title: Bond-disrupted 6

value: bond-disrupted

tag: time

value: Day 7 following bond-disruption


title: T24_Gem_C

status: Public on Dec 31 2023

type: SRA

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
19C
Group: T24_Gem
RNAseq_ensembl_raw_counts.txt

library_source: transcriptomic

data_processing:
Illumina adapters were removed, along with the first 12 base pairs using BBDuk and reads <50bp after trimming were discarded.
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (hg38.p12, release 96).
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset.
Differential gene expression was calculated using the voom function in limma.
Genome_build: GRCh38
Supplementary_files_format_and_content: RNAseq_ensembl_raw_counts.txt: Text file containing STAR gene count values.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: All cell lines were grown for several passages in the absence of antibiotics, gemcitabine or cisplatin in complete media (IMDM + 10% FBS).

extract_protocol:
RNA was extracted using the RNeasy Plus Kit (Qiagen). Cells were lysed and passed through QIAShredder column (Qiagen) according to the manufacturer’s protocol. gDNA elimination columns (Qiagen) were used to remove any residual gDNA from the purified RNA.
RNA library preparation was performed using the Universal Plus mRNA –Seq +UDI kit (Nugen Technologies).

treatment_protocol: Untreated

tag: cell line

tag: resistance

value: Gem


title: DIPG-IV_Control_C

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
counts_raw_onc201_2.tsv
DIPG4_control_C_S10_L006

data_processing: Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to human genome using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Functional enrichment analysis for the DEGs was performed using R package clusterProfiler (v4.2.2)

molecule: total RNA

source_name: parental cell line

growth_protocol: Cell lines were cultured at 37°C, in 5% CO2, in TSM media with growth factors as described previously (Grasso CS et al, Nat Med. 2015 Jul;21(7):827. PMID: 26151328).

extract_protocol:
RNA was isolated using a Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA). RNA quality/quantity of each samples was checked using RNA Nano assay using Bioanalyzer 2100 (Agilent Technologies - RNA RIN should be >8) and the RNA sample quantity was measured  using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Using 1000 ng of RNA from each sample to start library prep using TruSeq Stranded Total RNA Gold (Illumina RS-122-2303).
Sequencing library preparations were performed by Truseq Stranded Total RNA Sample Reference Guide (Illumina). RNA-seq  library quality/quantity checking was done using  Tape Station 2200 D1000 assay (Agilent Technologies) and QuantStudio 6 Flex Real time PCR System (Applied Biosystem). RNA-seq libraries were sequenced in Hiseq 3000 (Illumina) and the sequence type used was Paired End with 75 cycles.

treatment_protocol: Cells were treated with DMSO control and 5 uM, 3.0 uM, and 3.5 uM, rough IC50 values of ONC201 for 72 hours, respectively.

value: DIPG

tag: cell type

value: brain tumor cell line

tag: disease state

value: Diffuse intrinsic pontine glioma (DIPG)


title: virgin 4

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the Peromyscus californicus reference genome using STAR | version 2.7.2 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GCF_007827085.1_ASM782708v3_genomic
Supplementary files format and content: tab-delimited text files include gene counts for each sample

organism: Peromyscus californicus

source_name: lung

extract_protocol:
Pair bonding :The bonded mice were paired for a period of four months. Afterwards, mice were scarified and lung tissues were collected for RNA extraction.
bond-disrupting: The bond-disrupted mice were paired for four months, then the male was removed from the mating cage, and lung tissue was collected one week later after bond-disruption for RNA isolation.
Virgin: For virgin mice, tissues were collected from mice of similar age housed in groups of three in each cage.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext dA tailling and Ultra II Directional RNA Library prep Kit(E#7600) following the manufacturer's protocols.

tag: tissue

value: lung

tag: Sex

value: Male

tag: genotype

value: virgin


title: P7A9_T24_Saline_d15 [P7A9_ct_combinedruns.txt]

description:
Amplicon DNA
P7A9_ct_combinedruns.txt

library_source: genomic

data_processing:
Library strategy: CRISPR Screen
sgRNA counts were extracted directly from R1 raw sequence reads using a custom perl script that uses regular expression string matching to exactly match sgRNA sequence flanked by 10 bases of vector sequence. The vector sequence was allowed to have one error before and after the sgRNA sequence.
The sgRNA IDs of the Brunello library were updated to current HGNC gene names using the Total Approved Symbols download from HGNC, accessed on 9/1/2020 (https://www.genenames.org/download/statistics-and-files/). Transcript IDs were matched when possible and when matches were not found, past symbols and aliases were updated to current names. Finally, 5 sgRNAs with missing updated gene names were manually curated using literature searches.
The DESeq2 R package (Love et al., 2014) was used to calculate differential abundance of genes. Gene counts were generated using the sum of counts for sgRNAs of the same gene.
Synthetic Lethality compared GemCis day 19 and GemCis day 25 vs. Saline day 19 and Saline day 25 with the day as a covariate. In the comparison integrating all cell lines, cell line was additionally modeled as a covariate. Gene essentiality was calculated by comparing Saline day 25 to Saline day 0 and in the integrated all cell lines comparison, cell line was modeled as a covariate.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing sgRNA counts

molecule: genomic DNA

growth_protocol: Gemcitabine and cisplatin resistant cell lines were grown for 10 days in IMDM + 10% FBS and passaged every 2 days in drug free media to deplete essential genes.  On day 10, cells were treated with either gemcitabine and cisplatin (GC) combination treatment or saline (control) and passaged for an additional 15 days. During treatment, cells were passaged every 3 days and maintained at subconfluent densities. All GC-resistant cell lines  in the GC treatment arm were grown in the presence of both gemcitabine and cisplatin continuously from day 10 through 25 of each screen.

extract_protocol:
Cell pellets of 2.0 x 107 were snap frozen in liquid nitrogen in 1.5mL tubes and stored at -80 prior to extraction. When possible at least 8.0 x 107 cell were used for 4 separate genomic DNA isolation which were pooled to account for any variation with pellet size. DNA isolation was performed using the Puregene cell and tissue kit (Qiagen, Cat. Number: 158388) with the addition of RNase A Solution (Qiagen, Cat Number: 158924) according to manufacturer’s instructions. DNA concentration was measured in quadruplicate using either a nanodrop spectrophotometer (Thermo), Qubit® dsDNA assay (Life Technologies) and the average DNA content per cell was determined.
Library preparation was performed using primers sequences designed by the Broad Institute’s Genetic Perturbation Platform to amplify sgRNA sequences in the LentiCRISPRv2 backbone. Each unique sample utilized a pool of eight P5 primers with to introduce a stagger in reads associated with each library and sample specific P7 primer that contained a unique sample index sequence for each timepoint, replicate, or treatment condition to be sequenced in the same pool.

treatment_protocol: Beginning at day 10 of each screen, cells in the GC treatment arm received 20ng/mL gemcitabine and 1000ng/mL cisplatin, with the exception of the KU1919-GC cells which were treated with 2000ng/mL cisplatin.

tag: treatment

value: Saline

tag: time point


title: Bond-disrupted 5


title: DIPG-IV_Control_B

description:
counts_raw_onc201_2.tsv
DIPG4_control_B_S9_L006


title: T24_Gem_B

description:
19B
Group: T24_Gem
RNAseq_ensembl_raw_counts.txt


title: Bond-disrupted 4


title: P7A9_253J_Saline_d15 [P7A9_BV_S9_L004_R1_001]

description:
Amplicon DNA
P7A9_BV_S9_L004_R1_001


title: DIPG-IV_Control_A

description:
counts_raw_onc201_2.tsv
DIPG4_control_A_S8_L006


title: DIPG-VII_Control_C

description:
counts_raw_onc201_2.tsv
DIPG7_control_C_S18_L007


title: P7A8_TCCSUP_Saline_d9 [P7A8_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A8_TCCSUP_combined.txt

source_name: TCCSUP


title: T24_Gem_A

description:
19A
Group: T24_Gem
RNAseq_ensembl_raw_counts.txt


title: Bond-disrupted 2


title: P7A8_T24_Saline_d15 [P7A8_ct_combinedruns.txt]

description:
Amplicon DNA
P7A8_ct_combinedruns.txt


title: DIPG-XIII_Control_B

description:
counts_raw_onc201_2.tsv
DIPG13_control_B_S23_L008


title: Bond-disrupted 3


title: T24_Cis_C

description:
18C
Group: T24_Cis
RNAseq_ensembl_raw_counts.txt

value: Cis


title: DIPG-VII_Control_B

description:
counts_raw_onc201_2.tsv
DIPG7_control_B_S17_L007


title: P7A8_253J_GC_d9 [P7A8_BV_S8_L004_R1_001]

description:
Amplicon DNA
P7A8_BV_S8_L004_R1_001

value: GC


title: Bond-disrupted 1


title: P7A7_TCCSUP_Saline_d9 [P7A7_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A7_TCCSUP_combined.txt


title: DIPG-XIII_Treated_B

description:
counts_raw_onc201_1.tsv
DIPG13_Treated_B_S44_L006

source_name: +ONC201 (treated, 72hrs)


title: DIPG-VII_Control_A

description:
counts_raw_onc201_2.tsv
DIPG7_control_A_S16_L007


title: T24_Cis_B

description:
18B
Group: T24_Cis
RNAseq_ensembl_raw_counts.txt


title: P7A7_T24_Saline_d15 [P7A7_ct_combinedruns.txt]

description:
Amplicon DNA
P7A7_ct_combinedruns.txt


title: Pair bond 5

value: bonded


title: T24_Parental_B

description:
17B
Group: T24_Parental
RNAseq_ensembl_raw_counts.txt

value: Parental


title: T24_Parental_C

description:
17C
Group: T24_Parental
RNAseq_ensembl_raw_counts.txt


title: T24_Cis_A

description:
18A
Group: T24_Cis
RNAseq_ensembl_raw_counts.txt


title: P7A7_253J_GC_d9 [P7A7_BV_S7_L004_R1_001]

description:
Amplicon DNA
P7A7_BV_S7_L004_R1_001


title: DIPG-XIII_Treated_A

description:
counts_raw_onc201_1.tsv
DIPG13_Treated_A_S43_L006


title: DIPG-XIII_Untreated_B

description:
counts_raw_onc201_1.tsv
DIPG13_Control_B_S42_L006

source_name: -ONC201 (untreated)


title: Pair bond 4


title: P7A6_TCCSUP_T0 [P7A6_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A6_TCCSUP_combined.txt


title: KU1919_Gem_and_Cis_C

description:
12C
Group: KU1919_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: DIPG-IV_Treated_B

description:
counts_raw_onc201_1.tsv
DIPG4_Treated_B_S36_L005


title: DIPG-XIII_Untreated_A

description:
counts_raw_onc201_1.tsv
DIPG13_Control_A_S41_L006


title: P7A6_T24_GC_d9 [P7A6_ct_combinedruns.txt]

description:
Amplicon DNA
P7A6_ct_combinedruns.txt


title: Pair bond 3


title: Pair bond 2


title: T24_Parental_A

description:
17A
Group: T24_Parental
RNAseq_ensembl_raw_counts.txt


title: Pair bond 1


title: DIPG-IV_Treated_A

description:
counts_raw_onc201_1.tsv
DIPG4_Treated_A_S35_L005


title: Pair bond 6


title: P7A6_253J_GC_d9 [P7A6_BV_S6_L004_R1_001]

description:
Amplicon DNA
P7A6_BV_S6_L004_R1_001


title: KU1919_Gem_and_Cis_B

description:
12B
Group: KU1919_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: P7A5_TCCSUP_T0 [P7A5_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A5_TCCSUP_combined.txt


title: KU1919_Gem_and_Cis_A

description:
12A
Group: KU1919_Gem_and_Cis
RNAseq_ensembl_raw_counts.txt


title: DIPG-IV_Untreated_B

description:
counts_raw_onc201_1.tsv
DIPG4_Control_B_S34_L005


title: P7A5_T24_GC_d9 [P7A5_ct_combinedruns.txt]

description:
Amplicon DNA
P7A5_ct_combinedruns.txt


title: KU1919_Gem_C

description:
11C
Group: KU1919_Gem
RNAseq_ensembl_raw_counts.txt


title: DIPG-IV_Untreated_A

description:
counts_raw_onc201_1.tsv
DIPG4_Control_A_S33_L005


title: P7A5_253J_Saline_d9 [P7A5_BV_S5_L004_R1_001]

description:
Amplicon DNA
P7A5_BV_S5_L004_R1_001


title: KU1919_Gem_B

description:
11B
Group: KU1919_Gem
RNAseq_ensembl_raw_counts.txt


title: KU1919_Gem_A

description:
11A
Group: KU1919_Gem
RNAseq_ensembl_raw_counts.txt


title: P7A4_TCCSUP_T0 [P7A4_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A4_TCCSUP_combined.txt


title: DIPG-VII_Treated_B

description:
counts_raw_onc201_1.tsv
DIPG7_Treated_B_S40_L006


title: DIPG-VII_Treated_A

description:
counts_raw_onc201_1.tsv
DIPG7_Treated_A_S39_L006


title: lkh1 mutant basal sample_3

city: Jeongeup-si

first: Sunhak

last: Kwon

address: 29, Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to "GCF_000149245.1_CNA3" whole genome by using Bowtie version 1.1.2 with parameter -S -m 1 -I 0 -X 500 --fr --max --un -a --best -1 {read1} -2 {read2}
FPKM were calculated by using HTseq (htseq-count) version 0.10.0, with parameter -f bam -r name -t exon -i gene_id -m intersection-nonempty -s reverse -o {output} --nonunique none {alignment_file(.bam)} {gff/gtf_file}
Assembly: GCF_000149245.1_CNA3
Supplementary files format and content: *_FPKM.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Cryptococcus neoformans H99

source_name: lkh1 mutant basal sample

growth_protocol: Strains were grown in a 30 ml liquid YPD medium for 16 hr at 30℃. Then, overnight culture was inoculated into 100 ml fresh YPD medium and adjusted to OD600=0.2. The cells were further incubated until OD600 reached approximately 0.6.

