TBRG4 RNA-Seq in K562

General Information


RBP	TBRG4
Cell_Line	K562
Method	shRNA
Exp_Name	TBRG4-BGKLV08-K562
ENCODE_series_ID	ENCSR645FAT
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR079IPT
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	TBRG4-LV08-59
Rep2	TBRG4-LV08-60
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	59.5
Rep2_qPCR	47.2
Rep1_WB	60.6
Rep2_WB	59.9
Antibody Cat#	A301-392A
Antibody Lot#	A301-392A
Antibody DCC ID	ENCAB890JXZ
Status	Released
Project	ENCODE3
ID	303

Experiment Information (Status: Released)

	BGKLV08-59	BGKLV08-60
idx	64	65
TRCN#_or_BGC#	TRCN0000154962	TRCN0000154962
shRNA_or_gRNA_sequence	GATGCCCACTTTCATCAACTT	GATGCCCACTTTCATCAACTT
PAM
Name	TBRG4	TBRG4
Sample_ID	BGKLV08-59	BGKLV08-60
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	TBRG4	TBRG4
qPCR_result	59.5	47.2
Ave_qPCR	53.4
RT-qPCR_primer-F	ATGGAGGTCAGCGGTGGT
RT-qPCR_primer-R	GACGAGCAGCTTCTCTCAGG
protein_conc	2845	2948
WB_result	60.6	59.9
Ave_WB	60.3
WB_DONE_date	6/24/2015
MW	71kDa
IP	1	1
antibody_Cat#	A301-392A	A301-392A
Antibody DCC ID	ENCAB890JXZ	ENCAB890JXZ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	40.897659	0
Rep2_TPM	28.1630822	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	69	70

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-59	BGKLV08-60
Sample_ID	BGKLV08-59	BGKLV08-60
Sample Name	TBRG4-LV08-59	TBRG4-LV08-60
Sample Name	TBRG4-LV08-59	TBRG4-LV08-60
RBP	TBRG4	TBRG4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	318	319

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-59	BGKLV08-60
Sample #
Sample Name	TBRG4-BGKLV08-59	TBRG4-BGKLV08-60
Sample_Name_Alias	TBRG4-LV08-59	TBRG4-LV08-60
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set5/E1.png	DNA_Library_LV08/set5/F1.png
RIN	9.4	9.3
libSample_RNA_Well	RNA_Library_LV08/set4/E1.png	RNA_Library_LV08/set4/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-59	BGKLV08-60
RBP	TBRG4	TBRG4
Batch_ID	BGKLV08	BGKLV08
WB_result	60.600	59.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1938	1939

Sequencing Information

	BGKLV08-59	BGKLV08-60
Sample_ID	BGKLV08-59	BGKLV08-60
Sample Name	TBRG4-LV08-59	TBRG4-LV08-60
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	42,670,000	51,030,000
total_aligned_reads	39,463,862	46,106,086
unique_aligned_reads	36,072,444	41,974,792
percent_uniqueAligned	0.84538	0.82255
correlation_replicates	0.990369	0.990369
spikein_reads	257,446	350,866
percent_spikeins	0.00603	0.00688
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	638	639

Data Submission Information

	BGKLV08-59	BGKLV08-59
ENCODE_alias	brenton-graveley:TBRG4-LV08	brenton-graveley:TBRG4-BGKLV08-K562
ENCODE_accession	ENCSR079IPT	ENCSR645FAT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-59	BGKLV08-59
Sample Name	TBRG4-LV08-59	TBRG4-LV08-59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2708	7004

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
TBRG4-LV08-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59_TTAGGC_L008_R1_001.fastq.gz,TBRG4-LV08-59_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	12025
TBRG4-LV08-59_TTAGGC_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	638	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12081
TBRG4-LV08-59_TTAGGC_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	638	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12137
TBRG4-LV08-59_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	12193
TBRG4-LV08-59_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	12249
TBRG4-LV08-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	12305
TBRG4-LV08-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	12361
TBRG4-LV08-59_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	638					GRCh38	V40	TBRG4-LV08-59_TTAGGC_L008_R1_001.fastq.gz,TBRG4-LV08-59_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	13360
TBRG4-LV08-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gz,TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gz		ENCORE2	12026
TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	639	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12082
TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	639	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12138
TBRG4-LV08-60_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	12194
TBRG4-LV08-60_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	12250
TBRG4-LV08-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	12306
TBRG4-LV08-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	12362
TBRG4-LV08-60_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	639					GRCh38	V40	TBRG4-LV08-60_TGACCA_L008_R1_001.fastq.gz,TBRG4-LV08-60_TGACCA_L008_R2_001.fastq.gz		ENCORE2	13361