CCNT1 RNA-Seq in K562

General Information


RBP	CCNT1
Cell_Line	K562
Method	CRISPR
Exp_Name	CCNT1-BGKcLV26-K562
ENCODE_series_ID	ENCSR296EDR
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR035MKJ
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CCNT1-BGKcLV26-65
Rep2	CCNT1-BGKcLV26-66
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	74.6
Rep2_WB	72.5
Antibody Cat#	A303-496A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB283VHI
Status	Released
Project	ENCODE4
ID	805

Experiment Information (Status: Released)

	BGKcLV26-65	BGKcLV26-65	BGKcLV26-66	BGKcLV26-66
idx	928	928	929	929
TRCN#_or_BGC#	BGC#0000673	BGC#0000673	BGC#0000673	BGC#0000673
shRNA_or_gRNA_sequence	CCACGCCAAAACGACGGGAT	CCACGCCAAAACGACGGGAT	CCACGCCAAAACGACGGGAT	CCACGCCAAAACGACGGGAT
PAM	GGG	GGG	GGG	GGG
Name	CCNT1_98	CCNT1_98	CCNT1_98	CCNT1_98
Sample_ID	BGKcLV26-65	BGKcLV26-65	BGKcLV26-66	BGKcLV26-66
transduction_Date	3/30/21	3/30/21	3/30/21	3/30/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CCNT1	CCNT1	CCNT1	CCNT1
qPCR_result	50.3	50.3	71.8	71.8
Ave_qPCR	61.0	61.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5849	5849	4315	4315
WB_result	74.6	96.3	72.5	96.7
Ave_WB	73.5	96.5
WB_DONE_date	5/17/21	7/6/22	jess	licor
MW	81kDa	81kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A303-496A	A303-497A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB283VHI	ENCAB973MTR	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/01/21		09/01/21
repeat_library
Note
ID	5060	5062	5061	5063

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCNT1	Product_ID: A303-496A Lot_ID: 1 Source: Bethyl Labs Target Name: CCNT1-human
CCNT1	Product_ID: A303-497A Lot_ID: 1 Source: Bethyl Labs Target Name: CCNT1-human

Experiment Status

	BGKcLV26-65	BGKcLV26-66
Sample_ID	BGKcLV26-65	BGKcLV26-66
Sample Name
Sample Name	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-66
RBP	CCNT1	CCNT1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9791	9792

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-65	BGKcLV26-66
Sample #	49	50
Sample Name	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-66
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	265	271
Peak_Molarity	72.70	68.50
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/A7.png	DNA_Library_set48-49/set1/B7.png
RIN	9.2	9.5
libSample_RNA_Well	RNA_Library_set48-49/set1/A7.png	RNA_Library_set48-49/set1/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-65	BGKcLV26-66
RBP	CCNT1	CCNT1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	74.600	72.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1608	1609

Sequencing Information

	BGKcLV26-65	BGKcLV26-66
Sample_ID	BGKcLV26-65	BGKcLV26-66
Sample Name	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-66
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	94,966,400	80,903,900
total_aligned_reads	73,220,984	60,436,260
unique_aligned_reads	66,984,524	55,244,282
percent_uniqueAligned	0.70535	0.68284
correlation_replicates	0.998831	0.998831
spikein_reads	90,330	36,792
percent_spikeins	0.00095	0.00045
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1785	1786

Data Submission Information

	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-66	BGKcLV26-66	BGKcLV26-66	BGKcLV26-66
ENCODE_alias	brenton-graveley:CCNT1-BGKcLV26	brenton-graveley:CCNT1-BGKcLV26-65	brenton-graveley:L-CCNT1-BGKcLV26-65	brenton-graveley:CCNT1-BGKcLV26-65_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCNT1-BGKcLV26-65_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCNT1-BGKcLV26-K562	brenton-graveley:CCNT1-BGKcLV26-66	brenton-graveley:L-CCNT1-BGKcLV26-66	brenton-graveley:CCNT1-BGKcLV26-66_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCNT1-BGKcLV26-66_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR035MKJ	ENCBS773ARL	ENCLB968GDN	ENCFF231CJL	ENCFF699YNW	ENCSR296EDR	ENCBS999TYZ	ENCLB821TNP	ENCFF913DXL	ENCFF661PEY
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	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-65	BGKcLV26-66	BGKcLV26-66	BGKcLV26-66	BGKcLV26-66
Sample Name	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-65	CCNT1-BGKcLV26-66	CCNT1-BGKcLV26-66	CCNT1-BGKcLV26-66	CCNT1-BGKcLV26-66
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		CCNT1-BGKcLV26-65.pdf	L-CCNT1-BGKcLV26-65.pdf				CCNT1-BGKcLV26-66.pdf	L-CCNT1-BGKcLV26-66.pdf
ID	3470	3574	3708	3842	3976	7121	3575	3709	3843	3977

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
CCNT1-BGKcLV26-65_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1785	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3878
CCNT1-BGKcLV26-65_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1785	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3928
CCNT1-BGKcLV26-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGKcLV26-65_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25565
CCNT1-BGKcLV26-65_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65_S55_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGKcLV26-65_S55_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25615
CCNT1-BGKcLV26-65_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65/Aligned.sortedByCoord.out.bam		ENCORE2	26581
CCNT1-BGKcLV26-65_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65/Aligned.sortedByCoord.out.bam		ENCORE2	26631
CCNT1-BGKcLV26-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65/Aligned.sortedByCoord.out.bam		ENCORE2	26681
CCNT1-BGKcLV26-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1785					GRCh38	V40	CCNT1-BGKcLV26-65/Aligned.sortedByCoord.out.bam		ENCORE2	26731
CCNT1-BGKcLV26-66_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1786	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3879
CCNT1-BGKcLV26-66_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1786	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3929
CCNT1-BGKcLV26-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGKcLV26-66_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25566
CCNT1-BGKcLV26-66_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66_S56_L003_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGKcLV26-66_S56_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25616
CCNT1-BGKcLV26-66_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66/Aligned.sortedByCoord.out.bam		ENCORE2	26582
CCNT1-BGKcLV26-66_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66/Aligned.sortedByCoord.out.bam		ENCORE2	26632
CCNT1-BGKcLV26-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66/Aligned.sortedByCoord.out.bam		ENCORE2	26682
CCNT1-BGKcLV26-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1786					GRCh38	V40	CCNT1-BGKcLV26-66/Aligned.sortedByCoord.out.bam		ENCORE2	26732