CPSF2 RNA-Seq in HepG2

General Information


RBP	CPSF2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CPSF2-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR950QXS
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR224XSS
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CPSF2-BGHcLV29-33
Rep2	CPSF2-BGHcLV29-34
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	66.4
Rep2_qPCR	69.7
Rep1_WB	52.8
Rep2_WB	51.2
Antibody Cat#	A301-581A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB512SAR
Status	Submitted
Project	ENCODE4
ID	855

Experiment Information (Status: Released)

	BGHcLV29-33	BGHcLV29-33	BGHcLV29-34	BGHcLV29-34
idx	866	866	867	867
TRCN#_or_BGC#	BGC#0000709	BGC#0000709	BGC#0000709	BGC#0000709
shRNA_or_gRNA_sequence	CTTTCCGACAGCATACGGGA	CTTTCCGACAGCATACGGGA	CTTTCCGACAGCATACGGGA	CTTTCCGACAGCATACGGGA
PAM	GGG	GGG	GGG	GGG
Name	CPSF2_95	CPSF2_95	CPSF2_95	CPSF2_95
Sample_ID	BGHcLV29-33	BGHcLV29-33	BGHcLV29-34	BGHcLV29-34
transduction_Date	7/20	7/20	7/20	7/20
days	D6	D6	D6	D6
RBP_name	CPSF2	CPSF2	CPSF2	CPSF2
qPCR_result	66.4	66.4	69.7	69.7
Ave_qPCR	68.05	68.05
RT-qPCR_primer-F	tgtggatgcagcctttgata	tgtggatgcagcctttgata
RT-qPCR_primer-R	cagctggcagaggtgtgata	cagctggcagaggtgtgata
protein_conc	4192	4192	4698	4698
WB_result	52.8		51.2
Ave_WB	52.0
WB_DONE_date	7/30/21		JESS
MW	88kd	88kd
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A301-581A	A301-582A	LOT #1
Antibody DCC ID	ENCAB512SAR
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/5/21		11/5/21
repeat_library
Note
ID	7043	7045	7044	7046

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF2	Product_ID: A301-581A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF2-human

Experiment Status

	BGHcLV29-33	BGHcLV29-34
Sample_ID	BGHcLV29-33	BGHcLV29-34
Sample Name
Sample Name	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-34
RBP	CPSF2	CPSF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9995	9996

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-33	BGHcLV29-34
Sample #	23	24
Sample Name	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-34
Sample_Name_Alias
Index Well Position	G03	H03
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	287	320
Peak_Molarity	43.00	21.70
libSampleQC_DNA_Well	DNA_Library_set50/set1/G3.png	DNA_Library_set50/set1/H3.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set50/set1/G9.png	RNA_Library_set50/set1/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-33	BGHcLV29-34
RBP	CPSF2	CPSF2
Batch_ID	BGHcLV29	BGHcLV29
WB_result	52.800	51.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3110	3111

Sequencing Information

	BGHcLV29-33	BGHcLV29-34
Sample_ID	BGHcLV29-33	BGHcLV29-34
Sample Name	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-34
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	87,616,946	99,089,148
total_aligned_reads	80,265,078	86,985,926
unique_aligned_reads	75,718,420	81,883,724
percent_uniqueAligned	0.86420	0.82636
correlation_replicates	0.996921	0.996921
spikein_reads	16,280	17,754
percent_spikeins	0.00019	0.00018
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1891	1892

Data Submission Information

	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-34	BGHcLV29-34	BGHcLV29-34	BGHcLV29-34
ENCODE_alias	brenton-graveley:CPSF2-BGHcLV29	brenton-graveley:CPSF2-BGHcLV29-33	brenton-graveley:L-CPSF2-BGHcLV29-33	brenton-graveley:CPSF2-BGHcLV29-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGHcLV29-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGHcLV29-HepG2	brenton-graveley:CPSF2-BGHcLV29-34	brenton-graveley:L-CPSF2-BGHcLV29-34	brenton-graveley:CPSF2-BGHcLV29-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGHcLV29-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR224XSS	ENCBS174HKA	ENCLB936RIK	ENCFF957IQW	ENCFF872BAV	ENCSR950QXS	ENCBS253TGN	ENCLB035XKP	ENCFF732SFJ	ENCFF123MJP
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	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-33	BGHcLV29-34	BGHcLV29-34	BGHcLV29-34	BGHcLV29-34
Sample Name	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-33	CPSF2-BGHcLV29-34	CPSF2-BGHcLV29-34	CPSF2-BGHcLV29-34	CPSF2-BGHcLV29-34
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		CPSF2-BGHcLV29-33.pdf	L-CPSF2-BGHcLV29-33.pdf				CPSF2-BGHcLV29-34.pdf	L-CPSF2-BGHcLV29-34.pdf
ID	5853	5899	5971	6043	6115	6176	5900	5972	6044	6116

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
CPSF2-BGHcLV29-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1891	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	5779
CPSF2-BGHcLV29-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1891	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	5821
CPSF2-BGHcLV29-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1891					GRCh38	V40	CPSF2-BGHcLV29-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGHcLV29-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18946
CPSF2-BGHcLV29-33_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	1891					GRCh38	V40	CPSF2-BGHcLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	19004
CPSF2-BGHcLV29-33_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	1891					GRCh38	V40	CPSF2-BGHcLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	19050
CPSF2-BGHcLV29-33_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	1891					GRCh38	V40	CPSF2-BGHcLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	19096
CPSF2-BGHcLV29-33_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	1891					GRCh38	V40	CPSF2-BGHcLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	19142
CPSF2-BGHcLV29-33_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1891					GRCh38	V40	CPSF2-BGHcLV29-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGHcLV29-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19188
CPSF2-BGHcLV29-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1892	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	5780
CPSF2-BGHcLV29-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1892	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	5822
CPSF2-BGHcLV29-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1892					GRCh38	V40	CPSF2-BGHcLV29-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGHcLV29-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18947
CPSF2-BGHcLV29-34_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	1892					GRCh38	V40	CPSF2-BGHcLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	19005
CPSF2-BGHcLV29-34_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	1892					GRCh38	V40	CPSF2-BGHcLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	19051
CPSF2-BGHcLV29-34_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	1892					GRCh38	V40	CPSF2-BGHcLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	19097
CPSF2-BGHcLV29-34_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	1892					GRCh38	V40	CPSF2-BGHcLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	19143
CPSF2-BGHcLV29-34_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1892					GRCh38	V40	CPSF2-BGHcLV29-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGHcLV29-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19189