RPL5 RNA-Seq in K562

General Information


RBP	RPL5
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL5-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPL5-BGKcLV46-63
Rep2	RPL5-BGKcLV46-64
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	47.4
Rep2_qPCR	51.6
Rep1_WB	69.4
Rep2_WB	64.8
Antibody Cat#	A303-933A
Antibody Lot#	lot# 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1648

Experiment Information (Status: Submitting)

	BGKcLV46-63	BGKcLV46-64
idx	0	0
TRCN#_or_BGC#	BGC#0001258	BGC#0001258
shRNA_or_gRNA_sequence	TTTAGTACCAAACGATTCCC	TTTAGTACCAAACGATTCCC
PAM	TGG	TGG
Name	RPL5_81MISS)	RPL5_81MISS)
Sample_ID	BGKcLV46-63	BGKcLV46-64
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RPL5	RPL5
qPCR_result	47.4	51.6
Ave_qPCR	49.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3292	2859
WB_result	69.4	64.8
Ave_WB
WB_DONE_date	1/2/24,1/6/25,1/15/2
MW	34kd
IP
antibody_Cat#	A303-933A	lot# 3
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	6059	6060

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

	BGKcLV46-63	BGKcLV46-64
Sample_ID	BGKcLV46-63	BGKcLV46-64
Sample Name
Sample Name	RPL5-BGKcLV46-63	RPL5-BGKcLV46-64
RBP	RPL5	RPL5
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14050	14051

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-63	BGKcLV46-64
Sample #	29	30
Sample Name	RPL5-BGKcLV46-63	RPL5-BGKcLV46-64
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	313	311
Peak_Molarity	77.60	91.80
libSampleQC_DNA_Well	DNA_Library_set77/set1/E10.png	DNA_Library_set77/set1/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/E4.png	RNA_Library_set77/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-63	BGKcLV46-64
RBP	RPL5	RPL5
Batch_ID	BGKcLV46	BGKcLV46
WB_result	69.400	64.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4688	4689

Sequencing Information

	BGKcLV46-63	BGKcLV46-64
Sample_ID	BGKcLV46-63	BGKcLV46-64
Sample Name	RPL5-BGKcLV46-63	RPL5-BGKcLV46-64
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	57,225,989	51,640,376
total_aligned_reads	54,027,267	48,290,126
unique_aligned_reads	49,833,250	44,590,773
percent_uniqueAligned	0.87082	0.86349
correlation_replicates	0.998885	0.998885
spikein_reads	42,544	54,820
percent_spikeins	0.00074	0.00106
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3393	3394

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-BGKcLV46-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3393	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32178
RPL5-BGKcLV46-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3393	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32228
RPL5-BGKcLV46-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGKcLV46-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32278
RPL5-BGKcLV46-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_Aligned.sortedByCoord.out.bam		ENCORE2	32328
RPL5-BGKcLV46-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_Aligned.sortedByCoord.out.bam		ENCORE2	32378
RPL5-BGKcLV46-63_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_Aligned.sortedByCoord.out.bam		ENCORE2	32428
RPL5-BGKcLV46-63_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_Aligned.sortedByCoord.out.bam		ENCORE2	32478
RPL5-BGKcLV46-63_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3393					GRCh38	V40	RPL5-BGKcLV46-63_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGKcLV46-63_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32528
RPL5-BGKcLV46-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3394	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32179
RPL5-BGKcLV46-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3394	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32229
RPL5-BGKcLV46-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGKcLV46-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32279
RPL5-BGKcLV46-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_Aligned.sortedByCoord.out.bam		ENCORE2	32329
RPL5-BGKcLV46-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_Aligned.sortedByCoord.out.bam		ENCORE2	32379
RPL5-BGKcLV46-64_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_Aligned.sortedByCoord.out.bam		ENCORE2	32429
RPL5-BGKcLV46-64_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_Aligned.sortedByCoord.out.bam		ENCORE2	32479
RPL5-BGKcLV46-64_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3394					GRCh38	V40	RPL5-BGKcLV46-64_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL5-BGKcLV46-64_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32529