PUF60 RNA-Seq in K562

General Information


RBP	PUF60
Cell_Line	K562
Method	shRNA
Exp_Name	PUF60-BGKLV25-K562
ENCODE_series_ID	ENCSR294TLQ
Batch_ID	BGKLV25
Pool ID	Pool-151101
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR558XNA
ENCODE_CN_Exp_ID	ENCSR620PUP
Rep1	PUF60-BGKLV25-43
Rep2	PUF60-BGKLV25-44
CN1	NT_BGKLV25-1
CN2	NT_BGKLV25-2
Rep1_qPCR	53.9
Rep2_qPCR	56.0
Rep1_WB	45.1
Rep2_WB	55.0
Antibody Cat#	A302-817A
Antibody Lot#	A302-817A
Antibody DCC ID	ENCAB280GIW
Status	Released
Project	ENCODE3
ID	622

Experiment Information (Status: Released)

	BGKLV25-43	BGKLV25-44
idx	446	447
TRCN#_or_BGC#	TRCN0000017248	TRCN0000017248
shRNA_or_gRNA_sequence	CGATGACATCAAGAGCGTGTT	CGATGACATCAAGAGCGTGTT
PAM
Name	PUF60	PUF60
Sample_ID	BGKLV25-43	BGKLV25-44
transduction_Date	3/15/2015	3/15/2015
days
RBP_name	PUF60	PUF60
qPCR_result	53.9	56.0
Ave_qPCR	54.9	day 4
RT-qPCR_primer-F	GCGTCTACGTGGGCTCTATC
RT-qPCR_primer-R	GGACATGTCGATGCTCTTGA
protein_conc	2756	2537
WB_result	45.1	55.0
Ave_WB	50.0
WB_DONE_date	4/1/2015
MW	60kDa
IP	1	1
antibody_Cat#	A302-817A	A302-817A
Antibody DCC ID	ENCAB280GIW	ENCAB280GIW
submitted_to_DCC_date	5/4/2015
Rep1_TPM	24.8779434	0
Rep2_TPM	20.580289	0
Action
Library_start_date	6/23/2015	6/23/2015
repeat_library
Note
ID	517	518

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUF60	Product_ID: A302-817A Lot_ID: 1 Source: Bethyl Labs Target Name: PUF60-human

Experiment Status

	BGKLV25-43	BGKLV25-44
Sample_ID	BGKLV25-43	BGKLV25-44
Sample Name	PUF60-BGKLV25-43	PUF60-BGKLV25-44
Sample Name	PUF60-BGKLV25-43	PUF60-BGKLV25-44
RBP	PUF60	PUF60
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	924	925

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-43	BGKLV25-44
Sample #
Sample Name	PUF60-BGKLV25-43	PUF60-BGKLV25-44
Sample_Name_Alias	PUF60-BGKLV25-43	PUF60-BGKLV25-44
Index Well Position	S05	S06
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/E3.png	DNA_Library_LV24-25-26/set1/F3.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G11.png	RNA_Library_LV22-23-25/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-43	BGKLV25-44
RBP	PUF60	PUF60
Batch_ID	BGKLV25	BGKLV25
WB_result	45.100	55.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2616	2617

Sequencing Information

	BGKLV25-43	BGKLV25-44
Sample_ID	BGKLV25-43	BGKLV25-44
Sample Name	PUF60-BGKLV25-43	PUF60-BGKLV25-44
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set25	set25
total_reads	126,724,052	63,384,506
total_aligned_reads	128,601,908	65,237,102
unique_aligned_reads	117,970,110	59,882,314
percent_uniqueAligned	0.93092	0.94475
correlation_replicates	0.983190	0.983190
spikein_reads	1,178,590	439,182
percent_spikeins	0.00930	0.00693
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1258	1259

Data Submission Information

	BGKLV25-43	BGKLV25-43
ENCODE_alias	brenton-graveley:PUF60-BGKLV25	brenton-graveley:PUF60-BGKLV25-K562
ENCODE_accession	ENCSR558XNA	ENCSR294TLQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-43	BGKLV25-43
Sample Name	PUF60-BGKLV25-43	PUF60-BGKLV25-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3011	6878

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
PUF60-BGKLV25-43_ACAGTG_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1258	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19586
PUF60-BGKLV25-43_ACAGTG_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1258	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19622
PUF60-BGKLV25-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1258					GRCh38	V40	PUF60-BGKLV25-43_ACAGTG_L007_001.R1.fastq.gz,PUF60-BGKLV25-43_ACAGTG_L007_001.R2.fastq.gz		ENCORE2	19658
PUF60-BGKLV25-43_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	1258					GRCh38	V40	PUF60-BGKLV25-43/Aligned.sortedByCoord.out.bam		ENCORE2	19694
PUF60-BGKLV25-43_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	1258					GRCh38	V40	PUF60-BGKLV25-43/Aligned.sortedByCoord.out.bam		ENCORE2	19730
PUF60-BGKLV25-43_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	1258					GRCh38	V40	PUF60-BGKLV25-43/Aligned.sortedByCoord.out.bam		ENCORE2	19766
PUF60-BGKLV25-43_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	1258					GRCh38	V40	PUF60-BGKLV25-43/Aligned.sortedByCoord.out.bam		ENCORE2	19802
PUF60-BGKLV25-43_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1258					GRCh38	V40	PUF60-BGKLV25-43_ACAGTG_L007_001.R1.fastq.gz,PUF60-BGKLV25-43_ACAGTG_L007_001.R2.fastq.gz		ENCORE2	19992
PUF60-BGKLV25-44_GCCAAT_L007_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1259	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1_GATCAG_L004_001.R1.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R1.fastq.gz	ENCODE3	19587
PUF60-BGKLV25-44_GCCAAT_L007_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1259	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1_GATCAG_L004_001.R2.fastq.gz,NT_BGKLV25-2_TAGCTT_L004_001.R2.fastq.gz	ENCODE3	19623
PUF60-BGKLV25-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1259					GRCh38	V40	PUF60-BGKLV25-44_GCCAAT_L007_001.R1.fastq.gz,PUF60-BGKLV25-44_GCCAAT_L007_001.R2.fastq.gz		ENCORE2	19659
PUF60-BGKLV25-44_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	1259					GRCh38	V40	PUF60-BGKLV25-44/Aligned.sortedByCoord.out.bam		ENCORE2	19695
PUF60-BGKLV25-44_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	1259					GRCh38	V40	PUF60-BGKLV25-44/Aligned.sortedByCoord.out.bam		ENCORE2	19731
PUF60-BGKLV25-44_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	1259					GRCh38	V40	PUF60-BGKLV25-44/Aligned.sortedByCoord.out.bam		ENCORE2	19767
PUF60-BGKLV25-44_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	1259					GRCh38	V40	PUF60-BGKLV25-44/Aligned.sortedByCoord.out.bam		ENCORE2	19803
PUF60-BGKLV25-44_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1259					GRCh38	V40	PUF60-BGKLV25-44_GCCAAT_L007_001.R1.fastq.gz,PUF60-BGKLV25-44_GCCAAT_L007_001.R2.fastq.gz		ENCORE2	19993