TARDBP RNA-Seq in K562

General Information


RBP	TARDBP
Cell_Line	K562
Method	shRNA
Exp_Name	TARDBP-BGKLV11-K562
ENCODE_series_ID	ENCSR630HSM
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR134JRE
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	TARDBP-LV11-57
Rep2	TARDBP-LV11-58
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	64.3
Rep2_qPCR	70.2
Rep1_WB	69.3
Rep2_WB	71.7
Antibody Cat#	A303-223A
Antibody Lot#	A303-223A
Antibody DCC ID	ENCAB057RGG
Status	Released
Project	ENCODE3
ID	326

Experiment Information (Status: Released)

	BGKLV11-57	BGKLV11-57	BGKLV11-58	BGKLV11-58
idx	126	0	127	0
TRCN#_or_BGC#	TRCN0000016038	TRCN0000016038	TRCN0000016038	TRCN0000016038
shRNA_or_gRNA_sequence	GCTCTAATTCTGGTGCAGCAA	GCTCTAATTCTGGTGCAGCAA	GCTCTAATTCTGGTGCAGCAA	GCTCTAATTCTGGTGCAGCAA
PAM
Name	TARDBP	TARDBP	TARDBP	TARDBP
Sample_ID	BGKLV11-57	BGKLV11-57	BGKLV11-58	BGKLV11-58
transduction_Date	5/1/2014	5/1/2014	5/1/2014	5/1/2014
days
RBP_name	TARDBP	TARDBP	TARDBP	TARDBP
qPCR_result	64.3	64.3	70.2	70.2
Ave_qPCR	67.3	67.3
RT-qPCR_primer-F	GATGGACGATGGTGTGACTG	GATGGACGATGGTGTGACTG
RT-qPCR_primer-R	AGAACTCCCGCAGCTCATC	AGAACTCCCGCAGCTCATC
protein_conc	1822	1822	1918	1918
WB_result	69.3	96.7	71.7	96.7
Ave_WB	70.5	96.7
WB_DONE_date	6/24/2015	11/27/18
MW	45kDa	45kDa
IP	1		1
antibody_Cat#	A303-223A	711051	A303-223A	Lot# SI259917
Antibody DCC ID	ENCAB057RGG	ENCAB349KOV	ENCAB057RGG
submitted_to_DCC_date	8/6/2015	3/11/2019
Rep1_TPM	148.339946	148.339946	0	0
Rep2_TPM	111.944725	111.944725	0	0
Action	Ready	Ready	Ready	Ready
Library_start_date	5/19/2014	5/19/2014	5/19/2014	5/19/2014
repeat_library
Note
ID	139	141	140	142

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TARDBP	Product_ID: 711051 Lot_ID: SI259917 Source: Thermo Fisher Target Name: TARDBP-human
TARDBP	Product_ID: A303-223A Lot_ID: 1 Source: Bethyl Labs Target Name: TARDBP-human

Experiment Status

	BGKLV11-57	BGKLV11-58
Sample_ID	BGKLV11-57	BGKLV11-58
Sample Name	TARDBP-LV11-57	TARDBP-LV11-58
Sample Name	TARDBP-LV11-57	TARDBP-LV11-58
RBP	TARDBP	TARDBP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	366	367

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-57	BGKLV11-58
Sample #
Sample Name	TARDBP-BGKLV11-57	TARDBP-BGKLV11-58
Sample_Name_Alias	TARDBP-LV11-57	TARDBP-LV11-58
Index Well Position	S20	S21
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/set3/F2.png	DNA_Library_LV11/set3/G2.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV11/set1/C6.png	RNA_Library_LV11/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-57	BGKLV11-58
RBP	TARDBP	TARDBP
Batch_ID	BGKLV11	BGKLV11
WB_result	69.300	71.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1988	1989

Sequencing Information

	BGKLV11-57	BGKLV11-58
Sample_ID	BGKLV11-57	BGKLV11-58
Sample Name	TARDBP-LV11-57	TARDBP-LV11-58
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	55,400,000	57,280,000
total_aligned_reads	44,484,398	47,979,630
unique_aligned_reads	40,426,488	43,710,494
percent_uniqueAligned	0.72972	0.76310
correlation_replicates	0.994795	0.994795
spikein_reads	218,630	267,772
percent_spikeins	0.00395	0.00467
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	688	689

Data Submission Information

	BGKLV11-57	BGKLV11-57
ENCODE_alias	brenton-graveley:TARDBP-LV11	brenton-graveley:TARDBP-BGKLV11-K562
ENCODE_accession	ENCSR134JRE	ENCSR630HSM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-57	BGKLV11-57
Sample Name	TARDBP-LV11-57	TARDBP-LV11-57
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2732	7002

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
TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	688	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12409
TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	688	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12457
TARDBP-LV11-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	688					GRCh38	V40	TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gz,TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	12505
TARDBP-LV11-57_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	688					GRCh38	V40	TARDBP-LV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	12553
TARDBP-LV11-57_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	688					GRCh38	V40	TARDBP-LV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	12601
TARDBP-LV11-57_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	688					GRCh38	V40	TARDBP-LV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	12649
TARDBP-LV11-57_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	688					GRCh38	V40	TARDBP-LV11-57/Aligned.sortedByCoord.out.bam		ENCORE2	12697
TARDBP-LV11-57_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	688					GRCh38	V40	TARDBP-LV11-57_GTGGCC_L008_R1_001.fastq.gz,TARDBP-LV11-57_GTGGCC_L008_R2_001.fastq.gz		ENCORE2	12745
TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	689	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12410
TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	689	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12458
TARDBP-LV11-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	689					GRCh38	V40	TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gz,TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	12506
TARDBP-LV11-58_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	689					GRCh38	V40	TARDBP-LV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	12554
TARDBP-LV11-58_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	689					GRCh38	V40	TARDBP-LV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	12602
TARDBP-LV11-58_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	689					GRCh38	V40	TARDBP-LV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	12650
TARDBP-LV11-58_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	689					GRCh38	V40	TARDBP-LV11-58/Aligned.sortedByCoord.out.bam		ENCORE2	12698
TARDBP-LV11-58_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	689					GRCh38	V40	TARDBP-LV11-58_GTTTCG_L008_R1_001.fastq.gz,TARDBP-LV11-58_GTTTCG_L008_R2_001.fastq.gz		ENCORE2	12746