CPSF3 RNA-Seq in K562

General Information


RBP	CPSF3
Cell_Line	K562
Method	CRISPR
Exp_Name	CPSF3-BGKcLV28-K562
ENCODE_series_ID	ENCSR249YGF
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR970WRV
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CPSF3-BGKcLV28-35
Rep2	CPSF3-BGKcLV28-36
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	80.1
Rep2_qPCR	78.5
Rep1_WB	69.0
Rep2_WB	72.8
Antibody Cat#	A301-090A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB903JBS
Status	Released
Project	ENCODE4
ID	832

Experiment Information (Status: Released)

	BGKcLV28-35	BGKcLV28-35	BGKcLV28-36	BGKcLV28-36
idx	973	975	974	976
TRCN#_or_BGC#	BGC#0000712	BGC#0000712	BGC#0000712	BGC#0000712
shRNA_or_gRNA_sequence	GTCCACGATATTGTAAACAG	GTCCACGATATTGTAAACAG	GTCCACGATATTGTAAACAG	GTCCACGATATTGTAAACAG
PAM	AGG	AGG	AGG	AGG
Name	CPSF3_85	CPSF3_85	CPSF3_85	CPSF3_85
Sample_ID	BGKcLV28-35	BGKcLV28-35	BGKcLV28-36	BGKcLV28-36
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CPSF3	CPSF3	CPSF3	CPSF3
qPCR_result	80.1	80.1	78.5	78.5
Ave_qPCR	79.3	79.3
RT-qPCR_primer-F	tgaatgacaaaatccgcaaa	tgaatgacaaaatccgcaaa
RT-qPCR_primer-R	tgggaccaatgtcatcaaaa	tgggaccaatgtcatcaaaa
protein_conc	2208	2208	1740	1740
WB_result	69.0	59.2	72.8	59.5340072
Ave_WB	70.9	59.4
WB_DONE_date	6/25/21B	10/13/21	JESS	JESS
MW	77kd	77kd
IP
antibody_Cat#	A301-090A	A301-091A	LOT #1
Antibody DCC ID	ENCAB903JBS		1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5107	5109	5108	5110

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

	BGKcLV28-35	BGKcLV28-36
Sample_ID	BGKcLV28-35	BGKcLV28-36
Sample Name
Sample Name	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-36
RBP	CPSF3	CPSF3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9923	9924

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-35	BGKcLV28-36
Sample #	31	32
Sample Name	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-36
Sample_Name_Alias
Index Well Position	G08	H08
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	370	323
Peak_Molarity	74.20	120.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G4.png	DNA_Library_set48-49/set3/H4.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/G4.png	RNA_Library_set48-49/set2/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-35	BGKcLV28-36
RBP	CPSF3	CPSF3
Batch_ID	BGKcLV28	BGKcLV28
WB_result	69.000	72.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2092	2093

Sequencing Information

	BGKcLV28-35	BGKcLV28-36
Sample_ID	BGKcLV28-35	BGKcLV28-36
Sample Name	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-36
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	181,708,536	108,429,312
total_aligned_reads	174,326,752	102,858,056
unique_aligned_reads	160,209,872	94,564,174
percent_uniqueAligned	0.88169	0.87213
correlation_replicates	0.998236	0.998236
spikein_reads	37,912	24,356
percent_spikeins	0.00021	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1843	1844

Data Submission Information

	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-36	BGKcLV28-36	BGKcLV28-36	BGKcLV28-36
ENCODE_alias	brenton-graveley:CPSF3-BGKcLV28	brenton-graveley:CPSF3-BGKcLV28-35	brenton-graveley:L-CPSF3-BGKcLV28-35	brenton-graveley:CPSF3-BGKcLV28-35_S113_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGKcLV28-35_S113_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGKcLV28-K562	brenton-graveley:CPSF3-BGKcLV28-36	brenton-graveley:L-CPSF3-BGKcLV28-36	brenton-graveley:CPSF3-BGKcLV28-36_S114_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF3-BGKcLV28-36_S114_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR970WRV	ENCBS749HME	ENCLB195ICQ	ENCFF376NVK	ENCFF398VKK	ENCSR249YGF	ENCBS952HTR	ENCLB068EAQ	ENCFF944AXH	ENCFF494HUA
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	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-35	BGKcLV28-36	BGKcLV28-36	BGKcLV28-36	BGKcLV28-36
Sample Name	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-35	CPSF3-BGKcLV28-36	CPSF3-BGKcLV28-36	CPSF3-BGKcLV28-36	CPSF3-BGKcLV28-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	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		CPSF3-BGKcLV28-35.pdf	L-CPSF3-BGKcLV28-35.pdf				CPSF3-BGKcLV28-36.pdf	L-CPSF3-BGKcLV28-36.pdf
ID	3486	3606	3740	3874	4008	7153	3607	3741	3875	4009

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-BGKcLV28-35_S113_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1843	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	3960
CPSF3-BGKcLV28-35_S113_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1843	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	4018
CPSF3-BGKcLV28-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1843					GRCh38	V40	CPSF3-BGKcLV28-35_S113_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGKcLV28-35_S113_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19242
CPSF3-BGKcLV28-35_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	1843					GRCh38	V40	CPSF3-BGKcLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	19300
CPSF3-BGKcLV28-35_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	1843					GRCh38	V40	CPSF3-BGKcLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	19358
CPSF3-BGKcLV28-35_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	1843					GRCh38	V40	CPSF3-BGKcLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	19416
CPSF3-BGKcLV28-35_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	1843					GRCh38	V40	CPSF3-BGKcLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	19474
CPSF3-BGKcLV28-35_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1843					GRCh38	V40	CPSF3-BGKcLV28-35_S113_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGKcLV28-35_S113_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19532
CPSF3-BGKcLV28-36_S114_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1844	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	3961
CPSF3-BGKcLV28-36_S114_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1844	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	4019
CPSF3-BGKcLV28-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1844					GRCh38	V40	CPSF3-BGKcLV28-36_S114_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGKcLV28-36_S114_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19243
CPSF3-BGKcLV28-36_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	1844					GRCh38	V40	CPSF3-BGKcLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	19301
CPSF3-BGKcLV28-36_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	1844					GRCh38	V40	CPSF3-BGKcLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	19359
CPSF3-BGKcLV28-36_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	1844					GRCh38	V40	CPSF3-BGKcLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	19417
CPSF3-BGKcLV28-36_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	1844					GRCh38	V40	CPSF3-BGKcLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	19475
CPSF3-BGKcLV28-36_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1844					GRCh38	V40	CPSF3-BGKcLV28-36_S114_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF3-BGKcLV28-36_S114_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19533