BCLAF1 RNA-Seq in HepG2

General Information


RBP	BCLAF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	BCLAF1-BGHLV17-HepG2
ENCODE_series_ID	ENCSR580SXH
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR481AYC
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	BCLAF1_BGHLV17_5
Rep2	BCLAF1_BGHLV17_6
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	75.0
Rep2_qPCR	81.6
Rep1_WB	99.4
Rep2_WB	98.3
Antibody Cat#	A300-608A
Antibody Lot#	A300-608A
Antibody DCC ID	ENCAB012FUX
Status	Released
Project	ENCODE3
ID	428

Experiment Information (Status: Released)

	BGHLV17-5	BGHLV17-6
idx	241	242
TRCN#_or_BGC#	TRCN0000336784	TRCN0000336784
shRNA_or_gRNA_sequence	GCGGTTCACTTCGTATCAGAA	GCGGTTCACTTCGTATCAGAA
PAM
Name	BCLAF1	BCLAF1
Sample_ID	BGHLV17-5	BGHLV17-6
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	BCLAF1	BCLAF1
qPCR_result	75.0	81.6
Ave_qPCR	78.3
RT-qPCR_primer-F	aatggcacctgttcctcttg
RT-qPCR_primer-R	ggatcggaattcttgctcct
protein_conc	2876	2894
WB_result	99.4	98.3
Ave_WB	98.9
WB_DONE_date	4/1/2015
MW	106kDa
IP	1	1
antibody_Cat#	A300-608A	A300-608A
Antibody DCC ID	ENCAB012FUX	ENCAB012FUX
submitted_to_DCC_date	5/4/2015
Rep1_TPM	44.9	0
Rep2_TPM	34.3	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2306	2307

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BCLAF1	Product_ID: A300-608A Lot_ID: 1 Source: Bethyl Labs Target Name: BCLAF1-human

Experiment Status

	BGHLV17-5	BGHLV17-6
Sample_ID	BGHLV17-5	BGHLV17-6
Sample Name	BCLAF1_BGHLV17_5	BCLAF1_BGHLV17_6
Sample Name	BCLAF1_BGHLV17_5	BCLAF1_BGHLV17_6
RBP	BCLAF1	BCLAF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	582	583

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-5	BGHLV17-6
Sample #
Sample Name	BCLAF1-BGHLV17-5	BCLAF1-BGHLV17-6
Sample_Name_Alias	BCLAF1_BGHLV17_5	BCLAF1_BGHLV17_6
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/E1.png	DNA_Library_LV16-17/set1/F1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E3.png	RNA_Library_LV16-17-18/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-5	BGHLV17-6
RBP	BCLAF1	BCLAF1
Batch_ID	BGHLV17	BGHLV17
WB_result	99.400	98.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2266	2267

Sequencing Information

	BGHLV17-5	BGHLV17-6
Sample_ID	BGHLV17-5	BGHLV17-6
Sample Name	BCLAF1_BGHLV17_5	BCLAF1_BGHLV17_6
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	72,940,000	50,410,000
total_aligned_reads	61,565,458	44,405,214
unique_aligned_reads	58,173,074	42,057,950
percent_uniqueAligned	0.79755	0.83432
correlation_replicates	0.996147	0.996147
spikein_reads	262,472	138,476
percent_spikeins	0.00360	0.00275
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	908	909

Data Submission Information

	BGHLV17-5	BGHLV17-5
ENCODE_alias	brenton-graveley:BCLAF1_BGHLV17	brenton-graveley:BCLAF1-BGHLV17-HepG2
ENCODE_accession	ENCSR481AYC	ENCSR580SXH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-5	BGHLV17-5
Sample Name	BCLAF1_BGHLV17_5	BCLAF1_BGHLV17_5
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2859	6602

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
BCLAF1_BGHLV17_5_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	908	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	14490
BCLAF1_BGHLV17_5_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	908	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	14528
BCLAF1_BGHLV17_5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	908					GRCh38	V40	BCLAF1_BGHLV17_5_ACAGTG_L001_R1_001.fastq.gz,BCLAF1_BGHLV17_5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	14566
BCLAF1_BGHLV17_5_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	908					GRCh38	V40	BCLAF1_BGHLV17_5/Aligned.sortedByCoord.out.bam		ENCORE2	14604
BCLAF1_BGHLV17_5_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	908					GRCh38	V40	BCLAF1_BGHLV17_5/Aligned.sortedByCoord.out.bam		ENCORE2	14642
BCLAF1_BGHLV17_5_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	908					GRCh38	V40	BCLAF1_BGHLV17_5/Aligned.sortedByCoord.out.bam		ENCORE2	14680
BCLAF1_BGHLV17_5_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	908					GRCh38	V40	BCLAF1_BGHLV17_5/Aligned.sortedByCoord.out.bam		ENCORE2	14718
BCLAF1_BGHLV17_5_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	908					GRCh38	V40	BCLAF1_BGHLV17_5_ACAGTG_L001_R1_001.fastq.gz,BCLAF1_BGHLV17_5_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	14756
BCLAF1_BGHLV17_6_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	909	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	14491
BCLAF1_BGHLV17_6_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	909	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	14529
BCLAF1_BGHLV17_6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	909					GRCh38	V40	BCLAF1_BGHLV17_6_GCCAAT_L001_R1_001.fastq.gz,BCLAF1_BGHLV17_6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	14567
BCLAF1_BGHLV17_6_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	909					GRCh38	V40	BCLAF1_BGHLV17_6/Aligned.sortedByCoord.out.bam		ENCORE2	14605
BCLAF1_BGHLV17_6_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	909					GRCh38	V40	BCLAF1_BGHLV17_6/Aligned.sortedByCoord.out.bam		ENCORE2	14643
BCLAF1_BGHLV17_6_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	909					GRCh38	V40	BCLAF1_BGHLV17_6/Aligned.sortedByCoord.out.bam		ENCORE2	14681
BCLAF1_BGHLV17_6_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	909					GRCh38	V40	BCLAF1_BGHLV17_6/Aligned.sortedByCoord.out.bam		ENCORE2	14719
BCLAF1_BGHLV17_6_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	909					GRCh38	V40	BCLAF1_BGHLV17_6_GCCAAT_L001_R1_001.fastq.gz,BCLAF1_BGHLV17_6_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	14757