CPSF4 RNA-Seq in HepG2

General Information


RBP	CPSF4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CPSF4-BGHcLV24-HepG2
ENCODE_series_ID	ENCSR242BBP
Batch_ID	BGHcLV24
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR740WAG
ENCODE_CN_Exp_ID	ENCSR671FDZ
Rep1	CPSF4-BGHcLV24-23
Rep2	CPSF4-BGHcLV24-24
CN1	NT-BGHcLV24-1
CN2	NT-BGHcLV24-2
Rep1_qPCR	65.6
Rep2_qPCR	57.7
Rep1_WB	51.0
Rep2_WB	53.8
Antibody Cat#	A301-584A
Antibody Lot#	LOT#1
Antibody DCC ID	ENCAB277YJI
Status	Released
Project	ENCODE4
ID	6

Experiment Information (Status: Released)

	BGHcLV24-23	BGHcLV24-24
idx	681	682
TRCN#_or_BGC#	BGC#0000503	BGC#0000503
shRNA_or_gRNA_sequence	AGGCACGGTACCTTTGCTGG	AGGCACGGTACCTTTGCTGG
PAM	AGG	AGG
Name	CPSF4_88	CPSF4_88
Sample_ID	BGHcLV24-23	BGHcLV24-24
transduction_Date	10/30/20	10/30/20
days	D6	D6
RBP_name	CPSF4	CPSF4
qPCR_result	65.6	57.7
Ave_qPCR	61.7
RT-qPCR_primer-F	GGGCCCTCGTGTAAATTCAT
RT-qPCR_primer-R	CTTTGCTGGAGGCTGTGTCT
protein_conc	5071	5697
WB_result	51.0	53.8
Ave_WB	52.4
WB_DONE_date	11/18/20
MW	30kDa
IP	Rabbit / I
antibody_Cat#	A301-584A	LOT#1
Antibody DCC ID	ENCAB277YJI
submitted_to_DCC_date	12/09/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	8884	8885

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF4	Product_ID: A301-584A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF4-human

Experiment Status

	BGHcLV24-23	BGHcLV24-24
Sample_ID	BGHcLV24-23	BGHcLV24-24
Sample Name
Sample Name	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-24
RBP	CPSF4	CPSF4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7791	7792

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV24-23	BGHcLV24-24
Sample #	13	14
Sample Name	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-24
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	302	302
Peak_Molarity	71.20	81.00
libSampleQC_DNA_Well	DNA_Library_set47/set1/E5.png	DNA_Library_set47/set1/F5.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set1/E2.png	RNA_Library_set47/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV24-23	BGHcLV24-24
RBP	CPSF4	CPSF4
Batch_ID	BGHcLV24	BGHcLV24
WB_result	51.000	53.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1476	1477

Sequencing Information

	BGHcLV24-23	BGHcLV24-24
Sample_ID	BGHcLV24-23	BGHcLV24-24
Sample Name	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-24
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	104,013,332	120,803,958
total_aligned_reads	95,933,528	108,344,452
unique_aligned_reads	90,502,524	102,118,532
percent_uniqueAligned	0.87011	0.84532
correlation_replicates	0.996258	0.996258
spikein_reads	36,904	40,368
percent_spikeins	0.00035	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	558	559

Data Submission Information

	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-24	BGHcLV24-24	BGHcLV24-24	BGHcLV24-24
ENCODE_alias	brenton-graveley:CPSF4-BGHcLV24	brenton-graveley:CPSF4-BGHcLV24-23	brenton-graveley:L-CPSF4-BGHcLV24-23	brenton-graveley:CPSF4-BGHcLV24-23_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF4-BGHcLV24-23_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF4-BGHcLV24-HepG2	brenton-graveley:CPSF4-BGHcLV24-24	brenton-graveley:L-CPSF4-BGHcLV24-24	brenton-graveley:CPSF4-BGHcLV24-24_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF4-BGHcLV24-24_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR740WAG	ENCBS458UWG	ENCLB134BFX	ENCFF844HTQ	ENCFF888NYR	ENCSR242BBP	ENCBS137YOG	ENCLB910KLA	ENCFF376WXG	ENCFF190MUK
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	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-23	BGHcLV24-24	BGHcLV24-24	BGHcLV24-24	BGHcLV24-24
Sample Name	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-23	CPSF4-BGHcLV24-24	CPSF4-BGHcLV24-24	CPSF4-BGHcLV24-24	CPSF4-BGHcLV24-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		CPSF4-BGHcLV24-23.pdf	L-CPSF4-BGHcLV24-23.pdf				CPSF4-BGHcLV24-24.pdf	L-CPSF4-BGHcLV24-24.pdf
ID	3241	3269	3313	3357	3401	7154	3270	3314	3358	3402

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
CPSF4-BGHcLV24-23_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	558	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3716
CPSF4-BGHcLV24-23_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	558	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3762
CPSF4-BGHcLV24-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGHcLV24-23_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25405
CPSF4-BGHcLV24-23_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23_S73_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGHcLV24-23_S73_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25449
CPSF4-BGHcLV24-23_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23/Aligned.sortedByCoord.out.bam		ENCORE2	26281
CPSF4-BGHcLV24-23_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23/Aligned.sortedByCoord.out.bam		ENCORE2	26325
CPSF4-BGHcLV24-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23/Aligned.sortedByCoord.out.bam		ENCORE2	26369
CPSF4-BGHcLV24-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	558					GRCh38	V40	CPSF4-BGHcLV24-23/Aligned.sortedByCoord.out.bam		ENCORE2	26413
CPSF4-BGHcLV24-24_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	559	NovaSeq6000	100	paired-ended	1				NT-BGHcLV24-1_S61_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3717
CPSF4-BGHcLV24-24_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	559	NovaSeq6000	100	paired-ended	2				NT-BGHcLV24-1_S61_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV24-2_S62_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3763
CPSF4-BGHcLV24-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGHcLV24-24_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25406
CPSF4-BGHcLV24-24_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24_S74_L002_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGHcLV24-24_S74_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25450
CPSF4-BGHcLV24-24_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24/Aligned.sortedByCoord.out.bam		ENCORE2	26282
CPSF4-BGHcLV24-24_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24/Aligned.sortedByCoord.out.bam		ENCORE2	26326
CPSF4-BGHcLV24-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24/Aligned.sortedByCoord.out.bam		ENCORE2	26370
CPSF4-BGHcLV24-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	559					GRCh38	V40	CPSF4-BGHcLV24-24/Aligned.sortedByCoord.out.bam		ENCORE2	26414