon source

extract_protocol:
RNA was extracted using the Speedtools total RNA extraction kit (Biotools, Spain). The integrity of the RNA was assessed using a 2100 Bioanalyser (Agilent). Only RNAs with a RIN >7.7 were used
The cDNA library was made with the TruSeq LT kit (Illumina). Given the relatively high GC content of the Y. lipolytica genome the following modifications were made to the standard protocol: 1) priming time with oligodT was extended to 10 min, 2) extension with reverse transcriptase was done at 45ºC, and 3) the subsequent library amplification was carried out for 15 cycles .

treatment_protocol: no particular treatment was done.


title: 68N

description:
9611518087 R04C02 Grn.idat
9611518087 R04C02 Red.idat
normal tissue


title: nag5_mutant-complemented-replica-1


title: Piglet_control_metformin_sample7


title: Piglet_control_vehicle_sample6


title: 80N

description:
9611518081 R05C01 Grn.idat
9611518081 R05C01 Red.idat
normal tissue


title: nag5_mutant-replica-2


title: 67N

description:
9611518098 R06C02 Grn.idat
9611518098 R06C02 Red.idat
normal tissue


title: nag5_mutant-replica-1


title: Piglet_control_metformin_sample4


title: Wild type-replica-2


title: ZNF675_F1-F11 construct replicate 1


title: Wild type-replica-1


title: Piglet_control_metformin_sample15


title: Piglet_control_metformin_sample2


title: 65T

description:
9611518081 R04C01 Grn.idat
9611518081 R04C01 Red.idat
tumor tiisue


title: 49T

description:
9611518081 R02C01 Grn.idat
9611518081 R02C01 Red.idat
tumor tiisue


title: Piglet_control_vehicle_sample3


title: Piglet_control_metformin_sample1


title: 65N

description:
9611518081 R03C01 Grn.idat
9611518081 R03C01 Red.idat
normal tissue


title: Piglet_restricted_metformin_sample17


title: tumor-BMS754807+hydroxychloroquine-6

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing: Transcriptome Analysis Console Software v 4.0 was used for basic data analysis and quality control.

source_name: tumor from BMS754807+hydroxychloroquine treated group

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Affymetrix Clariom S peg plate. The Affymetrix GeneChip® WT PLUS Reagent Kit Manual was followed to prepare the samples. the GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the kit. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays

extract_protocol: total RNA was isolated from tumor tissue by homogenization in trisol reagent, followed by purification with E.Z.N.A. RNA isolation (omega biotek)

value: BMS+HCQ


title: 49N

description:
9611518081 R01C01 Grn.idat
9611518081 R01C01 Red.idat
normal tissue


title: testis - IGG_rep1

city: Knoxville

first: Maxim

middle: Vladimirovich

last: Zagoskin

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

institute: The University of Tennessee, Knoxville

description:
IGG_male_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

data_processing:
Adapters were clipped and artifacts removed with FASTX Toolkit 0.0.13 (fastx_clipper and fastx_artifacts_filter).
18-30nt were filtered.
Annotated against local databases of rRNA, tRNA, mtRNA, miRNAs, repeats and transcripts with bowtie with following parameters: -f -v 1 --best.
Reads were mapped to Ascaris genome with bowtie2 with following parameters: -f -x
Genome_build: WGS Project JACCHR01 (assembly ASM1343314v1)
Supplementary_files_format_and_content: Nonredundant reads (nr) of processed fasta files: ids >1_23421, where 1 is order number of the read and 23421 is number of reads.

organism: Ascaris suum

source_name: total male germline

growth_protocol: Ascaris 4-cell embryos were developed in incubator at 30 C shaking at 100 rpm for 64hr.