extract_protocol:
1. Freeze cells in Liquid Nitrogen for 30min. 2. Lyophilize samples overnight. 3. Add 3ml of 3mm glass beads and vortex vigorously until fine powder is created. 4. Add 4ml of Easyblue (dissolve powder completely) and let them sit 5 minutes. 5. Add 800 ul of chloroform (invert 10 times). 6. Let them sit 3 minutes and transfer to 14 ml round bottle tubes. 7. Spin at 10,000 rpm for 15 minutes. 8. Transfer supernatant to new round-bottom tubes. 9. Add 1.6 ml of isopropanol and capping and gently invert. 10. Store for 10 minutes at room temperature. 11. Spin for 10 minutes at 10,000 rpm. 12. Pour off supernatant. 13. Add 4 ml of 75% RNase free-EtOH (made with DEPC dH2O) and invert 4-5 times. 14. Spin for 5 minutes at 8,000 rpm. 15. Pour off EtOH (Let tubes air-dry upside down). 16. Resuspend in appropriate volume of DEPC dH2O. 17. Heat at 55℃ for 10 minutes. 18. Transfer RNA to microtube and measuring the concentration. 19. For purification of the extracted total RNA, we used RNeasy spin column (Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 50 ml of cells were harvested for the basal sample and rapamycin (3 ng/ml) was treated to the remaining cells. After rapamycin treatment, cells were further incubated at 30℃ for 60 mins.

value: lkh1<delta> mutant

value: basal


title: lkh1 mutant rapamycin 60min sample_2

source_name: lkh1 mutant rapamycin 60min sample

value: rapamycin


title: lkh1 mutant rapamycin 60min sample_1


title: DIPG-VII_Untreated_B

description:
counts_raw_onc201_1.tsv
DIPG7_Control_B_S38_L005


title: lkh1 mutant basal sample_2


title: KU1919_Cis_C

description:
10C
Group: KU1919_Cis
RNAseq_ensembl_raw_counts.txt


title: P7A4_253J_T_min_10 [P7A4_253JGC_T.10R3Tah_S57_L003_R1_001]

description:
Amplicon DNA
P7A4_253JGC_T.10R3Tah_S57_L003_R1_001


title: KU1919_Cis_B

description:
10B
Group: KU1919_Cis
RNAseq_ensembl_raw_counts.txt


title: lkh1 mutant basal sample_1


title: DIPG-VII_Untreated_A

description:
counts_raw_onc201_1.tsv
DIPG7_Control_A_S37_L005


title: lkh1 mutant rapamycin 60min sample_3


title: KU1919_Cis_A

description:
10A
Group: KU1919_Cis
RNAseq_ensembl_raw_counts.txt


title: H99_rapamycin 60min sample_3

source_name: H99 rapamycin 60min sample

value: WT


title: P7A3_TCCSUP_T_min_10 [P7A3_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A3_TCCSUP_combined.txt


title: group2-3

city: Nanning

first: Lin

last: Deng

state: Guangxi

address: No.6 Shuangyong Road

department: Department of Radiation Oncology

country: China

institute: The First Affiliated Hospital of Guangxi Medical University

data_processing:
Off-Line Base Caller software, version 1.8
Illumina NovaSeq 6000 sequencer was used for RNA-seq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) was calculated by Ballgown,version 3.5.0
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: beas-2b cell

growth_protocol: Beas-2b cells were cultured in Dulbecco's Modified Eagle Medium, supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C, 5% CO2, and 95% humidity.

extract_protocol:
Total RNA was extracted from cells using TRIZOL reagent (Life Technologies, NY, USA), in accordance with the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the IR group that was exposed to 6 MV X-ray photon beam from a Varian linac (Varian Medical Systems, Palo Alto, CA, USA) with a source-to-skin distance of 100 cm, irradiation field of 20 × 20 cm, and irradiation dose of 6 Gy at a dose rate of 300 cGy min-1, and the control group that received no irradiation.

value: no radiation

value: human lung epithelial


title: U2OS ALKBH5 KD Rep#3

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 Casava v1.8.2 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
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: Osteosarcoma

growth_protocol: U2OS cells were cultured in  Dulbecco's Modified Eagle Medium (DMEM)  supplemented with 10% fetal bovine serum and 1% penicillin/streptamycin. Cells were maintained in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted  from U2OS cell lines 48 hours after transfection ,  using RNeasy Mini Kit (Qiagen)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: U2OS cells were grown in 6-well plates and transfected with with either scrambled-siRNA or ALKBH5-siRNAs (Sigma-Aldrich) for 48 hours. Transfection was carried out using the RNAiMAX Reagent (Thermofisher) according to the manufacturer’s protocol.

value: U2OS cell line

value: ALKBH5 knockdown

tag: harvest time

value: 48 hour


title: H99_rapamycin 60min sample_2


title: U2OS ALKBH5 KD Rep#2


title: P7A3_T24_Saline_d9 [P7A3_ct_combinedruns.txt]

description:
Amplicon DNA
P7A3_ct_combinedruns.txt


title: group2-2


title: P7A4_T24_GC_d9 [P7A4_ct_combinedruns.txt]

description:
Amplicon DNA
P7A4_ct_combinedruns.txt


title: H99_rapamycin 60min sample_1


title: P7A3_253J_T_min_10 [P7A3_253JGC_T.10_R1R2_S56_L003_R1_001]

description:
Amplicon DNA
P7A3_253JGC_T.10_R1R2_S56_L003_R1_001


title: H99 basal sample_3

source_name: H99 basal sample


title: group2-1


title: U2OS ALKBH5 KD Rep#1


title: P7A3_253J_Saline_d9 [P7A3_BV_S3_L004_R1_001]

description:
Amplicon DNA
P7A3_BV_S3_L004_R1_001


title: P7A4_253J_Saline_d9 [P7A4_BV_S4_L004_R1_001]

description:
Amplicon DNA
P7A4_BV_S4_L004_R1_001


title: H99 basal sample_2


title: U2OS Scrambled Rep#2

value: scrambled-siRNA control


title: P7B3_TCCSUP_Saline_d11 [P7B3_TCCSUP_combined.txt]

description:
Amplicon DNA
P7B3_TCCSUP_combined.txt


title: group1-3

value: radiation


title: group1-2


title: P7A2_T24_Saline_d9 [P7A2_ct_combinedruns.txt]

description:
Amplicon DNA
P7A2_ct_combinedruns.txt


title: H99 basal sample_1


title: P7A2_TCCSUP_T_min_10 [P7A2_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A2_TCCSUP_combined.txt


title: U2OS Scrambled Rep#1


title: THL_60min_biol_rep_2

city: Kunming

first: Yunkun

last: Dang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: School of Life Sciences

institute: Yunnan university

data_processing:
Sequcen reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore(Parameter: . Version: )
Trimmed sequence reads were mapped to NC10/hg38 and reads counts were calculated using STAR(Parameter: --outSAMtype BAM SortedByCoordinate --alignIntronMin 20 --alignIntronMax 50000 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMattributes Standard.Version:2.7.10b)
normalization of total mapped sequence reads in Neurospora crassa between samples were performed using multiBamSummary bins to calculate the scalefactors of spike-in(Parameter:--bamfiles --scalingFactors . Version: deeptools 3.5.1)
Assembly: NC12
Supplementary files format and content: tab-delimited tab file includes raw counts for each Sample
Supplementary files format and content: tab-delimited tab file includes normalized counts for each Sample

organism: Neurospora crassa

source_name: mycelia

extract_protocol:
mRNA was harvested by using TRIzol and poly-T dynabeads. 50 ng of Neurospora crass mRNA and 0.5 μg of human mRNA as spike-in was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep kit for MGI following manufacture's protocols.

value: mycelia


title: group1-1


title: P7A2_253J_T0 [P7A2_253JGC_T0_R3R4_S55_L003_R1_001]

description:
Amplicon DNA
P7A2_253JGC_T0_R3R4_S55_L003_R1_001


title: Kid2

city: nanjign

first: yi

middle: xuan

last: fan

address: No 1 weigang

institute: nanjing agricultural university

data_processing:
we remove the reads containing adaptor contamination, low quality bases and undetermined bases from raw data using Cutadapt
Then sequence quality was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The mapped reads were denovo assembled to circular RNAs by CIRCExplorer2 and CIRI at first; then, back splicing reads were identified in unmapped reads by tophat-fusion
We normalized circRNA contents as the number of uniquely mapped spliced reads per billion mapping (SRPBM)
Only the comparisons with “p value” less than 0.05 were regarded as showing differential expression by R package.
Assembly: capra hircus(GCF_001704415.1)
Supplementary files format and content: circRNAs expression

organism: Capra hircus

source_name: Skeletal muscle

extract_protocol:
A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations.
Total RNA was isolated from LD muscle samples by TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The concentration and quality of RNA were determined by NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) and Agilent 2100 with RIN number >7.0. Approximately 5 μg of total RNA was used to remove ribosomal RNA with the Ribo-Zero™ Kit (Illumina, San Diego, USA). Then ribosome-depleted RNA was treated with RNase R (Epicentre Inc, Madison, WI, USA) to remove linear RNAs and to enrich circRNAs. Then the enriched circRNAs were fragmented into small pieces using divalent cations under high temperature. Retrotranscription of cleaved RNA was performed with PrimeScript RT regent Kit (TaKaRa, Japan), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Single-or dual-index adapters containing a T-base overhang are ligated to the DNA fragments. The ligated cDNA products were purified with AMPure XP beads (Beckman Coulter, Beverly, MA, USA), and treated with uracil DNA glycosylase to remove the second-strand cDNA. The purified first-strand cDNA was amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 s, and extension at 72℃ for 30 s; and then final extension at 72℃ for 5 min. At last, the qualified library was sequenced using an Illumina NovaseqTM 6000 (Illumina, San Diego, CA, USA) on a 150 bp paired-end run.

tag: development stage

value: kid stage (1 day of age)

tag: strain

value: Haimen goat

value: Longissimus dorsi muscle


title: THL_40min_biol_rep_2


title: Kid3


title: ChIP_H3K4me1_D50_r2

city: Singapore

first: Ching Thong

last: Choo

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Read quality check was performed using FASTQC and adaptors were trimmed using Trim Galore
Reads were mapped to Drosophila reference genome (BDGP6.22.98) using STAR (v2.5.3a) with following parameters: --alignEndsType EndToEnd --alignIntronMax 1
Downstream analysis was performed using Galaxy platform. Peak calling was performed using MACS2 (v2.1.1), using an effective genome size of 120000000 --no model --extsize 147 --bdg
Assembly: Drosophila melanogaster reference genome (BDGP6.22.98)
Supplementary files format and content: Alignment files (bam format) were transformed into read coverage files (bigwig format) using DeepTools: bamCompare (v3.3.2), normalized by BPM
Supplementary files format and content: peak files generated from MACS2 callpeak

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Male Drosophila melanogaster, strain  w[1118], were cultured in standard fly media (6% cornmeal, 5% dextrose, 2.4% brewer’s yeast, 0.8% agarose and 0.3% nipagin) at 25◦C with 12-hour light/dark cycle.

