TRIM56 RNA-Seq in HepG2

General Information


RBP	TRIM56
Cell_Line	HepG2
Method	shRNA
Exp_Name	TRIM56-BGHLV20-HepG2
ENCODE_series_ID	ENCSR128QHC
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR309HXK
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	TRIM56-BGHLV20-61_17740
Rep2	TRIM56-BGHLV20-62_17741
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	77.4
Rep2_qPCR	59.6
Rep1_WB	64.1
Rep2_WB	59.8
Antibody Cat#	A301-212A
Antibody Lot#	A301-212A
Antibody DCC ID	ENCAB769WDY
Status	Released
Project	ENCODE3
ID	505

Experiment Information (Status: Released)

	BGHLV20-61	BGHLV20-62
idx	425	426
TRCN#_or_BGC#	TRCN0000073093	TRCN0000073093
shRNA_or_gRNA_sequence	CGTCTTCTAGTGTGTGAGAAT	CGTCTTCTAGTGTGTGAGAAT
PAM
Name	TRIM56	TRIM56
Sample_ID	BGHLV20-61	BGHLV20-62
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	TRIM56	TRIM56
qPCR_result	77.4	59.6
Ave_qPCR	68.5
RT-qPCR_primer-F	cccaaggcctcagaagacta
RT-qPCR_primer-R	ttttacaggccaggaagtcg
protein_conc	6296	6000
WB_result	64.1	59.8
Ave_WB	61.9
WB_DONE_date	4/7/2015
MW	81kDa
IP	1	1
antibody_Cat#	A301-212A	A301-212A
Antibody DCC ID	ENCAB769WDY	ENCAB769WDY
submitted_to_DCC_date	5/6/2015
Rep1_TPM	6.2	0
Rep2_TPM	6.7	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note	need change image/(qPCR redo)
ID	2492	2493

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

	BGHLV20-61	BGHLV20-62
Sample_ID	BGHLV20-61	BGHLV20-62
Sample Name	TRIM56-BGHLV20-61_17740	TRIM56-BGHLV20-62_17741
Sample Name	TRIM56-BGHLV20-61_17740	TRIM56-BGHLV20-62_17741
RBP	TRIM56	TRIM56
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	742	743

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-61	BGHLV20-62
Sample #
Sample Name	TRIM56-BGHLV20-61	TRIM56-BGHLV20-62
Sample_Name_Alias	TRIM56-BGHLV20-61_17740	TRIM56-BGHLV20-62_17741
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C5.png	DNA_Library_LV20-22-23/set1/D5.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/E11.png	RNA_Library_LV20-22-24/set1/F11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-61	BGHLV20-62
RBP	TRIM56	TRIM56
Batch_ID	BGHLV20	BGHLV20
WB_result	64.100	59.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2428	2429

Sequencing Information

	BGHLV20-61	BGHLV20-62
Sample_ID	BGHLV20-61	BGHLV20-62
Sample Name	TRIM56-BGHLV20-61_17740	TRIM56-BGHLV20-62_17741
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	59,840,000	48,250,000
total_aligned_reads	54,669,938	44,303,994
unique_aligned_reads	51,817,220	41,971,756
percent_uniqueAligned	0.86593	0.86988
correlation_replicates	0.996968	0.996968
spikein_reads	282,520	214,878
percent_spikeins	0.00472	0.00445
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1196	1197

Data Submission Information

	BGHLV20-61	BGHLV20-61
ENCODE_alias	brenton-graveley:TRIM56-BGHLV20	brenton-graveley:TRIM56-BGHLV20-HepG2
ENCODE_accession	ENCSR309HXK	ENCSR128QHC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-61	BGHLV20-61
Sample Name	TRIM56-BGHLV20-61_17740	TRIM56-BGHLV20-61_17740
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2920	7013

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-BGHLV20-61_17740_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1196	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15624
TRIM56-BGHLV20-61_17740_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1196	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15666
TRIM56-BGHLV20-61_17740_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740_GGCTAC_L005_R1_001.fastq.gz,TRIM56-BGHLV20-61_17740_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	15708
TRIM56-BGHLV20-61_17740_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740/Aligned.sortedByCoord.out.bam		ENCORE2	15750
TRIM56-BGHLV20-61_17740_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740/Aligned.sortedByCoord.out.bam		ENCORE2	15792
TRIM56-BGHLV20-61_17740_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740/Aligned.sortedByCoord.out.bam		ENCORE2	15834
TRIM56-BGHLV20-61_17740_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740/Aligned.sortedByCoord.out.bam		ENCORE2	15876
TRIM56-BGHLV20-61_17740_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1196					GRCh38	V40	TRIM56-BGHLV20-61_17740_GGCTAC_L005_R1_001.fastq.gz,TRIM56-BGHLV20-61_17740_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	15918
TRIM56-BGHLV20-62_17741_CTTGTA_L006_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1197	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15625
TRIM56-BGHLV20-62_17741_CTTGTA_L006_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1197	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15667
TRIM56-BGHLV20-62_17741_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741_CTTGTA_L006_R1_001.fastq.gz,TRIM56-BGHLV20-62_17741_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	15709
TRIM56-BGHLV20-62_17741_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741/Aligned.sortedByCoord.out.bam		ENCORE2	15751
TRIM56-BGHLV20-62_17741_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741/Aligned.sortedByCoord.out.bam		ENCORE2	15793
TRIM56-BGHLV20-62_17741_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741/Aligned.sortedByCoord.out.bam		ENCORE2	15835
TRIM56-BGHLV20-62_17741_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741/Aligned.sortedByCoord.out.bam		ENCORE2	15877
TRIM56-BGHLV20-62_17741_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1197					GRCh38	V40	TRIM56-BGHLV20-62_17741_CTTGTA_L006_R1_001.fastq.gz,TRIM56-BGHLV20-62_17741_CTTGTA_L006_R2_001.fastq.gz		ENCORE2	15919