CCT4 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-11	BGHcLV49-12
idx	1710	1711
TRCN#_or_BGC#	BGC#0000679	BGC#0000679
shRNA_or_gRNA_sequence	TCGCAGCACTCGGTCCATCT	TCGCAGCACTCGGTCCATCT
PAM	GGG	GGG
Name	CCT4_86	CCT4_86
Sample_ID	BGHcLV49-11	BGHcLV49-12
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	CCT4	CCT4
qPCR_result	61.4	52.3
Ave_qPCR	56.9
RT-qPCR_primer-F	tgtctcgacctgtggaactg
RT-qPCR_primer-R	gtggctgggtcaatcacttt
protein_conc	4665	3844
WB_result	55.6	50.2
Ave_WB
WB_DONE_date	6/17/25
MW	58kd
IP
antibody_Cat#	A304-725A	LOT# 1
Antibody DCC ID	ENCAB174YJK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9899	9900

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCT4	Product_ID: A304-725A Lot_ID: 1 Source: Bethyl Labs Target Name: CCT4-human

Experiment Status

	BGHcLV49-11	BGHcLV49-12
Sample_ID	BGHcLV49-11	BGHcLV49-12
Sample Name
Sample Name	CCT4-BGHcLV49-11	CCT4-BGHcLV49-12
RBP	CCT4	CCT4
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14332	14333

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-11	BGHcLV49-12
Sample #	29	30
Sample Name	CCT4-BGHcLV49-11	CCT4-BGHcLV49-12
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	255	258
Peak_Molarity	82.40	61.90
libSampleQC_DNA_Well	DNA_Library_set81/set1/G1.png	DNA_Library_set81/set1/H1.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set81/set1/G4.png	RNA_Library_set81/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-11	BGHcLV49-12
RBP	CCT4	CCT4
Batch_ID	BGHcLV49	BGHcLV49
WB_result	55.600	50.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4774	4775

Sequencing Information

	BGHcLV49-11	BGHcLV49-12
Sample_ID	BGHcLV49-11	BGHcLV49-12
Sample Name	CCT4-BGHcLV49-11	CCT4-BGHcLV49-12
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	28,444,102	28,513,154
total_aligned_reads	22,652,263	23,534,068
unique_aligned_reads	21,214,508	22,108,328
percent_uniqueAligned	0.74583	0.77537
correlation_replicates	0.997700	0.997700
spikein_reads	81,258	78,020
percent_spikeins	0.00286	0.00274
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3501	3502

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
CCT4-BGHcLV49-11_S114_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3501	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33170
CCT4-BGHcLV49-11_S114_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3501	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33216
CCT4-BGHcLV49-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_S114_L008_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGHcLV49-11_S114_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33262
CCT4-BGHcLV49-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_Aligned.sortedByCoord.out.bam		ENCORE2	33308
CCT4-BGHcLV49-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_Aligned.sortedByCoord.out.bam		ENCORE2	33354
CCT4-BGHcLV49-11_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_Aligned.sortedByCoord.out.bam		ENCORE2	33400
CCT4-BGHcLV49-11_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_Aligned.sortedByCoord.out.bam		ENCORE2	33446
CCT4-BGHcLV49-11_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3501					GRCh38	V40	CCT4-BGHcLV49-11_S114_L008_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGHcLV49-11_S114_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33492
CCT4-BGHcLV49-12_S131_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3502	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33171
CCT4-BGHcLV49-12_S131_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3502	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33217
CCT4-BGHcLV49-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_S131_L008_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGHcLV49-12_S131_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33263
CCT4-BGHcLV49-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_Aligned.sortedByCoord.out.bam		ENCORE2	33309
CCT4-BGHcLV49-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_Aligned.sortedByCoord.out.bam		ENCORE2	33355
CCT4-BGHcLV49-12_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_Aligned.sortedByCoord.out.bam		ENCORE2	33401
CCT4-BGHcLV49-12_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_Aligned.sortedByCoord.out.bam		ENCORE2	33447
CCT4-BGHcLV49-12_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3502					GRCh38	V40	CCT4-BGHcLV49-12_S131_L008_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGHcLV49-12_S131_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33493