BCCIP RNA-Seq in HepG2

General Information


RBP	BCCIP
Cell_Line	HepG2
Method	shRNA
Exp_Name	BCCIP-BGHLV17-HepG2
ENCODE_series_ID	ENCSR459URX
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR570CWH
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	BCCIP_BGHLV17_45
Rep2	BCCIP_BGHLV17_46
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	84.2
Rep2_qPCR	85.7
Rep1_WB	94.0
Rep2_WB	95.5
Antibody Cat#	A302-196A
Antibody Lot#	A302-196A
Antibody DCC ID	ENCAB586MIB
Status	Released
Project	ENCODE3
ID	427

Experiment Information (Status: Released)

	BGHLV17-45	BGHLV17-46
idx	281	282
TRCN#_or_BGC#	TRCN0000072762	TRCN0000072762
shRNA_or_gRNA_sequence	GCCTTCTCCTAAGTGAAAGAT	GCCTTCTCCTAAGTGAAAGAT
PAM
Name	BCCIP	BCCIP
Sample_ID	BGHLV17-45	BGHLV17-46
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	BCCIP	BCCIP
qPCR_result	84.2	85.7
Ave_qPCR	84.9
RT-qPCR_primer-F	ttaatgtccctccacagatcg
RT-qPCR_primer-R	gcacttcccacatggcttat
protein_conc	2352	2319
WB_result	94.0	95.5
Ave_WB	94.7
WB_DONE_date	1/12/2015
MW
IP	1	1
antibody_Cat#	A302-196A	A302-196A
Antibody DCC ID	ENCAB586MIB	ENCAB586MIB
submitted_to_DCC_date	4/2/2015
Rep1_TPM	78	0
Rep2_TPM	59	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2346	2347

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCCIP	Product_ID: A302-196A Lot_ID: 1 Source: Bethyl Labs Target Name: BCCIP-human

Experiment Status

	BGHLV17-45	BGHLV17-46
Sample_ID	BGHLV17-45	BGHLV17-46
Sample Name	BCCIP_BGHLV17_45	BCCIP_BGHLV17_46
Sample Name	BCCIP_BGHLV17_45	BCCIP_BGHLV17_46
RBP	BCCIP	BCCIP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	580	581

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-45	BGHLV17-46
Sample #
Sample Name	BCCIP-BGHLV17-45	BCCIP-BGHLV17-46
Sample_Name_Alias	BCCIP_BGHLV17_45	BCCIP_BGHLV17_46
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E4.png	DNA_Library_LV16-17/set1/F4.png
RIN	8.2	8.3
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E6.png	RNA_Library_LV16-17-18/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-45	BGHLV17-46
RBP	BCCIP	BCCIP
Batch_ID	BGHLV17	BGHLV17
WB_result	94.000	95.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2264	2265

Sequencing Information

	BGHLV17-45	BGHLV17-46
Sample_ID	BGHLV17-45	BGHLV17-46
Sample Name	BCCIP_BGHLV17_45	BCCIP_BGHLV17_46
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	66,420,000	63,640,000
total_aligned_reads	60,780,970	58,619,098
unique_aligned_reads	57,221,800	55,265,854
percent_uniqueAligned	0.86151	0.86841
correlation_replicates	0.998026	0.998026
spikein_reads	212,810	203,476
percent_spikeins	0.00320	0.00320
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	906	907

Data Submission Information

	BGHLV17-45	BGHLV17-45
ENCODE_alias	brenton-graveley:BCCIP_BGHLV17	brenton-graveley:BCCIP-BGHLV17-HepG2
ENCODE_accession	ENCSR570CWH	ENCSR459URX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-45	BGHLV17-45
Sample Name	BCCIP_BGHLV17_45	BCCIP_BGHLV17_45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2858	6600

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
BCCIP_BGHLV17_45_ACAGTG_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	906	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14488
BCCIP_BGHLV17_45_ACAGTG_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	906	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14526
BCCIP_BGHLV17_45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45_ACAGTG_L004_R1_001.fastq.gz,BCCIP_BGHLV17_45_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	14564
BCCIP_BGHLV17_45_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45/Aligned.sortedByCoord.out.bam		ENCORE2	14602
BCCIP_BGHLV17_45_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45/Aligned.sortedByCoord.out.bam		ENCORE2	14640
BCCIP_BGHLV17_45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45/Aligned.sortedByCoord.out.bam		ENCORE2	14678
BCCIP_BGHLV17_45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45/Aligned.sortedByCoord.out.bam		ENCORE2	14716
BCCIP_BGHLV17_45_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	906					GRCh38	V40	BCCIP_BGHLV17_45_ACAGTG_L004_R1_001.fastq.gz,BCCIP_BGHLV17_45_ACAGTG_L004_R2_001.fastq.gz		ENCORE2	14754
BCCIP_BGHLV17_46_GCCAAT_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	907	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14489
BCCIP_BGHLV17_46_GCCAAT_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	907	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14527
BCCIP_BGHLV17_46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46_GCCAAT_L004_R1_001.fastq.gz,BCCIP_BGHLV17_46_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	14565
BCCIP_BGHLV17_46_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46/Aligned.sortedByCoord.out.bam		ENCORE2	14603
BCCIP_BGHLV17_46_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46/Aligned.sortedByCoord.out.bam		ENCORE2	14641
BCCIP_BGHLV17_46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46/Aligned.sortedByCoord.out.bam		ENCORE2	14679
BCCIP_BGHLV17_46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46/Aligned.sortedByCoord.out.bam		ENCORE2	14717
BCCIP_BGHLV17_46_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	907					GRCh38	V40	BCCIP_BGHLV17_46_GCCAAT_L004_R1_001.fastq.gz,BCCIP_BGHLV17_46_GCCAAT_L004_R2_001.fastq.gz		ENCORE2	14755