TRIM56 RNA-Seq in K562

General Information


RBP	TRIM56
Cell_Line	K562
Method	shRNA
Exp_Name	TRIM56-BGKLV21-K562
ENCODE_series_ID	ENCSR912QQL
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR300QFQ
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	TRIM56_BGKLV21_63_17590
Rep2	TRIM56_BGKLV21_64_17591
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	43.7
Rep2_qPCR	46.0
Rep1_WB	81.3
Rep2_WB	75.7
Antibody Cat#	A301-212A
Antibody Lot#	A301-212A
Antibody DCC ID	ENCAB769WDY
Status	Released
Project	ENCODE3
ID	521

Experiment Information (Status: Released)

	BGKLV21-63	BGKLV21-64
idx	334	335
TRCN#_or_BGC#	TRCN0000073093	TRCN0000073093
shRNA_or_gRNA_sequence	CGTCTTCTAGTGTGTGAGAAT	CGTCTTCTAGTGTGTGAGAAT
PAM
Name	TRIM56	TRIM56
Sample_ID	BGKLV21-63	BGKLV21-64
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	TRIM56	TRIM56
qPCR_result	43.7	46.0
Ave_qPCR	44.9
RT-qPCR_primer-F	cccaaggcctcagaagacta
RT-qPCR_primer-R	ttttacaggccaggaagtcg
protein_conc	3400	3260
WB_result	81.3	75.7
Ave_WB	78.5
WB_DONE_date	1/21/2015
MW
IP	1	1
antibody_Cat#	A301-212A	A301-212A
Antibody DCC ID	ENCAB769WDY	ENCAB769WDY
submitted_to_DCC_date	5/4/2015
Rep1_TPM	8.48720123	0
Rep2_TPM	13.184794	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	375	376

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TRIM56	Product_ID: A301-212A Lot_ID: 1 Source: Bethyl Labs Target Name: TRIM56-human

Experiment Status

	BGKLV21-63	BGKLV21-64
Sample_ID	BGKLV21-63	BGKLV21-64
Sample Name	TRIM56_BGKLV21_63_17590	TRIM56_BGKLV21_64_17591
Sample Name	TRIM56_BGKLV21_63_17590	TRIM56_BGKLV21_64_17591
RBP	TRIM56	TRIM56
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	776	777

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-63	BGKLV21-64
Sample #
Sample Name	TRIM56-BGKLV21-63	TRIM56-BGKLV21-64
Sample_Name_Alias	TRIM56_BGKLV21_63_17590	TRIM56_BGKLV21_64_17591
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A9.png	DNA_Library_LV21-24/set1/B9.png
RIN	9.6	9.3
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/A12.png	RNA_Library_LV19-21-24/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-63	BGKLV21-64
RBP	TRIM56	TRIM56
Batch_ID	BGKLV21	BGKLV21
WB_result	81.300	75.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2462	2463

Sequencing Information

	BGKLV21-63	BGKLV21-64
Sample_ID	BGKLV21-63	BGKLV21-64
Sample Name	TRIM56_BGKLV21_63_17590	TRIM56_BGKLV21_64_17591
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	38,610,000	52,650,000
total_aligned_reads	35,837,566	48,729,978
unique_aligned_reads	32,884,656	44,551,278
percent_uniqueAligned	0.85171	0.84618
correlation_replicates	0.999251	0.999251
spikein_reads	29,122	217,538
percent_spikeins	0.00075	0.00413
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1068	1069

Data Submission Information

	BGKLV21-63	BGKLV21-63
ENCODE_alias	brenton-graveley:TRIM56_BGKLV21	brenton-graveley:TRIM56-BGKLV21-K562
ENCODE_accession	ENCSR300QFQ	ENCSR912QQL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-63	BGKLV21-63
Sample Name	TRIM56_BGKLV21_63_17590	TRIM56_BGKLV21_63_17590
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2974	7014

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
TRIM56_BGKLV21_63_17590_GATCAG_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1068	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15960
TRIM56_BGKLV21_63_17590_GATCAG_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1068	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16004
TRIM56_BGKLV21_63_17590_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590_GATCAG_L004_R1_001.fastq.gz,TRIM56_BGKLV21_63_17590_GATCAG_L004_R2_001.fastq.gz		ENCORE2	16048
TRIM56_BGKLV21_63_17590_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590/Aligned.sortedByCoord.out.bam		ENCORE2	16092
TRIM56_BGKLV21_63_17590_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590/Aligned.sortedByCoord.out.bam		ENCORE2	16136
TRIM56_BGKLV21_63_17590_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590/Aligned.sortedByCoord.out.bam		ENCORE2	16180
TRIM56_BGKLV21_63_17590_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590/Aligned.sortedByCoord.out.bam		ENCORE2	16224
TRIM56_BGKLV21_63_17590_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1068					GRCh38	V40	TRIM56_BGKLV21_63_17590_GATCAG_L004_R1_001.fastq.gz,TRIM56_BGKLV21_63_17590_GATCAG_L004_R2_001.fastq.gz		ENCORE2	16268
TRIM56_BGKLV21_64_17591_TAGCTT_L004_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1069	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15961
TRIM56_BGKLV21_64_17591_TAGCTT_L004_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1069	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	16005
TRIM56_BGKLV21_64_17591_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591_TAGCTT_L004_R1_001.fastq.gz,TRIM56_BGKLV21_64_17591_TAGCTT_L004_R2_001.fastq.gz		ENCORE2	16049
TRIM56_BGKLV21_64_17591_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591/Aligned.sortedByCoord.out.bam		ENCORE2	16093
TRIM56_BGKLV21_64_17591_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591/Aligned.sortedByCoord.out.bam		ENCORE2	16137
TRIM56_BGKLV21_64_17591_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591/Aligned.sortedByCoord.out.bam		ENCORE2	16181
TRIM56_BGKLV21_64_17591_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591/Aligned.sortedByCoord.out.bam		ENCORE2	16225
TRIM56_BGKLV21_64_17591_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1069					GRCh38	V40	TRIM56_BGKLV21_64_17591_TAGCTT_L004_R1_001.fastq.gz,TRIM56_BGKLV21_64_17591_TAGCTT_L004_R2_001.fastq.gz		ENCORE2	16269