MBNL1 RNA-Seq in K562

General Information


RBP	MBNL1
Cell_Line	K562
Method	shRNA
Exp_Name	MBNL1-BGKLV32-K562
ENCODE_series_ID	ENCSR445PCG
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR222COT
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	MBNL1_BGKLV32-39
Rep2	MBNL1_BGKLV32-40
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	58.0
Rep2_qPCR	59.7
Rep1_WB	64.6
Rep2_WB	58.5
Antibody Cat#	GTX112624
Antibody Lot#	GTX112624
Antibody DCC ID	ENCAB536MGT
Status	Released
Project	ENCODE3
ID	711

Experiment Information (Status: Released)

	BGKLV32-39	BGKLV32-39	BGKLV32-40	BGKLV32-40
idx	638	638	639	639
TRCN#_or_BGC#	TRCN0000063963	TRCN0000063963	TRCN0000063963	TRCN0000063963
shRNA_or_gRNA_sequence	GCAGTCTTTAACACTGGTATT	CCGGGCAGTCTTTAACACTGGTATTCTCGAGAATACCAGTGTTAAAGACTGCTTTTTG	GCAGTCTTTAACACTGGTATT	CCGGGCAGTCTTTAACACTGGTATTCTCGAGAATACCAGTGTTAAAGACTGCTTTTTG
PAM
Name	MBNL1	MBNL1	MBNL1	MBNL1
Sample_ID	BGKLV32-39	BGKLV32-39	BGKLV32-40	BGKLV32-40
transduction_Date	10/1/2015	10/1/2015	10/1/2015	10/1/2015
days
RBP_name	MBNL1	MBNL1	MBNL1	MBNL1
qPCR_result	58.0	58.0	59.7	59.7
Ave_qPCR	58.9	58.9
RT-qPCR_primer-F	ctgccgaacatctgactagc	ctgccgaacatctgactagc
RT-qPCR_primer-R	atggctaatgacctcgtcct	atggctaatgacctcgtcct
protein_conc	2800	2800	2900	2900
WB_result	64.6	69.1	58.5	76.1
Ave_WB	61.5	72.6
WB_DONE_date	11/20/2015	3/21/2019
MW	41kDa
IP	1		1
antibody_Cat#	GTX112624	PA5-19739	GTX112624
Antibody DCC ID	ENCAB536MGT		ENCAB536MGT
submitted_to_DCC_date	12/7/2015
Rep1_TPM	14.03904218	0	0	0
Rep2_TPM	11.24537824	0	0	0
Action
Library_start_date	3/7/2016		3/7/2016
repeat_library
Note
ID	727	729	728	730

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MBNL1	Product_ID: PA5-19739 Lot_ID: TK2672742 Source: Thermo Fisher Target Name: MBNL1-human

Experiment Status

	BGKLV32-39	BGKLV32-40
Sample_ID	BGKLV32-39	BGKLV32-40
Sample Name	MBNL1_BGKLV32-39	MBNL1_BGKLV32-40
Sample Name	MBNL1_BGKLV32-39	MBNL1_BGKLV32-40
RBP	MBNL1	MBNL1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1171	1172

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-39	BGKLV32-40
Sample #
Sample Name	MBNL1-BGKLV32-39	MBNL1-BGKLV32-40
Sample_Name_Alias	MBNL1_BGKLV32-39	MBNL1_BGKLV32-40
Index Well Position	S22	S23
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/E8.png	DNA_Library_LV33-34-25B-32/set1/F8.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E1.png	RNA_Library_LV35_LV36/set1/D12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-39	BGKLV32-40
RBP	MBNL1	MBNL1
Batch_ID	BGKLV32	BGKLV32
WB_result	64.600	58.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2856	2857

Sequencing Information

	BGKLV32-39	BGKLV32-40
Sample_ID	BGKLV32-39	BGKLV32-40
Sample Name	MBNL1_BGKLV32-39	MBNL1_BGKLV32-40
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	134,000,000	85,908,596
total_aligned_reads	113,935,726	73,190,216
unique_aligned_reads	104,117,646	67,386,514
percent_uniqueAligned	0.77700	0.78440
correlation_replicates	0.999131	0.999131
spikein_reads	411,972	305,542
percent_spikeins	0.00307	0.00356
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1505	1506

Data Submission Information

	BGKLV32-39	BGKLV32-39
ENCODE_alias	brenton-graveley:MBNL1_BGKLV32	brenton-graveley:MBNL1-BGKLV32-K562
ENCODE_accession	ENCSR222COT	ENCSR445PCG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-39	BGKLV32-39
Sample Name	MBNL1_BGKLV32-39	MBNL1_BGKLV32-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3125	6809

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
MBNL1_BGKLV32-39_CGTACG_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1505	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21204
MBNL1_BGKLV32-39_CGTACG_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1505	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21234
MBNL1_BGKLV32-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1505					GRCh38	V40	MBNL1_BGKLV32-39_CGTACG_L003_001.R1.fastq.gz,MBNL1_BGKLV32-39_CGTACG_L003_001.R2.fastq.gz		ENCORE2	21264
MBNL1_BGKLV32-39_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	1505					GRCh38	V40	MBNL1_BGKLV32-39/Aligned.sortedByCoord.out.bam		ENCORE2	21294
MBNL1_BGKLV32-39_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	1505					GRCh38	V40	MBNL1_BGKLV32-39/Aligned.sortedByCoord.out.bam		ENCORE2	21324
MBNL1_BGKLV32-39_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	1505					GRCh38	V40	MBNL1_BGKLV32-39/Aligned.sortedByCoord.out.bam		ENCORE2	21354
MBNL1_BGKLV32-39_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	1505					GRCh38	V40	MBNL1_BGKLV32-39/Aligned.sortedByCoord.out.bam		ENCORE2	21384
MBNL1_BGKLV32-39_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1505					GRCh38	V40	MBNL1_BGKLV32-39_CGTACG_L003_001.R1.fastq.gz,MBNL1_BGKLV32-39_CGTACG_L003_001.R2.fastq.gz		ENCORE2	21414
MBNL1_BGKLV32-40_GAGTGG_L003_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1506	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21205
MBNL1_BGKLV32-40_GAGTGG_L003_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1506	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21235
MBNL1_BGKLV32-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1506					GRCh38	V40	MBNL1_BGKLV32-40_GAGTGG_L003_001.R1.fastq.gz,MBNL1_BGKLV32-40_GAGTGG_L003_001.R2.fastq.gz		ENCORE2	21265
MBNL1_BGKLV32-40_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	1506					GRCh38	V40	MBNL1_BGKLV32-40/Aligned.sortedByCoord.out.bam		ENCORE2	21295
MBNL1_BGKLV32-40_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	1506					GRCh38	V40	MBNL1_BGKLV32-40/Aligned.sortedByCoord.out.bam		ENCORE2	21325
MBNL1_BGKLV32-40_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	1506					GRCh38	V40	MBNL1_BGKLV32-40/Aligned.sortedByCoord.out.bam		ENCORE2	21355
MBNL1_BGKLV32-40_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	1506					GRCh38	V40	MBNL1_BGKLV32-40/Aligned.sortedByCoord.out.bam		ENCORE2	21385
MBNL1_BGKLV32-40_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1506					GRCh38	V40	MBNL1_BGKLV32-40_GAGTGG_L003_001.R1.fastq.gz,MBNL1_BGKLV32-40_GAGTGG_L003_001.R2.fastq.gz		ENCORE2	21415