CCT4 RNA-Seq in K562

General Information


RBP	CCT4
Cell_Line	K562
Method	CRISPR
Exp_Name	CCT4-BGKcLV28-K562
ENCODE_series_ID	ENCSR946GVC
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR995XEP
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CCT4-BGKcLV28-7
Rep2	CCT4-BGKcLV28-8
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	76.0
Rep2_qPCR	74.7
Rep1_WB	60.9
Rep2_WB	59.4
Antibody Cat#	A304-725A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB174YJK
Status	Released
Project	ENCODE4
ID	820

Experiment Information (Status: Released)

	BGKcLV28-7	BGKcLV28-7	BGKcLV28-8	BGKcLV28-8
idx	939	941	940	942
TRCN#_or_BGC#	BGC#0000679	BGC#0000679	BGC#0000679	BGC#0000679
shRNA_or_gRNA_sequence	TCGCAGCACTCGGTCCATCT	TCGCAGCACTCGGTCCATCT	TCGCAGCACTCGGTCCATCT	TCGCAGCACTCGGTCCATCT
PAM	GGG	GGG	GGG	GGG
Name	CCT4_86	CCT4_86	CCT4_86	CCT4_86
Sample_ID	BGKcLV28-7	BGKcLV28-7	BGKcLV28-8	BGKcLV28-8
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CCT4	CCT4	CCT4	CCT4
qPCR_result	76.0	76.0	74.7	74.7
Ave_qPCR	75.4	75.4
RT-qPCR_primer-F	tgtctcgacctgtggaactg	tgtctcgacctgtggaactg
RT-qPCR_primer-R	gtggctgggtcaatcacttt	gtggctgggtcaatcacttt
protein_conc	2039	2039	1994	1994
WB_result	60.9	50.2	59.4	51.0002788
Ave_WB	60.1	50.6
WB_DONE_date	6/23/21	2/14/22	JESS	JESS
MW	58kd	58kd
IP
antibody_Cat#	A304-725A	A304-726A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB174YJK		1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5073	5075	5074	5076

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

	BGKcLV28-7	BGKcLV28-8
Sample_ID	BGKcLV28-7	BGKcLV28-8
Sample Name
Sample Name	CCT4-BGKcLV28-7	CCT4-BGKcLV28-8
RBP	CCT4	CCT4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9899	9900

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-7	BGKcLV28-8
Sample #	7	8
Sample Name	CCT4-BGKcLV28-7	CCT4-BGKcLV28-8
Sample_Name_Alias
Index Well Position	G05	H05
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	309	313
Peak_Molarity	113.00	84.40
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G1.png	DNA_Library_set48-49/set3/H1.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set48-49/set2/G1.png	RNA_Library_set48-49/set2/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-7	BGKcLV28-8
RBP	CCT4	CCT4
Batch_ID	BGKcLV28	BGKcLV28
WB_result	60.900	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2068	2069

Sequencing Information

	BGKcLV28-7	BGKcLV28-8
Sample_ID	BGKcLV28-7	BGKcLV28-8
Sample Name	CCT4-BGKcLV28-7	CCT4-BGKcLV28-8
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	67,873,482	70,086,356
total_aligned_reads	64,101,094	65,567,314
unique_aligned_reads	58,923,724	60,110,968
percent_uniqueAligned	0.86814	0.85767
correlation_replicates	0.995605	0.995605
spikein_reads	19,618	14,662
percent_spikeins	0.00029	0.00021
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1819	1820

Data Submission Information

	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-8	BGKcLV28-8	BGKcLV28-8	BGKcLV28-8
ENCODE_alias	brenton-graveley:CCT4-BGKcLV28	brenton-graveley:CCT4-BGKcLV28-7	brenton-graveley:L-CCT4-BGKcLV28-7	brenton-graveley:CCT4-BGKcLV28-7_S89_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT4-BGKcLV28-7_S89_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT4-BGKcLV28-K562	brenton-graveley:CCT4-BGKcLV28-8	brenton-graveley:L-CCT4-BGKcLV28-8	brenton-graveley:CCT4-BGKcLV28-8_S90_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT4-BGKcLV28-8_S90_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR995XEP	ENCBS041CQT	ENCLB981GTZ	ENCFF501HQR	ENCFF043KOE	ENCSR946GVC	ENCBS537UUI	ENCLB960HUZ	ENCFF349EGZ	ENCFF366AMI
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	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-7	BGKcLV28-8	BGKcLV28-8	BGKcLV28-8	BGKcLV28-8
Sample Name	CCT4-BGKcLV28-7	CCT4-BGKcLV28-7	CCT4-BGKcLV28-7	CCT4-BGKcLV28-7	CCT4-BGKcLV28-7	CCT4-BGKcLV28-7	CCT4-BGKcLV28-8	CCT4-BGKcLV28-8	CCT4-BGKcLV28-8	CCT4-BGKcLV28-8
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		CCT4-BGKcLV28-7.pdf	L-CCT4-BGKcLV28-7.pdf				CCT4-BGKcLV28-8.pdf	L-CCT4-BGKcLV28-8.pdf
ID	3474	3582	3716	3850	3984	7124	3583	3717	3851	3985

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-BGKcLV28-7_S89_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1819	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	3936
CCT4-BGKcLV28-7_S89_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1819	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	3994
CCT4-BGKcLV28-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1819					GRCh38	V40	CCT4-BGKcLV28-7_S89_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGKcLV28-7_S89_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19218
CCT4-BGKcLV28-7_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	1819					GRCh38	V40	CCT4-BGKcLV28-7/Aligned.sortedByCoord.out.bam		ENCORE2	19276
CCT4-BGKcLV28-7_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	1819					GRCh38	V40	CCT4-BGKcLV28-7/Aligned.sortedByCoord.out.bam		ENCORE2	19334
CCT4-BGKcLV28-7_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	1819					GRCh38	V40	CCT4-BGKcLV28-7/Aligned.sortedByCoord.out.bam		ENCORE2	19392
CCT4-BGKcLV28-7_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	1819					GRCh38	V40	CCT4-BGKcLV28-7/Aligned.sortedByCoord.out.bam		ENCORE2	19450
CCT4-BGKcLV28-7_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1819					GRCh38	V40	CCT4-BGKcLV28-7_S89_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGKcLV28-7_S89_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19508
CCT4-BGKcLV28-8_S90_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1820	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	3937
CCT4-BGKcLV28-8_S90_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1820	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	3995
CCT4-BGKcLV28-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1820					GRCh38	V40	CCT4-BGKcLV28-8_S90_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGKcLV28-8_S90_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19219
CCT4-BGKcLV28-8_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	1820					GRCh38	V40	CCT4-BGKcLV28-8/Aligned.sortedByCoord.out.bam		ENCORE2	19277
CCT4-BGKcLV28-8_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	1820					GRCh38	V40	CCT4-BGKcLV28-8/Aligned.sortedByCoord.out.bam		ENCORE2	19335
CCT4-BGKcLV28-8_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	1820					GRCh38	V40	CCT4-BGKcLV28-8/Aligned.sortedByCoord.out.bam		ENCORE2	19393
CCT4-BGKcLV28-8_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	1820					GRCh38	V40	CCT4-BGKcLV28-8/Aligned.sortedByCoord.out.bam		ENCORE2	19451
CCT4-BGKcLV28-8_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1820					GRCh38	V40	CCT4-BGKcLV28-8_S90_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT4-BGKcLV28-8_S90_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19509