extract_protocol:
Isolate D10 to D50 fly heads (50mg) for each biological replicate. Fly heads were dounced 30 times with pestle A (Sigma) in 5 ml of A1 buffer (60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 15 mM HEPES pH 7.6, 0.5% NP-40, 0.5 mM DTT, 0.5 mM PMSF and protease inhibitors cocktail). Samples were filtered through MIRA cloth, and the lysate was incubated on ice for 15min. Samples was then centrifuged at 4000g for 5min at 4°C. After three additional rounds of A1 buffer wash and centrifugation, nuclear pellet was resuspended and dounced with pestle B (Sigma) in 3.3 ml of RIPA buffer (10 mM Tris pH 8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton, 0.1% SDS, 0.1% sodium deoxycholate, 0.5 mM DTT, 0.5 mM PMSF, protease inhibitors cocktail). 3.3 µl of 3M CaCl2 was added to 3.3 ml of nuclear lysate and incubated at 37°C for 3min. 5µl of MNase (i-DNA Biotech, Cat# LS004798) was then added to samples and incubated at 37°C for 15 min. MNase reaction was terminated by adding STOP buffer (5µM EDTA/EGTA). Samples were briefly sonicated (10sec ON, 50sec OFF, 5 times), followed by 10 min max speed centrifugation at 4°C. The supernatant was collected as the chromatin extract and 80 µl was kept as input. 5ul of H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729) antibody was added to remaining chromatin extract and incubate in 4°C overnight. On the following day, 20 μl of pre-blocked (0.5% BSA in PBS) Protein-G Dynabeads™ (Lifetech, Cat# 10003D) was added to the chromatin extract. Following 4 hours of incubation at 4°C, DNA-antibody-beads complex was isolated using magnetic stand. The beads complex was washed with RIPA buffer for 5 times, LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) once and Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA) once. The DNA fragments were eluted from the beads with 500 μl elution buffer (1 M NaHCO3, 0.5% SDS), while input was topped up to 420 µl with elution buffer and samples were incubated at 37°C overnight. On the next day, samples were treated with RNase A (20 μg/ml, 1 hr at 37°C) and proteinase K (40 μg/ml, 2 hr at 37°C). DNA was extracted by phenol/chloroform and ethanol precipitation.
ChIP-sequencing was carried at BGI (Hong Kong) according to company’s protocol. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified using KAPA library amplification kit (KK2702) with Illumina primers for 11 cycles and library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000.

treatment_protocol: Twenty flies were housed in one vial (diameter of 2.5 cm, height of 9.5 cm) and the food was changed every two days until the desired age of day 50.

value: Head

tag: age

value: D50 adult

value: Male

tag: antibody

value: H3K4me1 ChIP


title: U2OS Scrambled Rep#3


title: blood, B3

city: Jinan

first: cheng

middle: cheng

last: Li

state: Shandong

address: Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, No.107 Wenhuaxi Road, Jinan, Shandong, China

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital of Shandong University

description: after first bevacizumab treatment of patientB

data_processing:
Library quality was assessed on the Agilent Bioanalyzer 2100 system.
The raw data in the fastq format from the sequencer were checked for sequencing quality before further processing.
clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low quality reads from raw data
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2  R package (1.20.0)
Genome_build: HISAT2 v2.0.5
Supplementary_files_format_and_content: gene_fpkm.txt, BevvsControl.log2FC1_Pvalue0.05.txt

source_name: blood samples

extract_protocol:
RNA was harvested using Trizol reagent. And standard extraction methods were used to extract RNA from cells,1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bevacizumab (10mg/kg)

value: Ovarian cancer

tag: individual

value: patient B

value: blood


title: P7A2_253J.BV_T0 [P7A2_BV_S2_L004_R1_001]

description:
Amplicon DNA
P7A2_BV_S2_L004_R1_001


title: Kid1


title: THL_20min_biol_rep_2

value: WT


title: blood, B2

description: after second bevacizumab treatment of patientA

value: patient A


title: P7A12_TCCSUP_GC_d9 [P7A12_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A12_TCCSUP_combined.txt

value: GC


title: P7A12_T24_GC_d15 [P7A12_ct_combinedruns.txt]

description:
Amplicon DNA
P7A12_ct_combinedruns.txt


title: THL_0min_biol_rep_2


title: blood, B1

description: after first bevacizumab treatment of patientA


title: Fetus2

value: embryonic stage(75 day of pregnancy )


title: blood, C4

description: before second bevacizumab treatment of patientB

value: Control (before treatment)


title: blood, B4

description: after second bevacizumab treatment of patientB


title: THL_60min_biol_rep_1

value: mycelia


title: P7A12_253J_GC_d15 [P7A12_BV_S12_L004_R1_001]

description:
Amplicon DNA
P7A12_BV_S12_L004_R1_001


title: THL_40min_biol_rep_1


title: THL_20min_biol_rep_1


title: blood, C3

description: before first bevacizumab treatment of patientB


title: RRL with FVBeta-UGG-QW and SRI-41315, replicate 2

city: Boston

first: Sichen

last: Shao

state: MA

address: 240 Longwood Ave. Room C2-451

department: Cell Biology

institute: Harvard Medical School

data_processing:
Adaptor trimming by Trim Galore! (default parameters)
rRNA subtraction by Bowtie (--best -m1 -v2)
Read alignment to OryCun2.0 genome by STAR (default parameters)
P-site mapping using Plastid (default parameters)
Assembly: OryCun2.0
Supplementary files format and content: Profiles of mapped P-site density in WIG files

organism: Oryctolagus cuniculus

source_name: Reticulocyte lysate

extract_protocol:
625 µL ncT2 reactions were assembled and allowed to proceed for 30 minutes. 5 µM of SRI-41315 or 1 µM of recombinant eRF1-AAQ was supplemented when required. CaCl2 was added to a final concentration of 5 mM, and the samples were digested with 150 U of micrococcal nuclease (Roche) for 40 minutes at 25° C on a thermomixer at 750 rpm. Nuclease digestion was stopped by adding EGTA to a final concentration of 6.25 mM. 600 µL of digested sample was layered onto 4 mL of 34% (w/v) sucrose cushion solution (250 mM NaCl, 15 mM MgCl2, 50 mM Tris-HCl pH 8.0) and centrifuged in SW 55 Ti (Beckman) rotor at 33,000 rpm for 2.5 hours. After centrifugation, supernatant was aspirated, and pellet was resuspended in 200 µL 10 mM Tris-HCl pH 8.0. RNA was extracted using TRIzol LS (Invitrogen) and size-selected (28 to 34 nucleotides) on a 15% tris-borate EDTA (TBE)-urea gel.
All libraries were generated using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's protocols. RNA was dephosphorylated by incubating with T4 polynucleotide kinase (NEB) for 1 hour at 37° C, size-selected, and ligated to the 3’ adapter by incubating with T4 RNA ligase 2 truncated K227Q mutant (NEB) and 1 µg of pre-adenylated adapter (5’rAppCTGTAGGCACCATCAAT/3ddc/) for 2 hours at 25° C. The ligation product was size-selected on a 10% TBE-urea gel and depleted of rRNA using the QIAseq FastSelect -rRNA HMR kit (Qiagen). Reverse transcription was performed with Superscript III (Invitrogen) using the Illumina Tru-Seq RT primer: /5Phos/AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSp18/CACTCA/iSp18/TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG and the reaction was quenched by incubating with 0.1 M NaOH for 20 minutes at 98° C. cDNA library was circularized using CircLigase (Epicentre) and amplified by 5 PCR cycles.

treatment_protocol: In vitro transcription and translation reactions were performed using a homemade system as previously described (Feng and Shao, Methods 2018). When necessary, SRI-41315 was added to a final concentration of 5 µM and recombinant eRF1-AAQ to a final concentraion of 1 µM

value: Reticulocyte lysate

value: Added in vitro transcribed FVBeta-UGG-QW and 5 uM SRI-41315


title: Fetus1

value: Haimen goat

value: Longissimus dorsi muscle


title: P7A11_T24_GC_d15 [P7A11_ct_combinedruns.txt]

description:
Amplicon DNA
P7A11_ct_combinedruns.txt


title: THL_0min_biol_rep_1


title: blood, C2

description: before second bevacizumab treatment of patientA


title: P7A10_TCCSUP_GC_d9 [P7A10_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A10_TCCSUP_combined.txt


title: RRL with FVBeta-UGG and eRF1-AAQ, replicate 2

value: Added in vitro transcribed FVBeta-UGG and 1 uM eRF1-AAQ


title: SKOV3_Bev-3

data_processing:
The raw data in the fastq format from the sequencer were checked for sequencing quality before further processing.
The adapter sequences and low quality reads were removed by fastp (v0.20.0).
Clean reads alignment was performed against  human genome version GRCh38 with HISAT2 (version 2.1.0).
Aligned reads were analyzed with featureCounts(v1.6.5) to extract the for gene expression based on readscounts and FPKM
Differentially expression were performed in edgeR in R program (v3.5.1) and ranked based on p value or FDR
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel

growth_protocol: SKOV3 cells were grown  in RPMI-1640 medium, with 10% fetal bovine serum,100 U/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SKOV3 cells in experimental group were treated by 150ug/ml bevacizumab for 24 hours

tag: disease

value: ovarian cancer


title: blood, C1

description: before first bevacizumab treatment of patientA


title: RRL with FVBeta-UGG and SRI-41315, replicate 2

value: Added in vitro transcribed FVBeta-UGG and 5 uM SRI-41315


title: P7A11_TCCSUP_GC_d9 [P7A11_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A11_TCCSUP_combined.txt


title: P7A11_253J_Saline_d15 [P7A11_BV_S11_L004_R1_001]

description:
Amplicon DNA
P7A11_BV_S11_L004_R1_001

value: Saline


title: Fetus3


title: RRL with FVBeta-UGG, replicate 2

value: Added in vitro transcribed FVBeta-UGG


title: P7A10_T24_GC_d15 [P7A10_ct_combinedruns.txt]

description:
Amplicon DNA
P7A10_ct_combinedruns.txt


title: SKOV3_Bev-2


title: RRL with FVBeta-UGA and SRI-41315, replicate 2

value: Added in vitro transcribed FVBeta-UGA and 5 uM SRI-41315


title: SKOV3_Bev-1


title: P7A1_TCCSUP_T_min_10 [P7A1_TCCSUP_combined.txt]

description:
Amplicon DNA
P7A1_TCCSUP_combined.txt


title: pancreas tumor, MEKi_2days_rep2

type: RNA

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description: Sample name: short_MEKi_2

hyb_protocol: Each samples were hybridized with Capture ProbeSet for at least 16 hours at 65° according to  nCounter XT Gene Expression Assay protocol.

scan_protocol: 30 μL of each hybridized sample was loaded into the nCounter cartridge and scanned on  nCounter SPRINT profiler according to default settings.

data_processing:
The matrix of counts was then used for differential expression analysis with DESeq2 Bioconductor package. DESeq2 was used in combination with RUVSeq in order to control housekeeping genes expression and for normalization purposes. A batch factor of variation was calculated from the expression of the housekeeping genes, and such factor was then added to the DESeq2 design formula.
Values in the matrix represent VST normalized expression intensities from the variance stabilizing transformation of DESeq2 package

label: biotin

organism: Mus musculus

source_name: pancreas tumor

label_protocol: 25 ng of total RNA was labeled with target-specific oligonucleotide probe pairs, fluorescently-labeled specific Reporter Tags, and a biotinylated universal Capture Tag, collectively called a  TagSet. In particular, Probe A hybridizes to a specific Reporter Tag and the 5’ region of the target  nucleic acid sequence. Probe B hybridizes to the universal Capture Tag and the 3’ region of the  target nucleic acid sequence.

extract_protocol: RNA was extracted from freshly isolated tissues (isografts) using TRIzol (Invitrogen), followed by column-based purification with the PureLink RNA Mini Kit (Ambion)

treatment_protocol: Mice were treated with vehicle or trametinib (1mg/kg) daily, by oral gavage

value: pancreas tumor

value: MEKi

tag: time


title: pancreas tumor, MEKi_2days_rep3

description: Sample name: short_MEKi_3


title: pancreas tumor, MEKi_2days_rep1

description: Sample name: short_MEKi_1


title: RRL with FVBeta-UGA, replicate 2

value: WT

value: Added in vitro transcribed FVBeta-UGA


title: RRL with FVBeta-UGG-QW and SRI-41315, replicate 1


title: pancreas tumor, Ctrl_for MEKi 2days_rep4

description: Sample name: CTRL_4

value: Vehicle

value: control


title: RRL with FVBeta-UGA and SRI-41315, replicate 1


title: P7A1_253J_T_min_10 [P7A1_BV_S1_L004_R1_001]

description:
Amplicon DNA
P7A1_BV_S1_L004_R1_001


title: RRL with FVBeta-UGG and SRI-41315, replicate 1


title: RRL with FVBeta-UGG and eRF1-AAQ, replicate 1


title: SKOV3_Control1

tag: cell line

value: control(condition medium)


title: SKOV3_Control2


title: P7A1_T24_Saline_d9 [P7A1_ct_combinedruns.txt]

description:
Amplicon DNA
P7A1_ct_combinedruns.txt


title: RRL with FVBeta-UGA, replicate 1

value: Reticulocyte lysate


title: P7A1_253J_T0 [P7A1_253JGC_T0_R1R2_S54_L003_R1_001]

description:
Amplicon DNA
P7A1_253JGC_T0_R1R2_S54_L003_R1_001


title: RRL with FVBeta-UGG, replicate 1


title: IDD5

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < 5000;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV file contain counts for each sample

source_name: nucleus pulposus

growth_protocol: No growth are needed

extract_protocol:
The tissue are then digested using Collagenase for 3 hours. The cell viability are tested and viable sample are send to sequencing.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

treatment_protocol: Nucleus pulposus cells are extracted from the tissue immediately after acquiring the tissue from surgery. Degenerated intervertebral disc nuclesus pulposus samples are collected from lumbar disc herniation patients, and normal samples are collected from the lumbar disc of motor vehicle accident patients.

