RBMX RNA-Seq in HepG2

General Information


RBP	RBMX
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBMX-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBMX-BGHcLV45-59
Rep2	RBMX-BGHcLV45-60
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	33.2
Rep2_qPCR	42.2
Rep1_WB	95.5
Rep2_WB	95.8
Antibody Cat#	14794S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1626

Experiment Information (Status: Submitting)

	BGHcLV45-59	BGHcLV45-60
idx	1217	1217
TRCN#_or_BGC#	BGC#0001182	BGC#0001182
shRNA_or_gRNA_sequence	ATTTTTGATGCAGATGACGG	ATTTTTGATGCAGATGACGG
PAM	TGG	TGG
Name	RBMX_83	RBMX_83
Sample_ID	BGHcLV45-59	BGHcLV45-60
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	RBMX	RBMX
qPCR_result	33.2	42.2
Ave_qPCR	37.7
RT-qPCR_primer-F	cattggtgggcttaatacgg
RT-qPCR_primer-R	ttgttggtttcacggtctttc
protein_conc	3733	3833
WB_result	95.5	95.8
Ave_WB
WB_DONE_date	10/18/24,10/25/24
MW	42kd
IP
antibody_Cat#	14794S	lot # 1
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	9749	9750

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBMX	Product_ID: 14794S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RBMX-human

Experiment Status

	BGHcLV45-59	BGHcLV45-60
Sample_ID	BGHcLV45-59	BGHcLV45-60
Sample Name
Sample Name	RBMX-BGHcLV45-59	RBMX-BGHcLV45-60
RBP	RBMX	RBMX
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13710	13711

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-59	BGHcLV45-60
Sample #	25	26
Sample Name	RBMX-BGHcLV45-59	RBMX-BGHcLV45-60
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	297	294
Peak_Molarity	80.40	61.30
libSampleQC_DNA_Well	DNA_Library_set76/set1/A10.png	DNA_Library_set76/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/A4.png	RNA_Library_set76/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-59	BGHcLV45-60
RBP	RBMX	RBMX
Batch_ID	BGHcLV45	BGHcLV45
WB_result	95.500	95.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4634	4635

Sequencing Information

	BGHcLV45-59	BGHcLV45-60
Sample_ID	BGHcLV45-59	BGHcLV45-60
Sample Name	RBMX-BGHcLV45-59	RBMX-BGHcLV45-60
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	35,339,038	35,192,258
total_aligned_reads	31,561,210	32,338,805
unique_aligned_reads	29,739,160	30,475,449
percent_uniqueAligned	0.84154	0.86597
correlation_replicates	0.997891	0.997891
spikein_reads	54,728	31,314
percent_spikeins	0.00155	0.00089
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3345	3346

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
RBMX-BGHcLV45-59_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3345	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31836
RBMX-BGHcLV45-59_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3345	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31878
RBMX-BGHcLV45-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBMX-BGHcLV45-59_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31920
RBMX-BGHcLV45-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_Aligned.sortedByCoord.out.bam		ENCORE2	31962
RBMX-BGHcLV45-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_Aligned.sortedByCoord.out.bam		ENCORE2	32004
RBMX-BGHcLV45-59_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_Aligned.sortedByCoord.out.bam		ENCORE2	32046
RBMX-BGHcLV45-59_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_Aligned.sortedByCoord.out.bam		ENCORE2	32088
RBMX-BGHcLV45-59_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3345					GRCh38	V40	RBMX-BGHcLV45-59_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBMX-BGHcLV45-59_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32130
RBMX-BGHcLV45-60_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3346	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31837
RBMX-BGHcLV45-60_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3346	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31879
RBMX-BGHcLV45-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBMX-BGHcLV45-60_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31921
RBMX-BGHcLV45-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_Aligned.sortedByCoord.out.bam		ENCORE2	31963
RBMX-BGHcLV45-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_Aligned.sortedByCoord.out.bam		ENCORE2	32005
RBMX-BGHcLV45-60_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_Aligned.sortedByCoord.out.bam		ENCORE2	32047
RBMX-BGHcLV45-60_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_Aligned.sortedByCoord.out.bam		ENCORE2	32089
RBMX-BGHcLV45-60_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3346					GRCh38	V40	RBMX-BGHcLV45-60_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBMX-BGHcLV45-60_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32131