MTPAP RNA-Seq in K562

General Information


RBP	MTPAP
Cell_Line	K562
Method	shRNA
Exp_Name	MTPAP-BGKLV34-K562
ENCODE_series_ID	ENCSR564CIP
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR631RFX
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	MTPAP_BGKLV34-23
Rep2	MTPAP_BGKLV34-24
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	46.7
Rep2_qPCR	43.5
Rep1_WB	76.4
Rep2_WB	77.3
Antibody Cat#	A303-904A
Antibody Lot#	A303-904A
Antibody DCC ID	ENCAB235DTM
Status	Released
Project	ENCODE3
ID	722

Experiment Information (Status: Released)

	BGKLV34-23	BGKLV34-24
idx	686	687
TRCN#_or_BGC#	TRCN0000160380	TRCN0000160380
shRNA_or_gRNA_sequence	CGTTGGCAATGAATACATTAA	CGTTGGCAATGAATACATTAA
PAM
Name	MTPAP	MTPAP
Sample_ID	BGKLV34-23	BGKLV34-24
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	MTPAP	MTPAP
qPCR_result	46.7	43.5
Ave_qPCR	45.1
RT-qPCR_primer-F	ttggcaattttgctttcgat
RT-qPCR_primer-R	tggattctgaatgtacagaggaga
protein_conc	2259	2844
WB_result	76.4	77.3
Ave_WB	76.9
WB_DONE_date	2/16/2016
MW	88kda	WES
IP	1	1
antibody_Cat#	A303-904A	A303-904A
Antibody DCC ID	ENCAB235DTM	ENCAB235DTM
submitted_to_DCC_date	3/8/2016
Rep1_TPM	6.14658791	0
Rep2_TPM	3.50832717	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	777	778

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MTPAP	Product_ID: A303-904A Lot_ID: 1 Source: Bethyl Labs Target Name: MTPAP-human

Experiment Status

	BGKLV34-23	BGKLV34-24
Sample_ID	BGKLV34-23	BGKLV34-24
Sample Name	MTPAP_BGKLV34-23	MTPAP_BGKLV34-24
Sample Name	MTPAP_BGKLV34-23	MTPAP_BGKLV34-24
RBP	MTPAP	MTPAP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1231	1232

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-23	BGKLV34-24
Sample #
Sample Name	MTPAP-BGKLV34-23	MTPAP-BGKLV34-24
Sample_Name_Alias	MTPAP_BGKLV34-23	MTPAP_BGKLV34-24
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/A3.png	DNA_Library_LV33-34-25B-32/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/G4.png	RNA_Library_LV32-33-34/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-23	BGKLV34-24
RBP	MTPAP	MTPAP
Batch_ID	BGKLV34	BGKLV34
WB_result	76.400	77.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2916	2917

Sequencing Information

	BGKLV34-23	BGKLV34-24
Sample_ID	BGKLV34-23	BGKLV34-24
Sample Name	MTPAP_BGKLV34-23	MTPAP_BGKLV34-24
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	57,542,666	66,318,258
total_aligned_reads	48,427,156	56,108,126
unique_aligned_reads	44,143,450	51,146,236
percent_uniqueAligned	0.76714	0.77122
correlation_replicates	0.999002	0.999002
spikein_reads	266,096	274,668
percent_spikeins	0.00462	0.00414
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1565	1566

Data Submission Information

	BGKLV34-23	BGKLV34-23
ENCODE_alias	brenton-graveley:MTPAP_BGKLV34	brenton-graveley:MTPAP-BGKLV34-K562
ENCODE_accession	ENCSR631RFX	ENCSR564CIP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-23	BGKLV34-23
Sample Name	MTPAP_BGKLV34-23	MTPAP_BGKLV34-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3155	6815

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
MTPAP_BGKLV34-23_ATCACG_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1565	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21524
MTPAP_BGKLV34-23_ATCACG_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1565	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21544
MTPAP_BGKLV34-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23_ATCACG_L003_001.R1.fastq.gz,MTPAP_BGKLV34-23_ATCACG_L003_001.R2.fastq.gz		ENCORE2	21564
MTPAP_BGKLV34-23_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	21584
MTPAP_BGKLV34-23_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	21604
MTPAP_BGKLV34-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	21624
MTPAP_BGKLV34-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23/Aligned.sortedByCoord.out.bam		ENCORE2	21644
MTPAP_BGKLV34-23_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1565					GRCh38	V40	MTPAP_BGKLV34-23_ATCACG_L003_001.R1.fastq.gz,MTPAP_BGKLV34-23_ATCACG_L003_001.R2.fastq.gz		ENCORE2	21664
MTPAP_BGKLV34-24_CGATGT_L003_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1566	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21525
MTPAP_BGKLV34-24_CGATGT_L003_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1566	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21545
MTPAP_BGKLV34-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24_CGATGT_L003_001.R1.fastq.gz,MTPAP_BGKLV34-24_CGATGT_L003_001.R2.fastq.gz		ENCORE2	21565
MTPAP_BGKLV34-24_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	21585
MTPAP_BGKLV34-24_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	21605
MTPAP_BGKLV34-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	21625
MTPAP_BGKLV34-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24/Aligned.sortedByCoord.out.bam		ENCORE2	21645
MTPAP_BGKLV34-24_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1566					GRCh38	V40	MTPAP_BGKLV34-24_CGATGT_L003_001.R1.fastq.gz,MTPAP_BGKLV34-24_CGATGT_L003_001.R2.fastq.gz		ENCORE2	21665