extract_protocol:
Male and female germline tissues were extracted from worms and washed in PBS, frozen whole or following dissection in liquid nitrogen, and stored at -80°C. Argonaute IPs were carried out using affinity purified rabbit antibodies pre-bound to Protein A Dynabeads (Fisher Scientific) (5-10 ug of antibody per 100 ul of beads). Germline or embryo whole cell lysates were mixed with Protein A Dynabeads and rotated overnight at 4°C. Protein A Dynabeads were recovered and washed with high-salt buffer (50 mM Tris–HCl, pH 7.4, 1M NaCl, 1mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) three times. The beads were resuspended in 250 ul of Proteinase K buffer containing 200 µg/ml Proteinase K and incubated for 1 hr at 37°C. RNA was extracted using Trizol LS (Invitrogen) adapted for small RNA recovery by precipitation using 2 volumes of isopropanol, 15 µg of GlycoBlue (Invitrogen), and 30 minutes incubation at -80°C followed by centrifugation at 18,500 x g for 35 minutes at 4°C. The RNA was treated with RppH (25 units, New England Biolabs) in Thermopol buffer for 5’ independent cloning. Both untreated and RppH-treated samples were done for AsALG-1 and AsALG-4 samples. Following RppH treatment, samples were repurified with Trizol LS (Invitrogen) (adopted for small RNAs extraction) and stored at -80°C. RNA was isolated using Trizol or LS Trizol (Invitrogen). Total RNA samples were fractionated into small RNA (< 200 nt) and long RNA (>200nt) using the Monarch RNA cleaner (New England Biolabs).
Small RNA libraries were prepared using the Small RNA-Seq Library Prep Kit (Lexogen). Both 5’-phosphate and 5’-phosphate independent libraries (RppH-treated) were prepared. Libraries from 4-cell embryos were also prepared using 18-30 nt gel purified RNA using the SMARTer smRNA-Seq Kit (Clontech) and NEXTflex-Small-RNA-Seq (New England Biolabs) with similar results. RNA >200 nt was treated with TURBO DNase (Ambion) and rRNA depletion carried out using RiboCop rRNA Depletion Kit for Human/Mouse/Rat (Lexogen). Long RNA (>200 nt) libraries were made using CORALL Total RNA-Seq Library Prep Kit (Lexogen). Both small and long RNA libraries were sequenced 150 nt from both ends using the Illumina NovaSeq 6000 System.

value: total male germline

tag: 5'-end modification

value: mono- and triphosphate

tag: argonaute ip antibody

value: IGG

value: RNA 5' Pyrophosphohydrolase


title: testis - IGG_rep3

description:
IGG_male_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: testis - IGG_rep2

description:
IGG_male_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: tumor-BMS754807+hydroxychloroquine-5

scan_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.


title: MUC29213_S3: Barcode dataset of STICR-E14  in olfactory bulbs

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute of Neurobiology.

data_processing:
- Transcritpomic dataset: Sequencing reads in FASTQ files were aligned to a reference transcriptome (mm10-2.1.0) and collapsed into unique molecular identifier counts using the 10x Genomics Cell Ranger software (version 3.0.2 and 5.0.1).Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome (applied cut-offs see Supplementary Data 1, Bandler et al. 2021).
- Barcode dataset STICR: First, BBMap (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/) was used to remove low quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments which were then aligned to our pre-defined fragment reference sets using Bowtie (v5.2.1), allowing for up to 2 mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using Awk. Finally, UMI-tools (v.0.5.1) was used to remove duplicate STICR barcode/cell barcode reads by UMI, allowing for 1 bp mismatch in the UMI. STICR barcodes/CBC pairings with at least 5 distinct UMIs were retained for clonal analysis. Among cells with multiple STICR barcodes passing these criteria, we attempted to find a “dominant” STICR barcode that we defined as containing greater than or equal to 5 times the number of UMI counts compared to the next most abundance STICR barcode. “Dominant” STICR barcodes meeting these criteria were considered to be the clonal barcode of their respective cells and retained for further analysis. Finally, we applied an additional UMI threshold to STICR barcodes, requiring that all STICR barcode/CBC pairings used for clonal analysis have at least 9 distinct UMIs.
- Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Genome_build: mm10-2.1.0
Supplementary_files_format_and_content: - Processed_Transcript: Filtered count matrix
Supplementary_files_format_and_content: - Processed_LBC STICR: Csv files with columns for "CBC", "VBC_Count", "Tier", "Sequence", "UMI", "Final.VBC.call", and "Library"
Supplementary_files_format_and_content: - Processed_LBC TRACKERseq: Csv files with columns for "CBC" and "Lineage-Barcode"

source_name: Forebrain

extract_protocol:
embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custumed primers with standard Illumina adapters.

