RTF1 RNA-Seq in K562

General Information


RBP	RTF1
Cell_Line	K562
Method	shRNA
Exp_Name	RTF1-BGKLV13-K562
ENCODE_series_ID	ENCSR954LPI
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR783YSQ
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	RTF1_BGKLV13_19
Rep2	RTF1_BGKLV13_20
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	44.1
Rep2_qPCR	58.2
Rep1_WB	58.0
Rep2_WB	63.4
Antibody Cat#	A300-178A
Antibody Lot#	A300-178A
Antibody DCC ID	ENCAB664NPT
Status	Released
Project	ENCODE3
ID	366

Experiment Information (Status: Released)

	BGKLV13-19	BGKLV13-20
idx	152	153
TRCN#_or_BGC#	TRCN0000022360	TRCN0000022360
shRNA_or_gRNA_sequence	GCCAAACAAATCCAAGATCAA	GCCAAACAAATCCAAGATCAA
PAM
Name	RTF1	RTF1
Sample_ID	BGKLV13-19	BGKLV13-20
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	RTF1	RTF1
qPCR_result	44.1	58.2
Ave_qPCR	51.2
RT-qPCR_primer-F	acgcgtgttccgtttagag
RT-qPCR_primer-R	gcatgccagcagagaacat
protein_conc	1962	1800
WB_result	58.0	63.4
Ave_WB	60.7
WB_DONE_date	2/16/2016
MW	80kDa	WES
IP	1	1
antibody_Cat#	A300-178A	A300-178A
Antibody DCC ID	ENCAB664NPT
submitted_to_DCC_date	3/8/2016
Rep1_TPM	21.7522447	0
Rep2_TPM	17.4619507	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	167	168

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RTF1	Product_ID: A300-178A Lot_ID: 1 Source: Bethyl Labs Target Name: RTF1-human

Experiment Status

	BGKLV13-19	BGKLV13-20
Sample_ID	BGKLV13-19	BGKLV13-20
Sample Name	RTF1_BGKLV13_19	RTF1_BGKLV13_20
Sample Name	RTF1_BGKLV13_19	RTF1_BGKLV13_20
RBP	RTF1	RTF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	470	471

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-19	BGKLV13-20
Sample #
Sample Name	RTF1-BGKLV13-19	RTF1-BGKLV13-20
Sample_Name_Alias	RTF1_BGKLV13_19	RTF1_BGKLV13_20
Index Well Position	S15	S16
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/H2.png	DNA_Library_LV13-14/set1/A3.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/C11.png	RNA_Library_LV12/set1/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-19	BGKLV13-20
RBP	RTF1	RTF1
Batch_ID	BGKLV13	BGKLV13
WB_result	58.000	63.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2134	2135

Sequencing Information

	BGKLV13-19	BGKLV13-20
Sample_ID	BGKLV13-19	BGKLV13-20
Sample Name	RTF1_BGKLV13_19	RTF1_BGKLV13_20
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	51,450,000	50,010,000
total_aligned_reads	48,340,038	46,451,498
unique_aligned_reads	44,739,512	43,065,194
percent_uniqueAligned	0.86957	0.86113
correlation_replicates	0.996653	0.996653
spikein_reads	150,872	118,208
percent_spikeins	0.00293	0.00236
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	776	777

Data Submission Information

	BGKLV13-19	BGKLV13-19
ENCODE_alias	brenton-graveley:RTF1_BGKLV13	brenton-graveley:RTF1-BGKLV13-K562
ENCODE_accession	ENCSR783YSQ	ENCSR954LPI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-19	BGKLV13-19
Sample Name	RTF1_BGKLV13_19	RTF1_BGKLV13_19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2784	6926

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
RTF1_BGKLV13_19_ATGTCA_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	776	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13398
RTF1_BGKLV13_19_ATGTCA_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	776	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13450
RTF1_BGKLV13_19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	776					GRCh38	V40	RTF1_BGKLV13_19_ATGTCA_L003_R1_001.fastq.gz,RTF1_BGKLV13_19_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	13502
RTF1_BGKLV13_19_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	776					GRCh38	V40	RTF1_BGKLV13_19/Aligned.sortedByCoord.out.bam		ENCORE2	13554
RTF1_BGKLV13_19_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	776					GRCh38	V40	RTF1_BGKLV13_19/Aligned.sortedByCoord.out.bam		ENCORE2	13606
RTF1_BGKLV13_19_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	776					GRCh38	V40	RTF1_BGKLV13_19/Aligned.sortedByCoord.out.bam		ENCORE2	13658
RTF1_BGKLV13_19_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	776					GRCh38	V40	RTF1_BGKLV13_19/Aligned.sortedByCoord.out.bam		ENCORE2	13710
RTF1_BGKLV13_19_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	776					GRCh38	V40	RTF1_BGKLV13_19_ATGTCA_L003_R1_001.fastq.gz,RTF1_BGKLV13_19_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	13762
RTF1_BGKLV13_20_CCGTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	777	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13399
RTF1_BGKLV13_20_CCGTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	777	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13451
RTF1_BGKLV13_20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	777					GRCh38	V40	RTF1_BGKLV13_20_CCGTCC_L003_R1_001.fastq.gz,RTF1_BGKLV13_20_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	13503
RTF1_BGKLV13_20_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	777					GRCh38	V40	RTF1_BGKLV13_20/Aligned.sortedByCoord.out.bam		ENCORE2	13555
RTF1_BGKLV13_20_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	777					GRCh38	V40	RTF1_BGKLV13_20/Aligned.sortedByCoord.out.bam		ENCORE2	13607
RTF1_BGKLV13_20_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	777					GRCh38	V40	RTF1_BGKLV13_20/Aligned.sortedByCoord.out.bam		ENCORE2	13659
RTF1_BGKLV13_20_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	777					GRCh38	V40	RTF1_BGKLV13_20/Aligned.sortedByCoord.out.bam		ENCORE2	13711
RTF1_BGKLV13_20_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	777					GRCh38	V40	RTF1_BGKLV13_20_CCGTCC_L003_R1_001.fastq.gz,RTF1_BGKLV13_20_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	13763