RPL5 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-53	BGHcLV47-54
idx	1657	1658
TRCN#_or_BGC#	BGC#0001258	BGC#0001258
shRNA_or_gRNA_sequence	TTTAGTACCAAACGATTCCC	TTTAGTACCAAACGATTCCC
PAM	TGG	TGG
Name	RPL5_81MISS)	RPL5_81MISS)
Sample_ID	BGHcLV47-53	BGHcLV47-54
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	RPL5	RPL5
qPCR_result	72.8	61.4
Ave_qPCR	67.1
RT-qPCR_primer-F	attatgctcggaaacgcttg
RT-qPCR_primer-R	tacgctgcgcagactatcat
protein_conc	3688	4432
WB_result	73.4	74.6
Ave_WB
WB_DONE_date	2/10/25
MW	34KD
IP
antibody_Cat#	A303-933A	LOT #3
Antibody DCC ID	ENCAB324CNX
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9846	9847

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL5	Product_ID: A303-933A Lot_ID: 3 Source: Bethyl Labs Target Name: RPL5-human

Experiment Status

	BGHcLV47-53	BGHcLV47-54
Sample_ID	BGHcLV47-53	BGHcLV47-54
Sample Name
Sample Name	RPL5-BGHcLV47-53	RPL5-BGHcLV47-54
RBP	RPL5	RPL5
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14170	14171

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-53	BGHcLV47-54
Sample #	23	24
Sample Name	RPL5-BGHcLV47-53	RPL5-BGHcLV47-54
Sample_Name_Alias
Index Well Position	G10	H10
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	256	259
Peak_Molarity	52.00	63.40
libSampleQC_DNA_Well	DNA_Library_set78/set1/G8.png	DNA_Library_set78/set1/H8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set78/set1/G3.png	RNA_Library_set78/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-53	BGHcLV47-54
RBP	RPL5	RPL5
Batch_ID	BGHcLV47	BGHcLV47
WB_result	73.400	74.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4734	4735

Sequencing Information

	BGHcLV47-53	BGHcLV47-54
Sample_ID	BGHcLV47-53	BGHcLV47-54
Sample Name	RPL5-BGHcLV47-53	RPL5-BGHcLV47-54
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	27,530,344	20,225,537
total_aligned_reads	24,932,975	17,934,819
unique_aligned_reads	23,514,357	16,899,904
percent_uniqueAligned	0.85413	0.83557
correlation_replicates	0.997018	0.997018
spikein_reads	16,212	22,216
percent_spikeins	0.00059	0.00110
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3437	3438

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
RPL5-BGHcLV47-53_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3437	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	32570
RPL5-BGHcLV47-53_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3437	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	32604
RPL5-BGHcLV47-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3437					GRCh38	V40	RPL5-BGHcLV47-53_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGHcLV47-53_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32638
RPL5-BGHcLV47-53_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	3437					GRCh38	V40	RPL5-BGHcLV47-53_Aligned.sortedByCoord.out.bam		ENCORE2	32672
RPL5-BGHcLV47-53_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	3437					GRCh38	V40	RPL5-BGHcLV47-53_Aligned.sortedByCoord.out.bam		ENCORE2	32706
RPL5-BGHcLV47-53_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	3437					GRCh38	V40	RPL5-BGHcLV47-53_Aligned.sortedByCoord.out.bam		ENCORE2	32740
RPL5-BGHcLV47-53_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	3437					GRCh38	V40	RPL5-BGHcLV47-53_Aligned.sortedByCoord.out.bam		ENCORE2	32774
RPL5-BGHcLV47-53_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3437					GRCh38	V40	RPL5-BGHcLV47-53_S64_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGHcLV47-53_S64_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32808
RPL5-BGHcLV47-54_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3438	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	32571
RPL5-BGHcLV47-54_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3438	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	32605
RPL5-BGHcLV47-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3438					GRCh38	V40	RPL5-BGHcLV47-54_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGHcLV47-54_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32639
RPL5-BGHcLV47-54_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	3438					GRCh38	V40	RPL5-BGHcLV47-54_Aligned.sortedByCoord.out.bam		ENCORE2	32673
RPL5-BGHcLV47-54_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	3438					GRCh38	V40	RPL5-BGHcLV47-54_Aligned.sortedByCoord.out.bam		ENCORE2	32707
RPL5-BGHcLV47-54_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	3438					GRCh38	V40	RPL5-BGHcLV47-54_Aligned.sortedByCoord.out.bam		ENCORE2	32741
RPL5-BGHcLV47-54_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	3438					GRCh38	V40	RPL5-BGHcLV47-54_Aligned.sortedByCoord.out.bam		ENCORE2	32775
RPL5-BGHcLV47-54_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3438					GRCh38	V40	RPL5-BGHcLV47-54_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGHcLV47-54_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32809