tag: strain

value: Forebrain

value: FACSorted for GFP


title: ovary - IGG_rep2

description:
IGG_female_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total female germline

value: total female germline


title: MUC29212_S2: Barcode dataset of STICR-E14 in amygdala


title: tumor-BMS754807+hydroxychloroquine-3


title: 31T

description:
9611518098 R01C01 Grn.idat
9611518098 R01C01 Red.idat
tumor tiisue


title: 82T

description:
9611518087 R02C02 Grn.idat
9611518087 R02C02 Red.idat
tumor tiisue


title: MUC29214_S4: Barcode dataset of STICR-E14 in striatum


title: 32T

description:
9611518077 R04C02 Grn.idat
9611518077 R04C02 Red.idat
tumor tiisue


title: tumor-BMS754807+hydroxychloroquine-2


title: 43N

description:
9611518077 R05C02 Grn.idat
9611518077 R05C02 Red.idat
normal tissue


title: tumor-BMS754807+hydroxychloroquine-4


title: MUC28072_t: Transcriptomic dataset of TrackerSeq-E12


title: Piglet_control_vehicle_sample5

value: 28 days

value: vehicle


title: MUC29204_t: Transcriptomic dataset of STICR-E14 in amygdala


title: DMD_Input_2 (RIP-Seq)

city: Wuhan

first: Shiyong

last: Liu

institute: Huazhong University of Science and Technology

description:
iRIP-seq
1 end reads

data_processing:
remove adapter sequences with cutadapt and set the parameter as “cutadapt -a AGATCGGAAGAGC -u 3 -m 16”.
remove bases with quality below 20, and retain reads longer than 16 bases with FASTX-Toolkit package by setting parameter “fastq_quality_trimmer -t 20 -l 16 -Q 33”
remove reads if it has more than 30% base with quality below 20 (“fastq_quality_filter -q 20 -p 70 -Q 33”)
discard NN, polyG and polyA, retention reads longer than 16 bases(cutadapt -a N -m 16 -O 1 -N - | cutadapt -a GGGGGGGGGGGGGG -O 4 -e 0.1 -n 5 - | cutadapt -a AAAAAAAAAAAAAAA -m 16 --label clean -O 4 -e 0.1)
end2 in the double-ended sequencing data performs reverse complementation by fastx_reverse_complement of FASTX-Toolkit package and then cats to end1 to form single-ended data
Peaks called by Piranha or CIMS software.
Genome_build: GRCH38
Supplementary_files_format_and_content: bed files are all included in a tar archive available on the series record.

source_name: HeLa cell

extract_protocol:
For iRIP-seq, the libraries were prepared following the manufacturer's instructions and applied to Illumina Nextseq500 system for 150 nt paired-end sequencing by Ablife. For CLIP-seq, the libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).
For iRIP-seq, the cDNA libraries used the Illumina ScriptSeq? v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing. For CLIP-seq, the recovered RNA was used to generate paired-end sequencing library with Balancer NGS Library Preparation Kit for small/microRNA (Gnomegen) following the manufacture instructions. Libraries corresponding to 150-250 bps were purified, quantified and stored at -80C until used for sequencing. The libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).

tag: cell line

value: HeLa

tag: rip target

value: none (input)


title: 4cell embryo - IGG

description:
IGG_64hr
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: 4 cells embryos

tag: tissue

value: 4 cells embryos


title: Male germline region M7 - long RNA INPUT

description:
INPUT_maleR4_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M7

value: male germline region M7

value: monophosphate


title: MUC29205_t: Transcriptomic dataset of STICR-E14  in olfactory bulbs


title: tumor-BMS754807+hydroxychloroquine-1


title: DMD_Input_1 (RIP-Seq)

description:
iRIP-seq
1 end reads


title: 26T

description:
9611518077 R06C01 Grn.idat
9611518077 R06C01 Red.idat
tumor tiisue

value: resected tissue

value: tumor tissue

value: Colorectal cancer


title: 28N

description:
9611518077 R01C02 Grn.idat
9611518077 R01C02 Red.idat
normal tissue

value: normal tissue


title: Male germline region M6 - long RNA INPUT

description:
INPUT_maleR3c_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M6

value: male germline region M6


title: 31N

description:
9611518087 R06C02 Grn.idat
9611518087 R06C02 Red.idat
normal tissue


title: MUC29206_t: Transcriptomic dataset of STICR-E14 in striatum


title: tumor-hydroxychloroquine-4

source_name: tumor from hydroxychloroquine treated group

value: HCQ


title: DMD_IP_1 (RIP-Seq)

