RBM42 RNA-Seq in HepG2

General Information


RBP	RBM42
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RBM42-BGHcLV50-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV50
Pool ID	Pool-251003
Local_Set_Name	set80
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBM42-BGHcLV50-91
Rep2	RBM42-BGHcLV50-92
CN1	NT-BGHcLV50-1
CN2	NT-BGHcLV50-2
Rep1_qPCR	63.3
Rep2_qPCR	64.0
Rep1_WB	64.1
Rep2_WB	51.6
Antibody Cat#	A305-139A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1692

Experiment Information (Status: Submitting)

	BGHcLV50-91	BGHcLV50-91	BGHcLV50-92	BGHcLV50-92
idx	1912	1914	1913	1915
TRCN#_or_BGC#	BGC#0001364	BGC#0001364	BGC#0001364	BGC#0001364
shRNA_or_gRNA_sequence	TGTTGGTCGCGATAATTGGG	TGTTGGTCGCGATAATTGGG	TGTTGGTCGCGATAATTGGG	TGTTGGTCGCGATAATTGGG
PAM	CGG	CGG	CGG	CGG
Name	RBM42_93	RBM42_93	RBM42_93	RBM42_93
Sample_ID	BGHcLV50-91	BGHcLV50-91	BGHcLV50-92	BGHcLV50-92
transduction_Date	7/29/25	7/29/25	7/29/25	7/29/25
days	D6	D6	D6	D6
RBP_name	RBM42	RBM42	RBM42	RBM42
qPCR_result	63.3		64.0
Ave_qPCR	63.7
RT-qPCR_primer-F	atgatgctgccaccaatg
RT-qPCR_primer-R	caccactgcctcttccttct
protein_conc	3574	3574	3102	3102
WB_result	64.1	51.1	51.6	56.9
Ave_WB
WB_DONE_date	8/21/25	9/16/25
MW	50KD	50KD
IP
antibody_Cat#	A305-139A	A305-138A	LOT #1	LOT #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	10101	10103	10102	10104

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-91	BGHcLV50-91	BGHcLV50-92	BGHcLV50-92
Sample_ID	BGHcLV50-91	BGHcLV50-91	BGHcLV50-92	BGHcLV50-92
Sample Name
Sample Name	RBM42-BGHcLV50-91		RBM42-BGHcLV50-92
RBP	RBM42	RBM42	RBM42	RBM42
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2026-10-30	2025-09-30	2026-10-30	2025-09-30
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14466	14546	14467	14547

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-91	BGHcLV50-92
Sample #	19	20
Sample Name	RBM42-BGHcLV50-91	RBM42-BGHcLV50-92
Sample_Name_Alias
Index Well Position	C12	D12
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-10-01	2025-10-01
Lib_ID	Lib-251001	Lib-251001
Tecan_Location
Tecan
Tecan_date
Size_bp	292	287
Peak_Molarity	71.10	65.00
libSampleQC_DNA_Well	DNA_Library_set80/set1/C12.png	DNA_Library_set80/set1/D12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set80/set1/C9.png	RNA_Library_set80/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-91	BGHcLV50-92
RBP	RBM42	RBM42
Batch_ID	BGHcLV50	BGHcLV50
WB_result	64.100	51.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4834	4835

Sequencing Information

	BGHcLV50-91	BGHcLV50-92
Sample_ID	BGHcLV50-91	BGHcLV50-92
Sample Name	RBM42-BGHcLV50-91	RBM42-BGHcLV50-92
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	15,593,411	19,610,106
total_aligned_reads	14,097,088	17,987,962
unique_aligned_reads	13,344,844	17,009,419
percent_uniqueAligned	0.85580	0.86738
correlation_replicates	0.991876	0.991876
spikein_reads	94,200	58,052
percent_spikeins	0.00604	0.00296
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3489	3490

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-BGHcLV50-91_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3489	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32992
RBM42-BGHcLV50-91_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3489	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33016
RBM42-BGHcLV50-91_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BGHcLV50-91_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33040
RBM42-BGHcLV50-91_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_Aligned.sortedByCoord.out.bam		ENCORE2	33064
RBM42-BGHcLV50-91_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_Aligned.sortedByCoord.out.bam		ENCORE2	33088
RBM42-BGHcLV50-91_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_Aligned.sortedByCoord.out.bam		ENCORE2	33112
RBM42-BGHcLV50-91_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_Aligned.sortedByCoord.out.bam		ENCORE2	33136
RBM42-BGHcLV50-91_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3489					GRCh38	V40	RBM42-BGHcLV50-91_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BGHcLV50-91_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33160
RBM42-BGHcLV50-92_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3490	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32993
RBM42-BGHcLV50-92_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3490	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33017
RBM42-BGHcLV50-92_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BGHcLV50-92_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33041
RBM42-BGHcLV50-92_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_Aligned.sortedByCoord.out.bam		ENCORE2	33065
RBM42-BGHcLV50-92_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_Aligned.sortedByCoord.out.bam		ENCORE2	33089
RBM42-BGHcLV50-92_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_Aligned.sortedByCoord.out.bam		ENCORE2	33113
RBM42-BGHcLV50-92_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_Aligned.sortedByCoord.out.bam		ENCORE2	33137
RBM42-BGHcLV50-92_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3490					GRCh38	V40	RBM42-BGHcLV50-92_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM42-BGHcLV50-92_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33161