RACK1 RNA-Seq in K562

General Information


RBP	RACK1
Cell_Line	K562
Method	CRISPR
Exp_Name	RACK1-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RACK1-BGKcLV44-49
Rep2	RACK1-BGKcLV44-50
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	85.9
Rep2_qPCR	82.3
Rep1_WB	61.0
Rep2_WB	65.9
Antibody Cat#	5432S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1605

Experiment Information (Status: Submitting)

	BGKcLV44-49	BGKcLV44-50
idx	0	0
TRCN#_or_BGC#	BGC#0001046	BGC#0001046
shRNA_or_gRNA_sequence	TTAGTCCGTACCTCGAGAGG	TTAGTCCGTACCTCGAGAGG
PAM	CGG	CGG
Name	RACK1_96	RACK1_96
Sample_ID	BGKcLV44-49	BGKcLV44-50
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	RACK1	RACK1
qPCR_result	85.9	82.3
Ave_qPCR	84.1
RT-qPCR_primer-F	taaccgctactggctgtgtg
RT-qPCR_primer-R	gccttgctgctggtactgat
protein_conc	4909	4403
WB_result	61.0	65.9
Ave_WB	63.4
WB_DONE_date	8/13/24
MW	35kd
IP
antibody_Cat#	5432S	lot # 2
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	5928	5929

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RACK1	Product_ID: 5432S Lot_ID: 2 Source: Cell Signaling Technology Target Name: RACK1-human

Experiment Status

	BGKcLV44-49	BGKcLV44-50
Sample_ID	BGKcLV44-49	BGKcLV44-50
Sample Name
Sample Name	RACK1-BGKcLV44-49	RACK1-BGKcLV44-50
RBP	RACK1	RACK1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13602	13603

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-49	BGKcLV44-50
Sample #	31	32
Sample Name	RACK1-BGKcLV44-49	RACK1-BGKcLV44-50
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	295	286
Peak_Molarity	67.70	65.70
libSampleQC_DNA_Well	DNA_Library_set75/set1/G9.png	DNA_Library_set75/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/G3.png	RNA_Library_set75/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-49	BGKcLV44-50
RBP	RACK1	RACK1
Batch_ID	BGKcLV44	BGKcLV44
WB_result	61.000	65.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4590	4591

Sequencing Information

	BGKcLV44-49	BGKcLV44-50
Sample_ID	BGKcLV44-49	BGKcLV44-50
Sample Name	RACK1-BGKcLV44-49	RACK1-BGKcLV44-50
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	50,614,709	58,720,587
total_aligned_reads	47,951,044	54,961,460
unique_aligned_reads	44,656,621	51,006,284
percent_uniqueAligned	0.88229	0.86863
correlation_replicates	0.996083	0.996083
spikein_reads	64,820	112,178
percent_spikeins	0.00128	0.00191
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3301	3302

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
RACK1-BGKcLV44-49_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3301	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30958
RACK1-BGKcLV44-49_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3301	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31000
RACK1-BGKcLV44-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGKcLV44-49_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31042
RACK1-BGKcLV44-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_Aligned.sortedByCoord.out.bam		ENCORE2	31084
RACK1-BGKcLV44-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_Aligned.sortedByCoord.out.bam		ENCORE2	31126
RACK1-BGKcLV44-49_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_Aligned.sortedByCoord.out.bam		ENCORE2	31168
RACK1-BGKcLV44-49_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_Aligned.sortedByCoord.out.bam		ENCORE2	31210
RACK1-BGKcLV44-49_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3301					GRCh38	V40	RACK1-BGKcLV44-49_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGKcLV44-49_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31252
RACK1-BGKcLV44-50_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3302	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30959
RACK1-BGKcLV44-50_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3302	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31001
RACK1-BGKcLV44-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGKcLV44-50_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31043
RACK1-BGKcLV44-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_Aligned.sortedByCoord.out.bam		ENCORE2	31085
RACK1-BGKcLV44-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_Aligned.sortedByCoord.out.bam		ENCORE2	31127
RACK1-BGKcLV44-50_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_Aligned.sortedByCoord.out.bam		ENCORE2	31169
RACK1-BGKcLV44-50_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_Aligned.sortedByCoord.out.bam		ENCORE2	31211
RACK1-BGKcLV44-50_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3302					GRCh38	V40	RACK1-BGKcLV44-50_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RACK1-BGKcLV44-50_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31253