RBM42 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-77	BG293LV05-78
idx	0	0
TRCN#_or_BGC#	TRCN0000148512	TRCN0000148512
shRNA_or_gRNA_sequence	CCGGCGTGAGATGAATGGGAAGTATCTCGAGATACTTCCCATTCATCTCACGTTTTTTG	CCGGCGTGAGATGAATGGGAAGTATCTCGAGATACTTCCCATTCATCTCACGTTTTTTG
PAM
Name	RBM42	RBM42
Sample_ID	BG293LV05-77	BG293LV05-78
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	RBM42	RBM42
qPCR_result	85.9	80.5
Ave_qPCR	83.2
RT-qPCR_primer-F	atgatgctgccaccaatg
RT-qPCR_primer-R	caccactgcctcttccttct
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	10049	10050

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-77	BG293LV05-78
Sample_ID	BG293LV05-77	BG293LV05-78
Sample Name
Sample Name	RBM42-BG293LV05-77	RBM42-BG293LV05-78
RBP	RBM42	RBM42
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12868	12869

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-77	BG293LV05-78
Sample #	35	36
Sample Name	RBM42-BG293LV05-77	RBM42-BG293LV05-78
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	276	276
Peak_Molarity	86.50	95.20
libSampleQC_DNA_Well	DNA_Library_set69/set1/C5.png	DNA_Library_set69/set1/D5.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set69/set1/E10.png	RNA_Library_set69/set1/F10.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-77	BG293LV05-78
RBP	RBM42	RBM42
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4216	4217

Sequencing Information

	BG293LV05-77	BG293LV05-78
Sample_ID	BG293LV05-77	BG293LV05-78
Sample Name	RBM42-BG293LV05-77	RBM42-BG293LV05-78
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	15,700,483	15,727,104
total_aligned_reads	13,952,258	13,559,685
unique_aligned_reads	12,875,992	12,558,225
percent_uniqueAligned	0.82010	0.79851
correlation_replicates	0.976819	0.976819
spikein_reads	3,688	1,008
percent_spikeins	0.00023	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2935	2936

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
RBM42-BG293LV05-77_S167_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2935	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28519
RBM42-BG293LV05-77_S167_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2935	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28563
RBM42-BG293LV05-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77_S167_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV05-77_S167_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28607
RBM42-BG293LV05-77_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77/Aligned.sortedByCoord.out.bam		ENCORE2	28651
RBM42-BG293LV05-77_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77/Aligned.sortedByCoord.out.bam		ENCORE2	28695
RBM42-BG293LV05-77_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77/Aligned.sortedByCoord.out.bam		ENCORE2	28739
RBM42-BG293LV05-77_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77/Aligned.sortedByCoord.out.bam		ENCORE2	28783
RBM42-BG293LV05-77_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2935					GRCh38	V40	RBM42-BG293LV05-77_S167_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV05-77_S167_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28827
RBM42-BG293LV05-78_S168_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2936	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28520
RBM42-BG293LV05-78_S168_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2936	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28564
RBM42-BG293LV05-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78_S168_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV05-78_S168_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28608
RBM42-BG293LV05-78_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78/Aligned.sortedByCoord.out.bam		ENCORE2	28652
RBM42-BG293LV05-78_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78/Aligned.sortedByCoord.out.bam		ENCORE2	28696
RBM42-BG293LV05-78_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78/Aligned.sortedByCoord.out.bam		ENCORE2	28740
RBM42-BG293LV05-78_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78/Aligned.sortedByCoord.out.bam		ENCORE2	28784
RBM42-BG293LV05-78_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2936					GRCh38	V40	RBM42-BG293LV05-78_S168_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV05-78_S168_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28828