TBRG4 RNA-Seq in HepG2

General Information


RBP	TBRG4
Cell_Line	HepG2
Method	shRNA
Exp_Name	TBRG4-BGHLV27-HepG2
ENCODE_series_ID	ENCSR330RCO
Batch_ID	BGHLV27
Pool ID	Pool-151201
Local_Set_Name	set27
ENCODE_KD_Exp_ID	ENCSR741YCA
ENCODE_CN_Exp_ID	ENCSR246RRQ
Rep1	TBRG4_BGHLV27-55
Rep2	TBRG4_BGHLV27-56
CN1	non-target_BGHLV27-1
CN2	non-target_BGHLV27-2
Rep1_qPCR	41.2
Rep2_qPCR	40.2
Rep1_WB	82.5
Rep2_WB	83.4
Antibody Cat#	A301-392A
Antibody Lot#	A301-392A
Antibody DCC ID	ENCAB890JXZ
Status	Released
Project	ENCODE3
ID	646

Experiment Information (Status: Released)

	BGHLV27-55	BGHLV27-56
idx	675	676
TRCN#_or_BGC#	TRCN0000155887	TRCN0000155887
shRNA_or_gRNA_sequence	CACATTAGTGACCGTCATGAT	CACATTAGTGACCGTCATGAT
PAM
Name	TBRG4	TBRG4
Sample_ID	BGHLV27-55	BGHLV27-56
transduction_Date	6/9/2015	6/9/2015
days
RBP_name	TBRG4	TBRG4
qPCR_result	41.2	40.2
Ave_qPCR	40.7
RT-qPCR_primer-F	GCCAGAAGATAAAGGCTTGC
RT-qPCR_primer-R	GAGAGGGTACCATGCCAGAC
protein_conc	3184	2717
WB_result	82.5	83.4
Ave_WB	82.9
WB_DONE_date	7/24/2015
MW	72kDa
IP	1	1
antibody_Cat#	A301-392A	A301-392A
Antibody DCC ID	ENCAB890JXZ	ENCAB890JXZ
submitted_to_DCC_date	12/7/2015
Rep1_TPM	15.3	0
Rep2_TPM	20.8	0
Action
Library_start_date	9/28/2015	9/28/2015
repeat_library
Note	x	x
ID	2762	2763

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TBRG4	Product_ID: A301-392A Lot_ID: 1 Source: Bethyl Labs Target Name: TBRG4-human

Experiment Status

	BGHLV27-55	BGHLV27-56
Sample_ID	BGHLV27-55	BGHLV27-56
Sample Name	TBRG4_BGHLV27-55	TBRG4_BGHLV27-56
Sample Name	TBRG4_BGHLV27-55	TBRG4_BGHLV27-56
RBP	TBRG4	TBRG4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	978	979

Library-Prep
Sequencing

Library-Prep Information

	BGHLV27-55	BGHLV27-56
Sample #
Sample Name	TBRG4-BGHLV27-55	TBRG4-BGHLV27-56
Sample_Name_Alias	TBRG4_BGHLV27-55	TBRG4_BGHLV27-56
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-28	2015-09-28
Lib_ID	Lib-150928	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV27/set2/A1.png	DNA_Library_LV27/set2/B1.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/B7.png	RNA_Library_LV19-21-24/set2/C7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV27-55	BGHLV27-56
RBP	TBRG4	TBRG4
Batch_ID	BGHLV27	BGHLV27
WB_result	82.500	83.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2670	2671

Sequencing Information

	BGHLV27-55	BGHLV27-56
Sample_ID	BGHLV27-55	BGHLV27-56
Sample Name	TBRG4_BGHLV27-55	TBRG4_BGHLV27-56
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set27	set27
total_reads	84,194,674	73,751,880
total_aligned_reads	74,840,232	63,962,470
unique_aligned_reads	70,726,928	60,176,646
percent_uniqueAligned	0.84004	0.81593
correlation_replicates	0.982318	0.982318
spikein_reads	350,694	309,650
percent_spikeins	0.00417	0.00420
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1312	1313

Data Submission Information

	BGHLV27-55	BGHLV27-55
ENCODE_alias	brenton-graveley:TBRG4_BGHLV27	brenton-graveley:TBRG4-BGHLV27-HepG2
ENCODE_accession	ENCSR741YCA	ENCSR330RCO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV27-55	BGHLV27-55
Sample Name	TBRG4_BGHLV27-55	TBRG4_BGHLV27-55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3036	7003

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
TBRG4_BGHLV27-55_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1312	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20024
TBRG4_BGHLV27-55_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1312	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20046
TBRG4_BGHLV27-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55_1.fastq.gz,TBRG4_BGHLV27-55_2.fastq.gz		ENCORE2	20068
TBRG4_BGHLV27-55_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55/Aligned.sortedByCoord.out.bam		ENCORE2	20090
TBRG4_BGHLV27-55_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55/Aligned.sortedByCoord.out.bam		ENCORE2	20112
TBRG4_BGHLV27-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55/Aligned.sortedByCoord.out.bam		ENCORE2	20134
TBRG4_BGHLV27-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55/Aligned.sortedByCoord.out.bam		ENCORE2	20156
TBRG4_BGHLV27-55_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1312					GRCh38	V40	TBRG4_BGHLV27-55_1.fastq.gz,TBRG4_BGHLV27-55_2.fastq.gz		ENCORE2	20696
TBRG4_BGHLV27-56_1.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1313	HiSeq2500	100	paired-ended	1	GRCh38	V40		non-target_BGHLV27-1_1.fastq.gz,non-target_BGHLV27-2_1.fastq.gz	ENCODE3	20025
TBRG4_BGHLV27-56_2.fastq.gz	ENCODE_DATA/set27/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1313	HiSeq2500	100	paired-ended	2				non-target_BGHLV27-1_2.fastq.gz,non-target_BGHLV27-2_2.fastq.gz	ENCODE3	20047
TBRG4_BGHLV27-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56_1.fastq.gz,TBRG4_BGHLV27-56_2.fastq.gz		ENCORE2	20069
TBRG4_BGHLV27-56_Signal.Unique.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56/Aligned.sortedByCoord.out.bam		ENCORE2	20091
TBRG4_BGHLV27-56_Signal.Unique.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56/Aligned.sortedByCoord.out.bam		ENCORE2	20113
TBRG4_BGHLV27-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56/Aligned.sortedByCoord.out.bam		ENCORE2	20135
TBRG4_BGHLV27-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set27/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56/Aligned.sortedByCoord.out.bam		ENCORE2	20157
TBRG4_BGHLV27-56_quant.sf	ENCODE_DATA/set27/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1313					GRCh38	V40	TBRG4_BGHLV27-56_1.fastq.gz,TBRG4_BGHLV27-56_2.fastq.gz		ENCORE2	20697