value: nucleus pulposus

tag: gender

value: Male

tag: status

value: Degenerated


title: IDD8


title: pancreas tumor, Ctrl_for MEKi 2days_rep2

description: Sample name: CTRL_2


title: P7A10_253J_Saline_d15 [P7A10_BV_S10_L004_R1_001]

description:
Amplicon DNA
P7A10_BV_S10_L004_R1_001


title: IP_NDV-3-2

city: wuhan

first: Weifeng

last: Yuan

state: hubei

address: hubei province wuhan wuchang

institute: Wuhan University

data_processing:
library strategy: meRIP-seq
Remove 3 ′ adaptor-trimming and low-quality reads
Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.1.0)
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps.
denovo motif analysis was performed on 101 nucleotides centered around the identified m6A peaks using DREME software
Assembly: GCF_000002315.6_GRCg6a
Supplementary files format and content: Number of raw junction read

organism: Gallus gallus

source_name: CEF

growth_protocol: Chicken embryo fibroblasts  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA extraction protocol

treatment_protocol:
CEF group were maintained in DMEM supplemented with 2% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
NDV group were NDV infected (MOI = 1) 1h, then maintained in DMEM supplemented with 2% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: CEF

tag: cell type

value: Chicken embryo fibroblasts  cells

value: NDV infected (MOI = 1)

value: 24 hpi


title: IDD4

tag: tissue


title: pancreas tumor, Ctrl_for MEKi 2days_rep1

description: Sample name: CTRL_1


title: Input_NDV-3


title: pancreas tumor, MEKi_2w_rep4

description: Sample name: m135

hyb_protocol: Each sample was hybridized with Capture ProbeSet for at least 16 hours at 65° according to  nCounter XT Gene Expression Assay protocol.

source_name: pancreas tumor, MEKi_2w


title: IDD3


title: pancreas tumor, Ctrl_for MEKi 2days_rep3

description: Sample name: CTRL_3


title: SKOV3_Control3

value: ovarian cancer


title: IDD6


title: IDD7

value: female


title: pancreas tumor, MEKi_1w_rep3

description: Sample name: m138

source_name: pancreas tumor, MEKi_1w

value: pancreas tumor


title: pancreas tumor, MEKi_1w_rep4

description: Sample name: m141

value: MEKi


title: IP_NDV-2-2

value: WT


title: pancreas tumor, MEKi_2w_rep3

description: Sample name: m143


title: pancreas tumor, MEKi_2w_rep2

description: Sample name: m130


title: IDD1


title: IP_NDV-1-2


title: pancreas tumor, MEKi_2w_rep1

description: Sample name: m127


title: CTL8

value: Relatively normal


title: CTL6


title: Input_NDV-2


title: pancreas tumor, MEKi_1w_rep2

description: Sample name: m132


title: IDD2


title: pancreas tumor, MEKi_1w_rep1

description: Sample name: m129


title: Input_CEF-3


title: CTL4


title: pancreas tumor, Ctrl_for MEKi 1w 2w_rep5

description: Sample name: m140

source_name: pancreas tumor, Ctrl

value: Vehicle


title: CTL7


title: Input_NDV-1


title: IP_CEF-3-2


title: Input_CEF-2


title: CTL3


title: pancreas tumor, Ctrl_for MEKi 1w 2w_rep4

description: Sample name: m139

value: control


title: pancreas tumor, Ctrl_for MEKi 1w 2w_rep3

description: Sample name: m137


title: IP_CEF-2-2


title: Input_CEF-1


title: Sample 3_Doxy+2

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

description:
single cell cDNA library (droplet v3.1)
OSKM_c_seurat.rds

library_source: transcriptomic single cell

data_processing:
The sequencing data were aligned to mouse reference genome (mm10) using CellRanger (v3.0.2).
The matrix data was filtered with 2000< nFeature< 8500, nCount< 100000, and percent.mt< 15. After the log normalization and scaling, unsupervised clustering and UMAP visualization were performed. The low cell number and low nFeature clusters were further excluded.
DEG identification, gene ontology analysis, and GSVA were performed by FindMarkers, enrichGO, and gsva functions, respectively.
Peudotime and trajectory inference were decided by monocle3 package. Gene clustering with pseudotime was determined by pheatmap function with kmeans_k=6.
Assembly: mm10
Supplementary files format and content: Seurat object with annotated single-cell transcriptomes in rds file.

source_name: mouse primary embryonic fibroblast

growth_protocol: Cultured in DMEM with 10% FBS and 1X antibiotics under 5%O2 hypoxia incubator

extract_protocol:
The single cell cDNA libraries were generated through Chromium Single Cell 3' Reagent Kits User Guide (v3.1).
The pooled libraries were sequenced on a DNBSEQ-G400RS (MGI Tech) using paired-end mode (2×100 bp).

treatment_protocol: Cellular senescence was firstly synchronized by 16 hours 9 mM RO3306, and then induced by 5 mM Nutlin 3a for 48 hours. After that, 100 nM BI-2536 and 500 nM  4-hydroxytamoxifen were treated to exclude proliferative cells and active CreERT2-loxP recombination for total 9 days. Senescent MEFs were further treated with or without 8 ug/ml doxycycline for 12 days to induce expression of OSKM.

value: mouse primary embryonic fibroblast

value: Senescence with docycycline dependent OSKM expression


title: IP_CEF-1-2


title: CTL2

value: nucleus pulposus


title: Sample 2_Doxy+1


title: pancreas tumor, Ctrl_for MEKi 1w 2w_rep2

description: Sample name: m133


title: CTL1

value: Male


title: Sample 1_Doxy-

value: Senescence


title: CTL5


title: Placenta E18.5 Male 2 Capture

status: Public on Dec 30 2023

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.36)
Alignment and methylation counts were performed with Bismark (v0.18.1)
Assembly: mm10
Supplementary files format and content: tab-delimited files including CpG sites coordinate, coverage, methylation values
Supplementary files format and content: Input files for the methylKit package
Library strategy: Methyl-Seq

source_name: Placenta

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen) following manufacturer's recommendations
Libraries were performed using SureSelectXT Methyl-Seq mouse Target Enrichment System (Agilent) following manufacturer's protocol

value: Placenta

tag: developmental stage

value: male


title: Placenta E18.5 Male 3 Capture


title: Placenta E18.5 Male 1 Capture


title: Placenta E18.5 Female 2 Capture


title: Placenta E18.5 Female 3 Capture


title: Placenta E18.5 Female 1 Capture


title: pancreas tumor, Ctrl_for MEKi 1w 2w_rep1

description: Sample name: m128


title: Placenta E18.5 Female 3 RNA-Seq

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.36)
Gene counts matrix and differentially expressed genes (DEGs) were obtained using the R package DESeq2 (v1.24.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

extract_protocol:
RNA was extracted using QIAamp Rneasy Mini kit (Qiagen) following manufacturer's recommendations
Libraries were performed using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocol


title: Placenta E18.5 Female 2 RNA-Seq


title: Placenta E18.5 Male 2 RNA-Seq


title: Placenta E18.5 Male 1 RNA-Seq


title: Placenta E18.5 Female 1 RNA-Seq


title: Placenta E18.5 Male 3 RNA-Seq


title: WJL4158_RLF_N033

city: Stanford

first: Jinglong

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads from human and mouse were mapped to the hg19 and mm9 reference genomes, respectively, using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19, mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

source_name: vAbl DNA-PKcs KD/KD #C3

growth_protocol: K562 and its derived cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).  The DNA-PKcs-modified HCT116 cell lines were cultured at 37°C and 5% CO2 in Hyclone α-minimum Eagle's medium supplemented with 5% newborn calf serum, 5% fetal bovine serum (Sigma), and 1× penicillin/streptomycin (Gibco). DNA-PKcs catalytically dead v-Abl cells were cultured in same condition as K562 cells but for the DMEM base medium.

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1/G0-arrested K562-Bcl2, K562-Bcl2 PKcs-/- and K562-iCas9 cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with pX330-Cas9-sgRNA or pMCB320-sgRNA to generated twined  DSBs in different compound-treated conditions. The v-Abl cells were arrested by STI-571 for four days to induce V(D)J recombination.

value: vAbl DNA-PKcs KD/KD #C3

value: pro-B cells

tag: genotype

value: DNA-PKcs KD/KD

tag: dsb induction_(bait_site)

tag: dsb induction_(prey_sites)

value: RAG-VKs


title: WJL4154_RLF_N033

source_name: vAbl DNA-PKcs KD/KD #C1

value: vAbl DNA-PKcs KD/KD #C1

tag: treatment


title: WJL4157_RLF_N033


title: WJL4145_RLF_N033


title: WJL4150_RLF_N033

source_name: vAbl DNA-PKcs KD/KD #C3-1

value: vAbl DNA-PKcs KD/KD #C3-1


title: WJL4162_RLF_N033


title: WJL4155_RLF_N033


title: WJL4144_RLF_N033


title: WJL4159_RLF_N033


title: WJL4161_RLF_N033


title: WJL4156_RLF_N033


title: WJL4148_RLF_N033


title: WJL4147_RLF_N033


title: WJL4143_RLF_N033


title: WJL4146_RLF_N033


title: WJL4149_RLF_N033


title: WJL4160_RLF_N033


title: AEC_VC1

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Brain

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice were infused with angiotensin II (0.7mg/kg/d) or saline (0.9%) via an osmotic minipump for 2 weeks. After 2 weeks, the mice  culled and the brain was collected.

value: Brain

value: WT C57Bl6

value: Vehicle + AEC

tag: Sex

tag: disease state

value: Control


title: AEC_VC3


title: AEC_VC2


title: AEC_V6

value: Vehicle


title: AEC_V5


title: AEC_VC5


title: AEC_VC6


title: AEC_V4


title: AEC_V3


title: AEC_V1


title: AEC_AC6

value: Angiotensin II +AEC

value: Hypertension


title: AEC_AC1

value: Male


title: AEC_AC3


title: AEC_AC4


title: AEC_AC5


title: AEC_AC2


title: AEC_A2

value: Angiotensin II


title: AEC_A6


title: AEC_A1


title: AEC_A3


title: AEC_A4


title: AEC_VC4


title: WJL1969_RLF_N021_Ku70-/-_G1/G0-sorted_BMN673_Rep2

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

institute: Stanford University

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. Indicated inhibitors were added to some of the samples the same day as STI-571.

