CPSF3 RNA-Seq in HepG2

General Information


RBP	CPSF3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CPSF3-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR820HEO
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR958OFR
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CPSF3-BGHcLV29-35
Rep2	CPSF3-BGHcLV29-36
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	59.1
Rep2_qPCR	62.7
Rep1_WB	53.4
Rep2_WB	54.2
Antibody Cat#	A301-090A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB903JBS
Status	Submitted
Project	ENCODE4
ID	856

Experiment Information (Status: Released)

	BGHcLV29-35	BGHcLV29-36
idx	868	869
TRCN#_or_BGC#	BGC#0000712	BGC#0000712
shRNA_or_gRNA_sequence	GTCCACGATATTGTAAACAG	GTCCACGATATTGTAAACAG
PAM	AGG	AGG
Name	CPSF3_85	CPSF3_85
Sample_ID	BGHcLV29-35	BGHcLV29-36
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CPSF3	CPSF3
qPCR_result	59.1	62.7
Ave_qPCR	60.9
RT-qPCR_primer-F	tgaatgacaaaatccgcaaa
RT-qPCR_primer-R	tgggaccaatgtcatcaaaa
protein_conc	5435	3584
WB_result	53.4	54.2
Ave_WB	53.8
WB_DONE_date	7/30/21	JESS
MW	77kd
IP	Rabbit / I
antibody_Cat#	A301-090A	LOT #1
Antibody DCC ID	ENCAB903JBS
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	7047	7048

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF3	Product_ID: A301-090A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF3-human

Experiment Status

	BGHcLV29-35	BGHcLV29-36
Sample_ID	BGHcLV29-35	BGHcLV29-36
Sample Name
Sample Name	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-36
RBP	CPSF3	CPSF3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9997	9998

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-35	BGHcLV29-36
Sample #	25	26
Sample Name	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-36
Sample_Name_Alias
Index Well Position	A04	B04
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	295	294
Peak_Molarity	36.80	36.20
libSampleQC_DNA_Well	DNA_Library_set50/set1/A4.png	DNA_Library_set50/set1/B4.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_set50/set1/A10.png	RNA_Library_set50/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-35	BGHcLV29-36
RBP	CPSF3	CPSF3
Batch_ID	BGHcLV29	BGHcLV29
WB_result	53.400	54.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3112	3113

Sequencing Information

	BGHcLV29-35	BGHcLV29-36
Sample_ID	BGHcLV29-35	BGHcLV29-36
Sample Name	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-36
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	93,725,464	61,849,534
total_aligned_reads	86,990,804	54,906,214
unique_aligned_reads	82,034,944	51,760,882
percent_uniqueAligned	0.87527	0.83688
correlation_replicates	0.998094	0.998094
spikein_reads	30,922	12,028
percent_spikeins	0.00033	0.00019
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1893	1894

Data Submission Information

	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-36	BGHcLV29-36	BGHcLV29-36	BGHcLV29-36
ENCODE_alias	brenton-graveley:CPSF3-BGHcLV29	brenton-graveley:CPSF3-BGHcLV29-35	brenton-graveley:L-CPSF3-BGHcLV29-35	brenton-graveley:CPSF3-BGHcLV29-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGHcLV29-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGHcLV29-HepG2	brenton-graveley:CPSF3-BGHcLV29-36	brenton-graveley:L-CPSF3-BGHcLV29-36	brenton-graveley:CPSF3-BGHcLV29-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGHcLV29-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR958OFR	ENCBS875FPP	ENCLB140KZJ	ENCFF541MRW	ENCFF845IWQ	ENCSR820HEO	ENCBS924UAE	ENCLB448KBD	ENCFF082ZSR	ENCFF463QCB
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	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-35	BGHcLV29-36	BGHcLV29-36	BGHcLV29-36	BGHcLV29-36
Sample Name	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-35	CPSF3-BGHcLV29-36	CPSF3-BGHcLV29-36	CPSF3-BGHcLV29-36	CPSF3-BGHcLV29-36
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		CPSF3-BGHcLV29-35.pdf	L-CPSF3-BGHcLV29-35.pdf				CPSF3-BGHcLV29-36.pdf	L-CPSF3-BGHcLV29-36.pdf
ID	5854	5901	5973	6045	6117	6177	5902	5974	6046	6118

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
CPSF3-BGHcLV29-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1893	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	5781
CPSF3-BGHcLV29-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1893	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	5823
CPSF3-BGHcLV29-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1893					GRCh38	V40	CPSF3-BGHcLV29-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGHcLV29-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18948
CPSF3-BGHcLV29-35_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	1893					GRCh38	V40	CPSF3-BGHcLV29-35/Aligned.sortedByCoord.out.bam		ENCORE2	19006
CPSF3-BGHcLV29-35_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	1893					GRCh38	V40	CPSF3-BGHcLV29-35/Aligned.sortedByCoord.out.bam		ENCORE2	19052
CPSF3-BGHcLV29-35_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	1893					GRCh38	V40	CPSF3-BGHcLV29-35/Aligned.sortedByCoord.out.bam		ENCORE2	19098
CPSF3-BGHcLV29-35_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	1893					GRCh38	V40	CPSF3-BGHcLV29-35/Aligned.sortedByCoord.out.bam		ENCORE2	19144
CPSF3-BGHcLV29-35_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1893					GRCh38	V40	CPSF3-BGHcLV29-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGHcLV29-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19190
CPSF3-BGHcLV29-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1894	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	5782
CPSF3-BGHcLV29-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1894	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	5824
CPSF3-BGHcLV29-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1894					GRCh38	V40	CPSF3-BGHcLV29-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGHcLV29-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18949
CPSF3-BGHcLV29-36_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	1894					GRCh38	V40	CPSF3-BGHcLV29-36/Aligned.sortedByCoord.out.bam		ENCORE2	19007
CPSF3-BGHcLV29-36_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	1894					GRCh38	V40	CPSF3-BGHcLV29-36/Aligned.sortedByCoord.out.bam		ENCORE2	19053
CPSF3-BGHcLV29-36_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	1894					GRCh38	V40	CPSF3-BGHcLV29-36/Aligned.sortedByCoord.out.bam		ENCORE2	19099
CPSF3-BGHcLV29-36_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	1894					GRCh38	V40	CPSF3-BGHcLV29-36/Aligned.sortedByCoord.out.bam		ENCORE2	19145
CPSF3-BGHcLV29-36_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1894					GRCh38	V40	CPSF3-BGHcLV29-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGHcLV29-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19191