MAK16 RNA-Seq in K562

General Information


RBP	MAK16
Cell_Line	K562
Method	shRNA
Exp_Name	MAK16-BGKLV32-K562
ENCODE_series_ID	ENCSR849CWX
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR517JHY
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	MAK16_BGKLV32-37
Rep2	MAK16_BGKLV32-38
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	82.1
Rep2_qPCR	75.2
Rep1_WB	58.8
Rep2_WB	56.0
Antibody Cat#	A301-232A
Antibody Lot#	A301-232A
Antibody DCC ID	ENCAB777CMB
Status	Released
Project	ENCODE3
ID	710

Experiment Information (Status: Released)

	BGKLV32-37	BGKLV32-38
idx	636	637
TRCN#_or_BGC#	TRCN0000134315	TRCN0000134315
shRNA_or_gRNA_sequence	GACACAAATGTAAGCAGAGAT	GACACAAATGTAAGCAGAGAT
PAM
Name	MAK16	MAK16
Sample_ID	BGKLV32-37	BGKLV32-38
transduction_Date	10/1/2015	10/1/2015
days
RBP_name	MAK16	MAK16
qPCR_result	82.1	75.2
Ave_qPCR	78.6
RT-qPCR_primer-F	atgccactattaaagaagagaaagga
RT-qPCR_primer-R	aggaaaagccgctcgttcta
protein_conc	2287	2614
WB_result	58.8	56.0
Ave_WB	57.4
WB_DONE_date	10/20/2015
MW	35kDa
IP	1	1
antibody_Cat#	A301-232A	A301-232A
Antibody DCC ID	ENCAB777CMB	ENCAB777CMB
submitted_to_DCC_date	12/7/2015
Rep1_TPM	15.50706847	0
Rep2_TPM	7.77072126	0
Action
Library_start_date	3/7/2016	3/7/2016
repeat_library
Note
ID	719	720

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MAK16	Product_ID: A301-232A Lot_ID: 1 Source: Bethyl Labs Target Name: MAK16-human

Experiment Status

	BGKLV32-37	BGKLV32-38
Sample_ID	BGKLV32-37	BGKLV32-38
Sample Name	MAK16_BGKLV32-37	MAK16_BGKLV32-38
Sample Name	MAK16_BGKLV32-37	MAK16_BGKLV32-38
RBP	MAK16	MAK16
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1169	1170

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-37	BGKLV32-38
Sample #
Sample Name	MAK16-BGKLV32-37	MAK16-BGKLV32-38
Sample_Name_Alias	MAK16_BGKLV32-37	MAK16_BGKLV32-38
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/C8.png	DNA_Library_LV33-34-25B-32/set1/D8.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C1.png	RNA_Library_LV32-33-34/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-37	BGKLV32-38
RBP	MAK16	MAK16
Batch_ID	BGKLV32	BGKLV32
WB_result	58.800	56.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2854	2855

Sequencing Information

	BGKLV32-37	BGKLV32-38
Sample_ID	BGKLV32-37	BGKLV32-38
Sample Name	MAK16_BGKLV32-37	MAK16_BGKLV32-38
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	57,156,290	116,000,000
total_aligned_reads	48,173,516	96,832,334
unique_aligned_reads	44,185,846	88,279,996
percent_uniqueAligned	0.77307	0.76103
correlation_replicates	0.997410	0.997410
spikein_reads	208,924	416,288
percent_spikeins	0.00366	0.00359
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1503	1504

Data Submission Information

	BGKLV32-37	BGKLV32-37
ENCODE_alias	brenton-graveley:MAK16_BGKLV32	brenton-graveley:MAK16-BGKLV32-K562
ENCODE_accession	ENCSR517JHY	ENCSR849CWX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-37	BGKLV32-37
Sample Name	MAK16_BGKLV32-37	MAK16_BGKLV32-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3124	6805

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
MAK16_BGKLV32-37_GTGGCC_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1503	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21202
MAK16_BGKLV32-37_GTGGCC_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1503	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21232
MAK16_BGKLV32-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37_GTGGCC_L003_001.R1.fastq.gz,MAK16_BGKLV32-37_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	21262
MAK16_BGKLV32-37_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	21292
MAK16_BGKLV32-37_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	21322
MAK16_BGKLV32-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	21352
MAK16_BGKLV32-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	21382
MAK16_BGKLV32-37_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1503					GRCh38	V40	MAK16_BGKLV32-37_GTGGCC_L003_001.R1.fastq.gz,MAK16_BGKLV32-37_GTGGCC_L003_001.R2.fastq.gz		ENCORE2	21412
MAK16_BGKLV32-38_GTTTCG_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1504	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21203
MAK16_BGKLV32-38_GTTTCG_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1504	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21233
MAK16_BGKLV32-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38_GTTTCG_L003_001.R1.fastq.gz,MAK16_BGKLV32-38_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	21263
MAK16_BGKLV32-38_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	21293
MAK16_BGKLV32-38_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	21323
MAK16_BGKLV32-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	21353
MAK16_BGKLV32-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	21383
MAK16_BGKLV32-38_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1504					GRCh38	V40	MAK16_BGKLV32-38_GTTTCG_L003_001.R1.fastq.gz,MAK16_BGKLV32-38_GTTTCG_L003_001.R2.fastq.gz		ENCORE2	21413