RPS28 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-95	BGHcLV49-96
idx	1798	1799
TRCN#_or_BGC#	BGC#0000823	BGC#0000823
shRNA_or_gRNA_sequence	TTCGGGCCCCCACCTCACCC	TTCGGGCCCCCACCTCACCC
PAM	TGG	TGG
Name	RPS28_55	RPS28_55
Sample_ID	BGHcLV49-95	BGHcLV49-96
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	RPS28	RPS28
qPCR_result	50.3	48.0
Ave_qPCR	49.2
RT-qPCR_primer-F	gaccggttctcagggacagt
RT-qPCR_primer-R	tttacattgcggatgatgga
protein_conc	3004	3597
WB_result	52.2	54.0
Ave_WB
WB_DONE_date	7/1/25
MW	7.8kd
IP
antibody_Cat#	A305-095A	LOT #1
Antibody DCC ID	ENCAB557DQG
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9987	9988

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS28	Product_ID: A305-095A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS28-human

Experiment Status

	BGHcLV49-95	BGHcLV49-96
Sample_ID	BGHcLV49-95	BGHcLV49-96
Sample Name
Sample Name	RPS28-BGHcLV49-95	RPS28-BGHcLV49-96
RBP	RPS28	RPS28
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14362	14363

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-95	BGHcLV49-96
Sample #	59	60
Sample Name	RPS28-BGHcLV49-95	RPS28-BGHcLV49-96
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	264	260
Peak_Molarity	71.20	75.00
libSampleQC_DNA_Well	DNA_Library_set81/set1/E5.png	DNA_Library_set81/set1/F5.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set81/set1/E8.png	RNA_Library_set81/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-95	BGHcLV49-96
RBP	RPS28	RPS28
Batch_ID	BGHcLV49	BGHcLV49
WB_result	52.200	54.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4804	4805

Sequencing Information

	BGHcLV49-95	BGHcLV49-96
Sample_ID	BGHcLV49-95	BGHcLV49-96
Sample Name	RPS28-BGHcLV49-95	RPS28-BGHcLV49-96
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	25,291,908	56,165,542
total_aligned_reads	18,976,282	47,169,581
unique_aligned_reads	17,863,104	44,609,736
percent_uniqueAligned	0.70628	0.79425
correlation_replicates	0.993468	0.993468
spikein_reads	43,894	80,266
percent_spikeins	0.00174	0.00143
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3529	3530

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
RPS28-BGHcLV49-95_S112_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3529	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33204
RPS28-BGHcLV49-95_S112_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3529	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33250
RPS28-BGHcLV49-95_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_S112_L008_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGHcLV49-95_S112_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33296
RPS28-BGHcLV49-95_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_Aligned.sortedByCoord.out.bam		ENCORE2	33342
RPS28-BGHcLV49-95_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_Aligned.sortedByCoord.out.bam		ENCORE2	33388
RPS28-BGHcLV49-95_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_Aligned.sortedByCoord.out.bam		ENCORE2	33434
RPS28-BGHcLV49-95_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_Aligned.sortedByCoord.out.bam		ENCORE2	33480
RPS28-BGHcLV49-95_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3529					GRCh38	V40	RPS28-BGHcLV49-95_S112_L008_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGHcLV49-95_S112_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33526
RPS28-BGHcLV49-96_S134_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3530	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33205
RPS28-BGHcLV49-96_S134_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3530	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33251
RPS28-BGHcLV49-96_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_S134_L008_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGHcLV49-96_S134_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33297
RPS28-BGHcLV49-96_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_Aligned.sortedByCoord.out.bam		ENCORE2	33343
RPS28-BGHcLV49-96_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_Aligned.sortedByCoord.out.bam		ENCORE2	33389
RPS28-BGHcLV49-96_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_Aligned.sortedByCoord.out.bam		ENCORE2	33435
RPS28-BGHcLV49-96_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_Aligned.sortedByCoord.out.bam		ENCORE2	33481
RPS28-BGHcLV49-96_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3530					GRCh38	V40	RPS28-BGHcLV49-96_S134_L008_R1_001.filtered.trimmed.paired.fastq.gz,RPS28-BGHcLV49-96_S134_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33527