CCT2 RNA-Seq in K562

General Information


RBP	CCT2
Cell_Line	K562
Method	CRISPR
Exp_Name	CCT2-BGKcLV28-K562
ENCODE_series_ID	ENCSR292MQU
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR688ZJS
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CCT2-BGKcLV28-3
Rep2	CCT2-BGKcLV28-4
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	73.9
Rep2_qPCR	67.9
Rep1_WB	54.3
Rep2_WB	55.9
Antibody Cat#	A303-478A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB291TYE
Status	Released
Project	ENCODE4
ID	818

Experiment Information (Status: Released)

	BGKcLV28-3	BGKcLV28-3	BGKcLV28-4	BGKcLV28-4
idx	933	935	934	936
TRCN#_or_BGC#	BGC#0000676	BGC#0000676	BGC#0000676	BGC#0000676
shRNA_or_gRNA_sequence	CACAGACCATCATAGCGGGT	CACAGACCATCATAGCGGGT	CACAGACCATCATAGCGGGT	CACAGACCATCATAGCGGGT
PAM	TGG	TGG	TGG	TGG
Name	CCT2_92	CCT2_92	CCT2_92	CCT2_92
Sample_ID	BGKcLV28-3	BGKcLV28-3	BGKcLV28-4	BGKcLV28-4
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	CCT2	CCT2	CCT2	CCT2
qPCR_result	73.9	73.9	67.9	67.9
Ave_qPCR	70.9	70.9
RT-qPCR_primer-F	gctgacaatgcaggctatga	gctgacaatgcaggctatga
RT-qPCR_primer-R	tatctccaatggtgccttcc	tatctccaatggtgccttcc
protein_conc	1817	1817	1959	1959
WB_result	54.3	55.5	55.9	50.552483
Ave_WB	55.1	53.0
WB_DONE_date	6/23/21	2/14/22	JESS
MW	57kd	57kd
IP
antibody_Cat#	A303-478A	A303-479A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB291TYE		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	5067	5069	5068	5070

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCT2	Product_ID: A303-478A Lot_ID: 1 Source: Bethyl Labs Target Name: CCT2-human

Experiment Status

	BGKcLV28-3	BGKcLV28-4
Sample_ID	BGKcLV28-3	BGKcLV28-4
Sample Name
Sample Name	CCT2-BGKcLV28-3	CCT2-BGKcLV28-4
RBP	CCT2	CCT2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9895	9896

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-3	BGKcLV28-4
Sample #	3	4
Sample Name	CCT2-BGKcLV28-3	CCT2-BGKcLV28-4
Sample_Name_Alias
Index Well Position	C05	D05
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	307	312
Peak_Molarity	142.00	141.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C1.png	DNA_Library_set48-49/set3/D1.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/C1.png	RNA_Library_set48-49/set2/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-3	BGKcLV28-4
RBP	CCT2	CCT2
Batch_ID	BGKcLV28	BGKcLV28
WB_result	54.300	55.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2064	2065

Sequencing Information

	BGKcLV28-3	BGKcLV28-4
Sample_ID	BGKcLV28-3	BGKcLV28-4
Sample Name	CCT2-BGKcLV28-3	CCT2-BGKcLV28-4
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	98,482,662	61,732,904
total_aligned_reads	94,468,684	58,169,486
unique_aligned_reads	86,699,384	53,469,894
percent_uniqueAligned	0.88035	0.86615
correlation_replicates	0.997940	0.997940
spikein_reads	50,588	12,252
percent_spikeins	0.00051	0.00020
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1815	1816

Data Submission Information

	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-4	BGKcLV28-4	BGKcLV28-4	BGKcLV28-4
ENCODE_alias	brenton-graveley:CCT2-BGKcLV28	brenton-graveley:CCT2-BGKcLV28-3	brenton-graveley:L-CCT2-BGKcLV28-3	brenton-graveley:CCT2-BGKcLV28-3_S85_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT2-BGKcLV28-3_S85_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT2-BGKcLV28-K562	brenton-graveley:CCT2-BGKcLV28-4	brenton-graveley:L-CCT2-BGKcLV28-4	brenton-graveley:CCT2-BGKcLV28-4_S86_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT2-BGKcLV28-4_S86_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR688ZJS	ENCBS492BTH	ENCLB274BFN	ENCFF775VPQ	ENCFF977ULQ	ENCSR292MQU	ENCBS663RQN	ENCLB637YEK	ENCFF694EEJ	ENCFF292UOP
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	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-3	BGKcLV28-4	BGKcLV28-4	BGKcLV28-4	BGKcLV28-4
Sample Name	CCT2-BGKcLV28-3	CCT2-BGKcLV28-3	CCT2-BGKcLV28-3	CCT2-BGKcLV28-3	CCT2-BGKcLV28-3	CCT2-BGKcLV28-3	CCT2-BGKcLV28-4	CCT2-BGKcLV28-4	CCT2-BGKcLV28-4	CCT2-BGKcLV28-4
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		CCT2-BGKcLV28-3.pdf	L-CCT2-BGKcLV28-3.pdf				CCT2-BGKcLV28-4.pdf	L-CCT2-BGKcLV28-4.pdf
ID	3472	3578	3712	3846	3980	7122	3579	3713	3847	3981

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
CCT2-BGKcLV28-3_S85_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1815	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	3932
CCT2-BGKcLV28-3_S85_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1815	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	3990
CCT2-BGKcLV28-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1815					GRCh38	V40	CCT2-BGKcLV28-3_S85_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT2-BGKcLV28-3_S85_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19214
CCT2-BGKcLV28-3_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	1815					GRCh38	V40	CCT2-BGKcLV28-3/Aligned.sortedByCoord.out.bam		ENCORE2	19272
CCT2-BGKcLV28-3_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	1815					GRCh38	V40	CCT2-BGKcLV28-3/Aligned.sortedByCoord.out.bam		ENCORE2	19330
CCT2-BGKcLV28-3_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	1815					GRCh38	V40	CCT2-BGKcLV28-3/Aligned.sortedByCoord.out.bam		ENCORE2	19388
CCT2-BGKcLV28-3_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	1815					GRCh38	V40	CCT2-BGKcLV28-3/Aligned.sortedByCoord.out.bam		ENCORE2	19446
CCT2-BGKcLV28-3_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1815					GRCh38	V40	CCT2-BGKcLV28-3_S85_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT2-BGKcLV28-3_S85_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19504
CCT2-BGKcLV28-4_S86_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1816	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	3933
CCT2-BGKcLV28-4_S86_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1816	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	3991
CCT2-BGKcLV28-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1816					GRCh38	V40	CCT2-BGKcLV28-4_S86_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT2-BGKcLV28-4_S86_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19215
CCT2-BGKcLV28-4_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	1816					GRCh38	V40	CCT2-BGKcLV28-4/Aligned.sortedByCoord.out.bam		ENCORE2	19273
CCT2-BGKcLV28-4_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	1816					GRCh38	V40	CCT2-BGKcLV28-4/Aligned.sortedByCoord.out.bam		ENCORE2	19331
CCT2-BGKcLV28-4_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	1816					GRCh38	V40	CCT2-BGKcLV28-4/Aligned.sortedByCoord.out.bam		ENCORE2	19389
CCT2-BGKcLV28-4_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	1816					GRCh38	V40	CCT2-BGKcLV28-4/Aligned.sortedByCoord.out.bam		ENCORE2	19447
CCT2-BGKcLV28-4_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1816					GRCh38	V40	CCT2-BGKcLV28-4_S86_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT2-BGKcLV28-4_S86_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19505