SUB1 RNA-Seq in K562

General Information


RBP	SUB1
Cell_Line	K562
Method	shRNA
Exp_Name	SUB1-BGKLV13-K562
ENCODE_series_ID	ENCSR041FSP
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR047AJA
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	SUB1_BGKLV13_41
Rep2	SUB1_BGKLV13_42
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	92.7
Rep2_qPCR	93.2
Rep1_WB	92.3
Rep2_WB	95.2
Antibody Cat#	A301-161A
Antibody Lot#	A301-161A
Antibody DCC ID	ENCAB835QRD
Status	Released
Project	ENCODE3
ID	372

Experiment Information (Status: Released)

	BGKLV13-41	BGKLV13-42
idx	176	177
TRCN#_or_BGC#	TRCN0000014970	TRCN0000014970
shRNA_or_gRNA_sequence	GTACGTTAGTGTTCGCGATTT	GTACGTTAGTGTTCGCGATTT
PAM
Name	SUB1	SUB1
Sample_ID	BGKLV13-41	BGKLV13-42
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	SUB1	SUB1
qPCR_result	92.7	93.2
Ave_qPCR	93.0
RT-qPCR_primer-F	tcgcgattttaaaggcaaag
RT-qPCR_primer-R	ctggctccattgttctggat
protein_conc	2128	1900
WB_result	92.3	95.2
Ave_WB	93.7
WB_DONE_date	6/10/2015
MW	14kDa
IP	1	1
antibody_Cat#	A301-161A	A301-161A
Antibody DCC ID	ENCAB835QRD	ENCAB835QRD
submitted_to_DCC_date	8/6/2015
Rep1_TPM	45.2149623	0
Rep2_TPM	32.8932358	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	195	196

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SUB1	Product_ID: A301-161A Lot_ID: 1 Source: Bethyl Labs Target Name: SUB1-human

Experiment Status

	BGKLV13-41	BGKLV13-42
Sample_ID	BGKLV13-41	BGKLV13-42
Sample Name	SUB1_BGKLV13_41	SUB1_BGKLV13_42
Sample Name	SUB1_BGKLV13_41	SUB1_BGKLV13_42
RBP	SUB1	SUB1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	482	483

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-41	BGKLV13-42
Sample #
Sample Name	SUB1-BGKLV13-41	SUB1-BGKLV13-42
Sample_Name_Alias	SUB1_BGKLV13_41	SUB1_BGKLV13_42
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D4.png	DNA_Library_LV13-14/set1/E4.png
RIN	9.6	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/G12.png	RNA_Library_LV12/set1/H12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-41	BGKLV13-42
RBP	SUB1	SUB1
Batch_ID	BGKLV13	BGKLV13
WB_result	92.300	95.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2146	2147

Sequencing Information

	BGKLV13-41	BGKLV13-42
Sample_ID	BGKLV13-41	BGKLV13-42
Sample Name	SUB1_BGKLV13_41	SUB1_BGKLV13_42
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	45,130,000	51,230,000
total_aligned_reads	42,121,556	47,014,394
unique_aligned_reads	38,636,850	43,365,414
percent_uniqueAligned	0.85612	0.84648
correlation_replicates	0.996831	0.996831
spikein_reads	153,118	376,084
percent_spikeins	0.00339	0.00734
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	788	789

Data Submission Information

	BGKLV13-41	BGKLV13-41
ENCODE_alias	brenton-graveley:SUB1_BGKLV13	brenton-graveley:SUB1-BGKLV13-K562
ENCODE_accession	ENCSR047AJA	ENCSR041FSP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-41	BGKLV13-41
Sample Name	SUB1_BGKLV13_41	SUB1_BGKLV13_41
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2790	6989

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
SUB1_BGKLV13_41_TTAGGC_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	788	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13410
SUB1_BGKLV13_41_TTAGGC_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	788	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13462
SUB1_BGKLV13_41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41_TTAGGC_L004_R1_001.fastq.gz,SUB1_BGKLV13_41_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	13514
SUB1_BGKLV13_41_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41/Aligned.sortedByCoord.out.bam		ENCORE2	13566
SUB1_BGKLV13_41_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41/Aligned.sortedByCoord.out.bam		ENCORE2	13618
SUB1_BGKLV13_41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41/Aligned.sortedByCoord.out.bam		ENCORE2	13670
SUB1_BGKLV13_41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41/Aligned.sortedByCoord.out.bam		ENCORE2	13722
SUB1_BGKLV13_41_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	788					GRCh38	V40	SUB1_BGKLV13_41_TTAGGC_L004_R1_001.fastq.gz,SUB1_BGKLV13_41_TTAGGC_L004_R2_001.fastq.gz		ENCORE2	13774
SUB1_BGKLV13_42_TGACCA_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	789	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13411
SUB1_BGKLV13_42_TGACCA_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	789	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13463
SUB1_BGKLV13_42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42_TGACCA_L004_R1_001.fastq.gz,SUB1_BGKLV13_42_TGACCA_L004_R2_001.fastq.gz		ENCORE2	13515
SUB1_BGKLV13_42_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42/Aligned.sortedByCoord.out.bam		ENCORE2	13567
SUB1_BGKLV13_42_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42/Aligned.sortedByCoord.out.bam		ENCORE2	13619
SUB1_BGKLV13_42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42/Aligned.sortedByCoord.out.bam		ENCORE2	13671
SUB1_BGKLV13_42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42/Aligned.sortedByCoord.out.bam		ENCORE2	13723
SUB1_BGKLV13_42_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	789					GRCh38	V40	SUB1_BGKLV13_42_TGACCA_L004_R1_001.fastq.gz,SUB1_BGKLV13_42_TGACCA_L004_R2_001.fastq.gz		ENCORE2	13775