value: vAbl-ProB

tag: bait

tag: sample type


title: WJL4142_RLF_N033


title: WJL1971_RLF_N021_Ku70-/-_Cycling_Rep2


title: WJL1970_RLF_N021_Ku70-/-_Cycling_Rep1


title: WJL1973_RLF_N021_Ku70-/-_G1/G0-sorted_DMSO_Rep2


title: AEC_A5


title: AEC_V2


title: WJL1972_RLF_N021_Ku70-/-_G1/G0-sorted_DMSO_Rep1


title: WJL1990_RLF_N021_WT_G1/G0-sorted_DMSO_Rep1

value: WT


title: WJL1993_RLF_N021_WT_Cycling_Rep2


title: WJL1966_RLF_N021_Ku70-/-_G1/G0-sorted_Olaparib_Rep1


title: WJL1992_RLF_N021_WT_Cycling_Rep1


title: WJL1991_RLF_N021_WT_G1/G0-sorted_DMSO_Rep2


title: WJL1968_RLF_N021_Ku70-/-_G1/G0-sorted_BMN673_Rep1


title: WJL1967_RLF_N021_Ku70-/-_G1/G0-sorted_Olaparib_Rep2


title: WJL1986_RLF_N021_WT_G1/G0-sorted_Belinostat_Rep1


title: WJL1987_RLF_N021_WT_G1/G0-sorted_Belinostat_Rep2


title: WJL1989_RLF_N021_WT_G1/G0-sorted_PCI-24781_Rep2


title: WJL1988_RLF_N021_WT_G1/G0-sorted_PCI-24781_Rep1


title: WJL1982_RLF_N021_WT_G1/G0-sorted_AT13387_Rep1


title: WJL1984_RLF_N021_WT_G1/G0-sorted_Pracinostat_Rep1


title: WJL2203_RLF_N023_Lig4-/-_H12

tag: well

value: Proof-of-Principle


title: WJL2202_RLF_N023_Lig4-/-_H11

value: pro-B cells


title: WJL2201_RLF_N023_Lig4-/-_H10


title: WJL1983_RLF_N021_WT_G1/G0-sorted_AT13387_Rep2


title: WJL2200_RLF_N023_Lig4-/-_H9


title: WJL2197_RLF_N023_Ku70-/-_H6


title: WJL2196_RLF_N023_Ku70-/-_H5


title: WJL2194_RLF_N023_WT_H3


title: WJL2192_RLF_N023_WT_H1


title: WJL2199_RLF_N023_Ku70-/-_H8


title: WJL2193_RLF_N023_WT_H2


title: WJL2198_RLF_N023_Ku70-/-_H7


title: WJL2195_RLF_N023_WT_H4


title: WJL2190_RLF_N023_Lig4-/-_G11


title: WJL2187_RLF_N023_Ku70-/-_G8


title: WJL2191_RLF_N023_Lig4-/-_G12


title: WJL2186_RLF_N023_Ku70-/-_G7


title: WJL2185_RLF_N023_Ku70-/-_G6


title: WJL2189_RLF_N023_Lig4-/-_G10


title: WJL1985_RLF_N021_WT_G1/G0-sorted_Pracinostat_Rep2


title: WJL2184_RLF_N023_Ku70-/-_G5


title: WJL2182_RLF_N023_WT_G3


title: WJL2181_RLF_N023_WT_G2


title: WJL2183_RLF_N023_WT_G4


title: WJL2179_RLF_N023_Lig4-/-_F12


title: WJL2180_RLF_N023_WT_G1


title: WJL2178_RLF_N023_Lig4-/-_F11


title: WJL2175_RLF_N023_Ku70-/-_F8


title: WJL2176_RLF_N023_Lig4-/-_F9


title: WJL2188_RLF_N023_Lig4-/-_G9


title: WJL2174_RLF_N023_Ku70-/-_F7


title: WJL2177_RLF_N023_Lig4-/-_F10


title: WJL2171_RLF_N023_WT_F4


title: WJL2173_RLF_N023_Ku70-/-_F6


title: WJL2170_RLF_N023_WT_F3


title: WJL2162_RLF_N023_Ku70-/-_E7


title: WJL2168_RLF_N023_WT_F1


title: WJL2165_RLF_N023_Lig4-/-_E10


title: WJL2164_RLF_N023_Lig4-/-_E9


title: WJL2169_RLF_N023_WT_F2


title: WJL2167_RLF_N023_Lig4-/-_E12


title: WJL2157_RLF_N023_WT_E2


title: WJL2156_RLF_N023_WT_E1


title: WJL2158_RLF_N023_WT_E3


title: WJL2163_RLF_N023_Ku70-/-_E8


title: WJL2159_RLF_N023_WT_E4


title: WJL2155_RLF_N023_Lig4-/-_D12


title: WJL2154_RLF_N023_Lig4-/-_D11


title: WJL2153_RLF_N023_Lig4-/-_D10


title: WJL2160_RLF_N023_Ku70-/-_E5


title: WJL2172_RLF_N023_Ku70-/-_F5


title: WJL2150_RLF_N023_Ku70-/-_D7


title: WJL2152_RLF_N023_Lig4-/-_D9


title: WJL2151_RLF_N023_Ku70-/-_D8


title: WJL2166_RLF_N023_Lig4-/-_E11


title: WJL2161_RLF_N023_Ku70-/-_E6


title: WJL2145_RLF_N023_WT_D2


title: WJL2147_RLF_N023_WT_D4


title: WJL2149_RLF_N023_Ku70-/-_D6


title: WJL2144_RLF_N023_WT_D1


title: WJL2148_RLF_N023_Ku70-/-_D5


title: WJL2141_RLF_N023_Lig4-/-_C10


title: WJL2138_RLF_N023_Ku70-/-_C7


title: WJL2143_RLF_N023_Lig4-/-_C12


title: WJL2146_RLF_N023_WT_D3


title: WJL2142_RLF_N023_Lig4-/-_C11


title: WJL2140_RLF_N023_Lig4-/-_C9


title: WJL2136_RLF_N023_Ku70-/-_C5


title: WJL2137_RLF_N023_Ku70-/-_C6


title: WJL2131_RLF_N023_Lig4-/-_B12


title: WJL2132_RLF_N023_WT_C1


title: WJL2139_RLF_N023_Ku70-/-_C8


title: WJL2135_RLF_N023_WT_C4


title: WJL2133_RLF_N023_WT_C2


title: WJL2134_RLF_N023_WT_C3


title: WJL2130_RLF_N023_Lig4-/-_B11


title: WJL2129_RLF_N023_Lig4-/-_B10


title: WJL2127_RLF_N023_Ku70-/-_B8


title: WJL2128_RLF_N023_Lig4-/-_B9


title: WJL2125_RLF_N023_Ku70-/-_B6


title: WJL2126_RLF_N023_Ku70-/-_B7


title: WJL2124_RLF_N023_Ku70-/-_B5


title: WJL2122_RLF_N023_WT_B3


title: WJL2123_RLF_N023_WT_B4


title: WJL2120_RLF_N023_WT_B1


title: WJL2117_RLF_N023_Lig4-/-_A10


title: WJL2121_RLF_N023_WT_B2


title: WJL2115_RLF_N023_Ku70-/-_A8


title: WJL2119_RLF_N023_Lig4-/-_A12


title: WJL2116_RLF_N023_Lig4-/-_A9


title: WJL2118_RLF_N023_Lig4-/-_A11


title: WJL2111_RLF_N023_WT_A4


title: WJL2108_RLF_N023_WT_A1


title: WJ1929_RLF_N020_Ku70-/-_H12

value: Cycling


title: WJ1928_RLF_N020_Ku70-/-_H11

value: Pyrimethamine


title: WJ1926_RLF_N020_Ku70-/-_H9

value: Pralatrexate


title: WJL2114_RLF_N023_Ku70-/-_A7


title: WJ1924_RLF_N020_Ku70-/-_H7

value: Trilostane


title: WJL2109_RLF_N023_WT_A2


title: WJ1922_RLF_N020_Ku70-/-_H5

value: Aminophylline


title: WJL2113_RLF_N023_Ku70-/-_A6


title: WJ1921_RLF_N020_Ku70-/-_H4

value: Ozagrel


title: WJ1923_RLF_N020_Ku70-/-_H6

value: Methotrexate


title: WJL2110_RLF_N023_WT_A3


title: WJ1916_RLF_N020_Ku70-/-_G11

value: Pimobendan


title: WJ1920_RLF_N020_Ku70-/-_H3

value: Dyphylline


title: WJ1918_RLF_N020_Ku70-/-_H1

value: Apixaban


title: WJ1915_RLF_N020_Ku70-/-_G10

value: Rivaroxaban


title: WJ1917_RLF_N020_Ku70-/-_G12


title: WJ1914_RLF_N020_Ku70-/-_G9

value: Cilostazol


title: WJ1911_RLF_N020_Ku70-/-_G6

value: Isotretinoin


title: WJ1927_RLF_N020_Ku70-/-_H10

value: vAbl-ProB

value: Anagrelide HCl


title: WJL2112_RLF_N023_Ku70-/-_A5

value: Proof-of-Principle


title: WJ1910_RLF_N020_Ku70-/-_G5

value: pro-B cells

value: Cilomilast


title: WJ1912_RLF_N020_Ku70-/-_G7

value: Avanafil


title: WJ1909_RLF_N020_Ku70-/-_G4

value: Rolipram


title: WJ1907_RLF_N020_Ku70-/-_G2

value: TAK-700 (Orteronel)


title: WJ1925_RLF_N020_Ku70-/-_H8

value: S- (+)-Rolipram


title: WJ1900_RLF_N020_Ku70-/-_F7

value: Roflumilast


title: WJ1901_RLF_N020_Ku70-/-_F8

value: Voriconazole


title: WJ1904_RLF_N020_Ku70-/-_F11

value: Vardenafil HCl Trihydrate


title: WJ1903_RLF_N020_Ku70-/-_F10

value: Clarithromycin


title: WJ1898_RLF_N020_Ku70-/-_F5

value: Ketoconazole


title: WJ1899_RLF_N020_Ku70-/-_F6

value: Apremilast (CC-10004)


title: WJ1905_RLF_N020_Ku70-/-_F12

value: Cycling


title: WJ1895_RLF_N020_Ku70-/-_F2

value: Ciprofibrate


title: WJ1913_RLF_N020_Ku70-/-_G8

value: vAbl-ProB

value: Mycophenolate Mofetil


title: WJ1897_RLF_N020_Ku70-/-_F4

value: Cobicistat (GS-9350)


title: WJ1896_RLF_N020_Ku70-/-_F3

value: pro-B cells

value: Rosiglitazone HCl


title: WJ1891_RLF_N020_Ku70-/-_E10

value: Abiraterone


title: WJ1890_RLF_N020_Ku70-/-_E9

value: Amuvatinib (MP-470, HPK 56)


title: WJ1892_RLF_N020_Ku70-/-_E11

value: Rosiglitazone maleate


title: WJ1887_RLF_N020_Ku70-/-_E6

value: Tipifarnib (Zarnestra)


title: WJ1906_RLF_N020_Ku70-/-_G1

value: Pioglitazone HCl


title: WJ1886_RLF_N020_Ku70-/-_E5


title: WJ1889_RLF_N020_Ku70-/-_E8

value: Methylprednisolone


title: WJ1883_RLF_N020_Ku70-/-_E2

value: Pomalidomide (CC-4047)


title: WJ1884_RLF_N020_Ku70-/-_E3

value: Thalidomide


title: WJ1888_RLF_N020_Ku70-/-_E7

value: Cyclophosphamide monohydrate


title: WJ1885_RLF_N020_Ku70-/-_E4

value: Birinapant (TL32711)


title: WJ1908_RLF_N020_Ku70-/-_G3

value: Tadalafil


title: WJ1881_RLF_N020_Ku70-/-_D12


title: WJ1880_RLF_N020_Ku70-/-_D11

value: 2-Methoxyestradiol (2-MeOE2)


title: WJ1902_RLF_N020_Ku70-/-_F9

value: vAbl-ProB

value: Sildenafil Citrate


title: WJ1879_RLF_N020_Ku70-/-_D10


title: WJ1875_RLF_N020_Ku70-/-_D6

value: Entacapone


title: WJ1877_RLF_N020_Ku70-/-_D8

value: pro-B cells


title: WJ1894_RLF_N020_Ku70-/-_F1

value: Rosiglitazone


title: WJ1893_RLF_N020_Ku70-/-_E12


title: WJ1876_RLF_N020_Ku70-/-_D7

value: Thioguanine


title: WJ1873_RLF_N020_Ku70-/-_D4


title: WJ1874_RLF_N020_Ku70-/-_D5

value: Iniparib (BSI-201)


title: WJ1872_RLF_N020_Ku70-/-_D3


title: WJ1882_RLF_N020_Ku70-/-_E1

value: Lenalidomide (CC-5013)


title: WJ1869_RLF_N020_Ku70-/-_C12

value: DMSO


title: WJ1870_RLF_N020_Ku70-/-_D1


title: WJ1871_RLF_N020_Ku70-/-_D2

value: BMN 673


title: WJ1866_RLF_N020_Ku70-/-_C9


title: WJ1868_RLF_N020_Ku70-/-_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJ1865_RLF_N020_Ku70-/-_C8

value: Tofacitinib (CP-690550) Citrate


title: WJ1867_RLF_N020_Ku70-/-_C10

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJ1864_RLF_N020_Ku70-/-_C7

value: Barasertib (AZD1152-HQPA)


title: WJ1861_RLF_N020_Ku70-/-_C4

value: Sodium Phenylbutyrate


title: WJ1859_RLF_N020_Ku70-/-_C2


title: WJ1860_RLF_N020_Ku70-/-_C3

value: Valproic acid sodium salt (Sodium valproate)


title: WJ1862_RLF_N020_Ku70-/-_C5

value: MLN8237 (Alisertib)


title: WJ1857_RLF_N020_Ku70-/-_B12

value: vAbl-ProB


title: WJ1856_RLF_N020_Ku70-/-_B11

value: Pracinostat (SB939)


title: WJ1855_RLF_N020_Ku70-/-_B10


title: WJ1858_RLF_N020_Ku70-/-_C1

value: Belinostat (PXD101)


title: WJ1854_RLF_N020_Ku70-/-_B9

value: pro-B cells

value: Mocetinostat (MGCD0103, MG0103)


title: WJ1878_RLF_N020_Ku70-/-_D9

value: Resveratrol


title: WJ1852_RLF_N020_Ku70-/-_B7

value: Rocilinostat (ACY-1215)


title: WJ1853_RLF_N020_Ku70-/-_B8

value: Vorinostat (SAHA, MK0683)


title: WJ1849_RLF_N020_Ku70-/-_B4

value: Captopril


title: WJ1850_RLF_N020_Ku70-/-_B5

value: Moxonidine


title: WJ1848_RLF_N020_Ku70-/-_B3


title: WJ1847_RLF_N020_Ku70-/-_B2

value: Raltegravir (MK-0518)


title: WJ1851_RLF_N020_Ku70-/-_B6

value: Olmesartan medoxomil


title: WJ1846_RLF_N020_Ku70-/-_B1

value: Empty


title: WJ1843_RLF_N020_Ku70-/-_A10

value: Elvitegravir (GS-9137)


title: WJ1844_RLF_N020_Ku70-/-_A11

value: Fluorouracil (Adrucil)


title: WJ1845_RLF_N020_Ku70-/-_A12


title: WJ1842_RLF_N020_Ku70-/-_A9


title: WJ1863_RLF_N020_Ku70-/-_C6

value: VX-680 (MK-0457,Tozasertib)


title: WJ1841_RLF_N020_Ku70-/-_A8


title: WJ1838_RLF_N020_Ku70-/-_A5

value: Marimastat


title: WJ1837_RLF_N020_Ku70-/-_A4

value: vAbl-ProB

value: Atazanavir sulfate (BMS-232632-05)


