CPSF4 RNA-Seq in K562

General Information


RBP	CPSF4
Cell_Line	K562
Method	CRISPR
Exp_Name	CPSF4-BGKcLV21-K562
ENCODE_series_ID	ENCSR135RBH
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR854MSP
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	CPSF4-BGKcLV21-11
Rep2	CPSF4-BGKcLV21-12
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	20.0
Rep2_qPCR	0.0
Rep1_WB	66.7
Rep2_WB	66.1505675
Antibody Cat#	A301-584A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB277YJI
Status	Released
Project	ENCODE4
ID	64

Experiment Information (Status: Released)

	BGKcLV21-11	BGKcLV21-12
idx	744	745
TRCN#_or_BGC#	BGC#0000504	BGC#0000504
shRNA_or_gRNA_sequence	CATGACCCCGATGACCTGCG	CATGACCCCGATGACCTGCG
PAM	GGG	GGG
Name	CPSF4_90	CPSF4_90
Sample_ID	BGKcLV21-11	BGKcLV21-12
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	CPSF4	CPSF4
qPCR_result	20.0	0.0
Ave_qPCR	10.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3863	3685
WB_result	66.7	66.1505675
Ave_WB	66.4
WB_DONE_date	1/14/21
MW	30kDa
IP	Rabbit / I
antibody_Cat#	A301-584A	Lot# 1
Antibody DCC ID	ENCAB277YJI
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4864	4865

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

	BGKcLV21-11	BGKcLV21-12
Sample_ID	BGKcLV21-11	BGKcLV21-12
Sample Name
Sample Name	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-12
RBP	CPSF4	CPSF4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6119	6120

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-11	BGKcLV21-12
Sample #	37	38
Sample Name	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-12
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	300	297
Peak_Molarity	177.00	101.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/G4.png	DNA_Library_set45/set1/H4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set45/set1/G4.png	RNA_Library_set45/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-11	BGKcLV21-12
RBP	CPSF4	CPSF4
Batch_ID	BGKcLV21	BGKcLV21
WB_result	63.700	64.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	811	812

Sequencing Information

	BGKcLV21-11	BGKcLV21-12
Sample_ID	BGKcLV21-11	BGKcLV21-12
Sample Name	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-12
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	62,854,754	106,702,642
total_aligned_reads	62,157,350	106,522,306
unique_aligned_reads	56,757,026	97,171,566
percent_uniqueAligned	0.90299	0.91068
correlation_replicates	0.973267	0.973267
spikein_reads	29,804	49,628
percent_spikeins	0.00047	0.00047
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	442	443

Data Submission Information

	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-12	BGKcLV21-12	BGKcLV21-12	BGKcLV21-12
ENCODE_alias	brenton-graveley:CPSF4-BGKcLV21	brenton-graveley:CPSF4-BGKcLV21-11	brenton-graveley:L-CPSF4-BGKcLV21-11	brenton-graveley:CPSF4-BGKcLV21-11_S31_R1_001.fastq.gz	brenton-graveley:CPSF4-BGKcLV21-11_S31_R2_001.fastq.gz	brenton-graveley:CPSF4-BGKcLV21-K562	brenton-graveley:CPSF4-BGKcLV21-12	brenton-graveley:L-CPSF4-BGKcLV21-12	brenton-graveley:CPSF4-BGKcLV21-12_S32_R1_001.fastq.gz	brenton-graveley:CPSF4-BGKcLV21-12_S32_R2_001.fastq.gz
ENCODE_accession	ENCSR854MSP	ENCBS689YZE	ENCLB220LMM	ENCFF862IPI	ENCFF972NNI	ENCSR135RBH	ENCBS672XZR	ENCLB010SNF	ENCFF795CAW	ENCFF125PVH
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	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-11	BGKcLV21-12	BGKcLV21-12	BGKcLV21-12	BGKcLV21-12
Sample Name	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-11	CPSF4-BGKcLV21-12	CPSF4-BGKcLV21-12	CPSF4-BGKcLV21-12	CPSF4-BGKcLV21-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		CPSF4-BGKcLV21-11.pdf	L-CPSF4-BGKcLV21-11.pdf				CPSF4-BGKcLV21-12.pdf	L-CPSF4-BGKcLV21-12.pdf
ID	2105	2165	2235	2305	2375	7155	2166	2236	2306	2376

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-BGKcLV21-11_S31_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	442	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1214
CPSF4-BGKcLV21-11_S31_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	442	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1264
CPSF4-BGKcLV21-11_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11_S31_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGKcLV21-11_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25207
CPSF4-BGKcLV21-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11_S31_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGKcLV21-11_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27161
CPSF4-BGKcLV21-11_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11/Aligned.sortedByCoord.out.bam		ENCORE2	27211
CPSF4-BGKcLV21-11_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11/Aligned.sortedByCoord.out.bam		ENCORE2	27261
CPSF4-BGKcLV21-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11/Aligned.sortedByCoord.out.bam		ENCORE2	27311
CPSF4-BGKcLV21-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	442					GRCh38	V40	CPSF4-BGKcLV21-11/Aligned.sortedByCoord.out.bam		ENCORE2	27361
CPSF4-BGKcLV21-12_S32_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	443	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1215
CPSF4-BGKcLV21-12_S32_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	443	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1265
CPSF4-BGKcLV21-12_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12_S32_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGKcLV21-12_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25208
CPSF4-BGKcLV21-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12_S32_R1_001.filtered.trimmed.paired.fastq.gz,CPSF4-BGKcLV21-12_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27162
CPSF4-BGKcLV21-12_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12/Aligned.sortedByCoord.out.bam		ENCORE2	27212
CPSF4-BGKcLV21-12_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12/Aligned.sortedByCoord.out.bam		ENCORE2	27262
CPSF4-BGKcLV21-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12/Aligned.sortedByCoord.out.bam		ENCORE2	27312
CPSF4-BGKcLV21-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	443					GRCh38	V40	CPSF4-BGKcLV21-12/Aligned.sortedByCoord.out.bam		ENCORE2	27362