TUFM RNA-Seq in K562

General Information


RBP	TUFM
Cell_Line	K562
Method	shRNA
Exp_Name	TUFM-BGKLV25-K562
ENCODE_series_ID	ENCSR980RTI
Batch_ID	BGKLV25
Pool ID	Pool-151201
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR602AWR
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	TUFM-BGKLV25-59
Rep2	TUFM-BGKLV25-60
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	53.9
Rep2_qPCR	48.8
Rep1_WB	71.1
Rep2_WB	65.4
Antibody Cat#	GTX101763
Antibody Lot#	GTX101763
Antibody DCC ID	ENCAB531CVZ
Status	Released
Project	ENCODE3
ID	626

Experiment Information (Status: Released)

	BGKLV25-59	BGKLV25-60
idx	462	463
TRCN#_or_BGC#	TRCN0000165718	TRCN0000165718
shRNA_or_gRNA_sequence	CATAGCAAGAACATCCGCACT	CATAGCAAGAACATCCGCACT
PAM
Name	TUFM	TUFM
Sample_ID	BGKLV25-59	BGKLV25-60
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	TUFM	TUFM
qPCR_result	53.9	48.8
Ave_qPCR	51.4
RT-qPCR_primer-F	aggcccaggtttacatcctc
RT-qPCR_primer-R	tgtcccaagtcagggagaac
protein_conc	3362	2939
WB_result	71.1	65.4
Ave_WB	68.2
WB_DONE_date	5/11/2015
MW	50kDa
IP	1	1
antibody_Cat#	GTX101763	GTX101763
Antibody DCC ID	ENCAB531CVZ	ENCAB531CVZ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	159.374083	0
Rep2_TPM	111.260898	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	535	536

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TUFM	Product_ID: GTX101763 Lot_ID: 39694 Source: GeneTex Target Name: TUFM-human

Experiment Status

	BGKLV25-59	BGKLV25-60
Sample_ID	BGKLV25-59	BGKLV25-60
Sample Name	TUFM-BGKLV25-59	TUFM-BGKLV25-60
Sample Name	TUFM-BGKLV25-59	TUFM-BGKLV25-60
RBP	TUFM	TUFM
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	932	933

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-59	BGKLV25-60
Sample #
Sample Name	TUFM-BGKLV25-59	TUFM-BGKLV25-60
Sample_Name_Alias	TUFM-BGKLV25-59	TUFM-BGKLV25-60
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-23	2015-06-23
Lib_ID	Lib-150623	Lib-150623
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/E4.png	DNA_Library_LV24-25-26/set1/F4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G12.png	RNA_Library_LV22-23-25/set1/H12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-59	BGKLV25-60
RBP	TUFM	TUFM
Batch_ID	BGKLV25	BGKLV25
WB_result	71.100	65.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2624	2625

Sequencing Information

	BGKLV25-59	BGKLV25-60
Sample_ID	BGKLV25-59	BGKLV25-60
Sample Name	TUFM-BGKLV25-59	TUFM-BGKLV25-60
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set25	set25
total_reads	46,321,108	45,811,542
total_aligned_reads	44,070,426	43,911,788
unique_aligned_reads	40,390,174	40,200,170
percent_uniqueAligned	0.87196	0.87751
correlation_replicates	0.989877	0.989877
spikein_reads	220,900	199,748
percent_spikeins	0.00477	0.00436
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1266	1267

Data Submission Information

	BGKLV25-59	BGKLV25-59
ENCODE_alias	brenton-graveley:TUFM-BGKLV25	brenton-graveley:TUFM-BGKLV25-K562
ENCODE_accession	ENCSR602AWR	ENCSR980RTI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-59	BGKLV25-59
Sample Name	TUFM-BGKLV25-59	TUFM-BGKLV25-59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3015	7020

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
TUFM-BGKLV25-59_1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1266	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19594
TUFM-BGKLV25-59_2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1266	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19630
TUFM-BGKLV25-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59_1.fastq.gz,TUFM-BGKLV25-59_2.fastq.gz		ENCORE2	19666
TUFM-BGKLV25-59_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59/Aligned.sortedByCoord.out.bam		ENCORE2	19702
TUFM-BGKLV25-59_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59/Aligned.sortedByCoord.out.bam		ENCORE2	19738
TUFM-BGKLV25-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59/Aligned.sortedByCoord.out.bam		ENCORE2	19774
TUFM-BGKLV25-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59/Aligned.sortedByCoord.out.bam		ENCORE2	19810
TUFM-BGKLV25-59_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1266					GRCh38	V40	TUFM-BGKLV25-59_1.fastq.gz,TUFM-BGKLV25-59_2.fastq.gz		ENCORE2	20000
TUFM-BGKLV25-60_1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1267	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19595
TUFM-BGKLV25-60_2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1267	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19631
TUFM-BGKLV25-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60_1.fastq.gz,TUFM-BGKLV25-60_2.fastq.gz		ENCORE2	19667
TUFM-BGKLV25-60_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60/Aligned.sortedByCoord.out.bam		ENCORE2	19703
TUFM-BGKLV25-60_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60/Aligned.sortedByCoord.out.bam		ENCORE2	19739
TUFM-BGKLV25-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60/Aligned.sortedByCoord.out.bam		ENCORE2	19775
TUFM-BGKLV25-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60/Aligned.sortedByCoord.out.bam		ENCORE2	19811
TUFM-BGKLV25-60_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1267					GRCh38	V40	TUFM-BGKLV25-60_1.fastq.gz,TUFM-BGKLV25-60_2.fastq.gz		ENCORE2	20001