MARK2 RNA-Seq in HepG2

General Information


RBP	MARK2
Cell_Line	HepG2
Method	shRNA
Exp_Name	MARK2-BGHLV18-HepG2
ENCODE_series_ID	ENCSR044OFY
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR105OXX
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	MARK2_BGHLV18_27
Rep2	MARK2_BGHLV18_28
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	65.4
Rep2_qPCR	62.9
Rep1_WB	32.2
Rep2_WB	32.5
Antibody Cat#	A303-135A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB083FPU
Status	Released
Project	ENCODE3
ID	451

Experiment Information (Status: Released)

	BGHLV18-27	BGHLV18-28
idx	327	328
TRCN#_or_BGC#	TRCN0000001584	TRCN0000001584
shRNA_or_gRNA_sequence	AGATGATGAACTAAAGCCTTA	AGATGATGAACTAAAGCCTTA
PAM
Name	MARK2	MARK2
Sample_ID	BGHLV18-27	BGHLV18-28
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	MARK2	MARK2
qPCR_result	65.4	62.9
Ave_qPCR	64.1
RT-qPCR_primer-F	ccccatcccacaaggtacag
RT-qPCR_primer-R	tagaggtgggaatggcagga
protein_conc	4785	4433
WB_result	32.2	32.5
Ave_WB	32.3
WB_DONE_date	4/6/2015
MW
IP	1	1
antibody_Cat#	A303-135A	A303-135A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	4.2	0
Rep2_TPM	5.1	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2392	2393

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-27	BGHLV18-28
Sample_ID	BGHLV18-27	BGHLV18-28
Sample Name	MARK2_BGHLV18_27	MARK2_BGHLV18_28
Sample Name	MARK2_BGHLV18_27	MARK2_BGHLV18_28
RBP	MARK2	MARK2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	630	631

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-27	BGHLV18-28
Sample #
Sample Name	MARK2-BGHLV18-27	MARK2-BGHLV18-28
Sample_Name_Alias	MARK2_BGHLV18_27	MARK2_BGHLV18_28
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A3.png	DNA_Library_LV18-19/set1/B3.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/G9.png	RNA_Library_LV18-19/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-27	BGHLV18-28
RBP	MARK2	MARK2
Batch_ID	BGHLV18	BGHLV18
WB_result	32.200	32.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2314	2315

Sequencing Information

	BGHLV18-27	BGHLV18-28
Sample_ID	BGHLV18-27	BGHLV18-28
Sample Name	MARK2_BGHLV18_27	MARK2_BGHLV18_28
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	33,880,000	37,740,000
total_aligned_reads	29,609,592	34,057,600
unique_aligned_reads	27,981,638	32,156,312
percent_uniqueAligned	0.82590	0.85205
correlation_replicates	0.987179	0.987179
spikein_reads	60,210	129,732
percent_spikeins	0.00178	0.00344
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	956	957

Data Submission Information

	BGHLV18-27	BGHLV18-27
ENCODE_alias	brenton-graveley:MARK2_BGHLV18	brenton-graveley:MARK2-BGHLV18-HepG2
ENCODE_accession	ENCSR105OXX	ENCSR044OFY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-27	BGHLV18-27
Sample Name	MARK2_BGHLV18_27	MARK2_BGHLV18_27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2832	6806

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_BGHLV18_27_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	956	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14804
MARK2_BGHLV18_27_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	956	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14842
MARK2_BGHLV18_27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27_GTCCGC_L003_R1_001.fastq.gz,MARK2_BGHLV18_27_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	14880
MARK2_BGHLV18_27_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27/Aligned.sortedByCoord.out.bam		ENCORE2	14918
MARK2_BGHLV18_27_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27/Aligned.sortedByCoord.out.bam		ENCORE2	14956
MARK2_BGHLV18_27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27/Aligned.sortedByCoord.out.bam		ENCORE2	14994
MARK2_BGHLV18_27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27/Aligned.sortedByCoord.out.bam		ENCORE2	15032
MARK2_BGHLV18_27_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	956					GRCh38	V40	MARK2_BGHLV18_27_GTCCGC_L003_R1_001.fastq.gz,MARK2_BGHLV18_27_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	15070
MARK2_BGHLV18_28_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	957	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14805
MARK2_BGHLV18_28_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	957	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14843
MARK2_BGHLV18_28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28_GTGAAA_L003_R1_001.fastq.gz,MARK2_BGHLV18_28_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	14881
MARK2_BGHLV18_28_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28/Aligned.sortedByCoord.out.bam		ENCORE2	14919
MARK2_BGHLV18_28_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28/Aligned.sortedByCoord.out.bam		ENCORE2	14957
MARK2_BGHLV18_28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28/Aligned.sortedByCoord.out.bam		ENCORE2	14995
MARK2_BGHLV18_28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28/Aligned.sortedByCoord.out.bam		ENCORE2	15033
MARK2_BGHLV18_28_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	957					GRCh38	V40	MARK2_BGHLV18_28_GTGAAA_L003_R1_001.fastq.gz,MARK2_BGHLV18_28_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	15071