MARK2 RNA-Seq in K562

General Information


RBP	MARK2
Cell_Line	K562
Method	shRNA
Exp_Name	MARK2-BGKLV36-K562
ENCODE_series_ID	ENCSR030HRJ
Batch_ID	BGKLV36
Pool ID	Pool-180109
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR016OIX
ENCODE_CN_Exp_ID	ENCSR619PCR
Rep1	MARK2-BGKLV36-33
Rep2	MARK2-BGKLV36-34
CN1	NT-BGKLV36-1C
CN2	NT-BGKLV36-2C
Rep1_qPCR	4.2
Rep2_qPCR	27.7
Rep1_WB	56.5
Rep2_WB	58.1
Antibody Cat#	A303-135A
Antibody Lot#	A303-135A
Antibody DCC ID	ENCAB083FPU
Status	Released
Project	ENCODE4
ID	272

Experiment Information (Status: Released)

	BGKLV36-33	BGKLV36-34
idx	756	757
TRCN#_or_BGC#	TRCN0000001581	TRCN0000001581
shRNA_or_gRNA_sequence	TGCACAGAGTATTTCGCCTAA	TGCACAGAGTATTTCGCCTAA
PAM
Name	MARK2	MARK2
Sample_ID	BGKLV36-33	BGKLV36-34
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	MARK2	MARK2
qPCR_result	4.2	27.7
Ave_qPCR	16.0
RT-qPCR_primer-F	ccccatcccacaaggtacag
RT-qPCR_primer-R	tagaggtgggaatggcagga
protein_conc	5172	4488
WB_result	56.5	58.1
Ave_WB	57.3
WB_DONE_date	6/15/16	WES
MW	88kDa
IP	1	1
antibody_Cat#	A303-135A	A303-135A
Antibody DCC ID	ENCAB083FPU	ENCAB083FPU
submitted_to_DCC_date	11/16/17
Rep1_TPM	10	0
Rep2_TPM	8.9	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	849	850

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MARK2	Product_ID: A303-135A Lot_ID: 1 Source: Bethyl Labs Target Name: MARK2-human

Experiment Status

	BGKLV36-33	BGKLV36-34
Sample_ID	BGKLV36-33	BGKLV36-34
Sample Name
Sample Name	MARK2-BGKLV36-33	MARK2-BGKLV36-34
RBP	MARK2	MARK2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6467	6468

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-33	BGKLV36-34
Sample #	51	52
Sample Name	MARK2-BGKLV36-33C	MARK2-BGKLV36-34C
Sample_Name_Alias	MARK2-BGKLV36-33	MARK2-BGKLV36-34
Index Well Position	S01	S02
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	280	275
Peak_Molarity	14.30	10.50
libSampleQC_DNA_Well	DNA_Library_LV36/set1/A3.png	DNA_Library_LV36/set1/B3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/C6.png	RNA_Library_LV35_LV36/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2016-07-29	2016-07-29
Sample_ID	BGKLV36-33	BGKLV36-34
RBP	MARK2	MARK2
Batch_ID	BGKLV36	BGKLV36
WB_result	56.500	58.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	974	975

Sequencing Information

	BGKLV36-33	BGKLV36-34
Sample_ID	BGKLV36-33	BGKLV36-34
Sample Name	MARK2-BGKLV36-33	MARK2-BGKLV36-34
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	31,547,490	48,474,876
total_aligned_reads	27,585,132	42,227,830
unique_aligned_reads	25,205,278	38,591,652
percent_uniqueAligned	0.79896	0.79612
correlation_replicates	0.988975	0.988975
spikein_reads	80,834	120,102
percent_spikeins	0.00256	0.00248
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	377	378

Data Submission Information

	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-34	BGKLV36-34	BGKLV36-34	BGKLV36-34
ENCODE_alias	brenton-graveley:MARK2-BGKLV36-C	brenton-graveley:MARK2-BGKLV36-33	brenton-graveley:L-MARK2-BGKLV36-33	brenton-graveley:MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R1.fastq.gz	brenton-graveley:MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R2.fastq.gz	brenton-graveley:MARK2-BGKLV36-K562	brenton-graveley:MARK2-BGKLV36-34	brenton-graveley:L-MARK2-BGKLV36-34	brenton-graveley:MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R1.fastq.gz	brenton-graveley:MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R2.fastq.gz
ENCODE_accession	ENCSR016OIX	ENCBS705OBP	ENCLB801KTL	ENCFF603KPT	ENCFF841ZSG	ENCSR030HRJ	ENCBS477ORG	ENCLB630WQU	ENCFF495PXY	ENCFF138OWF
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	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-33	BGKLV36-34	BGKLV36-34	BGKLV36-34	BGKLV36-34
Sample Name	MARK2-BGKLV36-33	MARK2-BGKLV36-33	MARK2-BGKLV36-33	MARK2-BGKLV36-33	MARK2-BGKLV36-33	MARK2-BGKLV36-33	MARK2-BGKLV36-34	MARK2-BGKLV36-34	MARK2-BGKLV36-34	MARK2-BGKLV36-34
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		MARK2-BGKLV36-33.pdf	L-MARK2-BGKLV36-33.pdf				MARK2-BGKLV36-34.pdf	L-MARK2-BGKLV36-34.pdf
ID	1439	1476	1532	1651	1684	7251	1477	1533	1652	1685

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
MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	377	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	730
MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	377	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	773
MARK2-BGKLV36-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	377					GRCh38	V40	MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R1.fastq.gz,MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23476
MARK2-BGKLV36-33_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	377					GRCh38	V40	MARK2-BGKLV36-33/Aligned.sortedByCoord.out.bam		ENCORE2	23510
MARK2-BGKLV36-33_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	377					GRCh38	V40	MARK2-BGKLV36-33/Aligned.sortedByCoord.out.bam		ENCORE2	23544
MARK2-BGKLV36-33_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	377					GRCh38	V40	MARK2-BGKLV36-33/Aligned.sortedByCoord.out.bam		ENCORE2	23578
MARK2-BGKLV36-33_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	377					GRCh38	V40	MARK2-BGKLV36-33/Aligned.sortedByCoord.out.bam		ENCORE2	23612
MARK2-BGKLV36-33_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	377					GRCh38	V40	MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R1.fastq.gz,MARK2-BGKLV36-33_ATCACG_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23646
MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	378	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	731
MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	378	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	774
MARK2-BGKLV36-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	378					GRCh38	V40	MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R1.fastq.gz,MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23477
MARK2-BGKLV36-34_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	378					GRCh38	V40	MARK2-BGKLV36-34/Aligned.sortedByCoord.out.bam		ENCORE2	23511
MARK2-BGKLV36-34_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	378					GRCh38	V40	MARK2-BGKLV36-34/Aligned.sortedByCoord.out.bam		ENCORE2	23545
MARK2-BGKLV36-34_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	378					GRCh38	V40	MARK2-BGKLV36-34/Aligned.sortedByCoord.out.bam		ENCORE2	23579
MARK2-BGKLV36-34_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	378					GRCh38	V40	MARK2-BGKLV36-34/Aligned.sortedByCoord.out.bam		ENCORE2	23613
MARK2-BGKLV36-34_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	378					GRCh38	V40	MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R1.fastq.gz,MARK2-BGKLV36-34_CGATGT_ACBYWVANXX_L008_001.R2.fastq.gz		ENCORE2	23647