TUFM RNA-Seq in HepG2

General Information


RBP	TUFM
Cell_Line	HepG2
Method	shRNA
Exp_Name	TUFM-BGHLV23-HepG2
ENCODE_series_ID	ENCSR139HZN
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR459EMR
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	TUFM-BGHLV23-53
Rep2	TUFM-BGHLV23-54
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	71.4
Rep2_qPCR	62.6
Rep1_WB	77.0
Rep2_WB	72.2
Antibody Cat#	GTX101763
Antibody Lot#	GTX101763
Antibody DCC ID	ENCAB531CVZ
Status	Released
Project	ENCODE3
ID	553

Experiment Information (Status: Released)

	BGHLV23-53	BGHLV23-54
idx	545	546
TRCN#_or_BGC#	TRCN0000165718	TRCN0000165718
shRNA_or_gRNA_sequence	CATAGCAAGAACATCCGCACT	CATAGCAAGAACATCCGCACT
PAM
Name	TUFM	TUFM
Sample_ID	BGHLV23-53	BGHLV23-54
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	TUFM	TUFM
qPCR_result	71.4	62.6
Ave_qPCR	67.0
RT-qPCR_primer-F	aggcccaggtttacatcctc
RT-qPCR_primer-R	tgtcccaagtcagggagaac
protein_conc	5632	5715
WB_result	77.0	72.2
Ave_WB	74.6
WB_DONE_date	5/11/2015
MW	50kDa
IP	1	1
antibody_Cat#	GTX101763	GTX101763
Antibody DCC ID	ENCAB531CVZ	ENCAB531CVZ
submitted_to_DCC_date	8/6/2015
Rep1_TPM	72.8	0
Rep2_TPM	76.3	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2626	2627

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TUFM	Product_ID: GTX101763 Lot_ID: 39694 Source: GeneTex Target Name: TUFM-human

Experiment Status

	BGHLV23-53	BGHLV23-54
Sample_ID	BGHLV23-53	BGHLV23-54
Sample Name	TUFM-BGHLV23-53	TUFM-BGHLV23-54
Sample Name	TUFM-BGHLV23-53	TUFM-BGHLV23-54
RBP	TUFM	TUFM
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	844	845

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-53	BGHLV23-54
Sample #
Sample Name	TUFM-BGHLV23-53	TUFM-BGHLV23-54
Sample_Name_Alias	TUFM-BGHLV23-53	TUFM-BGHLV23-54
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E10.png	DNA_Library_LV20-22-23/set1/F10.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E8.png	RNA_Library_LV22-23-25/set1/F8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-53	BGHLV23-54
RBP	TUFM	TUFM
Batch_ID	BGHLV23	BGHLV23
WB_result	77.000	72.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2532	2533

Sequencing Information

	BGHLV23-53	BGHLV23-54
Sample_ID	BGHLV23-53	BGHLV23-54
Sample Name	TUFM-BGHLV23-53	TUFM-BGHLV23-54
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	57,670,000	55,400,000
total_aligned_reads	51,994,004	50,126,122
unique_aligned_reads	49,180,568	47,318,644
percent_uniqueAligned	0.85279	0.85413
correlation_replicates	0.995606	0.995606
spikein_reads	290,536	197,578
percent_spikeins	0.00504	0.00357
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1154	1155

Data Submission Information

	BGHLV23-53	BGHLV23-53
ENCODE_alias	brenton-graveley:TUFM-BGHLV23	brenton-graveley:TUFM-BGHLV23-HepG2
ENCODE_accession	ENCSR459EMR	ENCSR139HZN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-53	BGHLV23-53
Sample Name	TUFM-BGHLV23-53	TUFM-BGHLV23-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2954	7019

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
TUFM-BGHLV23-53_AGTCAA_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1154	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16684
TUFM-BGHLV23-53_AGTCAA_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1154	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16722
TUFM-BGHLV23-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53_AGTCAA_L008_R1_001.fastq.gz,TUFM-BGHLV23-53_AGTCAA_L008_R2_001.fastq.gz		ENCORE2	16760
TUFM-BGHLV23-53_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	16798
TUFM-BGHLV23-53_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	16836
TUFM-BGHLV23-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	16874
TUFM-BGHLV23-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	16912
TUFM-BGHLV23-53_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1154					GRCh38	V40	TUFM-BGHLV23-53_AGTCAA_L008_R1_001.fastq.gz,TUFM-BGHLV23-53_AGTCAA_L008_R2_001.fastq.gz		ENCORE2	16950
TUFM-BGHLV23-54_AGTTCC_L008_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1155	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16685
TUFM-BGHLV23-54_AGTTCC_L008_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1155	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16723
TUFM-BGHLV23-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54_AGTTCC_L008_R1_001.fastq.gz,TUFM-BGHLV23-54_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	16761
TUFM-BGHLV23-54_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	16799
TUFM-BGHLV23-54_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	16837
TUFM-BGHLV23-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	16875
TUFM-BGHLV23-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	16913
TUFM-BGHLV23-54_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1155					GRCh38	V40	TUFM-BGHLV23-54_AGTTCC_L008_R1_001.fastq.gz,TUFM-BGHLV23-54_AGTTCC_L008_R2_001.fastq.gz		ENCORE2	16951