RBM42 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-85	BG293LV06-86
idx	0	0
TRCN#_or_BGC#	TRCN0000180790	TRCN0000180790
shRNA_or_gRNA_sequence	CCGGGCGTGAGATGAATGGGAAGTACTCGAGTACTTCCCATTCATCTCACGCTTTTTTG	CCGGGCGTGAGATGAATGGGAAGTACTCGAGTACTTCCCATTCATCTCACGCTTTTTTG
PAM
Name	RBM42	RBM42
Sample_ID	BG293LV06-85	BG293LV06-86
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	RBM42	RBM42
qPCR_result	97.8	86.6
Ave_qPCR	92.2
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	12220	12221

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-85	BG293LV06-86
Sample_ID	BG293LV06-85	BG293LV06-86
Sample Name
Sample Name	RBM42-BG293LV06-85B	RBM42-BG293LV06-86B
RBP	RBM42	RBM42
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13522	13523

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-85	BG293LV06-86
Sample #	85	86
Sample Name	RBM42-BG293LV06-85B	RBM42-BG293LV06-86B
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	285	288
Peak_Molarity	81.80	100.00
libSampleQC_DNA_Well	DNA_Library_set72/set1/E4.png	DNA_Library_set72/set1/F4.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set72/set1/E4.png	RNA_Library_set72/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-85	BG293LV06-86
RBP	RBM42	RBM42
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4510	4511

Sequencing Information

	BG293LV06-85	BG293LV06-86
Sample_ID	BG293LV06-85	BG293LV06-86
Sample Name	RBM42-BG293LV06-85B	RBM42-BG293LV06-86B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	55,793,878	31,587,021
total_aligned_reads	51,940,603	29,540,866
unique_aligned_reads	48,460,927	27,741,977
percent_uniqueAligned	0.86857	0.87827
correlation_replicates	0.994534	0.994534
spikein_reads	211,606	107,332
percent_spikeins	0.00379	0.00340
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3079	3080

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-BG293LV06-85B_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3079	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29808
RBM42-BG293LV06-85B_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3079	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29880
RBM42-BG293LV06-85B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV06-85B_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29952
RBM42-BG293LV06-85B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_Aligned.sortedByCoord.out.bam		ENCORE2	30024
RBM42-BG293LV06-85B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_Aligned.sortedByCoord.out.bam		ENCORE2	30096
RBM42-BG293LV06-85B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_Aligned.sortedByCoord.out.bam		ENCORE2	30168
RBM42-BG293LV06-85B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_Aligned.sortedByCoord.out.bam		ENCORE2	30240
RBM42-BG293LV06-85B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3079					GRCh38	V40	RBM42-BG293LV06-85B_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV06-85B_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30312
RBM42-BG293LV06-86B_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3080	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29809
RBM42-BG293LV06-86B_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3080	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29881
RBM42-BG293LV06-86B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV06-86B_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29953
RBM42-BG293LV06-86B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_Aligned.sortedByCoord.out.bam		ENCORE2	30025
RBM42-BG293LV06-86B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_Aligned.sortedByCoord.out.bam		ENCORE2	30097
RBM42-BG293LV06-86B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_Aligned.sortedByCoord.out.bam		ENCORE2	30169
RBM42-BG293LV06-86B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_Aligned.sortedByCoord.out.bam		ENCORE2	30241
RBM42-BG293LV06-86B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3080					GRCh38	V40	RBM42-BG293LV06-86B_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BG293LV06-86B_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30313