RRP8 RNA-Seq in K562

General Information


RBP	RRP8
Cell_Line	K562
Method	CRISPR
Exp_Name	RRP8-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	RRP8-BGKcLV46-83
Rep2	RRP8-BGKcLV46-84
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	45.6
Rep2_qPCR	50.4
Rep1_WB	60.4
Rep2_WB	85.7
Antibody Cat#	A304-201A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1652

Experiment Information (Status: Submitting)

	BGKcLV46-83	BGKcLV46-84
idx	0	0
TRCN#_or_BGC#	BGC#0000832	BGC#0000832
shRNA_or_gRNA_sequence	AATCTCACGACCTCCGCCTG	AATCTCACGACCTCCGCCTG
PAM	CGG	CGG
Name	RRP8_91	RRP8_91
Sample_ID	BGKcLV46-83	BGKcLV46-84
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RRP8	RRP8
qPCR_result	45.6	50.4
Ave_qPCR	48.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4429	4121
WB_result	60.4	85.7
Ave_WB
WB_DONE_date	1/23/25
MW
IP
antibody_Cat#	A304-201A	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	6079	6080

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RRP8	Product_ID: A304-201A Lot_ID: 1 Source: Bethyl Labs Target Name: RRP8-human

Experiment Status

	BGKcLV46-83	BGKcLV46-84
Sample_ID	BGKcLV46-83	BGKcLV46-84
Sample Name
Sample Name	RRP8-BGKcLV46-83	RRP8-BGKcLV46-84
RBP	RRP8	RRP8
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14060	14061

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-83	BGKcLV46-84
Sample #	39	40
Sample Name	RRP8-BGKcLV46-83	RRP8-BGKcLV46-84
Sample_Name_Alias
Index Well Position	G05	H05
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	302	300
Peak_Molarity	62.90	67.50
libSampleQC_DNA_Well	DNA_Library_set77/set1/G11.png	DNA_Library_set77/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/G5.png	RNA_Library_set77/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-83	BGKcLV46-84
RBP	RRP8	RRP8
Batch_ID	BGKcLV46	BGKcLV46
WB_result	60.400	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4698	4699

Sequencing Information

	BGKcLV46-83	BGKcLV46-84
Sample_ID	BGKcLV46-83	BGKcLV46-84
Sample Name	RRP8-BGKcLV46-83	RRP8-BGKcLV46-84
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	74,301,812	74,660,466
total_aligned_reads	69,791,861	69,788,076
unique_aligned_reads	64,407,688	64,414,504
percent_uniqueAligned	0.86684	0.86277
correlation_replicates	0.996241	0.996241
spikein_reads	99,934	173,920
percent_spikeins	0.00134	0.00233
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3401	3402

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
RRP8-BGKcLV46-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3401	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	32188
RRP8-BGKcLV46-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3401	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	32238
RRP8-BGKcLV46-83_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3401					GRCh38	V40	RRP8-BGKcLV46-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,RRP8-BGKcLV46-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32288
RRP8-BGKcLV46-83_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	3401					GRCh38	V40	RRP8-BGKcLV46-83_Aligned.sortedByCoord.out.bam		ENCORE2	32338
RRP8-BGKcLV46-83_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	3401					GRCh38	V40	RRP8-BGKcLV46-83_Aligned.sortedByCoord.out.bam		ENCORE2	32388
RRP8-BGKcLV46-83_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	3401					GRCh38	V40	RRP8-BGKcLV46-83_Aligned.sortedByCoord.out.bam		ENCORE2	32438
RRP8-BGKcLV46-83_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	3401					GRCh38	V40	RRP8-BGKcLV46-83_Aligned.sortedByCoord.out.bam		ENCORE2	32488
RRP8-BGKcLV46-83_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3401					GRCh38	V40	RRP8-BGKcLV46-83_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,RRP8-BGKcLV46-83_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32538
RRP8-BGKcLV46-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3402	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	32189
RRP8-BGKcLV46-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3402	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	32239
RRP8-BGKcLV46-84_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3402					GRCh38	V40	RRP8-BGKcLV46-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,RRP8-BGKcLV46-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32289
RRP8-BGKcLV46-84_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	3402					GRCh38	V40	RRP8-BGKcLV46-84_Aligned.sortedByCoord.out.bam		ENCORE2	32339
RRP8-BGKcLV46-84_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	3402					GRCh38	V40	RRP8-BGKcLV46-84_Aligned.sortedByCoord.out.bam		ENCORE2	32389
RRP8-BGKcLV46-84_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	3402					GRCh38	V40	RRP8-BGKcLV46-84_Aligned.sortedByCoord.out.bam		ENCORE2	32439
RRP8-BGKcLV46-84_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	3402					GRCh38	V40	RRP8-BGKcLV46-84_Aligned.sortedByCoord.out.bam		ENCORE2	32489
RRP8-BGKcLV46-84_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3402					GRCh38	V40	RRP8-BGKcLV46-84_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,RRP8-BGKcLV46-84_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32539