description:
iRIP-seq
1 end reads

value: DMD


title: tumor-hydroxychloroquine-5


title: 67T

description:
9611518087 R03C02 Grn.idat
9611518087 R03C02 Red.idat
tumor tiisue

source_name: Colorectal cancer tumor


title: tumor-hydroxychloroquine-6


title: 28T

description:
9611518077 R02C02 Grn.idat
9611518077 R02C02 Red.idat
tumor tiisue


title: LV1_MUC21171_t: Transcriptomic dataset of STICR-E10 #1

description: Transcriptomic dataset of STICR-E10 #1

value: Forebrain


title: CLIP1_IP_1 (RIP-Seq)

description:
iRIP-seq
1 end reads


title: Male germline region M4 - long RNA INPUT

description:
INPUT_maleR2b3a_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M4

value: male germline region M4


title: LV3_MUC21172_t: Transcriptomic dataset of STICR-E10 #2

description: Transcriptomic dataset of STICR-E10 #2

value: FACSorted for GFP


title: CLIP1_Input_2 (RIP-Seq)

description:
iRIP-seq
1 end reads


title: Male germline region M5 - long RNA INPUT

description:
INPUT_maleR3b_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M5

value: male germline region M5


title: 26N

description:
9611518077 R05C01 Grn.idat
9611518077 R05C01 Red.idat
normal tissue

source_name: Colorectal cancer normal


title: 43T

description:
9611518077 R06C02 Grn.idat
9611518077 R06C02 Red.idat
tumor tiisue


title: 6N

description:
9611518098 R02C01 Grn.idat
9611518098 R02C01 Red.idat
normal tissue


title: CLIP1_Input_1 (RIP-Seq)

description:
iRIP-seq
1 end reads


title: LV4_MUC21173_t: Tracsnriptomic dataset of STICR-E10 #3

description: Tracsnriptomic dataset of STICR-E10 #3


title: Male germline region M2 - long RNA INPUT

description:
INPUT_maleR1b_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M2

value: male germline region M2


title: Male germline region M3 - long RNA INPUT

description:
INPUT_maleR2a_longRNAs
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M3

value: male germline region M3


title: 6T

description:
9611518098 R03C01 Grn.idat
9611518098 R03C01 Red.idat
tumor tiisue


title: tumor-hydroxychloroquine-2


title: tumor-hydroxychloroquine-3


title: LV7_MUC21174_t: Transcriptomic dataset of STICR-E10 #4

description: Transcriptomic dataset of STICR-E10 #4


title: 16N

description:
9611518087 R05C01 Grn.idat
9611518087 R05C01 Red.idat
normal tissue


title: Male germline region M1 - long RNA INPUT_rep2

description:
INPUT_maleR1a_longRNAs_rep2
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

source_name: male germline region M1

value: male germline region M1


title: CA298_t: Transcritomic dataset of wt MGE E13

description: Transcritomic dataset of wt MGE E13

source_name: MGE

value: SW

value: MGE

value: wild type


title: 27-KO-HFD

city: Los Angeles

first: Georges Doumet

last: HELOU

state: California

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M16 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M. Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10

source_name: CD11c+ hepatic cells from HFD-treated Atg5 CD11c KO mice

extract_protocol:
Total RNA was isolated from freshly isolated cells using MicroRNAeasy (Qiagen). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD11c+ cells were isolated from the livers of WT and Atg5 CD11cKO mice fed HFD for 14 weeks

value: 4-8 weeks

value: CD11c+ hepatic cells

tag: genotype

value: Atg5 CD11c KO mice


title: CA299_t: Transcritomic dataset of wt CGE E13

description: Transcritomic dataset of wt CGE E13

source_name: CGE

value: CGE


title: 16T

description:
9611518087 R06C01 Grn.idat
9611518087 R06C01 Red.idat
tumor tiisue

value: resected tissue

value: tumor tissue

value: Colorectal cancer


title: ovary - IGG_rep1

description:
IGG_female_rep1
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total female germline

value: mono- and triphosphate

value: IGG

value: RNA 5' Pyrophosphohydrolase


title: tumor-hydroxychloroquine-1

value: HCQ


title: 25-KO-HFD


title: 23-WT-HFD

source_name: CD11c+ hepatic cells from HFD-treated WT mice

value: WT


title: Male germline region M1 - long RNA INPUT_rep1

description:
INPUT_maleR1a_longRNAs_rep1
long RNA
Library made with Lexogen - CORALL Total RNA-Seq Library Prep Kit

