RBM4 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-47	BG293LV06-48
idx	0	0
TRCN#_or_BGC#	TRCN0000160719	TRCN0000160719
shRNA_or_gRNA_sequence	CCGGCCTGTTCTTCTGTCCTTCAATCTCGAGATTGAAGGACAGAAGAACAGGTTTTTTG	CCGGCCTGTTCTTCTGTCCTTCAATCTCGAGATTGAAGGACAGAAGAACAGGTTTTTTG
PAM
Name	RBM4	RBM4
Sample_ID	BG293LV06-47	BG293LV06-48
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	RBM4	RBM4
qPCR_result	85.1	88.6
Ave_qPCR	86.9
RT-qPCR_primer-F
RT-qPCR_primer-R
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	12182	12183

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-47	BG293LV06-48
Sample_ID	BG293LV06-47	BG293LV06-48
Sample Name
Sample Name	RBM4-BG293LV06-47	RBM4-BG293LV06-48
RBP	RBM4	RBM4
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13484	13485

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-47	BG293LV06-48
Sample #	49	50
Sample Name	RBM4-BG293LV06-47	RBM4-BG293LV06-48
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	277	273
Peak_Molarity	84.20	89.10
libSampleQC_DNA_Well	DNA_Library_set71/set1/A7.png	DNA_Library_set71/set1/B7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/A7.png	RNA_Library_set71/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-47	BG293LV06-48
RBP	RBM4	RBM4
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4474	4475

Sequencing Information

	BG293LV06-47	BG293LV06-48
Sample_ID	BG293LV06-47	BG293LV06-48
Sample Name	RBM4-BG293LV06-47	RBM4-BG293LV06-48
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	46,847,362	39,684,737
total_aligned_reads	43,665,857	36,370,630
unique_aligned_reads	40,998,159	34,030,574
percent_uniqueAligned	0.87514	0.85752
correlation_replicates	0.995438	0.995438
spikein_reads	171,628	113,068
percent_spikeins	0.00366	0.00285
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3043	3044

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
RBM4-BG293LV06-47_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3043	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29365
RBM4-BG293LV06-47_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3043	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29429
RBM4-BG293LV06-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3043					GRCh38	V40	RBM4-BG293LV06-47_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV06-47_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29494
RBM4-BG293LV06-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3043					GRCh38	V40	RBM4-BG293LV06-47_Aligned.sortedByCoord.out.bam		ENCORE2	29558
RBM4-BG293LV06-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3043					GRCh38	V40	RBM4-BG293LV06-47_Aligned.sortedByCoord.out.bam		ENCORE2	29622
RBM4-BG293LV06-47_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3043					GRCh38	V40	RBM4-BG293LV06-47_Aligned.sortedByCoord.out.bam		ENCORE2	29686
RBM4-BG293LV06-47_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3043					GRCh38	V40	RBM4-BG293LV06-47_S49_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV06-47_S49_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29750
RBM4-BG293LV06-48_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3044	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29366
RBM4-BG293LV06-48_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3044	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29430
RBM4-BG293LV06-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3044					GRCh38	V40	RBM4-BG293LV06-48_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV06-48_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29495
RBM4-BG293LV06-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3044					GRCh38	V40	RBM4-BG293LV06-48_Aligned.sortedByCoord.out.bam		ENCORE2	29559
RBM4-BG293LV06-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3044					GRCh38	V40	RBM4-BG293LV06-48_Aligned.sortedByCoord.out.bam		ENCORE2	29623
RBM4-BG293LV06-48_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3044					GRCh38	V40	RBM4-BG293LV06-48_Aligned.sortedByCoord.out.bam		ENCORE2	29687
RBM4-BG293LV06-48_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3044					GRCh38	V40	RBM4-BG293LV06-48_S50_L002_R1_001.filtered.trimmed.paired.fastq.gz,RBM4-BG293LV06-48_S50_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29751