MATR3 RNA-Seq in K562

General Information


RBP	MATR3
Cell_Line	K562
Method	shRNA
Exp_Name	MATR3-BGKLV11-K562
ENCODE_series_ID	ENCSR634RWY
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR792XFP
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	MATR3-06-LV11-27
Rep2	MATR3-06-LV11-28
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	70.6
Rep2_qPCR	71.8
Rep1_WB	no clear band
Rep2_WB	no clear band
Antibody Cat#	ab151714
Antibody Lot#	GR108745-9
Antibody DCC ID	ENCAB789SRM
Status	Released
Project	ENCODE3
ID	315

Experiment Information (Status: Released)

	BGKLV11-27	BGKLV11-28
idx	96	97
TRCN#_or_BGC#	TRCN0000074906	TRCN0000074906
shRNA_or_gRNA_sequence	GAGACCGATCTTGCTAATTTA	GAGACCGATCTTGCTAATTTA
PAM
Name	MATR3_06	MATR3_06
Sample_ID	BGKLV11-27	BGKLV11-28
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	MATR3	MATR3
qPCR_result	70.6	71.8
Ave_qPCR	71.2
RT-qPCR_primer-F	TGGTTCTGAGGATTCCAAACA
RT-qPCR_primer-R	TTGGAGATTCTTTGCCATCTG
protein_conc	1886	2395
WB_result	no clear band	no clear band
Ave_WB
WB_DONE_date	2/23/2016	wes
MW	95kDa
IP
antibody_Cat#	ab151714	ab151714
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	63.25576	0
Rep2_TPM	48.4841377	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	109	110

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV11-27	BGKLV11-28
Sample_ID	BGKLV11-27	BGKLV11-28
Sample Name	MATR3-06-LV11-27	MATR3-06-LV11-28
Sample Name	MATR3-06-LV11-27	MATR3-06-LV11-28
RBP	MATR3	MATR3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	342	343

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-27	BGKLV11-28
Sample #
Sample Name	MATR3-BGKLV11-27	MATR3-BGKLV11-28
Sample_Name_Alias	MATR3-06-LV11-27	MATR3-06-LV11-28
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set2/G1.png	DNA_Library_LV11/set2/H1.png
RIN	9.0	9.0
libSample_RNA_Well	RNA_Library_LV11/set1/E3.png	RNA_Library_LV11/set1/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-27	BGKLV11-28
RBP	MATR3	MATR3
Batch_ID	BGKLV11	BGKLV11
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1964	1965

Sequencing Information

	BGKLV11-27	BGKLV11-28
Sample_ID	BGKLV11-27	BGKLV11-28
Sample Name	MATR3-06-LV11-27	MATR3-06-LV11-28
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	69,630,000	60,710,000
total_aligned_reads	55,585,282	49,029,070
unique_aligned_reads	50,623,598	44,504,218
percent_uniqueAligned	0.72704	0.73306
correlation_replicates	0.998245	0.998245
spikein_reads	518,898	418,992
percent_spikeins	0.00745	0.00690
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	664	665

Data Submission Information

	BGKLV11-27	BGKLV11-27
ENCODE_alias	brenton-graveley:MATR3-06-LV11	brenton-graveley:MATR3-BGKLV11-K562
ENCODE_accession	ENCSR792XFP	ENCSR634RWY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-27	BGKLV11-27
Sample Name	MATR3-06-LV11-27	MATR3-06-LV11-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2720	6808

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
MATR3-06-LV11-27_CGTACG_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	664	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12385
MATR3-06-LV11-27_CGTACG_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	664	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12433
MATR3-06-LV11-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27_CGTACG_L004_R1_001.fastq.gz,MATR3-06-LV11-27_CGTACG_L004_R2_001.fastq.gz		ENCORE2	12481
MATR3-06-LV11-27_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27/Aligned.sortedByCoord.out.bam		ENCORE2	12529
MATR3-06-LV11-27_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27/Aligned.sortedByCoord.out.bam		ENCORE2	12577
MATR3-06-LV11-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27/Aligned.sortedByCoord.out.bam		ENCORE2	12625
MATR3-06-LV11-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27/Aligned.sortedByCoord.out.bam		ENCORE2	12673
MATR3-06-LV11-27_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	664					GRCh38	V40	MATR3-06-LV11-27_CGTACG_L004_R1_001.fastq.gz,MATR3-06-LV11-27_CGTACG_L004_R2_001.fastq.gz		ENCORE2	12721
MATR3-06-LV11-28_GAGTGG_L004_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	665	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12386
MATR3-06-LV11-28_GAGTGG_L004_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	665	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12434
MATR3-06-LV11-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28_GAGTGG_L004_R1_001.fastq.gz,MATR3-06-LV11-28_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	12482
MATR3-06-LV11-28_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28/Aligned.sortedByCoord.out.bam		ENCORE2	12530
MATR3-06-LV11-28_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28/Aligned.sortedByCoord.out.bam		ENCORE2	12578
MATR3-06-LV11-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28/Aligned.sortedByCoord.out.bam		ENCORE2	12626
MATR3-06-LV11-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28/Aligned.sortedByCoord.out.bam		ENCORE2	12674
MATR3-06-LV11-28_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	665					GRCh38	V40	MATR3-06-LV11-28_GAGTGG_L004_R1_001.fastq.gz,MATR3-06-LV11-28_GAGTGG_L004_R2_001.fastq.gz		ENCORE2	12722