value: male germline region M1

value: monophosphate


title: testis - ALG4 - 5'end-monophosphate

description:
ALG4_male_mono
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total male germline

value: total male germline


title: tumor-BMS754807-6

source_name: tumor from BMS754807 treated group

value: BMS


title: tumor-BMS754807-5


title: tumor-BMS754807-4


title: CA300_t: Transcritomic dataset of wt LGE E13

description: Transcritomic dataset of wt LGE E13

source_name: LGE

value: SW

value: LGE

value: wild type


title: CA301_t: Transcritomic dataset of wt MGE E15

description: Transcritomic dataset of wt MGE E15

value: MGE


title: ovary - ALG4 - 5'end-monophosphate

description:
ALG4_female_mono
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

source_name: total female germline


title: 26-KO-HFD

value: 4-8 weeks

value: CD11c+ hepatic cells

value: Atg5 CD11c KO mice


title: 22-WT-HFD


title: tumor-BMS754807-3


title: testis - region R2 - 5'end-triphosphate_rep3

description:
Testis_R2_tri_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: CA303_t: Transcritomic dataset of wt LGE E15

description: Transcritomic dataset of wt LGE E15


title: DMD_IP_2 (RIP-Seq)

description:
iRIP-seq
1 end reads

source_name: HeLa cell

value: HeLa

value: DMD


title: testis - region R1 - 5'end-triphosphate_rep3

description:
Testis_R1_tri_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: mono- and triphosphate


title: Noise + cells specimen 20 [20_S48]

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas

data_processing:
Data processing carried out by commercial service (sequentiabiotech.com)
Reference Genome C67Bl/6
Processing using Noiseq protocol
Supplementary_files_format_and_content: Upregulated and down regulated genes provieded in .cvs format; raw counts in txt format

source_name: Left cochlea_Noise + cells

extract_protocol:
Trizol and phase lock heacy gel (Tiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: animals subjected to 16 kHz narrow band noise or noise and mesenchymal stem cells.  RNA extracted 2 days post treatement

value: Noise trauma +  MSCs derived from human umbilical cord Wharton’s jelly

value: Left cochlea


title: ES DRG at 19 DIV

city: Daegu

first: Aseer

last: Intisar

address: 333, Techno Jungang-daero, Hyeonpung-myeon, Dalseong-gun

institute: Daegu Gyeongbuk Institute of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Dorsal root ganglion explant culture

growth_protocol: DRGs were extracted from mouse embryos at E13 and seeded onto Matrigel-coated coverslips. DRGs were cultured in growth medium till DIV 8, after which medium was changed to myelination medium.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: ES DRGs were given electrical stimulation at DIV 10. Control DRGs were not given any electrical stimulation. After electrical stimulation, DRGs were cultured in myelination medium until further analysis.

value: Embryonic day 13

value: Electrical stimulation. 20 Hz, 50 mV/mm, 1h.


title: Control DRG at 19 DIV


title: Noise + cells specimen 18 [18_S46]


title: ES DRG at 11 DIV


title: tumor-BMS754807-2


title: Noise + cells specimen 13 [13_S45]


title: testis - region R2 - 5'end-triphosphate_rep2

description:
Testis_R2_tri_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: RNA 5' Pyrophosphohydrolase


title: 32N

description:
9611518077 R03C02 Grn.idat
9611518077 R03C02 Red.idat
normal tissue

value: resected tissue

value: normal tissue

value: Colorectal cancer


title: testis - region R3 - 5'end-triphosphate_rep3

description:
Testis_R3_tri_rep3
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: total male germline


title: tumor-BMS754807-1

value: BMS


title: CA302_t: Transcritomic dataset of wt CGE E15

description: Transcritomic dataset of wt CGE E15

value: SW

value: CGE

value: wild type


title: testis - region R3 - 5'end-triphosphate_rep2

description:
Testis_R3_tri_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit


title: 21-WT-HFD

value: 4-8 weeks

value: CD11c+ hepatic cells

value: WT


title: Control DRG at 11 DIV


title: Noise trauma specimen 10 [10_S44]

source_name: Left cochlea_Noise trauma

value: Noise trauma


title: testis - region R1 - 5'end-triphosphate_rep2

description:
Testis_R1_tri_rep2
small RNA
Library made with Lexogen - Small RNA-Seq Library Prep Kit

value: mono- and triphosphate