CCT3 RNA-Seq in K562

General Information


RBP	CCT3
Cell_Line	K562
Method	CRISPR
Exp_Name	CCT3-BGKcLV28-K562
ENCODE_series_ID	ENCSR909SOX
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR054DGN
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CCT3-BGKcLV28-5
Rep2	CCT3-BGKcLV28-6
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	80.6
Rep2_qPCR	74.6
Rep1_WB	58.2
Rep2_WB	63.5652336
Antibody Cat#	A303-459A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB809NWD
Status	Released
Project	ENCODE4
ID	819

Experiment Information (Status: Released)

	BGKcLV28-5	BGKcLV28-6
idx	937	938
TRCN#_or_BGC#	BGC#0000678	BGC#0000678
shRNA_or_gRNA_sequence	GGTGATCAGTGCTTACCGCA	GGTGATCAGTGCTTACCGCA
PAM	AGG	AGG
Name	CCT3_94	CCT3_94
Sample_ID	BGKcLV28-5	BGKcLV28-6
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CCT3	CCT3
qPCR_result	80.6	74.6
Ave_qPCR	77.6
RT-qPCR_primer-F	cctcgtaccctgatccagaa
RT-qPCR_primer-R	tccaccaaagtacccgtctc
protein_conc	1853	1725
WB_result	58.2	63.5652336
Ave_WB	60.9
WB_DONE_date	7/8/21,7/9/21	JESS
MW	61kd
IP
antibody_Cat#	A303-459A	LOT# 1
Antibody DCC ID	ENCAB809NWD	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5071	5072

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CCT3	Product_ID: A303-459A Lot_ID: 1 Source: Bethyl Labs Target Name: CCT3-human

Experiment Status

	BGKcLV28-5	BGKcLV28-6
Sample_ID	BGKcLV28-5	BGKcLV28-6
Sample Name
Sample Name	CCT3-BGKcLV28-5	CCT3-BGKcLV28-6
RBP	CCT3	CCT3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9897	9898

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-5	BGKcLV28-6
Sample #	5	6
Sample Name	CCT3-BGKcLV28-5	CCT3-BGKcLV28-6
Sample_Name_Alias
Index Well Position	E05	F05
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	323	337
Peak_Molarity	115.00	111.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E1.png	DNA_Library_set48-49/set3/F1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E1.png	RNA_Library_set48-49/set2/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-5	BGKcLV28-6
RBP	CCT3	CCT3
Batch_ID	BGKcLV28	BGKcLV28
WB_result	58.200	63.565
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2066	2067

Sequencing Information

	BGKcLV28-5	BGKcLV28-6
Sample_ID	BGKcLV28-5	BGKcLV28-6
Sample Name	CCT3-BGKcLV28-5	CCT3-BGKcLV28-6
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	79,869,690	64,672,434
total_aligned_reads	76,196,862	60,338,334
unique_aligned_reads	69,842,294	55,230,010
percent_uniqueAligned	0.87445	0.85400
correlation_replicates	0.989252	0.989252
spikein_reads	37,782	23,714
percent_spikeins	0.00047	0.00037
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1817	1818

Data Submission Information

	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-6	BGKcLV28-6	BGKcLV28-6	BGKcLV28-6
ENCODE_alias	brenton-graveley:CCT3-BGKcLV28	brenton-graveley:CCT3-BGKcLV28-5	brenton-graveley:L-CCT3-BGKcLV28-5	brenton-graveley:CCT3-BGKcLV28-5_S87_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT3-BGKcLV28-5_S87_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT3-BGKcLV28-K562	brenton-graveley:CCT3-BGKcLV28-6	brenton-graveley:L-CCT3-BGKcLV28-6	brenton-graveley:CCT3-BGKcLV28-6_S88_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CCT3-BGKcLV28-6_S88_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR054DGN	ENCBS711XJR	ENCLB742CJK	ENCFF587WLL	ENCFF688TLJ	ENCSR909SOX	ENCBS119KBU	ENCLB156QON	ENCFF868GHN	ENCFF958OHT
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	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-5	BGKcLV28-6	BGKcLV28-6	BGKcLV28-6	BGKcLV28-6
Sample Name	CCT3-BGKcLV28-5	CCT3-BGKcLV28-5	CCT3-BGKcLV28-5	CCT3-BGKcLV28-5	CCT3-BGKcLV28-5	CCT3-BGKcLV28-5	CCT3-BGKcLV28-6	CCT3-BGKcLV28-6	CCT3-BGKcLV28-6	CCT3-BGKcLV28-6
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		CCT3-BGKcLV28-5.pdf	L-CCT3-BGKcLV28-5.pdf				CCT3-BGKcLV28-6.pdf	L-CCT3-BGKcLV28-6.pdf
ID	3473	3580	3714	3848	3982	7123	3581	3715	3849	3983

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
CCT3-BGKcLV28-5_S87_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1817	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	3934
CCT3-BGKcLV28-5_S87_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1817	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	3992
CCT3-BGKcLV28-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1817					GRCh38	V40	CCT3-BGKcLV28-5_S87_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT3-BGKcLV28-5_S87_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19216
CCT3-BGKcLV28-5_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	1817					GRCh38	V40	CCT3-BGKcLV28-5/Aligned.sortedByCoord.out.bam		ENCORE2	19274
CCT3-BGKcLV28-5_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	1817					GRCh38	V40	CCT3-BGKcLV28-5/Aligned.sortedByCoord.out.bam		ENCORE2	19332
CCT3-BGKcLV28-5_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	1817					GRCh38	V40	CCT3-BGKcLV28-5/Aligned.sortedByCoord.out.bam		ENCORE2	19390
CCT3-BGKcLV28-5_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	1817					GRCh38	V40	CCT3-BGKcLV28-5/Aligned.sortedByCoord.out.bam		ENCORE2	19448
CCT3-BGKcLV28-5_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1817					GRCh38	V40	CCT3-BGKcLV28-5_S87_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT3-BGKcLV28-5_S87_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19506
CCT3-BGKcLV28-6_S88_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1818	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	3935
CCT3-BGKcLV28-6_S88_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1818	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	3993
CCT3-BGKcLV28-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1818					GRCh38	V40	CCT3-BGKcLV28-6_S88_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT3-BGKcLV28-6_S88_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19217
CCT3-BGKcLV28-6_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	1818					GRCh38	V40	CCT3-BGKcLV28-6/Aligned.sortedByCoord.out.bam		ENCORE2	19275
CCT3-BGKcLV28-6_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	1818					GRCh38	V40	CCT3-BGKcLV28-6/Aligned.sortedByCoord.out.bam		ENCORE2	19333
CCT3-BGKcLV28-6_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	1818					GRCh38	V40	CCT3-BGKcLV28-6/Aligned.sortedByCoord.out.bam		ENCORE2	19391
CCT3-BGKcLV28-6_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	1818					GRCh38	V40	CCT3-BGKcLV28-6/Aligned.sortedByCoord.out.bam		ENCORE2	19449
CCT3-BGKcLV28-6_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1818					GRCh38	V40	CCT3-BGKcLV28-6_S88_L004_R1_001.filtered.trimmed.paired.fastq.gz,CCT3-BGKcLV28-6_S88_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19507