RPS3 RNA-Seq in HepG2

General Information


RBP	RPS3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS3-BGHcLV47-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV47
Pool ID	Pool-250422
Local_Set_Name	set78
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPS3-BGHcLV47-61
Rep2	RPS3-BGHcLV47-62
CN1	NT-BGHcLV47-1
CN2	NT-BGHcLV47-2
Rep1_qPCR	66.7
Rep2_qPCR	62.6
Rep1_WB	50.1
Rep2_WB	61.9
Antibody Cat#	A303-840A
Antibody Lot#
Antibody DCC ID	ENCAB855QRN
Status	Submitted
Project	ENCORE2
ID	1670

Experiment Information (Status: Sequenced)

	BGHcLV47-61	BGHcLV47-62
idx	1665	1666
TRCN#_or_BGC#	BGC#0000048	BGC#0000048
shRNA_or_gRNA_sequence	CTTTCCAGAGGGCAGTGTAG	CTTTCCAGAGGGCAGTGTAG
PAM
Name	RPS3-3	RPS3-3
Sample_ID	BGHcLV47-61	BGHcLV47-62
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	RPS3	RPS3
qPCR_result	66.7	62.6
Ave_qPCR	64.7
RT-qPCR_primer-F	GTGCGAGTTACACCAACCAG
RT-qPCR_primer-R	ACAGCAGTCAGTTCCCGAAT
protein_conc	3204	3213
WB_result	50.1	61.9
Ave_WB
WB_DONE_date	3/25/25
MW	27 kDa
IP	1
antibody_Cat#	A303-840A
Antibody DCC ID	ENCAB855QRN
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9854	9855

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS3	Product_ID: A303-840A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS3-human

Experiment Status

	BGHcLV47-61	BGHcLV47-62
Sample_ID	BGHcLV47-61	BGHcLV47-62
Sample Name
Sample Name	RPS3-BGHcLV47-61	RPS3-BGHcLV47-62
RBP	RPS3	RPS3
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14174	14175

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-61	BGHcLV47-62
Sample #	27	28
Sample Name	RPS3-BGHcLV47-61	RPS3-BGHcLV47-62
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	274	280
Peak_Molarity	91.20	86.60
libSampleQC_DNA_Well	DNA_Library_set78/set1/C9.png	DNA_Library_set78/set1/D9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set78/set1/C4.png	RNA_Library_set78/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-61	BGHcLV47-62
RBP	RPS3	RPS3
Batch_ID	BGHcLV47	BGHcLV47
WB_result	50.100	61.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4738	4739

Sequencing Information

	BGHcLV47-61	BGHcLV47-62
Sample_ID	BGHcLV47-61	BGHcLV47-62
Sample Name	RPS3-BGHcLV47-61	RPS3-BGHcLV47-62
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	12,788,618	16,237,277
total_aligned_reads	11,375,542	14,258,525
unique_aligned_reads	10,743,225	13,483,838
percent_uniqueAligned	0.84006	0.83042
correlation_replicates	0.997475	0.997475
spikein_reads	11,816	15,726
percent_spikeins	0.00092	0.00097
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3441	3442

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
RPS3-BGHcLV47-61_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3441	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32574
RPS3-BGHcLV47-61_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3441	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32608
RPS3-BGHcLV47-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS3-BGHcLV47-61_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32642
RPS3-BGHcLV47-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_Aligned.sortedByCoord.out.bam		ENCORE2	32676
RPS3-BGHcLV47-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_Aligned.sortedByCoord.out.bam		ENCORE2	32710
RPS3-BGHcLV47-61_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_Aligned.sortedByCoord.out.bam		ENCORE2	32744
RPS3-BGHcLV47-61_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_Aligned.sortedByCoord.out.bam		ENCORE2	32778
RPS3-BGHcLV47-61_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3441					GRCh38	V40	RPS3-BGHcLV47-61_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS3-BGHcLV47-61_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32812
RPS3-BGHcLV47-62_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3442	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32575
RPS3-BGHcLV47-62_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3442	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32609
RPS3-BGHcLV47-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS3-BGHcLV47-62_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32643
RPS3-BGHcLV47-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_Aligned.sortedByCoord.out.bam		ENCORE2	32677
RPS3-BGHcLV47-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_Aligned.sortedByCoord.out.bam		ENCORE2	32711
RPS3-BGHcLV47-62_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_Aligned.sortedByCoord.out.bam		ENCORE2	32745
RPS3-BGHcLV47-62_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_Aligned.sortedByCoord.out.bam		ENCORE2	32779
RPS3-BGHcLV47-62_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3442					GRCh38	V40	RPS3-BGHcLV47-62_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPS3-BGHcLV47-62_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32813