LARP1 RNA-Seq in K562

General Information


RBP	LARP1
Cell_Line	K562
Method	CRISPR
Exp_Name	LARP1-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	LARP1-BGKcLV42-47
Rep2	LARP1-BGKcLV42-48
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	14.2
Rep2_qPCR	23.6
Rep1_WB	84.5
Rep2_WB	86.8
Antibody Cat#	70180S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1545

Experiment Information (Status: Submitting)

	BGKcLV42-47	BGKcLV42-48
idx	0	0
TRCN#_or_BGC#	BGC#0001151	BGC#0001151
shRNA_or_gRNA_sequence	GTCTGCCACCTACGTGCCCG	GTCTGCCACCTACGTGCCCG
PAM	TGG	TGG
Name	LARP1_92	LARP1_92
Sample_ID	BGKcLV42-47	BGKcLV42-48
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	LARP1	LARP1
qPCR_result	14.2	23.6
Ave_qPCR	18.9
RT-qPCR_primer-F	AACTGCAAGAATACCTCGGC
RT-qPCR_primer-R	CACTGAGTGTCGCTTGTGGT
protein_conc	2524	3333
WB_result	84.5	86.8
Ave_WB	85.6
WB_DONE_date	5/7/2002
MW	150kd
IP
antibody_Cat#	70180S	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	5809	5810

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARP1	Product_ID: 70180S Lot_ID: 1 Source: Cell Signaling Technology Target Name: LARP1-human

Experiment Status

	BGKcLV42-47	BGKcLV42-48
Sample_ID	BGKcLV42-47	BGKcLV42-48
Sample Name
Sample Name	LARP1-BGKcLV42-47	LARP1-BGKcLV42-48
RBP	LARP1	LARP1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13084	13085

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-47	BGKcLV42-48
Sample #	41	42
Sample Name	LARP1-BGKcLV42-47	LARP1-BGKcLV42-48
Sample_Name_Alias
Index Well Position	A06	B06
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	300	298
Peak_Molarity	113.00	90.00
libSampleQC_DNA_Well	DNA_Library_set73/set1/A6.png	DNA_Library_set73/set1/B6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set73/set1/A6.png	RNA_Library_set73/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-47	BGKcLV42-48
RBP	LARP1	LARP1
Batch_ID	BGKcLV42	BGKcLV42
WB_result	84.500	86.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4310	4311

Sequencing Information

	BGKcLV42-47	BGKcLV42-48
Sample_ID	BGKcLV42-47	BGKcLV42-48
Sample Name	LARP1-BGKcLV42-47	LARP1-BGKcLV42-48
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	44,614,746	50,468,966
total_aligned_reads	42,506,688	41,938,656
unique_aligned_reads	39,465,284	38,612,192
percent_uniqueAligned	0.88458	0.76507
correlation_replicates	0.995153	0.995153
spikein_reads	6,000	2,004
percent_spikeins	0.00013	0.00004
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3177	3178

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
LARP1-BGKcLV42-47_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3177	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	30378
LARP1-BGKcLV42-47_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3177	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	30468
LARP1-BGKcLV42-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3177					GRCh38	V40	LARP1-BGKcLV42-47_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGKcLV42-47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31310
LARP1-BGKcLV42-47_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	3177					GRCh38	V40	LARP1-BGKcLV42-47_Aligned.sortedByCoord.out.bam		ENCORE2	31400
LARP1-BGKcLV42-47_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	3177					GRCh38	V40	LARP1-BGKcLV42-47_Aligned.sortedByCoord.out.bam		ENCORE2	31490
LARP1-BGKcLV42-47_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	3177					GRCh38	V40	LARP1-BGKcLV42-47_Aligned.sortedByCoord.out.bam		ENCORE2	31580
LARP1-BGKcLV42-47_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	3177					GRCh38	V40	LARP1-BGKcLV42-47_Aligned.sortedByCoord.out.bam		ENCORE2	31670
LARP1-BGKcLV42-47_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3177					GRCh38	V40	LARP1-BGKcLV42-47_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGKcLV42-47_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31760
LARP1-BGKcLV42-48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3178	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	30379
LARP1-BGKcLV42-48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3178	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	30469
LARP1-BGKcLV42-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3178					GRCh38	V40	LARP1-BGKcLV42-48_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGKcLV42-48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31311
LARP1-BGKcLV42-48_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	3178					GRCh38	V40	LARP1-BGKcLV42-48_Aligned.sortedByCoord.out.bam		ENCORE2	31401
LARP1-BGKcLV42-48_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	3178					GRCh38	V40	LARP1-BGKcLV42-48_Aligned.sortedByCoord.out.bam		ENCORE2	31491
LARP1-BGKcLV42-48_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	3178					GRCh38	V40	LARP1-BGKcLV42-48_Aligned.sortedByCoord.out.bam		ENCORE2	31581
LARP1-BGKcLV42-48_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	3178					GRCh38	V40	LARP1-BGKcLV42-48_Aligned.sortedByCoord.out.bam		ENCORE2	31671
LARP1-BGKcLV42-48_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3178					GRCh38	V40	LARP1-BGKcLV42-48_L001_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGKcLV42-48_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31761