PSIP1 RNA-Seq in K562

General Information


RBP	PSIP1
Cell_Line	K562
Method	shRNA
Exp_Name	PSIP1-BGKLV21-K562
ENCODE_series_ID	ENCSR157QFT
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR611LQB
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	PSIP1_BGKLV21_45_17582
Rep2	PSIP1_BGKLV21_46_17583
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	70.2
Rep2_qPCR	56.8
Rep1_WB	94.3
Rep2_WB	89.7
Antibody Cat#	A300-848A
Antibody Lot#	A300-848A
Antibody DCC ID	ENCAB004FAZ
Status	Released
Project	ENCODE3
ID	517

Experiment Information (Status: Released)

	BGKLV21-45	BGKLV21-46
idx	316	317
TRCN#_or_BGC#	TRCN0000074819	TRCN0000074819
shRNA_or_gRNA_sequence	GCAGCAACTAAACAATCAAAT	GCAGCAACTAAACAATCAAAT
PAM
Name	PSIP1	PSIP1
Sample_ID	BGKLV21-45	BGKLV21-46
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	PSIP1	PSIP1
qPCR_result	70.2	56.8
Ave_qPCR	63.5
RT-qPCR_primer-F	tcaagtcaacaggcagcaac
RT-qPCR_primer-R	gctggctttttcttcatggt
protein_conc	3165	2873
WB_result	94.3	89.7
Ave_WB	92.0
WB_DONE_date	3/31/2015
MW
IP	1	1
antibody_Cat#	A300-848A	A300-848A
Antibody DCC ID	ENCAB004FAZ	ENCAB004FAZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	36.46741	0
Rep2_TPM	56.9682146	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	353	354

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PSIP1	Product_ID: A300-848A Lot_ID: 1 Source: Bethyl Labs Target Name: PSIP1-human

Experiment Status

	BGKLV21-45	BGKLV21-46
Sample_ID	BGKLV21-45	BGKLV21-46
Sample Name	PSIP1_BGKLV21_45_17582	PSIP1_BGKLV21_46_17583
Sample Name	PSIP1_BGKLV21_45_17582	PSIP1_BGKLV21_46_17583
RBP	PSIP1	PSIP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	768	769

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-45	BGKLV21-46
Sample #
Sample Name	PSIP1-BGKLV21-45	PSIP1-BGKLV21-46
Sample_Name_Alias	PSIP1_BGKLV21_45_17582	PSIP1_BGKLV21_46_17583
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A8.png	DNA_Library_LV21-24/set1/B8.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/F2.png	RNA_Library_LV19-21-24/set2/G2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-45	BGKLV21-46
RBP	PSIP1	PSIP1
Batch_ID	BGKLV21	BGKLV21
WB_result	94.300	89.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2454	2455

Sequencing Information

	BGKLV21-45	BGKLV21-46
Sample_ID	BGKLV21-45	BGKLV21-46
Sample Name	PSIP1_BGKLV21_45_17582	PSIP1_BGKLV21_46_17583
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	56,780,000	30,000,000
total_aligned_reads	52,378,742	27,704,822
unique_aligned_reads	48,197,212	25,476,372
percent_uniqueAligned	0.84884	0.84921
correlation_replicates	0.998432	0.998432
spikein_reads	262,480	147,430
percent_spikeins	0.00462	0.00491
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1060	1061

Data Submission Information

	BGKLV21-45	BGKLV21-45
ENCODE_alias	brenton-graveley:PSIP1_BGKLV21	brenton-graveley:PSIP1-BGKLV21-K562
ENCODE_accession	ENCSR611LQB	ENCSR157QFT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-45	BGKLV21-45
Sample Name	PSIP1_BGKLV21_45_17582	PSIP1_BGKLV21_45_17582
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2970	6873

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
PSIP1_BGKLV21_45_17582_ATCACG_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1060	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15952
PSIP1_BGKLV21_45_17582_ATCACG_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1060	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15996
PSIP1_BGKLV21_45_17582_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582_ATCACG_L003_R1_001.fastq.gz,PSIP1_BGKLV21_45_17582_ATCACG_L003_R2_001.fastq.gz		ENCORE2	16040
PSIP1_BGKLV21_45_17582_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582/Aligned.sortedByCoord.out.bam		ENCORE2	16084
PSIP1_BGKLV21_45_17582_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582/Aligned.sortedByCoord.out.bam		ENCORE2	16128
PSIP1_BGKLV21_45_17582_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582/Aligned.sortedByCoord.out.bam		ENCORE2	16172
PSIP1_BGKLV21_45_17582_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582/Aligned.sortedByCoord.out.bam		ENCORE2	16216
PSIP1_BGKLV21_45_17582_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1060					GRCh38	V40	PSIP1_BGKLV21_45_17582_ATCACG_L003_R1_001.fastq.gz,PSIP1_BGKLV21_45_17582_ATCACG_L003_R2_001.fastq.gz		ENCORE2	16260
PSIP1_BGKLV21_46_17583_CGATGT_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1061	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15953
PSIP1_BGKLV21_46_17583_CGATGT_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1061	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15997
PSIP1_BGKLV21_46_17583_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583_CGATGT_L003_R1_001.fastq.gz,PSIP1_BGKLV21_46_17583_CGATGT_L003_R2_001.fastq.gz		ENCORE2	16041
PSIP1_BGKLV21_46_17583_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583/Aligned.sortedByCoord.out.bam		ENCORE2	16085
PSIP1_BGKLV21_46_17583_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583/Aligned.sortedByCoord.out.bam		ENCORE2	16129
PSIP1_BGKLV21_46_17583_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583/Aligned.sortedByCoord.out.bam		ENCORE2	16173
PSIP1_BGKLV21_46_17583_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583/Aligned.sortedByCoord.out.bam		ENCORE2	16217
PSIP1_BGKLV21_46_17583_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1061					GRCh38	V40	PSIP1_BGKLV21_46_17583_CGATGT_L003_R1_001.fastq.gz,PSIP1_BGKLV21_46_17583_CGATGT_L003_R2_001.fastq.gz		ENCORE2	16261