BOP1 RNA-Seq in HepG2

General Information


RBP	BOP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	BOP1-BGHLV35-HepG2
ENCODE_series_ID	ENCSR738DNW
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR925SYZ
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	BOP1_BGHLV35-9
Rep2	BOP1_BGHLV35-10
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	63.4
Rep2_qPCR	58.3
Rep1_WB
Rep2_WB
Antibody Cat#	A302-184A
Antibody Lot#	A302-184A
Antibody DCC ID	wrong AB
Status	Released
Project	ENCODE3
ID	730

Experiment Information (Status: Released)

	BGHLV35-9	BGHLV35-10
idx	865	866
TRCN#_or_BGC#	TRCN0000078069	TRCN0000078069
shRNA_or_gRNA_sequence	CTTGGAGTGGTACGATGACTT	CTTGGAGTGGTACGATGACTT
PAM
Name	BOP1	BOP1
Sample_ID	BGHLV35-9	BGHLV35-10
transduction_Date	4/29/16	4/29/16
days
RBP_name	BOP1	BOP1
qPCR_result	63.4	58.3
Ave_qPCR	60.9
RT-qPCR_primer-F	ctgagactgacggatgagca
RT-qPCR_primer-R	ggctcataggggttgaagc
protein_conc	2200	2193
WB_result
Ave_WB		MW is too high?
WB_DONE_date	6/8/16	WES
MW	84kDa
IP	1	1
antibody_Cat#	A302-184A	A302-184A
Antibody DCC ID	wrong AB
submitted_to_DCC_date
Rep1_TPM	9.2	9.2
Rep2_TPM	13.1	13.1
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2954	2955

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV35-9	BGHLV35-10
Sample_ID	BGHLV35-9	BGHLV35-10
Sample Name	BOP1_BGHLV35-9	BOP1_BGHLV35-10
Sample Name	BOP1_BGHLV35-9	BOP1_BGHLV35-10
RBP	BOP1	BOP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1250	1249

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-9	BGHLV35-10
Sample #
Sample Name	BOP1-BGHLV35-9	BOP1-BGHLV35-10
Sample_Name_Alias	BOP1_BGHLV35-9	BOP1_BGHLV35-10
Index Well Position	S04	S03
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/C1.png	DNA_Library_LV35/set2/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/C1.png	RNA_Library_LV35_LV36/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-9	BGHLV35-10
RBP	BOP1	BOP1
Batch_ID	BGHLV35	BGHLV35
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2935	2934

Sequencing Information

	BGHLV35-9	BGHLV35-10
Sample_ID	BGHLV35-9	BGHLV35-10
Sample Name	BOP1_BGHLV35-9	BOP1_BGHLV35-10
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	74,538,108	78,239,568
total_aligned_reads	59,959,948	61,593,890
unique_aligned_reads	56,208,650	57,540,438
percent_uniqueAligned	0.75409	0.73544
correlation_replicates	0.999636	0.999636
spikein_reads	96,984	100,306
percent_spikeins	0.00130	0.00128
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1584	1583

Data Submission Information

	BGHLV35-9	BGHLV35-9
ENCODE_alias	brenton-graveley:BOP1_BGHLV35	brenton-graveley:BOP1-BGHLV35-HepG2
ENCODE_accession	ENCSR925SYZ	ENCSR738DNW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-9	BGHLV35-9
Sample Name	BOP1_BGHLV35-9	BOP1_BGHLV35-9
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3164	6604

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
BOP1_BGHLV35-9_TTAGGC_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1584	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21683
BOP1_BGHLV35-9_TTAGGC_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1584	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21709
BOP1_BGHLV35-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9_TTAGGC_L005_001.R1.fastq.gz,BOP1_BGHLV35-9_TTAGGC_L005_001.R2.fastq.gz		ENCORE2	21735
BOP1_BGHLV35-9_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	21761
BOP1_BGHLV35-9_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	21787
BOP1_BGHLV35-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	21813
BOP1_BGHLV35-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9/Aligned.sortedByCoord.out.bam		ENCORE2	21839
BOP1_BGHLV35-9_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1584					GRCh38	V40	BOP1_BGHLV35-9_TTAGGC_L005_001.R1.fastq.gz,BOP1_BGHLV35-9_TTAGGC_L005_001.R2.fastq.gz		ENCORE2	21865
BOP1_BGHLV35-10_TGACCA_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1583	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21682
BOP1_BGHLV35-10_TGACCA_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1583	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21708
BOP1_BGHLV35-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10_TGACCA_L005_001.R1.fastq.gz,BOP1_BGHLV35-10_TGACCA_L005_001.R2.fastq.gz		ENCORE2	21734
BOP1_BGHLV35-10_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	21760
BOP1_BGHLV35-10_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	21786
BOP1_BGHLV35-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	21812
BOP1_BGHLV35-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10/Aligned.sortedByCoord.out.bam		ENCORE2	21838
BOP1_BGHLV35-10_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1583					GRCh38	V40	BOP1_BGHLV35-10_TGACCA_L005_001.R1.fastq.gz,BOP1_BGHLV35-10_TGACCA_L005_001.R2.fastq.gz		ENCORE2	21864