PES1 RNA-Seq in K562

General Information


RBP	PES1
Cell_Line	K562
Method	CRISPR
Exp_Name	PES1-BGKcLV11-K562
ENCODE_series_ID	ENCSR163IXP
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR717XCO
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	PES1-BGKcLV11-69
Rep2	PES1-BGKcLV11-70
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	9.7
Rep2_qPCR	6.8
Rep1_WB	66.2
Rep2_WB	49.4
Antibody Cat#	A300-903A
Antibody Lot#
Antibody DCC ID	ENCAB170HXF
Status	Released
Project	ENCODE4
ID	183

Experiment Information (Status: Released)

	BGKcLV11-69	BGKcLV11-70
idx	385	386
TRCN#_or_BGC#	BGC#0000201	BGC#0000201
shRNA_or_gRNA_sequence	AAGCCCACGATGAGGCGGTG	AAGCCCACGATGAGGCGGTG
PAM	AGG	AGG
Name	PES1_84F	PES1_84F
Sample_ID	BGKcLV11-69	BGKcLV11-70
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	PES1	PES1
qPCR_result	9.7	6.8
Ave_qPCR	8.3
RT-qPCR_primer-F	ccaactacatcacccggaac
RT-qPCR_primer-R	aaatgcccttcagaatgcac
protein_conc	3126	2849
WB_result	66.2	49.4
Ave_WB	57.8
WB_DONE_date	8/14/18	wes
MW	68kda
IP	1
antibody_Cat#	A300-903A
Antibody DCC ID	ENCAB170HXF
submitted_to_DCC_date	2/22/19
Rep1_TPM	92.1	0
Rep2_TPM	79.6	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4487	4488

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PES1	Product_ID: A300-903A Lot_ID: 1 Source: Bethyl Labs Target Name: PES1-human

Experiment Status

	BGKcLV11-69	BGKcLV11-70
Sample_ID	BGKcLV11-69	BGKcLV11-70
Sample Name	PES1-BGKcLV11-69	PES1-BGKcLV11-70
Sample Name	PES1-BGKcLV11-69	PES1-BGKcLV11-70
RBP	PES1	PES1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2685	2686

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-69	BGKcLV11-70
Sample #	13	14
Sample Name	PES1-BGKcLV11-69	PES1-BGKcLV11-70
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-E2	1-F2
Tecan	46.19	49.97
Tecan_date	2019-03-13	2019-03-13
Size_bp	300	292
Peak_Molarity	116.00	99.20
libSampleQC_DNA_Well	DNA_Library_set42/set1/E2.png	DNA_Library_set42/set2/A1.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set42/set1/E2.png	RNA_Library_set42/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-69	BGKcLV11-70
RBP	PES1	PES1
Batch_ID	BGKcLV11	BGKcLV11
WB_result	66.200	49.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	13	14

Sequencing Information

	BGKcLV11-69	BGKcLV11-70
Sample_ID	BGKcLV11-69	BGKcLV11-70
Sample Name	PES1-BGKcLV11-69	PES1-BGKcLV11-70
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	47,586,970	45,092,910
total_aligned_reads	45,827,810	43,574,122
unique_aligned_reads	41,613,014	39,641,872
percent_uniqueAligned	0.87446	0.87912
correlation_replicates	0.997747	0.997747
spikein_reads	58,260	47,908
percent_spikeins	0.00122	0.00106
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	53	54

Data Submission Information

	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-70	BGKcLV11-70	BGKcLV11-70	BGKcLV11-70
ENCODE_alias	brenton-graveley:PES1-BGKcLV11	brenton-graveley:PES1-BGKcLV11-69	brenton-graveley:L-PES1-BGKcLV11-69	brenton-graveley:PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PES1-BGKcLV11-K562	brenton-graveley:PES1-BGKcLV11-70	brenton-graveley:L-PES1-BGKcLV11-70	brenton-graveley:PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR717XCO	ENCBS943XSM	ENCLB504QTA	ENCFF732BKK	ENCFF804LBS	ENCSR163IXP	ENCBS434FAM	ENCLB529UWT	ENCFF722YTG	ENCFF659AXY
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	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-69	BGKcLV11-70	BGKcLV11-70	BGKcLV11-70	BGKcLV11-70
Sample Name	PES1-BGKcLV11-69	PES1-BGKcLV11-69	PES1-BGKcLV11-69	PES1-BGKcLV11-69	PES1-BGKcLV11-69	PES1-BGKcLV11-69	PES1-BGKcLV11-70	PES1-BGKcLV11-70	PES1-BGKcLV11-70	PES1-BGKcLV11-70
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		PES1-BGKcLV11-69.pdf	L-PES1-BGKcLV11-69.pdf				PES1-BGKcLV11-70.pdf	L-PES1-BGKcLV11-70.pdf
ID	767	829	911	1003	1085	7282	830	912	1004	1086

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
PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	53	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	385
PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	53	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	467
PES1-BGKcLV11-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz,PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23724
PES1-BGKcLV11-69_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69/Aligned.sortedByCoord.out.bam		ENCORE2	23806
PES1-BGKcLV11-69_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69/Aligned.sortedByCoord.out.bam		ENCORE2	23888
PES1-BGKcLV11-69_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69/Aligned.sortedByCoord.out.bam		ENCORE2	23970
PES1-BGKcLV11-69_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69/Aligned.sortedByCoord.out.bam		ENCORE2	24052
PES1-BGKcLV11-69_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	53					GRCh38	V40	PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R1_001.filtered.trimmed.paired.fastq.gz,PES1-BGKcLV11-69_CCAAGTCT+AAGGATGA_HK3H2DSXX_S13_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24134
PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	54	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	386
PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	54	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	468
PES1-BGKcLV11-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz,PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23725
PES1-BGKcLV11-70_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70/Aligned.sortedByCoord.out.bam		ENCORE2	23807
PES1-BGKcLV11-70_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70/Aligned.sortedByCoord.out.bam		ENCORE2	23889
PES1-BGKcLV11-70_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70/Aligned.sortedByCoord.out.bam		ENCORE2	23971
PES1-BGKcLV11-70_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70/Aligned.sortedByCoord.out.bam		ENCORE2	24053
PES1-BGKcLV11-70_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	54					GRCh38	V40	PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R1_001.filtered.trimmed.paired.fastq.gz,PES1-BGKcLV11-70_TTGGACTC+GGAAGCAG_HK3H2DSXX_S14_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24135