GSPT2 RNA-Seq in K562

General Information


RBP	GSPT2
Cell_Line	K562
Method	CRISPR
Exp_Name	GSPT2-BGKcLV17-K562
ENCODE_series_ID	ENCSR114QMA
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR148XGX
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	GSPT2-BGKcLV17-27
Rep2	GSPT2-BGKcLV17-28
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	65.8
Rep2_WB	55.9951325
Antibody Cat#	RN119PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB053JZL
Status	Released
Project	ENCODE4
ID	88

Experiment Information (Status: Released)

	BGKcLV17-27	BGKcLV17-28
idx	634	635
TRCN#_or_BGC#	BGC#0000423	BGC#0000423
shRNA_or_gRNA_sequence	AAGTTCCGAGACCATGGATT	AAGTTCCGAGACCATGGATT
PAM	CGG	CGG
Name	GSPT2	GSPT2
Sample_ID	BGKcLV17-27	BGKcLV17-28
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	GSPT2	GSPT2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TTCTGGACGCACGTTTGATG
RT-qPCR_primer-R	CACCGCATTATAACCTGGGC
protein_conc	4032	4152
WB_result	65.8	55.9951325
Ave_WB	60.9
WB_DONE_date	7/23/19
MW	69KD
IP	Rabbit / I
antibody_Cat#	RN119PW	lot #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	2.4	0
Rep2_TPM	2.7	0
Action	Question	Question
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4750	4751

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GSPT2	Product_ID: RN119PW Lot_ID: 1 Source: MBLI Target Name: GSPT2-human

Experiment Status

	BGKcLV17-27	BGKcLV17-28
Sample_ID	BGKcLV17-27	BGKcLV17-28
Sample Name	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-28
Sample Name	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-28
RBP	GSPT2	GSPT2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5509	5510

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-27	BGKcLV17-28
Sample #	99	100
Sample Name	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-28
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-G2	1-H2
Tecan	40.11	28.86
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	282
Peak_Molarity	24.50	19.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C11.png	DNA_Library_set43-44/set1/D11.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/C6.png	RNA_Library_set43-44/set4/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-27	BGKcLV17-28
RBP	GSPT2	GSPT2
Batch_ID	BGKcLV17	BGKcLV17
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	675	676

Sequencing Information

	BGKcLV17-27	BGKcLV17-28
Sample_ID	BGKcLV17-27	BGKcLV17-28
Sample Name	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-28
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	133,399,770	127,614,858
total_aligned_reads	132,981,136	127,404,302
unique_aligned_reads	121,166,798	115,895,050
percent_uniqueAligned	0.90830	0.90816
correlation_replicates	0.999321	0.999321
spikein_reads	31,818	37,670
percent_spikeins	0.00024	0.00030
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	181	182

Data Submission Information

	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-28	BGKcLV17-28	BGKcLV17-28	BGKcLV17-28
ENCODE_alias	brenton-graveley:GSPT2-BGKcLV17	brenton-graveley:GSPT2-BGKcLV17-27	brenton-graveley:L-GSPT2-BGKcLV17-27	brenton-graveley:GSPT2-BGKcLV17-27_S29_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSPT2-BGKcLV17-27_S29_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSPT2-BGKcLV17-K562	brenton-graveley:GSPT2-BGKcLV17-28	brenton-graveley:L-GSPT2-BGKcLV17-28	brenton-graveley:GSPT2-BGKcLV17-28_S30_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSPT2-BGKcLV17-28_S30_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR148XGX	ENCBS609LOC	ENCLB345SJG	ENCFF992UMN	ENCFF158BNR	ENCSR114QMA	ENCBS475WDP	ENCLB854QCB	ENCFF490HGK	ENCFF743MHI
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-27	BGKcLV17-28	BGKcLV17-28	BGKcLV17-28	BGKcLV17-28
Sample Name	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-27	GSPT2-BGKcLV17-28	GSPT2-BGKcLV17-28	GSPT2-BGKcLV17-28	GSPT2-BGKcLV17-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		GSPT2-BGKcLV17-27.pdf	L-GSPT2-BGKcLV17-27.pdf				GSPT2-BGKcLV17-28.pdf	L-GSPT2-BGKcLV17-28.pdf
ID	74	228	394	696	726	7239	229	395	697	727

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
GSPT2-BGKcLV17-27_S29_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	181	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	283
GSPT2-BGKcLV17-27_S29_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	181	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	313
GSPT2-BGKcLV17-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27_S29_R1_001.filtered.trimmed.paired.fastq.gz,GSPT2-BGKcLV17-27_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24679
GSPT2-BGKcLV17-27_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27/Aligned.sortedByCoord.out.bam		ENCORE2	24709
GSPT2-BGKcLV17-27_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27/Aligned.sortedByCoord.out.bam		ENCORE2	24739
GSPT2-BGKcLV17-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27/Aligned.sortedByCoord.out.bam		ENCORE2	24769
GSPT2-BGKcLV17-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27/Aligned.sortedByCoord.out.bam		ENCORE2	24799
GSPT2-BGKcLV17-27_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	181					GRCh38	V40	GSPT2-BGKcLV17-27_S29_R1_001.filtered.trimmed.paired.fastq.gz,GSPT2-BGKcLV17-27_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24829
GSPT2-BGKcLV17-28_S30_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	182	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	284
GSPT2-BGKcLV17-28_S30_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	182	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	314
GSPT2-BGKcLV17-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28_S30_R1_001.filtered.trimmed.paired.fastq.gz,GSPT2-BGKcLV17-28_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24680
GSPT2-BGKcLV17-28_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28/Aligned.sortedByCoord.out.bam		ENCORE2	24710
GSPT2-BGKcLV17-28_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28/Aligned.sortedByCoord.out.bam		ENCORE2	24740
GSPT2-BGKcLV17-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28/Aligned.sortedByCoord.out.bam		ENCORE2	24770
GSPT2-BGKcLV17-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28/Aligned.sortedByCoord.out.bam		ENCORE2	24800
GSPT2-BGKcLV17-28_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	182					GRCh38	V40	GSPT2-BGKcLV17-28_S30_R1_001.filtered.trimmed.paired.fastq.gz,GSPT2-BGKcLV17-28_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24830