title: WJ1839_RLF_N020_Ku70-/-_A6


title: WJ1835_RLF_N020_Ku70-/-_A2

value: Vildagliptin (LAF-237)


title: WJ1836_RLF_N020_Ku70-/-_A3

value: pro-B cells

value: Alogliptin (SYR-322)


title: WJL1434_RLF_N019_Ku70-/-_H11

value: Pyrimethamine


title: WJ1834_RLF_N020_Ku70-/-_A1

value: Sitagliptin phosphate monohydrate


title: WJL1433_RLF_N019_Ku70-/-_H10

value: Anagrelide HCl


title: WJL1430_RLF_N019_Ku70-/-_H7

value: Trilostane


title: WJL1431_RLF_N019_Ku70-/-_H8

value: S- (+)-Rolipram


title: WJL1428_RLF_N019_Ku70-/-_H5

value: Aminophylline


title: WJL1429_RLF_N019_Ku70-/-_H6

value: Methotrexate


title: WJL1424_RLF_N019_Ku70-/-_H1

value: Apixaban


title: WJL1425_RLF_N019_Ku70-/-_H2

value: Gimeracil


title: WJL1426_RLF_N019_Ku70-/-_H3

value: Dyphylline


title: WJL1422_RLF_N019_Ku70-/-_G11

value: Pimobendan


title: WJL1423_RLF_N019_Ku70-/-_G12

value: Cycling


title: WJL1419_RLF_N019_Ku70-/-_G8

value: vAbl-ProB

value: Mycophenolate Mofetil


title: WJL1420_RLF_N019_Ku70-/-_G9

value: Cilostazol


title: WJ1840_RLF_N020_Ku70-/-_A7

value: pro-B cells

value: Doxycycline hyclate


title: WJL1417_RLF_N019_Ku70-/-_G6

value: Isotretinoin


title: WJL1414_RLF_N019_Ku70-/-_G3

value: Tadalafil


title: WJL1413_RLF_N019_Ku70-/-_G2

value: TAK-700 (Orteronel)


title: WJL1412_RLF_N019_Ku70-/-_G1

value: Pioglitazone HCl


title: WJL1415_RLF_N019_Ku70-/-_G4

value: Rolipram


title: WJL1411_RLF_N019_Ku70-/-_F12


title: WJL1432_RLF_N019_Ku70-/-_H9

value: Pralatrexate


title: WJL1435_RLF_N019_Ku70-/-_H12


title: WJL1409_RLF_N019_Ku70-/-_F10

value: Clarithromycin


title: WJL1410_RLF_N019_Ku70-/-_F11

value: Vardenafil HCl Trihydrate


title: WJL1407_RLF_N019_Ku70-/-_F8

value: Voriconazole


title: WJL1405_RLF_N019_Ku70-/-_F6

value: Apremilast (CC-10004)


title: WJL1406_RLF_N019_Ku70-/-_F7

value: Roflumilast


title: WJL1427_RLF_N019_Ku70-/-_H4

value: Ozagrel


title: WJL1404_RLF_N019_Ku70-/-_F5

value: vAbl-ProB

value: Ketoconazole


title: WJL1403_RLF_N019_Ku70-/-_F4

value: Cobicistat (GS-9350)


title: WJL1402_RLF_N019_Ku70-/-_F3

value: pro-B cells

value: Rosiglitazone HCl


title: WJL1418_RLF_N019_Ku70-/-_G7

value: Avanafil


title: WJL1421_RLF_N019_Ku70-/-_G10

value: Rivaroxaban


title: WJL1400_RLF_N019_Ku70-/-_F1

value: Rosiglitazone


title: WJL1401_RLF_N019_Ku70-/-_F2

value: Ciprofibrate


title: WJL1399_RLF_N019_Ku70-/-_E12


title: WJL1398_RLF_N019_Ku70-/-_E11

value: Rosiglitazone maleate


title: WJL1397_RLF_N019_Ku70-/-_E10

value: Abiraterone


title: WJL1416_RLF_N019_Ku70-/-_G5

value: Cilomilast


title: WJL1394_RLF_N019_Ku70-/-_E7

value: Cyclophosphamide monohydrate


title: WJL1395_RLF_N019_Ku70-/-_E8

value: Methylprednisolone


title: WJL1392_RLF_N019_Ku70-/-_E5


title: WJL1408_RLF_N019_Ku70-/-_F9

value: Sildenafil Citrate


title: WJL1391_RLF_N019_Ku70-/-_E4

value: Birinapant (TL32711)


title: WJL1396_RLF_N019_Ku70-/-_E9

value: Amuvatinib (MP-470, HPK 56)


title: WJL1386_RLF_N019_Ku70-/-_D11

value: vAbl-ProB

value: 2-Methoxyestradiol (2-MeOE2)


title: WJL1388_RLF_N019_Ku70-/-_E1

value: Lenalidomide (CC-5013)


title: WJL1385_RLF_N019_Ku70-/-_D10

value: pro-B cells


title: WJL1390_RLF_N019_Ku70-/-_E3

value: Thalidomide


title: WJL1384_RLF_N019_Ku70-/-_D9

value: Resveratrol


title: WJL1387_RLF_N019_Ku70-/-_D12


title: WJL1382_RLF_N019_Ku70-/-_D7

value: Thioguanine


title: WJL1379_RLF_N019_Ku70-/-_D4


title: WJL1378_RLF_N019_Ku70-/-_D3


title: WJL1381_RLF_N019_Ku70-/-_D6

value: Entacapone


title: WJL1380_RLF_N019_Ku70-/-_D5

value: Iniparib (BSI-201)


title: WJL1377_RLF_N019_Ku70-/-_D2

value: BMN 673


title: WJL1376_RLF_N019_Ku70-/-_D1


title: WJL1374_RLF_N019_Ku70-/-_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJL1373_RLF_N019_Ku70-/-_C10

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJ1919_RLF_N020_Ku70-/-_H2

value: Gimeracil


title: WJL1393_RLF_N019_Ku70-/-_E6

value: Tipifarnib (Zarnestra)


title: WJL1375_RLF_N019_Ku70-/-_C12

value: DMSO


title: WJL1370_RLF_N019_Ku70-/-_C7

value: Barasertib (AZD1152-HQPA)


title: WJL1372_RLF_N019_Ku70-/-_C9


title: WJL1369_RLF_N019_Ku70-/-_C6

value: VX-680 (MK-0457,Tozasertib)


title: WJL1368_RLF_N019_Ku70-/-_C5

value: vAbl-ProB

value: MLN8237 (Alisertib)


title: WJL1367_RLF_N019_Ku70-/-_C4

value: Sodium Phenylbutyrate


title: WJL1364_RLF_N019_Ku70-/-_C1

value: pro-B cells

value: Belinostat (PXD101)


title: WJL1383_RLF_N019_Ku70-/-_D8


title: WJL1365_RLF_N019_Ku70-/-_C2


title: WJL1366_RLF_N019_Ku70-/-_C3

value: Valproic acid sodium salt (Sodium valproate)


title: WJL1362_RLF_N019_Ku70-/-_B11

value: Pracinostat (SB939)


title: WJL1363_RLF_N019_Ku70-/-_B12


title: WJL1360_RLF_N019_Ku70-/-_B9

value: Mocetinostat (MGCD0103, MG0103)


title: WJL1357_RLF_N019_Ku70-/-_B6

value: Olmesartan medoxomil


title: WJL1361_RLF_N019_Ku70-/-_B10


title: WJL1359_RLF_N019_Ku70-/-_B8

value: Vorinostat (SAHA, MK0683)


title: WJL1358_RLF_N019_Ku70-/-_B7

value: Rocilinostat (ACY-1215)


title: WJL1356_RLF_N019_Ku70-/-_B5

value: Moxonidine


title: WJL1371_RLF_N019_Ku70-/-_C8

value: Tofacitinib (CP-690550) Citrate


title: WJL1351_RLF_N019_Ku70-/-_A12


title: WJL1350_RLF_N019_Ku70-/-_A11

value: Fluorouracil (Adrucil)


title: WJL1353_RLF_N019_Ku70-/-_B2

value: Raltegravir (MK-0518)


title: WJL1355_RLF_N019_Ku70-/-_B4

value: Captopril


title: WJL1389_RLF_N019_Ku70-/-_E2

value: Pomalidomide (CC-4047)


title: WJL1354_RLF_N019_Ku70-/-_B3

value: vAbl-ProB


title: WJL1352_RLF_N019_Ku70-/-_B1

value: Empty


title: WJL1345_RLF_N019_Ku70-/-_A6


title: WJL1348_RLF_N019_Ku70-/-_A9


title: WJL1347_RLF_N019_Ku70-/-_A8


title: WJL1346_RLF_N019_Ku70-/-_A7

value: Doxycycline hyclate


title: WJL1343_RLF_N019_Ku70-/-_A4

value: pro-B cells

value: Atazanavir sulfate (BMS-232632-05)


title: WJL1349_RLF_N019_Ku70-/-_A10

value: Elvitegravir (GS-9137)


title: WJL1342_RLF_N019_Ku70-/-_A3

value: Alogliptin (SYR-322)


title: WJL1021_RLF_N017_WT_H9

value: WT

value: Chloramphenicol


title: WJL1341_RLF_N019_Ku70-/-_A2

value: Vildagliptin (LAF-237)


title: WJL1020_RLF_N017_WT_H8

value: Carbenicillin, Disodium Salt


title: WJL1018_RLF_N017_WT_H6

value: Leucovorin Calcium


title: WJL1024_RLF_N017_WT_H12

value: Cycling


title: WJL1017_RLF_N017_WT_H5

value: Malotilate


title: WJL1023_RLF_N017_WT_H11

value: Gentamycin Sulfate


title: WJL1016_RLF_N017_WT_H4

value: Idarubicin HCl


title: WJL1022_RLF_N017_WT_H10

value: Geneticin, G-418 Sulfate


title: WJL1013_RLF_N017_WT_H1

value: vAbl-ProB

value: Fluoxetine HCl


title: WJL1344_RLF_N019_Ku70-/-_A5

value: Marimastat


title: WJL1011_RLF_N017_WT_G11

value: pro-B cells

value: Acarbose


title: WJL1009_RLF_N017_WT_G9

value: Floxuridine


title: WJL1007_RLF_N017_WT_G7

value: Cyclophosphamide


title: WJL1010_RLF_N017_WT_G10

value: WT

value: Acitretin


title: WJL1012_RLF_N017_WT_G12


title: WJL1008_RLF_N017_WT_G8

value: Mercaptopurine (6-MP)


title: WJL1005_RLF_N017_WT_G5


title: WJL1004_RLF_N017_WT_G4

value: Ellagic acid


title: WJL1340_RLF_N019_Ku70-/-_A1

value: Sitagliptin phosphate monohydrate


title: WJL1001_RLF_N017_WT_G1

value: Dacarbazine


title: WJL1002_RLF_N017_WT_G2

value: Genistein


title: WJL1003_RLF_N017_WT_G3

value: Tivozanib (AV-951)


title: WJL1019_RLF_N017_WT_H7

value: Ampicillin


title: WJL999_RLF_N017_WT_F11

value: Cladribine


title: WJL1015_RLF_N017_WT_H3

value: vAbl-ProB

value: Pamidronate Disodium


title: WJL998_RLF_N017_WT_F10

value: Lenvatinib (E7080)


title: WJL994_RLF_N017_WT_F6

value: pro-B cells

value: Saracatinib (AZD0530)


title: WJL996_RLF_N017_WT_F8

value: Dovitinib (TKI-258, CHIR-258)


title: WJL995_RLF_N017_WT_F7

value: Bosutinib (SKI-606)


title: WJL992_RLF_N017_WT_F4

value: WT

value: Doripenem Hydrate


title: WJL990_RLF_N017_WT_F2

value: Bendamustine HCl


title: WJL993_RLF_N017_WT_F5

value: Ifosfamide


title: WJL1006_RLF_N017_WT_G6

value: Dexamethasone (DHAP)


title: WJL997_RLF_N017_WT_F9

value: Carboplatin


title: WJL1014_RLF_N017_WT_H2

value: Epirubicin HCl


title: WJL989_RLF_N017_WT_F1

value: Etoposide


title: WJL991_RLF_N017_WT_F3

value: Plerixafor (AMD3100)


title: WJL986_RLF_N017_WT_E10


title: WJL988_RLF_N017_WT_E12


title: WJL984_RLF_N017_WT_E8

value: (-)-Huperzine A


title: WJL987_RLF_N017_WT_E11

value: vAbl-ProB

value: Etomidate


title: WJL985_RLF_N017_WT_E9

value: Carfilzomib (PR-171)


title: WJL979_RLF_N017_WT_E3

value: pro-B cells

value: Cediranib (AZD217)


title: WJL980_RLF_N017_WT_E4

value: E 64d


title: WJL981_RLF_N017_WT_E5

value: Decitabine (NSC127716, 5AZA-CdR)


