CPSF2 RNA-Seq in K562

General Information


RBP	CPSF2
Cell_Line	K562
Method	CRISPR
Exp_Name	CPSF2-BGKcLV28-K562
ENCODE_series_ID	ENCSR433VPP
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR887XCL
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CPSF2-BGKcLV28-33
Rep2	CPSF2-BGKcLV28-34
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	63.0
Rep2_qPCR	80.0
Rep1_WB	70.5
Rep2_WB	67.6
Antibody Cat#	A301-581A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB512SAR
Status	Released
Project	ENCODE4
ID	831

Experiment Information (Status: Released)

	BGKcLV28-33	BGKcLV28-34
idx	971	972
TRCN#_or_BGC#	BGC#0000709	BGC#0000709
shRNA_or_gRNA_sequence	CTTTCCGACAGCATACGGGA	CTTTCCGACAGCATACGGGA
PAM	GGG	GGG
Name	CPSF2_95	CPSF2_95
Sample_ID	BGKcLV28-33	BGKcLV28-34
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CPSF2	CPSF2
qPCR_result	63.0	70.0
Ave_qPCR	66.5
RT-qPCR_primer-F	tgtggatgcagcctttgata
RT-qPCR_primer-R	cagctggcagaggtgtgata
protein_conc	1966	1735
WB_result	70.5	67.6
Ave_WB	69.0
WB_DONE_date	6/25/21B	JESS
MW	88kd
IP
antibody_Cat#	A301-581A	LOT #1
Antibody DCC ID	ENCAB512SAR	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5105	5106

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

	BGKcLV28-33	BGKcLV28-34
Sample_ID	BGKcLV28-33	BGKcLV28-34
Sample Name
Sample Name	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-34
RBP	CPSF2	CPSF2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9921	9922

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-33	BGKcLV28-34
Sample #	29	30
Sample Name	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-34
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	353	325
Peak_Molarity	99.50	96.20
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E4.png	DNA_Library_set48-49/set3/F4.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E4.png	RNA_Library_set48-49/set2/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-33	BGKcLV28-34
RBP	CPSF2	CPSF2
Batch_ID	BGKcLV28	BGKcLV28
WB_result	70.500	67.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2090	2091

Sequencing Information

	BGKcLV28-33	BGKcLV28-34
Sample_ID	BGKcLV28-33	BGKcLV28-34
Sample Name	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-34
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	127,584,274	110,323,544
total_aligned_reads	119,770,248	107,328,220
unique_aligned_reads	109,873,790	98,784,018
percent_uniqueAligned	0.86119	0.89540
correlation_replicates	0.960575	0.960575
spikein_reads	22,764	24,004
percent_spikeins	0.00018	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1841	1842

Data Submission Information

	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-34	BGKcLV28-34	BGKcLV28-34	BGKcLV28-34
ENCODE_alias	brenton-graveley:CPSF2-BGKcLV28	brenton-graveley:CPSF2-BGKcLV28-33	brenton-graveley:L-CPSF2-BGKcLV28-33	brenton-graveley:CPSF2-BGKcLV28-33_S111_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGKcLV28-33_S111_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGKcLV28-K562	brenton-graveley:CPSF2-BGKcLV28-34	brenton-graveley:L-CPSF2-BGKcLV28-34	brenton-graveley:CPSF2-BGKcLV28-34_S112_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF2-BGKcLV28-34_S112_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR887XCL	ENCBS862OGM	ENCLB231RII	ENCFF680YRZ	ENCFF591UAA	ENCSR433VPP	ENCBS692WQE	ENCLB444SVC	ENCFF870OFO	ENCFF072RPK
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	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-33	BGKcLV28-34	BGKcLV28-34	BGKcLV28-34	BGKcLV28-34
Sample Name	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-33	CPSF2-BGKcLV28-34	CPSF2-BGKcLV28-34	CPSF2-BGKcLV28-34	CPSF2-BGKcLV28-34
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CPSF2-BGKcLV28-33.pdf	L-CPSF2-BGKcLV28-33.pdf				CPSF2-BGKcLV28-34.pdf	L-CPSF2-BGKcLV28-34.pdf
ID	3485	3604	3738	3872	4006	7152	3605	3739	3873	4007

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-BGKcLV28-33_S111_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1841	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3958
CPSF2-BGKcLV28-33_S111_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1841	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4016
CPSF2-BGKcLV28-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33_S111_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGKcLV28-33_S111_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19240
CPSF2-BGKcLV28-33_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33/Aligned.sortedByCoord.out.bam		ENCORE2	19298
CPSF2-BGKcLV28-33_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33/Aligned.sortedByCoord.out.bam		ENCORE2	19356
CPSF2-BGKcLV28-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33/Aligned.sortedByCoord.out.bam		ENCORE2	19414
CPSF2-BGKcLV28-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33/Aligned.sortedByCoord.out.bam		ENCORE2	19472
CPSF2-BGKcLV28-33_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1841					GRCh38	V40	CPSF2-BGKcLV28-33_S111_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGKcLV28-33_S111_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19530
CPSF2-BGKcLV28-34_S112_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1842	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3959
CPSF2-BGKcLV28-34_S112_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1842	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4017
CPSF2-BGKcLV28-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34_S112_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGKcLV28-34_S112_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19241
CPSF2-BGKcLV28-34_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34/Aligned.sortedByCoord.out.bam		ENCORE2	19299
CPSF2-BGKcLV28-34_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34/Aligned.sortedByCoord.out.bam		ENCORE2	19357
CPSF2-BGKcLV28-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34/Aligned.sortedByCoord.out.bam		ENCORE2	19415
CPSF2-BGKcLV28-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34/Aligned.sortedByCoord.out.bam		ENCORE2	19473
CPSF2-BGKcLV28-34_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1842					GRCh38	V40	CPSF2-BGKcLV28-34_S112_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF2-BGKcLV28-34_S112_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19531