PUS1 RNA-Seq in K562

General Information


RBP	PUS1
Cell_Line	K562
Method	shRNA
Exp_Name	PUS1-BGKLV32-K562
ENCODE_series_ID	ENCSR272DTK
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR618IQH
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	PUS1_BGKLV32-51
Rep2	PUS1_BGKLV32-52
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	70.1
Rep2_qPCR	72.5
Rep1_WB	72.4
Rep2_WB	70.4
Antibody Cat#	A301-651A
Antibody Lot#	A301-651A
Antibody DCC ID	ENCAB680DCY
Status	Released
Project	ENCODE3
ID	713

Experiment Information (Status: Released)

	BGKLV32-51	BGKLV32-52
idx	650	651
TRCN#_or_BGC#	TRCN0000045517	TRCN0000045517
shRNA_or_gRNA_sequence	GCACTTCGAGAAGTACAACCA	GCACTTCGAGAAGTACAACCA
PAM
Name	PUS1	PUS1
Sample_ID	BGKLV32-51	BGKLV32-52
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	PUS1	PUS1
qPCR_result	70.1	72.5
Ave_qPCR	71.3
RT-qPCR_primer-F	gtgctgctcatggcctattc
RT-qPCR_primer-R	cggacaccaagtcatcttca
protein_conc	3120	3326
WB_result	72.4	70.4
Ave_WB	71.4
WB_DONE_date	11/18/2015
MW	47kda
IP	1	1
antibody_Cat#	A301-651A	A301-651A
Antibody DCC ID	ENCAB680DCY	ENCAB680DCY
submitted_to_DCC_date	12/7/2015
Rep1_TPM	21.09490175	0
Rep2_TPM	12.27383905	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	737	738

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUS1	Product_ID: A301-651A Lot_ID: 1 Source: Bethyl Labs Target Name: PUS1-human

Experiment Status

	BGKLV32-51	BGKLV32-52
Sample_ID	BGKLV32-51	BGKLV32-52
Sample Name	PUS1_BGKLV32-51	PUS1_BGKLV32-52
Sample Name	PUS1_BGKLV32-51	PUS1_BGKLV32-52
RBP	PUS1	PUS1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1177	1178

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-51	BGKLV32-52
Sample #
Sample Name	PUS1-BGKLV32-51	PUS1-BGKLV32-52
Sample_Name_Alias	PUS1_BGKLV32-51	PUS1_BGKLV32-52
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A9.png	DNA_Library_LV33-34-25B-32/set1/B9.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/A2.png	RNA_Library_LV32-33-34/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-51	BGKLV32-52
RBP	PUS1	PUS1
Batch_ID	BGKLV32	BGKLV32
WB_result	72.400	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2862	2863

Sequencing Information

	BGKLV32-51	BGKLV32-52
Sample_ID	BGKLV32-51	BGKLV32-52
Sample Name	PUS1_BGKLV32-51	PUS1_BGKLV32-52
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	79,477,548	130,000,000
total_aligned_reads	67,401,000	110,968,002
unique_aligned_reads	61,484,980	101,137,634
percent_uniqueAligned	0.77361	0.77798
correlation_replicates	0.994650	0.994650
spikein_reads	442,592	665,446
percent_spikeins	0.00557	0.00512
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1511	1512

Data Submission Information

	BGKLV32-51	BGKLV32-51
ENCODE_alias	brenton-graveley:PUS1_BGKLV32	brenton-graveley:PUS1-BGKLV32-K562
ENCODE_accession	ENCSR618IQH	ENCSR272DTK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-51	BGKLV32-51
Sample Name	PUS1_BGKLV32-51	PUS1_BGKLV32-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3128	6884

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
PUS1_BGKLV32-51_ATCACG_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1511	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21210
PUS1_BGKLV32-51_ATCACG_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1511	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21240
PUS1_BGKLV32-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51_ATCACG_L004_001.R1.fastq.gz,PUS1_BGKLV32-51_ATCACG_L004_001.R2.fastq.gz		ENCORE2	21270
PUS1_BGKLV32-51_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51/Aligned.sortedByCoord.out.bam		ENCORE2	21300
PUS1_BGKLV32-51_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51/Aligned.sortedByCoord.out.bam		ENCORE2	21330
PUS1_BGKLV32-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51/Aligned.sortedByCoord.out.bam		ENCORE2	21360
PUS1_BGKLV32-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51/Aligned.sortedByCoord.out.bam		ENCORE2	21390
PUS1_BGKLV32-51_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1511					GRCh38	V40	PUS1_BGKLV32-51_ATCACG_L004_001.R1.fastq.gz,PUS1_BGKLV32-51_ATCACG_L004_001.R2.fastq.gz		ENCORE2	21420
PUS1_BGKLV32-52_CGATGT_L004_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1512	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21211
PUS1_BGKLV32-52_CGATGT_L004_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1512	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21241
PUS1_BGKLV32-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52_CGATGT_L004_001.R1.fastq.gz,PUS1_BGKLV32-52_CGATGT_L004_001.R2.fastq.gz		ENCORE2	21271
PUS1_BGKLV32-52_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52/Aligned.sortedByCoord.out.bam		ENCORE2	21301
PUS1_BGKLV32-52_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52/Aligned.sortedByCoord.out.bam		ENCORE2	21331
PUS1_BGKLV32-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52/Aligned.sortedByCoord.out.bam		ENCORE2	21361
PUS1_BGKLV32-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52/Aligned.sortedByCoord.out.bam		ENCORE2	21391
PUS1_BGKLV32-52_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1512					GRCh38	V40	PUS1_BGKLV32-52_CGATGT_L004_001.R1.fastq.gz,PUS1_BGKLV32-52_CGATGT_L004_001.R2.fastq.gz		ENCORE2	21421