title: WJL982_RLF_N017_WT_E6

value: WT


title: WJL983_RLF_N017_WT_E7

value: Macitentan


title: WJL1000_RLF_N017_WT_F12

value: Cycling


title: WJL977_RLF_N017_WT_E1

value: Pelitinib (EKB-569)


title: WJL976_RLF_N017_WT_D12


title: WJL978_RLF_N017_WT_E2

value: Bumetanide


title: WJL974_RLF_N017_WT_D10

value: Imatinib Mesylate (STI571)


title: WJL972_RLF_N017_WT_D8


title: WJL971_RLF_N017_WT_D7

value: Vatalanib (PTK787) 2HCl


title: WJL973_RLF_N017_WT_D9

value: Mianserin HCl


title: WJL975_RLF_N017_WT_D11

value: Doxorubicin (Adriamycin) HCl


title: WJL969_RLF_N017_WT_D5

value: Vincristine


title: WJL968_RLF_N017_WT_D4

value: vAbl-ProB

value: Tenofovir Disoproxil Fumarate


title: WJL967_RLF_N017_WT_D3

value: Ramelteon


title: WJL964_RLF_N017_WT_C12

value: pro-B cells

value: DMSO


title: WJL962_RLF_N017_WT_C10


title: WJL963_RLF_N017_WT_C11

value: Roscovitine (Seliciclib,CYC202)


title: WJL961_RLF_N017_WT_C9

value: Posaconazole


title: WJL960_RLF_N017_WT_C8

value: WT

value: Aprepitant


title: WJL959_RLF_N017_WT_C7

value: Enzastaurin (LY317615)


title: WJL958_RLF_N017_WT_C6

value: Celecoxib


title: WJL957_RLF_N017_WT_C5

value: Dutasteride


title: WJL956_RLF_N017_WT_C4

value: Dimesna


title: WJL953_RLF_N017_WT_C1

value: Dexrazoxane HCl (ICRF-187, ADR-529)


title: WJL954_RLF_N017_WT_C2

value: Prasugrel


title: WJL950_RLF_N017_WT_B10

value: Cilnidipine


title: WJL951_RLF_N017_WT_B11

value: Lidocaine


title: WJL948_RLF_N017_WT_B8

value: vAbl-ProB

value: Fulvestrant


title: WJL949_RLF_N017_WT_B9


title: WJL952_RLF_N017_WT_B12


title: WJL966_RLF_N017_WT_D2

value: Galanthamine HBr


title: WJL946_RLF_N017_WT_B6

value: pro-B cells

value: Clofarabine


title: WJL944_RLF_N017_WT_B4

value: Gemcitabine HCl


title: WJL945_RLF_N017_WT_B5

value: Rigosertib (ON-01910,Estybon)


title: WJL942_RLF_N017_WT_B2

value: WT

value: Biapenem


title: WJL955_RLF_N017_WT_C3

value: Epothilone B (EPO906, Patupilone)


title: WJL941_RLF_N017_WT_B1

value: Rocuronium Bromide


title: WJL943_RLF_N017_WT_B3

value: Nelarabine


title: WJL965_RLF_N017_WT_D1


title: WJL947_RLF_N017_WT_B7

value: Losartan Potassium (DuP 753)


title: WJL970_RLF_N017_WT_D6

value: Entecavir Hydrate


title: WJL938_RLF_N017_WT_A10

value: Mosapride Citrate


title: WJL933_RLF_N017_WT_A5

value: Adapalene


title: WJL934_RLF_N017_WT_A6

value: Granisetron HCl


title: WJL940_RLF_N017_WT_A12

value: vAbl-ProB

value: DMSO


title: WJL936_RLF_N017_WT_A8

value: Letrozole


title: WJL939_RLF_N017_WT_A11

value: pro-B cells

value: Zoledronic Acid


title: WJL937_RLF_N017_WT_A9

value: Gatifloxacin


title: WJL932_RLF_N017_WT_A4

value: Lansoprazole


title: WJL614_RLF_N014_WT_H9

value: WT

value: Chloramphenicol


title: WJL616_RLF_N014_WT_H11

value: Gentamycin Sulfate


title: WJL617_RLF_N014_WT_H12

value: Cycling


title: WJL615_RLF_N014_WT_H10

value: Geneticin, G-418 Sulfate


title: WJL931_RLF_N017_WT_A3

value: Daptomycin


title: WJL929_RLF_N017_WT_A1

value: Angiotensin II


title: WJL612_RLF_N014_WT_H7

value: Ampicillin


title: WJL930_RLF_N017_WT_A2

value: Levetiracetam


title: WJL613_RLF_N014_WT_H8

value: Carbenicillin, Disodium Salt


title: WJL607_RLF_N014_WT_H2

value: vAbl-ProB

value: Epirubicin HCl


title: WJL606_RLF_N014_WT_H1

value: Fluoxetine HCl


title: WJL610_RLF_N014_WT_H5

value: pro-B cells

value: Malotilate


title: WJL608_RLF_N014_WT_H3

value: Pamidronate Disodium


title: WJL603_RLF_N014_WT_G10

value: Acitretin


title: WJL611_RLF_N014_WT_H6

value: WT

value: Leucovorin Calcium


title: WJL604_RLF_N014_WT_G11

value: Acarbose


title: WJL600_RLF_N014_WT_G7

value: Cyclophosphamide


title: WJL609_RLF_N014_WT_H4

value: Idarubicin HCl


title: WJL602_RLF_N014_WT_G9

value: Floxuridine


title: WJL935_RLF_N017_WT_A7

value: Exemestane


title: WJL605_RLF_N014_WT_G12

value: Cycling


title: WJL601_RLF_N014_WT_G8

value: Mercaptopurine (6-MP)


title: WJL599_RLF_N014_WT_G6

value: Dexamethasone (DHAP)


title: WJL595_RLF_N014_WT_G2

value: vAbl-ProB

value: Genistein


title: WJL597_RLF_N014_WT_G4

value: Ellagic acid


title: WJL594_RLF_N014_WT_G1

value: pro-B cells

value: Dacarbazine


title: WJL598_RLF_N014_WT_G5


title: WJL593_RLF_N014_WT_F12


title: WJL592_RLF_N014_WT_F11

value: Cladribine


title: WJL596_RLF_N014_WT_G3

value: Tivozanib (AV-951)


title: WJL591_RLF_N014_WT_F10

value: WT

value: Lenvatinib (E7080)


title: WJL589_RLF_N014_WT_F8

value: Dovitinib (TKI-258, CHIR-258)


title: WJL590_RLF_N014_WT_F9

value: Carboplatin


title: WJL584_RLF_N014_WT_F3

value: Plerixafor (AMD3100)


title: WJL586_RLF_N014_WT_F5

value: Ifosfamide


title: WJL585_RLF_N014_WT_F4

value: Doripenem Hydrate


title: WJL588_RLF_N014_WT_F7

value: Bosutinib (SKI-606)


title: WJL583_RLF_N014_WT_F2

value: Bendamustine HCl


title: WJL582_RLF_N014_WT_F1

value: Etoposide


title: WJL580_RLF_N014_WT_E11

value: vAbl-ProB

value: Etomidate


title: WJL581_RLF_N014_WT_E12


title: WJL578_RLF_N014_WT_E9

value: Carfilzomib (PR-171)


title: WJL579_RLF_N014_WT_E10

value: pro-B cells


title: WJL576_RLF_N014_WT_E7

value: Macitentan


title: WJL572_RLF_N014_WT_E3

value: Cediranib (AZD217)


title: WJL573_RLF_N014_WT_E4

value: E 64d


title: WJL574_RLF_N014_WT_E5

value: WT

value: Decitabine (NSC127716, 5AZA-CdR)


title: WJL571_RLF_N014_WT_E2

value: Bumetanide


title: WJL575_RLF_N014_WT_E6


title: WJL570_RLF_N014_WT_E1

value: Pelitinib (EKB-569)


title: WJL568_RLF_N014_WT_D11

value: Doxorubicin (Adriamycin) HCl


title: WJL567_RLF_N014_WT_D10

value: Imatinib Mesylate (STI571)


title: WJL569_RLF_N014_WT_D12


title: WJL566_RLF_N014_WT_D9

value: Mianserin HCl


title: WJL565_RLF_N014_WT_D8


title: WJL564_RLF_N014_WT_D7

value: Vatalanib (PTK787) 2HCl


title: WJL562_RLF_N014_WT_D5

value: Vincristine


title: WJL587_RLF_N014_WT_F6

value: Saracatinib (AZD0530)


title: WJL561_RLF_N014_WT_D4

value: vAbl-ProB

value: Tenofovir Disoproxil Fumarate


title: WJL577_RLF_N014_WT_E8

value: (-)-Huperzine A


title: WJL560_RLF_N014_WT_D3

value: pro-B cells

value: Ramelteon


title: WJL559_RLF_N014_WT_D2

value: Galanthamine HBr


title: WJL558_RLF_N014_WT_D1


title: WJL545_RLF_N014_WT_B12

value: DMSO


title: WJL552_RLF_N014_WT_C7

value: WT

value: Enzastaurin (LY317615)


title: WJL546_RLF_N014_WT_C1

value: Dexrazoxane HCl (ICRF-187, ADR-529)


title: WJL553_RLF_N014_WT_C8

value: Aprepitant


title: WJL547_RLF_N014_WT_C2

value: Prasugrel


title: WJL556_RLF_N014_WT_C11

value: Roscovitine (Seliciclib,CYC202)


title: WJL554_RLF_N014_WT_C9

value: Posaconazole


title: WJL557_RLF_N014_WT_C12


title: WJL543_RLF_N014_WT_B10

value: Cilnidipine


title: WJL555_RLF_N014_WT_C10


title: WJL550_RLF_N014_WT_C5

value: Dutasteride


title: WJL549_RLF_N014_WT_C4

value: Dimesna


title: WJL563_RLF_N014_WT_D6

value: vAbl-ProB

value: Entecavir Hydrate


title: WJL541_RLF_N014_WT_B8

value: Fulvestrant


title: WJL540_RLF_N014_WT_B7

value: pro-B cells

value: Losartan Potassium (DuP 753)


title: WJL538_RLF_N014_WT_B5

value: Rigosertib (ON-01910,Estybon)


title: WJL539_RLF_N014_WT_B6

value: Clofarabine


title: WJL537_RLF_N014_WT_B4

value: WT

value: Gemcitabine HCl


title: WJL536_RLF_N014_WT_B3

value: Nelarabine


title: WJL551_RLF_N014_WT_C6

value: Celecoxib


title: WJL535_RLF_N014_WT_B2

value: Biapenem


title: WJL534_RLF_N014_WT_B1

value: Rocuronium Bromide


title: WJL533_RLF_N014_WT_A12

value: DMSO


title: WJL548_RLF_N014_WT_C3

value: Epothilone B (EPO906, Patupilone)


title: WJL531_RLF_N014_WT_A10

value: Mosapride Citrate


title: WJL532_RLF_N014_WT_A11

value: Zoledronic Acid


title: WJL544_RLF_N014_WT_B11

value: vAbl-ProB

value: Lidocaine


title: WJL529_RLF_N014_WT_A8

value: Letrozole


title: WJL530_RLF_N014_WT_A9

value: pro-B cells

value: Gatifloxacin


title: WJL542_RLF_N014_WT_B9


title: WJ1831_RLF_N020_WT_H10

value: Anagrelide HCl


title: WJ1832_RLF_N020_WT_H11

value: Pyrimethamine


title: WJL523_RLF_N014_WT_A2

value: WT

value: Levetiracetam


title: WJ1826_RLF_N020_WT_H5

value: Aminophylline


title: WJL525_RLF_N014_WT_A4

value: Lansoprazole


title: WJL528_RLF_N014_WT_A7

value: Exemestane


title: WJ1829_RLF_N020_WT_H8

value: S- (+)-Rolipram


title: WJ1830_RLF_N020_WT_H9

value: Pralatrexate


title: WJ1827_RLF_N020_WT_H6

value: Methotrexate


title: WJ1833_RLF_N020_WT_H12

value: Cycling


title: WJ1825_RLF_N020_WT_H4

value: Ozagrel


title: WJL527_RLF_N014_WT_A6

value: vAbl-ProB

value: Granisetron HCl


title: WJ1828_RLF_N020_WT_H7

value: Trilostane


title: WJL526_RLF_N014_WT_A5

value: pro-B cells

value: Adapalene


title: WJL522_RLF_N014_WT_A1

value: Angiotensin II


title: WJL524_RLF_N014_WT_A3

value: Daptomycin


title: WJ1822_RLF_N020_WT_H1

value: WT

value: Apixaban


title: WJ1823_RLF_N020_WT_H2

value: Gimeracil


title: WJ1824_RLF_N020_WT_H3

value: Dyphylline


title: WJ1821_RLF_N020_WT_G12


title: WJ1817_RLF_N020_WT_G8

value: Mycophenolate Mofetil


title: WJ1818_RLF_N020_WT_G9

value: Cilostazol


title: WJ1819_RLF_N020_WT_G10

value: Rivaroxaban


title: WJ1820_RLF_N020_WT_G11

value: Pimobendan


title: WJ1816_RLF_N020_WT_G7

value: Avanafil


title: WJ1811_RLF_N020_WT_G2

value: TAK-700 (Orteronel)


