CPSF6 RNA-Seq in HepG2

General Information


RBP	CPSF6
Cell_Line	HepG2
Method	shRNA
Exp_Name	CPSF6-BGHLV35-HepG2
ENCODE_series_ID	ENCSR109KPD
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR676EKU
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	CPSF6_BGHLV35-13
Rep2	CPSF6_BGHLV35-14
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	56.5
Rep2_qPCR	58.1
Rep1_WB	56.5
Rep2_WB	57.8
Antibody Cat#	A301-356A
Antibody Lot#	A301-356A
Antibody DCC ID	ENCAB652TTL
Status	Released
Project	ENCODE3
ID	731

Experiment Information (Status: Released)

	BGHLV35-13	BGHLV35-14
idx	869	870
TRCN#_or_BGC#	TRCN0000000154	TRCN0000000154
shRNA_or_gRNA_sequence	ACCATAGTAGATCACGAGAAA	ACCATAGTAGATCACGAGAAA
PAM
Name	CPSF6	CPSF6
Sample_ID	BGHLV35-13	BGHLV35-14
transduction_Date	4/29/16	4/29/16
days
RBP_name	CPSF6	CPSF6
qPCR_result	56.5	58.1
Ave_qPCR	57.3
RT-qPCR_primer-F	AGAGCGCGAATATCGTCATC
RT-qPCR_primer-R	CCCCCATGAAGACTGTTTTG
protein_conc	3671	3542
WB_result	56.5	57.8
Ave_WB	57.2
WB_DONE_date	5/10/2016	WES
MW	59kDa
IP	1	1
antibody_Cat#	A301-356A	A301-356A
Antibody DCC ID	ENCAB652TTL	ENCAB652TTL
submitted_to_DCC_date	10/26/16
Rep1_TPM	9.3	9.3
Rep2_TPM	10	10
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2958	2959

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF6	Product_ID: A301-356A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF6-human

Experiment Status

	BGHLV35-13	BGHLV35-14
Sample_ID	BGHLV35-13	BGHLV35-14
Sample Name	CPSF6_BGHLV35-13	CPSF6_BGHLV35-14
Sample Name	CPSF6_BGHLV35-13	CPSF6_BGHLV35-14
RBP	CPSF6	CPSF6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1251	1252

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-13	BGHLV35-14
Sample #
Sample Name	CPSF6-BGHLV35-13	CPSF6-BGHLV35-14
Sample_Name_Alias	CPSF6_BGHLV35-13	CPSF6_BGHLV35-14
Index Well Position	S05	S06
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/E1.png	DNA_Library_LV35/set2/F1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E1.png	RNA_Library_LV35_LV36/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-13	BGHLV35-14
RBP	CPSF6	CPSF6
Batch_ID	BGHLV35	BGHLV35
WB_result	56.500	57.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2936	2937

Sequencing Information

	BGHLV35-13	BGHLV35-14
Sample_ID	BGHLV35-13	BGHLV35-14
Sample Name	CPSF6_BGHLV35-13	CPSF6_BGHLV35-14
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	77,866,274	58,976,418
total_aligned_reads	58,521,990	45,611,696
unique_aligned_reads	55,225,052	42,978,306
percent_uniqueAligned	0.70923	0.72874
correlation_replicates	0.997601	0.997601
spikein_reads	99,222	97,392
percent_spikeins	0.00127	0.00165
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1585	1586

Data Submission Information

	BGHLV35-13	BGHLV35-13
ENCODE_alias	brenton-graveley:CPSF6_BGHLV35	brenton-graveley:CPSF6-BGHLV35-HepG2
ENCODE_accession	ENCSR676EKU	ENCSR109KPD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-13	BGHLV35-13
Sample Name	CPSF6_BGHLV35-13	CPSF6_BGHLV35-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3165	6626

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
CPSF6_BGHLV35-13_ACAGTG_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1585	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21684
CPSF6_BGHLV35-13_ACAGTG_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1585	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21710
CPSF6_BGHLV35-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1585					GRCh38	V40	CPSF6_BGHLV35-13_ACAGTG_L005_001.R1.fastq.gz,CPSF6_BGHLV35-13_ACAGTG_L005_001.R2.fastq.gz		ENCORE2	21736
CPSF6_BGHLV35-13_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	1585					GRCh38	V40	CPSF6_BGHLV35-13/Aligned.sortedByCoord.out.bam		ENCORE2	21762
CPSF6_BGHLV35-13_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	1585					GRCh38	V40	CPSF6_BGHLV35-13/Aligned.sortedByCoord.out.bam		ENCORE2	21788
CPSF6_BGHLV35-13_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	1585					GRCh38	V40	CPSF6_BGHLV35-13/Aligned.sortedByCoord.out.bam		ENCORE2	21814
CPSF6_BGHLV35-13_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	1585					GRCh38	V40	CPSF6_BGHLV35-13/Aligned.sortedByCoord.out.bam		ENCORE2	21840
CPSF6_BGHLV35-13_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1585					GRCh38	V40	CPSF6_BGHLV35-13_ACAGTG_L005_001.R1.fastq.gz,CPSF6_BGHLV35-13_ACAGTG_L005_001.R2.fastq.gz		ENCORE2	21866
CPSF6_BGHLV35-14_GCCAAT_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1586	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21685
CPSF6_BGHLV35-14_GCCAAT_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1586	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21711
CPSF6_BGHLV35-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1586					GRCh38	V40	CPSF6_BGHLV35-14_GCCAAT_L005_001.R1.fastq.gz,CPSF6_BGHLV35-14_GCCAAT_L005_001.R2.fastq.gz		ENCORE2	21737
CPSF6_BGHLV35-14_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	1586					GRCh38	V40	CPSF6_BGHLV35-14/Aligned.sortedByCoord.out.bam		ENCORE2	21763
CPSF6_BGHLV35-14_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	1586					GRCh38	V40	CPSF6_BGHLV35-14/Aligned.sortedByCoord.out.bam		ENCORE2	21789
CPSF6_BGHLV35-14_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	1586					GRCh38	V40	CPSF6_BGHLV35-14/Aligned.sortedByCoord.out.bam		ENCORE2	21815
CPSF6_BGHLV35-14_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	1586					GRCh38	V40	CPSF6_BGHLV35-14/Aligned.sortedByCoord.out.bam		ENCORE2	21841
CPSF6_BGHLV35-14_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1586					GRCh38	V40	CPSF6_BGHLV35-14_GCCAAT_L005_001.R1.fastq.gz,CPSF6_BGHLV35-14_GCCAAT_L005_001.R2.fastq.gz		ENCORE2	21867