RBM10 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-21	BGRSDLV04-22
idx	0	0
TRCN#_or_BGC#	TRCN0000233278	TRCN0000233278
shRNA_or_gRNA_sequence	CCGGTCCAACGTGCGCGTCATAAAGCTCGAGCTTTATGACGCGCACGTTGGATTTTTG	CCGGTCCAACGTGCGCGTCATAAAGCTCGAGCTTTATGACGCGCACGTTGGATTTTTG
PAM
Name	RBM10	RBM10
Sample_ID	BGRSDLV04-21	BGRSDLV04-22
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	RBM10	RBM10
qPCR_result	71.21147	72.50756
Ave_qPCR	71.859515
RT-qPCR_primer-F	agcccacttgtcagaaaacg
RT-qPCR_primer-R	acttcctcctcttgggctct
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9385	9386

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-21	BGRSDLV04-22
Sample_ID	BGRSDLV04-21	BGRSDLV04-22
Sample Name
Sample Name	RBM10-BGRSDLV04-21	RBM10-BGRSDLV04-22
RBP	RBM10	RBM10
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12662	12663

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-21	BGRSDLV04-22
Sample #	17	18
Sample Name	RBM10-BGRSDLV04-21	RBM10-BGRSDLV04-22
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	271	288
Peak_Molarity	60.70	35.10
libSampleQC_DNA_Well	DNA_Library_set68/set1/A3.png	DNA_Library_set68/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/A3.png	RNA_Library_set68/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-21	BGRSDLV04-22
RBP	RBM10	RBM10
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4090	4091

Sequencing Information

	BGRSDLV04-21	BGRSDLV04-22
Sample_ID	BGRSDLV04-21	BGRSDLV04-22
Sample Name	RBM10-BGRSDLV04-21	RBM10-BGRSDLV04-22
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	32,835,430	31,903,701
total_aligned_reads	25,048,542	26,106,409
unique_aligned_reads	23,372,959	24,378,008
percent_uniqueAligned	0.71182	0.76411
correlation_replicates	0.997473	0.997473
spikein_reads	14,124	13,290
percent_spikeins	0.00043	0.00042
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2853	2854

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RBM10-BGRSDLV04-21_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2853	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27645
RBM10-BGRSDLV04-21_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2853	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27709
RBM10-BGRSDLV04-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGRSDLV04-21_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27773
RBM10-BGRSDLV04-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21/Aligned.sortedByCoord.out.bam		ENCORE2	27837
RBM10-BGRSDLV04-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21/Aligned.sortedByCoord.out.bam		ENCORE2	27901
RBM10-BGRSDLV04-21_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21/Aligned.sortedByCoord.out.bam		ENCORE2	27965
RBM10-BGRSDLV04-21_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21/Aligned.sortedByCoord.out.bam		ENCORE2	28029
RBM10-BGRSDLV04-21_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2853					GRCh38	V40	RBM10-BGRSDLV04-21_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGRSDLV04-21_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28093
RBM10-BGRSDLV04-22_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2854	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27646
RBM10-BGRSDLV04-22_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2854	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27710
RBM10-BGRSDLV04-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGRSDLV04-22_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27774
RBM10-BGRSDLV04-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22/Aligned.sortedByCoord.out.bam		ENCORE2	27838
RBM10-BGRSDLV04-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22/Aligned.sortedByCoord.out.bam		ENCORE2	27902
RBM10-BGRSDLV04-22_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22/Aligned.sortedByCoord.out.bam		ENCORE2	27966
RBM10-BGRSDLV04-22_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22/Aligned.sortedByCoord.out.bam		ENCORE2	28030
RBM10-BGRSDLV04-22_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2854					GRCh38	V40	RBM10-BGRSDLV04-22_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGRSDLV04-22_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28094