title: WJ1812_RLF_N020_WT_G3

value: vAbl-ProB

value: Tadalafil


title: WJ1815_RLF_N020_WT_G6

value: Isotretinoin


title: WJ1807_RLF_N020_WT_F10

value: pro-B cells

value: Clarithromycin


title: WJ1814_RLF_N020_WT_G5

value: Cilomilast


title: WJ1810_RLF_N020_WT_G1

value: Pioglitazone HCl


title: WJ1806_RLF_N020_WT_F9

value: WT

value: Sildenafil Citrate


title: WJ1813_RLF_N020_WT_G4

value: Rolipram


title: WJ1802_RLF_N020_WT_F5

value: Ketoconazole


title: WJ1809_RLF_N020_WT_F12

value: Cycling


title: WJ1803_RLF_N020_WT_F6

value: Apremilast (CC-10004)


title: WJ1808_RLF_N020_WT_F11

value: Vardenafil HCl Trihydrate


title: WJ1801_RLF_N020_WT_F4

value: Cobicistat (GS-9350)


title: WJ1804_RLF_N020_WT_F7

value: Roflumilast


title: WJ1805_RLF_N020_WT_F8

value: Voriconazole


title: WJ1799_RLF_N020_WT_F2

value: vAbl-ProB

value: Ciprofibrate


title: WJ1798_RLF_N020_WT_F1

value: Rosiglitazone


title: WJ1800_RLF_N020_WT_F3

value: pro-B cells

value: Rosiglitazone HCl


title: WJ1787_RLF_N020_WT_E2

value: Pomalidomide (CC-4047)


title: WJ1790_RLF_N020_WT_E5


title: WJ1797_RLF_N020_WT_E12


title: WJ1786_RLF_N020_WT_E1

value: Lenalidomide (CC-5013)


title: WJ1794_RLF_N020_WT_E9

value: WT

value: Amuvatinib (MP-470, HPK 56)


title: WJ1788_RLF_N020_WT_E3

value: Thalidomide


title: WJ1795_RLF_N020_WT_E10

value: Abiraterone


title: WJ1793_RLF_N020_WT_E8

value: Methylprednisolone


title: WJ1789_RLF_N020_WT_E4

value: Birinapant (TL32711)


title: WJ1785_RLF_N020_WT_D12


title: WJ1792_RLF_N020_WT_E7

value: Cyclophosphamide monohydrate


title: WJ1781_RLF_N020_WT_D8


title: WJ1791_RLF_N020_WT_E6

value: Tipifarnib (Zarnestra)


title: WJ1796_RLF_N020_WT_E11

value: Rosiglitazone maleate


title: WJ1783_RLF_N020_WT_D10


title: WJ1777_RLF_N020_WT_D4


title: WJ1779_RLF_N020_WT_D6

value: Entacapone


title: WJ1771_RLF_N020_WT_C10

value: vAbl-ProB

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJ1773_RLF_N020_WT_C12

value: DMSO


title: WJ1776_RLF_N020_WT_D3

value: pro-B cells


title: WJ1774_RLF_N020_WT_D1


title: WJ1772_RLF_N020_WT_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJ1769_RLF_N020_WT_C8

value: Tofacitinib (CP-690550) Citrate


title: WJ1770_RLF_N020_WT_C9


title: WJ1768_RLF_N020_WT_C7

value: Barasertib (AZD1152-HQPA)


title: WJ1784_RLF_N020_WT_D11

value: WT

value: 2-Methoxyestradiol (2-MeOE2)


title: WJ1782_RLF_N020_WT_D9

value: Resveratrol


title: WJ1766_RLF_N020_WT_C5

value: MLN8237 (Alisertib)


title: WJ1767_RLF_N020_WT_C6

value: VX-680 (MK-0457,Tozasertib)


title: WJ1780_RLF_N020_WT_D7

value: Thioguanine


title: WJ1765_RLF_N020_WT_C4

value: Sodium Phenylbutyrate


title: WJ1764_RLF_N020_WT_C3

value: Valproic acid sodium salt (Sodium valproate)


title: WJ1762_RLF_N020_WT_C1

value: Belinostat (PXD101)


title: WJ1778_RLF_N020_WT_D5

value: Iniparib (BSI-201)


title: WJ1775_RLF_N020_WT_D2

value: vAbl-ProB

value: BMN 673


title: WJ1763_RLF_N020_WT_C2


title: WJ1757_RLF_N020_WT_B8

value: Vorinostat (SAHA, MK0683)


title: WJ1754_RLF_N020_WT_B5

value: pro-B cells

value: Moxonidine


title: WJ1756_RLF_N020_WT_B7

value: Rocilinostat (ACY-1215)


title: WJ1760_RLF_N020_WT_B11

value: Pracinostat (SB939)


title: WJ1759_RLF_N020_WT_B10

value: WT


title: WJ1758_RLF_N020_WT_B9

value: Mocetinostat (MGCD0103, MG0103)


title: WJ1761_RLF_N020_WT_B12

value: DMSO


title: WJ1752_RLF_N020_WT_B3


title: WJ1749_RLF_N020_WT_A12


title: WJ1748_RLF_N020_WT_A11

value: Fluorouracil (Adrucil)


title: WJ1751_RLF_N020_WT_B2

value: Raltegravir (MK-0518)


title: WJ1747_RLF_N020_WT_A10

value: Elvitegravir (GS-9137)


title: WJ1745_RLF_N020_WT_A8


title: WJ1746_RLF_N020_WT_A9


title: WJ1744_RLF_N020_WT_A7

value: Doxycycline hyclate


title: WJ1739_RLF_N020_WT_A2

value: Vildagliptin (LAF-237)


title: WJL1339_RLF_N019_WT_H12

value: Cycling


title: WJ1741_RLF_N020_WT_A4

value: Atazanavir sulfate (BMS-232632-05)


title: WJ1743_RLF_N020_WT_A6

value: vAbl-ProB


title: WJ1742_RLF_N020_WT_A5

value: Marimastat


title: WJ1738_RLF_N020_WT_A1

value: Sitagliptin phosphate monohydrate


title: WJ1750_RLF_N020_WT_B1

value: pro-B cells

value: Empty


title: WJL1338_RLF_N019_WT_H11

value: Pyrimethamine


title: WJ1740_RLF_N020_WT_A3

value: Alogliptin (SYR-322)


title: WJL1335_RLF_N019_WT_H8

value: WT

value: S- (+)-Rolipram


title: WJ1755_RLF_N020_WT_B6

value: Olmesartan medoxomil


title: WJL1334_RLF_N019_WT_H7

value: Trilostane


title: WJL1332_RLF_N019_WT_H5

value: Aminophylline


title: WJL1333_RLF_N019_WT_H6

value: Methotrexate


title: WJL1331_RLF_N019_WT_H4

value: Ozagrel


title: H751L.rep2.RNAseq

city: Worcester

first: Ye

last: Duan

address: 373 Plantation Street, Biotech Two, Suite 306

institute: Umass Medical School

description: mRNA (by rRNA depletion)

data_processing:
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA removal by Bowtie2/2.3.5.1 using C. elegans genome WS279
RPF were mapped to Genome WS279 by Star/2.7.6a with default setting
Gene counting by featureCounts(subread/1.6.2)
Assembly: WS279
Supplementary files format and content: comma-seperated values of gene counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) and fed with E. coli HB101. To obtain populations of synchronized developing worms, gravid adults were collected and washed twice with water. Pellets of centrifuged worms were treated with 5 ml 1N NaOH and 1% (v/v) sodium hypochlorite for 4 min with shaking to obtain embryos, and the embryos were rinsed with M9 buffer three times. The embryos were hatched in 10 ml M9 buffer at 20°C for 16-18 hrs with mild shaking. Hatched L1 larvae were transferred to plates at 30-50 worms per plate and replicate plates were cultured at 20°C for defined periods of time; samples of the population were examined by microscopy to confirm the developmental stages at the time of harvest.

extract_protocol:
Harvested worms were washed with M9 medium, centrifuged, and the worm pellets were flash-frozen in liquid nitrogen. The worm pellets were thawed and lysed by adding 4X volumes of QIAzol (Qiagen, Cat: 79306) and shaking vigorously at room temperature for 15 min. The total RNA was extracted by the addition of 0.85X volume chloroform, centrifugation, and recovery of the aqueous phase, which was then re-extracted with 1 volume phenol:chloroform:isoamyl alcohol (25:24:1, pH = 5.5). Total RNA was then precipitated by add 1 volume of isopropanol and 0.5 µl GlycoBlue (Invitrogen, Cat: AM9516), followed by incubation at -80oC for at least 30 min, and recovery by centrifugation at 25,000 rcf for 10 min at 4 °C. The supernatants were then removed, and the RNA pellets were subsequently washed twice by 70% (v/v) ethanol, dried in air for 5 min, dissolved in water, and stored at -80 °C. Worm samples for RNA-seq were aliquoted from the ribosome profiling harvests before the lysis step and frozen separately. The total RNA was extracted as described above. To enrich for mRNA, rRNA was depleted as described in detail elsewhere (Duan et al., 2020b). rRNA-depleted mRNA samples were then purified by RNA Clean & Concentrator-5 Kit (ZYMO, Cat: R1015)
Libraries were constructed by NEBNext Ultra II RNA Library Prep kit (NEB, Cat: E7775, E7335, E7500) and sequenced by Illumina NextSeq 500 system
RNAseq (rRNA depletion)

treatment_protocol: Synchronized populations of developing worms were cultured at 20 °C for 45 hrs after feeding. Harvested worms were washed with water three times and incubated at room temperature for 10 min to allow digestion of intestinal bacteria. Worms were then pelleted by centrifuge at 4,500 rcf for 2 min at room temperature and residual water was removed until the total volumes were twice as the worm pellets. The samples were then flashed frozen by liquid nitrogen and stored at -80 °C.

value: whole animal


title: null.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: null.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: WT.rep2.RNAseq

description: mRNA (by rRNA depletion)


title: null.rep2.RNAseq

description: mRNA (by rRNA depletion)


title: WT.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: H751L.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: H751L.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: E. coli K-12 WT 0

city: Hohhot

first: Xiaoli

last: Lv

address: NO.24 Zhao jun Street

institute: Inner Mongolia Universtiy

description: Gene expression data from WT cells without rifampicin-treatment

hyb_protocol: The corresponding volume of Hybridization Mix was injected into Affymetrix E. coli Genome 2.0 Array and then hybridized at 45℃for 16 hr. GeneChips were washed and stained using Affymetrix® GeneChip® Command Console® Software.

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

data_processing: The data were analyzed using RMA algorithm as normalization method.

organism: Escherichia coli

source_name: Wild-type (WT) cells without rifampicin-treatment

label_protocol: cDNA fragmentation and terminal labeling with biotinylated GeneChip® DNA labeling Reagent.

growth_protocol: WT cells and ΔcsdA mutant were grown in LB medium at 25℃. 50μg/ml of kanamycin were added for the selection in ΔcsdA mutant.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was reverse transcribed under random primers to synthesize cDNA strands. RNA was degraded with NaOH. cDNA was purified by column.

treatment_protocol: Exponentially growing cells in LB at 25°C with or without treatment of 300 μg/ml rifampicin for 40 min were collected by centrifugation at 4°C, freezed in liquid nitrogen for 5 min, and stored at -80℃.

tag: strain/genotype

value: without rifampicin-treatment


title: WJL1329_RLF_N019_WT_H2

value: Gimeracil


title: WJL1328_RLF_N019_WT_H1

value: vAbl-ProB

value: Apixaban


title: WJL1326_RLF_N019_WT_G11

value: Pimobendan


title: E. coli K-12 csdA mutant 40

description: Gene expression data from ΔcsdA mutant with rifampicin-treatment for 40 min

value: BW25113 csdA (deaD) mutant

value: with rifampicin-treatment for 40 min


title: WJL1327_RLF_N019_WT_G12

value: pro-B cells

value: Cycling


title: WJL1330_RLF_N019_WT_H3

value: WT

value: Dyphylline


title: E. coli K-12 WT 40

description: Gene expression data from WT cells with rifampicin-treatment for 40 min

source_name: Wild-type  (WT) cells with rifampicin-treatment for 40 min


title: V254I.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: V254I.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: V254I.rep2.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1336_RLF_N019_WT_H9

value: Pralatrexate


title: E. coli K-12 csdA mutant 0

description: Gene expression data from ΔcsdA mutant without rifampicin-treatment


title: WT.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1337_RLF_N019_WT_H10

value: Anagrelide HCl


title: G199S.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1325_RLF_N019_WT_G10

value: Rivaroxaban


title: WJL1324_RLF_N019_WT_G9

value: Cilostazol


title: G199S.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1321_RLF_N019_WT_G6

value: Isotretinoin


title: F180del.rep2.RNAseq

description: mRNA (by rRNA depletion)

value: whole animal


title: F180del.rep3.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1320_RLF_N019_WT_G5

value: Cilomilast


title: WJL1318_RLF_N019_WT_G3

value: Tadalafil