RBBP5 RNA-Seq in K562

General Information


RBP	RBBP5
Cell_Line	K562
Method	CRISPR
Exp_Name	RBBP5-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBBP5-BGKcLV42-75
Rep2	RBBP5-BGKcLV42-76
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	65.3
Rep2_qPCR	68.6
Rep1_WB	93.4
Rep2_WB	91.9
Antibody Cat#	13171S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1556

Experiment Information (Status: Submitting)

	BGKcLV42-75	BGKcLV42-76
idx	0	0
TRCN#_or_BGC#	BGC#0001178	BGC#0001178
shRNA_or_gRNA_sequence	CAAACATGTTGTTCTGCCGG	CAAACATGTTGTTCTGCCGG
PAM	TGG	TGG
Name	RBBP5_92	RBBP5_92
Sample_ID	BGKcLV42-75	BGKcLV42-76
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	RBBP5	RBBP5
qPCR_result	65.3	68.6
Ave_qPCR	66.9
RT-qPCR_primer-F	ctgttcgacccatcatagca
RT-qPCR_primer-R	tgcaaatgcactccagtttt
protein_conc	2109	2127
WB_result	93.4	91.9
Ave_WB	92.7
WB_DONE_date	4/30/24
MW	70kd
IP
antibody_Cat#	13171S	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	5841	5842

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBBP5	Product_ID: 13171S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RBBP5-human

Experiment Status

	BGKcLV42-75	BGKcLV42-76
Sample_ID	BGKcLV42-75	BGKcLV42-76
Sample Name
Sample Name	RBBP5-BGKcLV42-75	RBBP5-BGKcLV42-76
RBP	RBBP5	RBBP5
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13106	13107

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-75	BGKcLV42-76
Sample #	63	64
Sample Name	RBBP5-BGKcLV42-75	RBBP5-BGKcLV42-76
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	299	303
Peak_Molarity	93.50	67.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/G8.png	DNA_Library_set73/set1/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/G8.png	RNA_Library_set73/set1/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-75	BGKcLV42-76
RBP	RBBP5	RBBP5
Batch_ID	BGKcLV42	BGKcLV42
WB_result	93.400	91.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4332	4333

Sequencing Information

	BGKcLV42-75	BGKcLV42-76
Sample_ID	BGKcLV42-75	BGKcLV42-76
Sample Name	RBBP5-BGKcLV42-75	RBBP5-BGKcLV42-76
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	52,568,450	50,652,932
total_aligned_reads	49,410,958	47,184,834
unique_aligned_reads	45,598,623	43,538,465
percent_uniqueAligned	0.86741	0.85954
correlation_replicates	0.997929	0.997929
spikein_reads	6,246	7,516
percent_spikeins	0.00012	0.00015
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3199	3200

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
RBBP5-BGKcLV42-75_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3199	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30402
RBBP5-BGKcLV42-75_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3199	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30492
RBBP5-BGKcLV42-75_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBBP5-BGKcLV42-75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31334
RBBP5-BGKcLV42-75_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_Aligned.sortedByCoord.out.bam		ENCORE2	31424
RBBP5-BGKcLV42-75_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_Aligned.sortedByCoord.out.bam		ENCORE2	31514
RBBP5-BGKcLV42-75_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_Aligned.sortedByCoord.out.bam		ENCORE2	31604
RBBP5-BGKcLV42-75_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_Aligned.sortedByCoord.out.bam		ENCORE2	31694
RBBP5-BGKcLV42-75_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3199					GRCh38	V40	RBBP5-BGKcLV42-75_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBBP5-BGKcLV42-75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31784
RBBP5-BGKcLV42-76_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3200	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30403
RBBP5-BGKcLV42-76_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3200	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30493
RBBP5-BGKcLV42-76_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBBP5-BGKcLV42-76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31335
RBBP5-BGKcLV42-76_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_Aligned.sortedByCoord.out.bam		ENCORE2	31425
RBBP5-BGKcLV42-76_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_Aligned.sortedByCoord.out.bam		ENCORE2	31515
RBBP5-BGKcLV42-76_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_Aligned.sortedByCoord.out.bam		ENCORE2	31605
RBBP5-BGKcLV42-76_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_Aligned.sortedByCoord.out.bam		ENCORE2	31695
RBBP5-BGKcLV42-76_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3200					GRCh38	V40	RBBP5-BGKcLV42-76_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBBP5-BGKcLV42-76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31785