APTX RNA-Seq in K562

General Information


RBP	APTX
Cell_Line	K562
Method	CRISPR
Exp_Name	APTX-BGKcLV23-K562
ENCODE_series_ID	ENCSR049HPU
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR148HLA
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	APTX-BGKcLV23-15
Rep2	APTX-BGKcLV23-16
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	71.0
Rep2_WB	78.0264144
Antibody Cat#	PA5-92422
Antibody Lot#	LOT# UK2881303A
Antibody DCC ID	ENCAB069JSS
Status	Released
Project	ENCODE4
ID	23

Experiment Information (Status: Released)

	BGKcLV23-15	BGKcLV23-16
idx	801	802
TRCN#_or_BGC#	BGC#0000564	BGC#0000564
shRNA_or_gRNA_sequence	CGTGGTAGCCCAATCGGAAG	CGTGGTAGCCCAATCGGAAG
PAM	CGG	CGG
Name	APTX_97	APTX_97
Sample_ID	BGKcLV23-15	BGKcLV23-16
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	APTX	APTX
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	gccattccgagtatgagcca
RT-qPCR_primer-R	ccagcctcttgtaccatctcg
protein_conc	4087	3212
WB_result	71.0	78.0264144
Ave_WB	74.5
WB_DONE_date	12/14/20
MW	40.7KD
IP	Rabbit / I
antibody_Cat#	PA5-92422	LOT# UK2881303A
Antibody DCC ID	ENCAB069JSS
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4921	4922

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
APTX	Product_ID: PA5-92422 Lot_ID: UK2881303A Source: Thermo Fisher Target Name: APTX-human

Experiment Status

	BGKcLV23-15	BGKcLV23-16
Sample_ID	BGKcLV23-15	BGKcLV23-16
Sample Name
Sample Name	APTX-BGKcLV23-15	APTX-BGKcLV23-16
RBP	APTX	APTX
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7435	7436

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-15	BGKcLV23-16
Sample #	37	38
Sample Name	APTX-BGKcLV23-15	APTX-BGKcLV23-16
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	299	293
Peak_Molarity	87.40	148.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E5.png	DNA_Library_set46/set1/F5.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_set46/set2/E9.png	RNA_Library_set46/set2/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-15	BGKcLV23-16
RBP	APTX	APTX
Batch_ID	BGKcLV23	BGKcLV23
WB_result	61.400	65.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1412	1413

Sequencing Information

	BGKcLV23-15	BGKcLV23-16
Sample_ID	BGKcLV23-15	BGKcLV23-16
Sample Name	APTX-BGKcLV23-15	APTX-BGKcLV23-16
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	237,962,794	224,846,324
total_aligned_reads	218,658,140	206,066,202
unique_aligned_reads	198,887,902	187,530,734
percent_uniqueAligned	0.83579	0.83404
correlation_replicates	0.991318	0.991318
spikein_reads	187,882	109,212
percent_spikeins	0.00079	0.00049
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	518	519

Data Submission Information

	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-16	BGKcLV23-16	BGKcLV23-16	BGKcLV23-16
ENCODE_alias	brenton-graveley:APTX-BGKcLV23	brenton-graveley:APTX-BGKcLV23-15	brenton-graveley:L-APTX-BGKcLV23-15	brenton-graveley:APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGKcLV23-K562	brenton-graveley:APTX-BGKcLV23-16	brenton-graveley:L-APTX-BGKcLV23-16	brenton-graveley:APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR148HLA	ENCBS932ELT	ENCLB388JNG	ENCFF352CZZ	ENCFF923MEB	ENCSR049HPU	ENCBS346LUN	ENCLB267XPI	ENCFF749SNI	ENCFF465SJA
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	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-15	BGKcLV23-16	BGKcLV23-16	BGKcLV23-16	BGKcLV23-16
Sample Name	APTX-BGKcLV23-15	APTX-BGKcLV23-15	APTX-BGKcLV23-15	APTX-BGKcLV23-15	APTX-BGKcLV23-15	APTX-BGKcLV23-15	APTX-BGKcLV23-16	APTX-BGKcLV23-16	APTX-BGKcLV23-16	APTX-BGKcLV23-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		APTX-BGKcLV23-15.pdf	L-APTX-BGKcLV23-15.pdf				APTX-BGKcLV23-16.pdf	L-APTX-BGKcLV23-16.pdf
ID	2413	2463	2527	2621	2655	7091	2464	2528	2622	2656

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
APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	518	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1382
APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	518	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1446
APTX-BGKcLV23-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25285
APTX-BGKcLV23-15_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGKcLV23-15_TCGTAGTG+CCAAGTCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25319
APTX-BGKcLV23-15_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	26123
APTX-BGKcLV23-15_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	26157
APTX-BGKcLV23-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	26191
APTX-BGKcLV23-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	518					GRCh38	V40	APTX-BGKcLV23-15/Aligned.sortedByCoord.out.bam		ENCORE2	26225
APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	519	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1383
APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	519	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1447
APTX-BGKcLV23-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25286
APTX-BGKcLV23-16_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,APTX-BGKcLV23-16_CTACGACA+TTGGACTC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25320
APTX-BGKcLV23-16_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	26124
APTX-BGKcLV23-16_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	26158
APTX-BGKcLV23-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	26192
APTX-BGKcLV23-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	519					GRCh38	V40	APTX-BGKcLV23-16/Aligned.sortedByCoord.out.bam		ENCORE2	26226