LARP7 RNA-Seq in K562

General Information


RBP	LARP7
Cell_Line	K562
Method	shRNA
Exp_Name	LARP7-BGKLV21-K562
ENCODE_series_ID	ENCSR710HIK
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR770OWW
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	LARP7_BGKLV21_25_17571
Rep2	LARP7_BGKLV21_26_17572
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	87.5
Rep2_qPCR	89.8
Rep1_WB	77.1
Rep2_WB	72.3
Antibody Cat#	A303-723A
Antibody Lot#	A303-723A
Antibody DCC ID	ENCAB568DRS
Status	Released
Project	ENCODE3
ID	512

Experiment Information (Status: Released)

	BGKLV21-25	BGKLV21-26
idx	296	297
TRCN#_or_BGC#	TRCN0000122544	TRCN0000122544
shRNA_or_gRNA_sequence	CTTGAGCTGTTCTTGGGAGAT	CTTGAGCTGTTCTTGGGAGAT
PAM
Name	LARP7	LARP7
Sample_ID	BGKLV21-25	BGKLV21-26
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	LARP7	LARP7
qPCR_result	87.5	89.8
Ave_qPCR	88.6
RT-qPCR_primer-F	gctggaaactcgagatccttt
RT-qPCR_primer-R	ttttcccgaggctgattaag
protein_conc	3163	3191
WB_result	77.1	72.3
Ave_WB	74.7
WB_DONE_date	3/6/2015
MW	67kDa
IP	1	1
antibody_Cat#	A303-723A	A303-723A
Antibody DCC ID	ENCAB568DRS	ENCAB568DRS
submitted_to_DCC_date	4/2/2015
Rep1_TPM	33.5165496	0
Rep2_TPM	25.4006154	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	327	328

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LARP7	Product_ID: A303-723A Lot_ID: 1 Source: Bethyl Labs Target Name: LARP7-human

Experiment Status

	BGKLV21-25	BGKLV21-26
Sample_ID	BGKLV21-25	BGKLV21-26
Sample Name	LARP7_BGKLV21_25_17571	LARP7_BGKLV21_26_17572
Sample Name	LARP7_BGKLV21_25_17571	LARP7_BGKLV21_26_17572
RBP	LARP7	LARP7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	756	757

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-25	BGKLV21-26
Sample #
Sample Name	LARP7-BGKLV21-25	LARP7-BGKLV21-26
Sample_Name_Alias	LARP7_BGKLV21_25_17571	LARP7_BGKLV21_26_17572
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/G6.png	DNA_Library_LV21-24/set1/H6.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E9.png	RNA_Library_LV19-21-24/set1/F9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-25	BGKLV21-26
RBP	LARP7	LARP7
Batch_ID	BGKLV21	BGKLV21
WB_result	77.100	72.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2442	2443

Sequencing Information

	BGKLV21-25	BGKLV21-26
Sample_ID	BGKLV21-25	BGKLV21-26
Sample Name	LARP7_BGKLV21_25_17571	LARP7_BGKLV21_26_17572
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	49,340,000	41,630,000
total_aligned_reads	46,042,732	38,903,792
unique_aligned_reads	42,230,054	35,783,624
percent_uniqueAligned	0.85590	0.85956
correlation_replicates	0.994063	0.994063
spikein_reads	236,214	211,908
percent_spikeins	0.00479	0.00509
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1048	1049

Data Submission Information

	BGKLV21-25	BGKLV21-25
ENCODE_alias	brenton-graveley:LARP7_BGKLV21	brenton-graveley:LARP7-BGKLV21-K562
ENCODE_accession	ENCSR770OWW	ENCSR710HIK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-25	BGKLV21-25
Sample Name	LARP7_BGKLV21_25_17571	LARP7_BGKLV21_25_17571
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2964	6798

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
LARP7_BGKLV21_25_17571_ATGTCA_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1048	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15936
LARP7_BGKLV21_25_17571_ATGTCA_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1048	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15980
LARP7_BGKLV21_25_17571_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571_ATGTCA_L002_R1_001.fastq.gz,LARP7_BGKLV21_25_17571_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	16024
LARP7_BGKLV21_25_17571_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571/Aligned.sortedByCoord.out.bam		ENCORE2	16068
LARP7_BGKLV21_25_17571_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571/Aligned.sortedByCoord.out.bam		ENCORE2	16112
LARP7_BGKLV21_25_17571_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571/Aligned.sortedByCoord.out.bam		ENCORE2	16156
LARP7_BGKLV21_25_17571_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571/Aligned.sortedByCoord.out.bam		ENCORE2	16200
LARP7_BGKLV21_25_17571_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1048					GRCh38	V40	LARP7_BGKLV21_25_17571_ATGTCA_L002_R1_001.fastq.gz,LARP7_BGKLV21_25_17571_ATGTCA_L002_R2_001.fastq.gz		ENCORE2	16244
LARP7_BGKLV21_26_17572_CCGTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1049	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15937
LARP7_BGKLV21_26_17572_CCGTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1049	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15981
LARP7_BGKLV21_26_17572_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572_CCGTCC_L002_R1_001.fastq.gz,LARP7_BGKLV21_26_17572_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	16025
LARP7_BGKLV21_26_17572_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572/Aligned.sortedByCoord.out.bam		ENCORE2	16069
LARP7_BGKLV21_26_17572_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572/Aligned.sortedByCoord.out.bam		ENCORE2	16113
LARP7_BGKLV21_26_17572_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572/Aligned.sortedByCoord.out.bam		ENCORE2	16157
LARP7_BGKLV21_26_17572_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572/Aligned.sortedByCoord.out.bam		ENCORE2	16201
LARP7_BGKLV21_26_17572_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1049					GRCh38	V40	LARP7_BGKLV21_26_17572_CCGTCC_L002_R1_001.fastq.gz,LARP7_BGKLV21_26_17572_CCGTCC_L002_R2_001.fastq.gz		ENCORE2	16245