CPSF7 RNA-Seq in HepG2

General Information


RBP	CPSF7
Cell_Line	HepG2
Method	shRNA
Exp_Name	CPSF7-BGHLV30-HepG2
ENCODE_series_ID	ENCSR631XJU
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR594DNW
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	CPSF7_BGHLV30-21
Rep2	CPSF7_BGHLV30-22
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	80.9
Rep2_qPCR	76.8
Rep1_WB	92.0
Rep2_WB	88.7
Antibody Cat#	A301-359A
Antibody Lot#	A301-359A
Antibody DCC ID	ENCAB161FJH
Status	Released
Project	ENCODE3
ID	684

Experiment Information (Status: Released)

	BGHLV30-21	BGHLV30-22
idx	705	706
TRCN#_or_BGC#	TRCN0000161936	TRCN0000161936
shRNA_or_gRNA_sequence	GATCCAGGTTATTCGCTCTAT	GATCCAGGTTATTCGCTCTAT
PAM
Name	CPSF7	CPSF7
Sample_ID	BGHLV30-21	BGHLV30-22
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	CPSF7	CPSF7
qPCR_result	80.9	76.8
Ave_qPCR	78.9
RT-qPCR_primer-F	agccatgtcagaaggagtgg
RT-qPCR_primer-R	gtggctgtcagcacatcatc
protein_conc	4860	4914
WB_result	92.0	88.7
Ave_WB	90.3
WB_DONE_date	9/4/2015
MW	52kDa
IP	1	1
antibody_Cat#	A301-359A	A301-359A
Antibody DCC ID	ENCAB161FJH	ENCAB161FJH
submitted_to_DCC_date	12/7/2015
Rep1_TPM	5.5	0
Rep2_TPM	6.1	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2792	2793

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF7	Product_ID: A300-930A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF7-human

Experiment Status

	BGHLV30-21	BGHLV30-22
Sample_ID	BGHLV30-21	BGHLV30-22
Sample Name	CPSF7_BGHLV30-21	CPSF7_BGHLV30-22
Sample Name	CPSF7_BGHLV30-21	CPSF7_BGHLV30-22
RBP	CPSF7	CPSF7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1050	1051

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-21	BGHLV30-22
Sample #
Sample Name	CPSF7-BGHLV30-21	CPSF7-BGHLV30-22
Sample_Name_Alias	CPSF7_BGHLV30-21	CPSF7_BGHLV30-22
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C10.png	DNA_Library_LV28-29-30/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C5.png	RNA_Library_LV29-30-31-32/set1/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-21	BGHLV30-22
RBP	CPSF7	CPSF7
Batch_ID	BGHLV30	BGHLV30
WB_result	92.000	88.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2742	2743

Sequencing Information

	BGHLV30-21	BGHLV30-22
Sample_ID	BGHLV30-21	BGHLV30-22
Sample Name	CPSF7_BGHLV30-21	CPSF7_BGHLV30-22
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	84,389,754	101,087,960
total_aligned_reads	73,973,062	88,517,696
unique_aligned_reads	69,749,620	83,432,968
percent_uniqueAligned	0.82652	0.82535
correlation_replicates	0.997506	0.997506
spikein_reads	226,448	287,816
percent_spikeins	0.00268	0.00285
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1401	1402

Data Submission Information

	BGHLV30-21	BGHLV30-21
ENCODE_alias	brenton-graveley:CPSF7_BGHLV30	brenton-graveley:CPSF7-BGHLV30-HepG2
ENCODE_accession	ENCSR594DNW	ENCSR631XJU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-21	BGHLV30-21
Sample Name	CPSF7_BGHLV30-21	CPSF7_BGHLV30-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3074	6628

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
CPSF7_BGHLV30-21_TTAGGC_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1401	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20706
CPSF7_BGHLV30-21_TTAGGC_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1401	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20740
CPSF7_BGHLV30-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21_TTAGGC_L003_001.R1.fastq.gz,CPSF7_BGHLV30-21_TTAGGC_L003_001.R2.fastq.gz		ENCORE2	20774
CPSF7_BGHLV30-21_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21/Aligned.sortedByCoord.out.bam		ENCORE2	20808
CPSF7_BGHLV30-21_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21/Aligned.sortedByCoord.out.bam		ENCORE2	20842
CPSF7_BGHLV30-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21/Aligned.sortedByCoord.out.bam		ENCORE2	20876
CPSF7_BGHLV30-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21/Aligned.sortedByCoord.out.bam		ENCORE2	20910
CPSF7_BGHLV30-21_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1401					GRCh38	V40	CPSF7_BGHLV30-21_TTAGGC_L003_001.R1.fastq.gz,CPSF7_BGHLV30-21_TTAGGC_L003_001.R2.fastq.gz		ENCORE2	20944
CPSF7_BGHLV30-22_TGACCA_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1402	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20707
CPSF7_BGHLV30-22_TGACCA_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1402	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20741
CPSF7_BGHLV30-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22_TGACCA_L003_001.R1.fastq.gz,CPSF7_BGHLV30-22_TGACCA_L003_001.R2.fastq.gz		ENCORE2	20775
CPSF7_BGHLV30-22_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22/Aligned.sortedByCoord.out.bam		ENCORE2	20809
CPSF7_BGHLV30-22_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22/Aligned.sortedByCoord.out.bam		ENCORE2	20843
CPSF7_BGHLV30-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22/Aligned.sortedByCoord.out.bam		ENCORE2	20877
CPSF7_BGHLV30-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22/Aligned.sortedByCoord.out.bam		ENCORE2	20911
CPSF7_BGHLV30-22_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1402					GRCh38	V40	CPSF7_BGHLV30-22_TGACCA_L003_001.R1.fastq.gz,CPSF7_BGHLV30-22_TGACCA_L003_001.R2.fastq.gz		ENCORE2	20945