CCNT1 RNA-Seq in HepG2

General Information


RBP	CCNT1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CCNT1-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CCNT1-BGHcLV45-9
Rep2	CCNT1-BGHcLV45-10
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	83.7
Rep2_WB	84.2148
Antibody Cat#	81464S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1618

Experiment Information (Status: Submitting)

	BGHcLV45-9	BGHcLV45-10
idx	1442	1443
TRCN#_or_BGC#	BGC#0000674	BGC#0000674
shRNA_or_gRNA_sequence	TGGGTCCACGCCAAAACGAC	TGGGTCCACGCCAAAACGAC
PAM	GGG	GGG
Name	CCNT1_92	CCNT1_92
Sample_ID	BGHcLV45-9	BGHcLV45-10
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	CCNT1	CCNT1
qPCR_result	0.0	0.0
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3203	4091
WB_result	83.7	84.2148
Ave_WB
WB_DONE_date	10/9/24,11/1/24
MW	81kDa
IP
antibody_Cat#	81464S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9697	9698

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCNT1	Product_ID: 81464S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CCNT1-human

Experiment Status

	BGHcLV45-9	BGHcLV45-10
Sample_ID	BGHcLV45-9	BGHcLV45-10
Sample Name
Sample Name	CCNT1-BGHcLV45-9	CCNT1-BGHcLV45-10
RBP	CCNT1	CCNT1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13694	13695

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-9	BGHcLV45-10
Sample #	9	10
Sample Name	CCNT1-BGHcLV45-9	CCNT1-BGHcLV45-10
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	315	310
Peak_Molarity	93.00	91.40
libSampleQC_DNA_Well	DNA_Library_set76/set1/A8.png	DNA_Library_set76/set1/B8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set76/set1/A2.png	RNA_Library_set76/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-9	BGHcLV45-10
RBP	CCNT1	CCNT1
Batch_ID	BGHcLV45	BGHcLV45
WB_result	83.700	84.215
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4618	4619

Sequencing Information

	BGHcLV45-9	BGHcLV45-10
Sample_ID	BGHcLV45-9	BGHcLV45-10
Sample Name	CCNT1-BGHcLV45-9	CCNT1-BGHcLV45-10
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	32,621,252	33,332,506
total_aligned_reads	28,672,486	30,427,678
unique_aligned_reads	26,960,797	28,694,129
percent_uniqueAligned	0.82648	0.86085
correlation_replicates	0.998811	0.998811
spikein_reads	50,544	39,316
percent_spikeins	0.00155	0.00118
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3329	3330

Data Submission Information DCC submission information was not avaliable

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-BGHcLV45-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3329	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31819
CCNT1-BGHcLV45-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3329	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31861
CCNT1-BGHcLV45-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGHcLV45-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31903
CCNT1-BGHcLV45-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_Aligned.sortedByCoord.out.bam		ENCORE2	31945
CCNT1-BGHcLV45-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_Aligned.sortedByCoord.out.bam		ENCORE2	31987
CCNT1-BGHcLV45-9_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_Aligned.sortedByCoord.out.bam		ENCORE2	32029
CCNT1-BGHcLV45-9_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_Aligned.sortedByCoord.out.bam		ENCORE2	32071
CCNT1-BGHcLV45-9_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3329					GRCh38	V40	CCNT1-BGHcLV45-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGHcLV45-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32113
CCNT1-BGHcLV45-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3330	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31818
CCNT1-BGHcLV45-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3330	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31860
CCNT1-BGHcLV45-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGHcLV45-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31902
CCNT1-BGHcLV45-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_Aligned.sortedByCoord.out.bam		ENCORE2	31944
CCNT1-BGHcLV45-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_Aligned.sortedByCoord.out.bam		ENCORE2	31986
CCNT1-BGHcLV45-10_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_Aligned.sortedByCoord.out.bam		ENCORE2	32028
CCNT1-BGHcLV45-10_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_Aligned.sortedByCoord.out.bam		ENCORE2	32070
CCNT1-BGHcLV45-10_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3330					GRCh38	V40	CCNT1-BGHcLV45-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CCNT1-BGHcLV45-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32112