ABT1 RNA-Seq in K562

General Information


RBP	ABT1
Cell_Line	K562
Method	shRNA
Exp_Name	ABT1-BGKLV38-K562
ENCODE_series_ID	ENCSR954JGH
Batch_ID	BGKLV38
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR233UVM
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	ABT1-BGKLV38-5C
Rep2	ABT1-BGKLV38-6C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	88.7
Rep2_qPCR	82.7
Rep1_WB	57.1
Rep2_WB	58.4
Antibody Cat#	A304-044A
Antibody Lot#	A304-044A
Antibody DCC ID	ENCAB891MJI
Status	Released
Project	ENCODE4
ID	274

Experiment Information (Status: Released)

	BGKLV38-5	BGKLV38-6
idx	776	777
TRCN#_or_BGC#	TRCN0000017607	TRCN0000017607
shRNA_or_gRNA_sequence	CCGGTTCGTGAGACGCAAGAA	CCGGTTCGTGAGACGCAAGAA
PAM
Name	ABT1	ABT1
Sample_ID	BGKLV38-5	BGKLV38-6
transduction_Date	9/15/16	9/15/16
days
RBP_name	ABT1	ABT1
qPCR_result	88.7	82.7
Ave_qPCR	85.7
RT-qPCR_primer-F	cgtcttctttcaggctgagg
RT-qPCR_primer-R	ttggtgtaggaccgcttttt
protein_conc	3031	3102
WB_result	57.1	58.4
Ave_WB	57.7
WB_DONE_date	10/14/16
MW	31kDa
IP	1	1
antibody_Cat#	A304-044A	A304-044A
Antibody DCC ID	ENCAB891MJI	ENCAB891MJI
submitted_to_DCC_date	10/26/16
Rep1_TPM	20	0
Rep2_TPM	12.6	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note
ID	869	870

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ABT1	Product_ID: A304-044A Lot_ID: 1 Source: Bethyl Labs Target Name: ABT1-human

Experiment Status

	BGKLV38-5	BGKLV38-6
Sample_ID	BGKLV38-5	BGKLV38-6
Sample Name
Sample Name	ABT1-BGKLV38-5C	ABT1-BGKLV38-6C
RBP	ABT1	ABT1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6473	6474

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-5	BGKLV38-6
Sample #	57	58
Sample Name	ABT1-BGKLV38-5C	ABT1-BGKLV38-6C
Sample_Name_Alias
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	265	286
Peak_Molarity	6.66	11.00
libSampleQC_DNA_Well	DNA_Library_set40/set1/C9.png	DNA_Library_set40/set1/D9.png
RIN	9.2	9.1
libSample_RNA_Well	RNA_Library_set40/set1/C4.png	RNA_Library_set40/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-5	BGKLV38-6
RBP	ABT1	ABT1
Batch_ID	BGKLV38	BGKLV38
WB_result	57.100	58.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	980	981

Sequencing Information

	BGKLV38-5	BGKLV38-6
Sample_ID	BGKLV38-5	BGKLV38-6
Sample Name	ABT1-BGKLV38-5C	ABT1-BGKLV38-6C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	72,052,508	48,099,228
total_aligned_reads	57,336,780	39,747,642
unique_aligned_reads	51,952,574	36,069,666
percent_uniqueAligned	0.72104	0.74990
correlation_replicates	0.999519	0.999519
spikein_reads	12,444	13,716
percent_spikeins	0.00017	0.00029
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	383	384

Data Submission Information

	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-6	BGKLV38-6	BGKLV38-6	BGKLV38-6
ENCODE_alias	brenton-graveley:ABT1-BGKLV38-C	brenton-graveley:ABT1-BGKLV38-5C	brenton-graveley:L-ABT1-BGKLV38-5C	brenton-graveley:ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R2.fastq.gz	brenton-graveley:ABT1-BGKLV38-K562	brenton-graveley:ABT1-BGKLV38-6C	brenton-graveley:L-ABT1-BGKLV38-6C	brenton-graveley:ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R1.fastq.gz	brenton-graveley:ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R2.fastq.gz
ENCODE_accession	ENCSR233UVM	ENCBS886EYT	ENCLB237JDR	ENCFF973VXT	ENCFF876EDH	ENCSR954JGH	ENCBS711MRV	ENCLB914SSP	ENCFF918XMS	ENCFF342RXT
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	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-5	BGKLV38-6	BGKLV38-6	BGKLV38-6	BGKLV38-6
Sample Name	ABT1-BGKLV38-5C	ABT1-BGKLV38-5C	ABT1-BGKLV38-5C	ABT1-BGKLV38-5C	ABT1-BGKLV38-5C	ABT1-BGKLV38-5C	ABT1-BGKLV38-6C	ABT1-BGKLV38-6C	ABT1-BGKLV38-6C	ABT1-BGKLV38-6C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		ABT1-BGKLV38-5C.pdf	L-ABT1-BGKLV38-5C.pdf				ABT1-BGKLV38-6C.pdf	L-ABT1-BGKLV38-6C.pdf
ID	1431	1460	1516	1644	1677	7059	1461	1517	1645	1678

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
ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	383	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	721
ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	383	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	764
ABT1-BGKLV38-5C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R1.fastq.gz,ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23468
ABT1-BGKLV38-5C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C/Aligned.sortedByCoord.out.bam		ENCORE2	23502
ABT1-BGKLV38-5C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C/Aligned.sortedByCoord.out.bam		ENCORE2	23536
ABT1-BGKLV38-5C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C/Aligned.sortedByCoord.out.bam		ENCORE2	23570
ABT1-BGKLV38-5C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C/Aligned.sortedByCoord.out.bam		ENCORE2	23604
ABT1-BGKLV38-5C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	383					GRCh38	V40	ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R1.fastq.gz,ABT1-BGKLV38-5C_GGCTAC_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23638
ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	384	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	722
ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	384	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	765
ABT1-BGKLV38-6C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R1.fastq.gz,ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23469
ABT1-BGKLV38-6C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C/Aligned.sortedByCoord.out.bam		ENCORE2	23503
ABT1-BGKLV38-6C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C/Aligned.sortedByCoord.out.bam		ENCORE2	23537
ABT1-BGKLV38-6C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C/Aligned.sortedByCoord.out.bam		ENCORE2	23571
ABT1-BGKLV38-6C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C/Aligned.sortedByCoord.out.bam		ENCORE2	23605
ABT1-BGKLV38-6C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	384					GRCh38	V40	ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R1.fastq.gz,ABT1-BGKLV38-6C_CTTGTA_ACBYWVANXX_L005_001.R2.fastq.gz		ENCORE2	23639