LARP1 RNA-Seq in HepG2

General Information


RBP	LARP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	LARP1-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	LARP1-BGHcLV43-27
Rep2	LARP1-BGHcLV43-28
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	37.0
Rep2_qPCR	29.7
Rep1_WB	88.1
Rep2_WB	88.0
Antibody Cat#	70180S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1579

Experiment Information (Status: Submitting)

	BGHcLV43-27	BGHcLV43-28
idx	1395	1396
TRCN#_or_BGC#	BGC#0001153	BGC#0001153
shRNA_or_gRNA_sequence	GTCTGCCACCTACGTGCCCG	GTCTGCCACCTACGTGCCCG
PAM	TGG	TGG
Name	LARP1_92	LARP1_92
Sample_ID	BGHcLV43-27	BGHcLV43-28
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	LARP1	LARP1
qPCR_result	37.0	29.7
Ave_qPCR	33.4
RT-qPCR_primer-F	AACTGCAAGAATACCTCGGC
RT-qPCR_primer-R	CACTGAGTGTCGCTTGTGGT
protein_conc	3469	3556
WB_result	88.1	88.0
Ave_WB	88.1
WB_DONE_date	6/21/24
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	9648	9649

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

	BGHcLV43-27	BGHcLV43-28
Sample_ID	BGHcLV43-27	BGHcLV43-28
Sample Name
Sample Name	LARP1-BGHcLV43-27	LARP1-BGHcLV43-28
RBP	LARP1	LARP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13248	13249

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-27	BGHcLV43-28
Sample #	21	22
Sample Name	LARP1-BGHcLV43-27	LARP1-BGHcLV43-28
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	293	291
Peak_Molarity	87.50	98.70
libSampleQC_DNA_Well	DNA_Library_set74/set1/E3.png	DNA_Library_set74/set1/F3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/A9.png	RNA_Library_set74/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-27	BGHcLV43-28
RBP	LARP1	LARP1
Batch_ID	BGHcLV43	BGHcLV43
WB_result	88.100	88.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4380	4381

Sequencing Information

	BGHcLV43-27	BGHcLV43-28
Sample_ID	BGHcLV43-27	BGHcLV43-28
Sample Name	LARP1-BGHcLV43-27	LARP1-BGHcLV43-28
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	44,328,623	49,768,854
total_aligned_reads	39,113,613	45,505,707
unique_aligned_reads	36,891,692	42,909,935
percent_uniqueAligned	0.83223	0.86218
correlation_replicates	0.998171	0.998171
spikein_reads	22,476	31,756
percent_spikeins	0.00051	0.00064
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3247	3248

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-BGHcLV43-27_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3247	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30538
LARP1-BGHcLV43-27_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3247	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30590
LARP1-BGHcLV43-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGHcLV43-27_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30642
LARP1-BGHcLV43-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_Aligned.sortedByCoord.out.bam		ENCORE2	30694
LARP1-BGHcLV43-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_Aligned.sortedByCoord.out.bam		ENCORE2	30746
LARP1-BGHcLV43-27_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_Aligned.sortedByCoord.out.bam		ENCORE2	30798
LARP1-BGHcLV43-27_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_Aligned.sortedByCoord.out.bam		ENCORE2	30850
LARP1-BGHcLV43-27_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3247					GRCh38	V40	LARP1-BGHcLV43-27_S111_L003_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGHcLV43-27_S111_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30902
LARP1-BGHcLV43-28_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3248	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30539
LARP1-BGHcLV43-28_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3248	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30591
LARP1-BGHcLV43-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGHcLV43-28_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30643
LARP1-BGHcLV43-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_Aligned.sortedByCoord.out.bam		ENCORE2	30695
LARP1-BGHcLV43-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_Aligned.sortedByCoord.out.bam		ENCORE2	30747
LARP1-BGHcLV43-28_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_Aligned.sortedByCoord.out.bam		ENCORE2	30799
LARP1-BGHcLV43-28_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_Aligned.sortedByCoord.out.bam		ENCORE2	30851
LARP1-BGHcLV43-28_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3248					GRCh38	V40	LARP1-BGHcLV43-28_S112_L003_R1_001.filtered.trimmed.paired.fastq.gz,LARP1-BGHcLV43-28_S112_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30903