LARP4 RNA-Seq in K562

General Information


RBP	LARP4
Cell_Line	K562
Method	shRNA
Exp_Name	LARP4-BGKLV28-K562
ENCODE_series_ID	ENCSR274YYU
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR866XLI
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	LARP4_BGKLV28-25
Rep2	LARP4_BGKLV28-26
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	76.5
Rep2_qPCR	75.7
Rep1_WB	75.2
Rep2_WB	66.2
Antibody Cat#	A303-900A
Antibody Lot#	A303-900A
Antibody DCC ID	ENCAB580XQQ
Status	Released
Project	ENCODE3
ID	650

Experiment Information (Status: Released)

	BGKLV28-25	BGKLV28-26
idx	494	495
TRCN#_or_BGC#	TRCN0000161048	TRCN0000161048
shRNA_or_gRNA_sequence	GCTTTAATTCGCCAGGATCTT	GCTTTAATTCGCCAGGATCTT
PAM
Name	LARP4_48	LARP4_48
Sample_ID	BGKLV28-25	BGKLV28-26
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	LARP4	LARP4
qPCR_result	76.5	75.7
Ave_qPCR	76.1
RT-qPCR_primer-F	gggtgagaaagtgagaccaagt
RT-qPCR_primer-R	ggggcagttttcacttttga
protein_conc	2688	2522
WB_result	75.2	66.2
Ave_WB	70.7
WB_DONE_date	7/15/2015
MW	81kd
IP	1	1
antibody_Cat#	A303-900A	A303-900A
Antibody DCC ID	ENCAB580XQQ	ENCAB580XQQ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	9.52989713	0
Rep2_TPM	6.46078204	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	569	570

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARP4	Product_ID: A303-900A Lot_ID: 1 Source: Bethyl Labs Target Name: LARP4-human

Experiment Status

	BGKLV28-25	BGKLV28-26
Sample_ID	BGKLV28-25	BGKLV28-26
Sample Name	LARP4_BGKLV28-25	LARP4_BGKLV28-26
Sample Name	LARP4_BGKLV28-25	LARP4_BGKLV28-26
RBP	LARP4	LARP4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	984	985

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-25	BGKLV28-26
Sample #
Sample Name	LARP4-BGKLV28-25	LARP4-BGKLV28-26
Sample_Name_Alias	LARP4_BGKLV28-25	LARP4_BGKLV28-26
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G1.png	DNA_Library_LV28-29-30/set1/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/C7.png	RNA_Library_LV26-27-28-29/set1/D7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-25	BGKLV28-26
RBP	LARP4	LARP4
Batch_ID	BGKLV28	BGKLV28
WB_result	75.200	66.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2676	2677

Sequencing Information

	BGKLV28-25	BGKLV28-26
Sample_ID	BGKLV28-25	BGKLV28-26
Sample Name	LARP4_BGKLV28-25	LARP4_BGKLV28-26
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	84,731,920	111,876,538
total_aligned_reads	70,009,104	91,620,814
unique_aligned_reads	63,926,880	83,372,154
percent_uniqueAligned	0.75446	0.74522
correlation_replicates	0.994661	0.990000
spikein_reads	211,778	243,032
percent_spikeins	0.00250	0.00217
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1318	1319

Data Submission Information

	BGKLV28-25	BGKLV28-25
ENCODE_alias	brenton-graveley:LARP4_BGKLV28	brenton-graveley:LARP4-BGKLV28-K562
ENCODE_accession	ENCSR866XLI	ENCSR274YYU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-25	BGKLV28-25
Sample Name	LARP4_BGKLV28-25	LARP4_BGKLV28-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3041	6796

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
LARP4_BGKLV28-25_CAGATC_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1318	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20162
LARP4_BGKLV28-25_CAGATC_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1318	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20194
LARP4_BGKLV28-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25_CAGATC_L001_001.R1.fastq.gz,LARP4_BGKLV28-25_CAGATC_L001_001.R2.fastq.gz		ENCORE2	20226
LARP4_BGKLV28-25_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	20258
LARP4_BGKLV28-25_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	20290
LARP4_BGKLV28-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	20322
LARP4_BGKLV28-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	20354
LARP4_BGKLV28-25_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1318					GRCh38	V40	LARP4_BGKLV28-25_CAGATC_L001_001.R1.fastq.gz,LARP4_BGKLV28-25_CAGATC_L001_001.R2.fastq.gz		ENCORE2	20386
LARP4_BGKLV28-26_ACTTGA_L001_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1319	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20163
LARP4_BGKLV28-26_ACTTGA_L001_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1319	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20195
LARP4_BGKLV28-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26_ACTTGA_L001_001.R1.fastq.gz,LARP4_BGKLV28-26_ACTTGA_L001_001.R2.fastq.gz		ENCORE2	20227
LARP4_BGKLV28-26_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	20259
LARP4_BGKLV28-26_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	20291
LARP4_BGKLV28-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	20323
LARP4_BGKLV28-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	20355
LARP4_BGKLV28-26_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1319					GRCh38	V40	LARP4_BGKLV28-26_ACTTGA_L001_001.R1.fastq.gz,LARP4_BGKLV28-26_ACTTGA_L001_001.R2.fastq.gz		ENCORE2	20387