CPSF7 RNA-Seq in K562

General Information


RBP	CPSF7
Cell_Line	K562
Method	CRISPR
Exp_Name	CPSF7-BGKcLV28-K562
ENCODE_series_ID	ENCSR634BTM
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR709ILB
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CPSF7-BGKcLV28-39
Rep2	CPSF7-BGKcLV28-40
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	54.6
Rep2_qPCR	52.1
Rep1_WB	63.6
Rep2_WB	69.9
Antibody Cat#	A301-360A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB196XQB
Status	Released
Project	ENCODE4
ID	833

Experiment Information (Status: Released)

	BGKcLV28-39	BGKcLV28-40
idx	979	980
TRCN#_or_BGC#	BGC#0000716	BGC#0000716
shRNA_or_gRNA_sequence	GCAATTCTGTATACCTACAG	GCAATTCTGTATACCTACAG
PAM	TGG	TGG
Name	CPSF7_83	CPSF7_83
Sample_ID	BGKcLV28-39	BGKcLV28-40
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CPSF7	CPSF7
qPCR_result	54.6	52.1
Ave_qPCR	53.4
RT-qPCR_primer-F	tgtggatgcagcctttgata
RT-qPCR_primer-R	cagctggcagaggtgtgata
protein_conc	2357	2048
WB_result	63.6	69.9
Ave_WB	66.8
WB_DONE_date	6/25/21B	JESS
MW	52KD
IP
antibody_Cat#	A301-360A	LOT #1
Antibody DCC ID	ENCAB196XQB
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	5113	5114

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CPSF7	Product_ID: A301-360A Lot_ID: 1 Source: Bethyl Labs Target Name: CPSF7-human

Experiment Status

	BGKcLV28-39	BGKcLV28-40
Sample_ID	BGKcLV28-39	BGKcLV28-40
Sample Name
Sample Name	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-40
RBP	CPSF7	CPSF7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9925	9926

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-39	BGKcLV28-40
Sample #	33	34
Sample Name	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-40
Sample_Name_Alias
Index Well Position	A09	B09
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	311	334
Peak_Molarity	108.00	100.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A5.png	DNA_Library_set48-49/set3/B5.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/A5.png	RNA_Library_set48-49/set2/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-39	BGKcLV28-40
RBP	CPSF7	CPSF7
Batch_ID	BGKcLV28	BGKcLV28
WB_result	63.600	69.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2094	2095

Sequencing Information

	BGKcLV28-39	BGKcLV28-40
Sample_ID	BGKcLV28-39	BGKcLV28-40
Sample Name	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-40
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	103,574,318	91,344,908
total_aligned_reads	93,788,044	86,122,894
unique_aligned_reads	85,955,432	79,157,646
percent_uniqueAligned	0.82989	0.86658
correlation_replicates	0.998172	0.998172
spikein_reads	37,278	19,784
percent_spikeins	0.00036	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1845	1846

Data Submission Information

	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-40	BGKcLV28-40	BGKcLV28-40	BGKcLV28-40
ENCODE_alias	brenton-graveley:CPSF7-BGKcLV28	brenton-graveley:CPSF7-BGKcLV28-39	brenton-graveley:L-CPSF7-BGKcLV28-39	brenton-graveley:CPSF7-BGKcLV28-39_S115_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGKcLV28-39_S115_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGKcLV28-K562	brenton-graveley:CPSF7-BGKcLV28-40	brenton-graveley:L-CPSF7-BGKcLV28-40	brenton-graveley:CPSF7-BGKcLV28-40_S116_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CPSF7-BGKcLV28-40_S116_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR709ILB	ENCBS414SBT	ENCLB548YGS	ENCFF781MJV	ENCFF507LTI	ENCSR634BTM	ENCBS074OXD	ENCLB008IAX	ENCFF177FYQ	ENCFF789YAK
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	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-39	BGKcLV28-40	BGKcLV28-40	BGKcLV28-40	BGKcLV28-40
Sample Name	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-39	CPSF7-BGKcLV28-40	CPSF7-BGKcLV28-40	CPSF7-BGKcLV28-40	CPSF7-BGKcLV28-40
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		CPSF7-BGKcLV28-39.pdf	L-CPSF7-BGKcLV28-39.pdf				CPSF7-BGKcLV28-40.pdf	L-CPSF7-BGKcLV28-40.pdf
ID	3487	3608	3742	3876	4010	7156	3609	3743	3877	4011

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
CPSF7-BGKcLV28-39_S115_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1845	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	3962
CPSF7-BGKcLV28-39_S115_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1845	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	4020
CPSF7-BGKcLV28-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1845					GRCh38	V40	CPSF7-BGKcLV28-39_S115_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGKcLV28-39_S115_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19244
CPSF7-BGKcLV28-39_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	1845					GRCh38	V40	CPSF7-BGKcLV28-39/Aligned.sortedByCoord.out.bam		ENCORE2	19302
CPSF7-BGKcLV28-39_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	1845					GRCh38	V40	CPSF7-BGKcLV28-39/Aligned.sortedByCoord.out.bam		ENCORE2	19360
CPSF7-BGKcLV28-39_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	1845					GRCh38	V40	CPSF7-BGKcLV28-39/Aligned.sortedByCoord.out.bam		ENCORE2	19418
CPSF7-BGKcLV28-39_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	1845					GRCh38	V40	CPSF7-BGKcLV28-39/Aligned.sortedByCoord.out.bam		ENCORE2	19476
CPSF7-BGKcLV28-39_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1845					GRCh38	V40	CPSF7-BGKcLV28-39_S115_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGKcLV28-39_S115_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19534
CPSF7-BGKcLV28-40_S116_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1846	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	3963
CPSF7-BGKcLV28-40_S116_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1846	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	4021
CPSF7-BGKcLV28-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1846					GRCh38	V40	CPSF7-BGKcLV28-40_S116_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGKcLV28-40_S116_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19245
CPSF7-BGKcLV28-40_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	1846					GRCh38	V40	CPSF7-BGKcLV28-40/Aligned.sortedByCoord.out.bam		ENCORE2	19303
CPSF7-BGKcLV28-40_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	1846					GRCh38	V40	CPSF7-BGKcLV28-40/Aligned.sortedByCoord.out.bam		ENCORE2	19361
CPSF7-BGKcLV28-40_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	1846					GRCh38	V40	CPSF7-BGKcLV28-40/Aligned.sortedByCoord.out.bam		ENCORE2	19419
CPSF7-BGKcLV28-40_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	1846					GRCh38	V40	CPSF7-BGKcLV28-40/Aligned.sortedByCoord.out.bam		ENCORE2	19477
CPSF7-BGKcLV28-40_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1846					GRCh38	V40	CPSF7-BGKcLV28-40_S116_L004_R1_001.filtered.trimmed.paired.fastq.gz,CPSF7-BGKcLV28-40_S116_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19535