RPL4 RNA-Seq in K562

General Information


RBP	RPL4
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL4-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	RPL4-BGKcLV46-59
Rep2	RPL4-BGKcLV46-60
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	74.2
Rep2_qPCR	75.6
Rep1_WB	49.4
Rep2_WB	49.0771
Antibody Cat#	A305-046A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1647

Experiment Information (Status: Submitting)

	BGKcLV46-59	BGKcLV46-60
idx	0	0
TRCN#_or_BGC#	BGC#0001255	BGC#0001255
shRNA_or_gRNA_sequence	CGGAGTACACCGATATCAGT	CGGAGTACACCGATATCAGT
PAM	GGG	GGG
Name	RPL4_69	RPL4_69
Sample_ID	BGKcLV46-59	BGKcLV46-60
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RPL4	RPL4
qPCR_result	74.2	75.6
Ave_qPCR	74.9
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3121	2827
WB_result	49.4	49.0771
Ave_WB
WB_DONE_date	1/13/25,1/17/25
MW	48kd	tubulin
IP
antibody_Cat#	A305-046A	lot# 1
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	6055	6056

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL4	Product_ID: A305-046A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL4-human

Experiment Status

	BGKcLV46-59	BGKcLV46-60
Sample_ID	BGKcLV46-59	BGKcLV46-60
Sample Name
Sample Name	RPL4-BGKcLV46-59	RPL4-BGKcLV46-60
RBP	RPL4	RPL4
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14048	14049

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-59	BGKcLV46-60
Sample #	27	28
Sample Name	RPL4-BGKcLV46-59	RPL4-BGKcLV46-60
Sample_Name_Alias
Index Well Position	C04	D04
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	309	300
Peak_Molarity	69.20	78.80
libSampleQC_DNA_Well	DNA_Library_set77/set1/C10.png	DNA_Library_set77/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set2/H12.png	RNA_Library_set77/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-59	BGKcLV46-60
RBP	RPL4	RPL4
Batch_ID	BGKcLV46	BGKcLV46
WB_result	49.400	49.077
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4686	4687

Sequencing Information

	BGKcLV46-59	BGKcLV46-60
Sample_ID	BGKcLV46-59	BGKcLV46-60
Sample Name	RPL4-BGKcLV46-59	RPL4-BGKcLV46-60
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	75,943,885	53,655,884
total_aligned_reads	71,474,942	49,454,380
unique_aligned_reads	66,010,178	45,659,377
percent_uniqueAligned	0.86920	0.85097
correlation_replicates	0.996196	0.996196
spikein_reads	85,954	30,504
percent_spikeins	0.00113	0.00057
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3391	3392

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
RPL4-BGKcLV46-59_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3391	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	32176
RPL4-BGKcLV46-59_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3391	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	32226
RPL4-BGKcLV46-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3391					GRCh38	V40	RPL4-BGKcLV46-59_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL4-BGKcLV46-59_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32276
RPL4-BGKcLV46-59_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	3391					GRCh38	V40	RPL4-BGKcLV46-59_Aligned.sortedByCoord.out.bam		ENCORE2	32326
RPL4-BGKcLV46-59_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	3391					GRCh38	V40	RPL4-BGKcLV46-59_Aligned.sortedByCoord.out.bam		ENCORE2	32376
RPL4-BGKcLV46-59_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	3391					GRCh38	V40	RPL4-BGKcLV46-59_Aligned.sortedByCoord.out.bam		ENCORE2	32426
RPL4-BGKcLV46-59_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	3391					GRCh38	V40	RPL4-BGKcLV46-59_Aligned.sortedByCoord.out.bam		ENCORE2	32476
RPL4-BGKcLV46-59_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3391					GRCh38	V40	RPL4-BGKcLV46-59_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL4-BGKcLV46-59_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32526
RPL4-BGKcLV46-60_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3392	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	32177
RPL4-BGKcLV46-60_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3392	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	32227
RPL4-BGKcLV46-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3392					GRCh38	V40	RPL4-BGKcLV46-60_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL4-BGKcLV46-60_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32277
RPL4-BGKcLV46-60_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	3392					GRCh38	V40	RPL4-BGKcLV46-60_Aligned.sortedByCoord.out.bam		ENCORE2	32327
RPL4-BGKcLV46-60_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	3392					GRCh38	V40	RPL4-BGKcLV46-60_Aligned.sortedByCoord.out.bam		ENCORE2	32377
RPL4-BGKcLV46-60_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	3392					GRCh38	V40	RPL4-BGKcLV46-60_Aligned.sortedByCoord.out.bam		ENCORE2	32427
RPL4-BGKcLV46-60_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	3392					GRCh38	V40	RPL4-BGKcLV46-60_Aligned.sortedByCoord.out.bam		ENCORE2	32477
RPL4-BGKcLV46-60_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3392					GRCh38	V40	RPL4-BGKcLV46-60_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL4-BGKcLV46-60_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32527