CPSF7 RNA-Seq in HepG2

General Information


RBP	CPSF7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CPSF7-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR038ZCW
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR339XFB
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CPSF7-BGHcLV29-39
Rep2	CPSF7-BGHcLV29-40
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	8.2
Rep2_qPCR	19.3
Rep1_WB	79.0
Rep2_WB	78.8
Antibody Cat#	A301-360A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB196XQB
Status	Submitted
Project	ENCODE4
ID	857

Experiment Information (Status: Released)

	BGHcLV29-39	BGHcLV29-40
idx	872	873
TRCN#_or_BGC#	BGC#0000716	BGC#0000716
shRNA_or_gRNA_sequence	GCAATTCTGTATACCTACAG	GCAATTCTGTATACCTACAG
PAM	TGG	TGG
Name	CPSF7_83	CPSF7_83
Sample_ID	BGHcLV29-39	BGHcLV29-40
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CPSF7	CPSF7
qPCR_result	8.2	19.3
Ave_qPCR	13.75
RT-qPCR_primer-F	agccatgtcagaaggagtgg
RT-qPCR_primer-R	gtggctgtcagcacatcatc
protein_conc	4976	4838
WB_result	79.0	78.8
Ave_WB	78.9
WB_DONE_date	10/18/21	JESS
MW	52KD
IP	Rabbit / I
antibody_Cat#	A301-360A	LOT #1
Antibody DCC ID	ENCAB196XQB
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7051	7052

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF7	Product_ID: A301-360A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF7-human

Experiment Status

	BGHcLV29-39	BGHcLV29-40
Sample_ID	BGHcLV29-39	BGHcLV29-40
Sample Name
Sample Name	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-40
RBP	CPSF7	CPSF7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9999	10000

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-39	BGHcLV29-40
Sample #	27	28
Sample Name	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-40
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	289	292
Peak_Molarity	46.60	32.10
libSampleQC_DNA_Well	DNA_Library_set50/set1/C4.png	DNA_Library_set50/set1/D4.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set50/set1/C10.png	RNA_Library_set50/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-39	BGHcLV29-40
RBP	CPSF7	CPSF7
Batch_ID	BGHcLV29	BGHcLV29
WB_result	79.000	78.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3114	3115

Sequencing Information

	BGHcLV29-39	BGHcLV29-40
Sample_ID	BGHcLV29-39	BGHcLV29-40
Sample Name	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-40
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	107,757,610	82,068,608
total_aligned_reads	93,756,990	73,902,858
unique_aligned_reads	88,253,734	69,619,450
percent_uniqueAligned	0.81900	0.84831
correlation_replicates	0.998540	0.998540
spikein_reads	17,748	18,234
percent_spikeins	0.00016	0.00022
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1895	1896

Data Submission Information

	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-40	BGHcLV29-40	BGHcLV29-40	BGHcLV29-40
ENCODE_alias	brenton-graveley:CPSF7-BGHcLV29	brenton-graveley:CPSF7-BGHcLV29-39	brenton-graveley:L-CPSF7-BGHcLV29-39	brenton-graveley:CPSF7-BGHcLV29-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGHcLV29-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGHcLV29-HepG2	brenton-graveley:CPSF7-BGHcLV29-40	brenton-graveley:L-CPSF7-BGHcLV29-40	brenton-graveley:CPSF7-BGHcLV29-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGHcLV29-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR339XFB	ENCBS315ZKM	ENCLB627DOE	ENCFF576YYG	ENCFF476ROJ	ENCSR038ZCW	ENCBS512BUS	ENCLB303IHK	ENCFF303CIV	ENCFF084ZMM
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-39	BGHcLV29-40	BGHcLV29-40	BGHcLV29-40	BGHcLV29-40
Sample Name	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-39	CPSF7-BGHcLV29-40	CPSF7-BGHcLV29-40	CPSF7-BGHcLV29-40	CPSF7-BGHcLV29-40
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CPSF7-BGHcLV29-39.pdf	L-CPSF7-BGHcLV29-39.pdf				CPSF7-BGHcLV29-40.pdf	L-CPSF7-BGHcLV29-40.pdf
ID	5855	5903	5975	6047	6119	6178	5904	5976	6048	6120

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-BGHcLV29-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1895	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5783
CPSF7-BGHcLV29-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1895	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5825
CPSF7-BGHcLV29-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGHcLV29-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18950
CPSF7-BGHcLV29-39_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	19008
CPSF7-BGHcLV29-39_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	19054
CPSF7-BGHcLV29-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	19100
CPSF7-BGHcLV29-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39/Aligned.sortedByCoord.out.bam		ENCORE2	19146
CPSF7-BGHcLV29-39_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1895					GRCh38	V40	CPSF7-BGHcLV29-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGHcLV29-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19192
CPSF7-BGHcLV29-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1896	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5784
CPSF7-BGHcLV29-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1896	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5826
CPSF7-BGHcLV29-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGHcLV29-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18951
CPSF7-BGHcLV29-40_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	19009
CPSF7-BGHcLV29-40_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	19055
CPSF7-BGHcLV29-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	19101
CPSF7-BGHcLV29-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40/Aligned.sortedByCoord.out.bam		ENCORE2	19147
CPSF7-BGHcLV29-40_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1896					GRCh38	V40	CPSF7-BGHcLV29-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGHcLV29-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19193