CTTN RNA-Seq in K562

General Information


RBP	CTTN
Cell_Line	K562
Method	CRISPR
Exp_Name	CTTN-BGKcLV28-K562
ENCODE_series_ID	ENCSR230BMV
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR146YRO
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CTTN-BGKcLV28-51
Rep2	CTTN-BGKcLV28-52
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	53.8
Rep2_qPCR	65.9
Rep1_WB	66.5
Rep2_WB	59.5
Antibody Cat#	A302-607A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB014AIG
Status	Released
Project	ENCODE4
ID	836

Experiment Information (Status: Released)

	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52
idx	993	995	994	996
TRCN#_or_BGC#	BGC#0000727	BGC#0000727	BGC#0000727	BGC#0000727
shRNA_or_gRNA_sequence	CATCGCCCAGGATGACGCGG	CATCGCCCAGGATGACGCGG	CATCGCCCAGGATGACGCGG	CATCGCCCAGGATGACGCGG
PAM	GGG	GGG	GGG	GGG
Name	CTTN_93	CTTN_93	CTTN_93	CTTN_93
Sample_ID	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52
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	CTTN	CTTN	CTTN	CTTN
qPCR_result	53.8	53.8	65.9	65.9
Ave_qPCR	59.9	59.9
RT-qPCR_primer-F	agcaagccagagccaaaac	agcaagccagagccaaaac
RT-qPCR_primer-R	tcacagggcctctgtagctc	tcacagggcctctgtagctc
protein_conc	2606	2606	2610	2610
WB_result	66.5	77.6	59.5	74.656735
Ave_WB	63.0	76.2
WB_DONE_date	6/30/21	8/25/21	JESS	JESS
MW	62KD	62KD
IP
antibody_Cat#	A302-607A	A302-608A	LOT #1	LOT #1
Antibody DCC ID	ENCAB014AIG	ENCAB718XCE	1/19/22	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	5127	5129	5128	5130

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CTTN	Product_ID: A302-607A Lot_ID: 1 Source: Bethyl Labs Target Name: CTTN-human
CTTN	Product_ID: A302-608A Lot_ID: 1 Source: Bethyl Labs Target Name: CTTN-human

Experiment Status

	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52
Sample_ID	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52
Sample Name
Sample Name	CTTN-BGKcLV28-51		CTTN-BGKcLV28-52
RBP	CTTN	CTTN	CTTN	CTTN
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-01-29	2021-09-16	2022-01-29	2021-09-16
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9931	9965	9932	9966

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-51	BGKcLV28-52
Sample #	39	40
Sample Name	CTTN-BGKcLV28-51	CTTN-BGKcLV28-52
Sample_Name_Alias
Index Well Position	G09	H09
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	317	316
Peak_Molarity	106.00	107.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G5.png	DNA_Library_set48-49/set3/H5.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/G5.png	RNA_Library_set48-49/set2/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-51	BGKcLV28-52
RBP	CTTN	CTTN
Batch_ID	BGKcLV28	BGKcLV28
WB_result	66.500	59.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2100	2101

Sequencing Information

	BGKcLV28-51	BGKcLV28-52
Sample_ID	BGKcLV28-51	BGKcLV28-52
Sample Name	CTTN-BGKcLV28-51	CTTN-BGKcLV28-52
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	171,636,294	91,621,830
total_aligned_reads	162,880,538	77,548,422
unique_aligned_reads	149,932,664	71,240,034
percent_uniqueAligned	0.87355	0.77754
correlation_replicates	0.992691	0.992691
spikein_reads	45,500	17,476
percent_spikeins	0.00027	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1851	1852

Data Submission Information

	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52	BGKcLV28-52	BGKcLV28-52
ENCODE_alias	brenton-graveley:CTTN-BGKcLV28	brenton-graveley:CTTN-BGKcLV28-51	brenton-graveley:L-CTTN-BGKcLV28-51	brenton-graveley:CTTN-BGKcLV28-51_S121_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGKcLV28-51_S121_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGKcLV28-K562	brenton-graveley:CTTN-BGKcLV28-52	brenton-graveley:L-CTTN-BGKcLV28-52	brenton-graveley:CTTN-BGKcLV28-52_S122_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CTTN-BGKcLV28-52_S122_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR146YRO	ENCBS056LXD	ENCLB319GWQ	ENCFF437VHH	ENCFF580OTI	ENCSR230BMV	ENCBS909SFC	ENCLB202FEW	ENCFF191VQU	ENCFF199SMJ
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	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-51	BGKcLV28-52	BGKcLV28-52	BGKcLV28-52	BGKcLV28-52
Sample Name	CTTN-BGKcLV28-51	CTTN-BGKcLV28-51	CTTN-BGKcLV28-51	CTTN-BGKcLV28-51	CTTN-BGKcLV28-51	CTTN-BGKcLV28-51	CTTN-BGKcLV28-52	CTTN-BGKcLV28-52	CTTN-BGKcLV28-52	CTTN-BGKcLV28-52
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		CTTN-BGKcLV28-51.pdf	L-CTTN-BGKcLV28-51.pdf				CTTN-BGKcLV28-52.pdf	L-CTTN-BGKcLV28-52.pdf
ID	3490	3614	3748	3882	4016	7163	3615	3749	3883	4017

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
CTTN-BGKcLV28-51_S121_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1851	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	3968
CTTN-BGKcLV28-51_S121_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1851	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	4026
CTTN-BGKcLV28-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1851					GRCh38	V40	CTTN-BGKcLV28-51_S121_L004_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGKcLV28-51_S121_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19250
CTTN-BGKcLV28-51_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	1851					GRCh38	V40	CTTN-BGKcLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	19308
CTTN-BGKcLV28-51_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	1851					GRCh38	V40	CTTN-BGKcLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	19366
CTTN-BGKcLV28-51_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	1851					GRCh38	V40	CTTN-BGKcLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	19424
CTTN-BGKcLV28-51_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	1851					GRCh38	V40	CTTN-BGKcLV28-51/Aligned.sortedByCoord.out.bam		ENCORE2	19482
CTTN-BGKcLV28-51_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1851					GRCh38	V40	CTTN-BGKcLV28-51_S121_L004_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGKcLV28-51_S121_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19540
CTTN-BGKcLV28-52_S122_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1852	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	3969
CTTN-BGKcLV28-52_S122_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1852	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	4027
CTTN-BGKcLV28-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1852					GRCh38	V40	CTTN-BGKcLV28-52_S122_L004_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGKcLV28-52_S122_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19251
CTTN-BGKcLV28-52_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	1852					GRCh38	V40	CTTN-BGKcLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	19309
CTTN-BGKcLV28-52_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	1852					GRCh38	V40	CTTN-BGKcLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	19367
CTTN-BGKcLV28-52_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	1852					GRCh38	V40	CTTN-BGKcLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	19425
CTTN-BGKcLV28-52_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	1852					GRCh38	V40	CTTN-BGKcLV28-52/Aligned.sortedByCoord.out.bam		ENCORE2	19483
CTTN-BGKcLV28-52_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1852					GRCh38	V40	CTTN-BGKcLV28-52_S122_L004_R1_001.filtered.trimmed.paired.fastq.gz,CTTN-BGKcLV28-52_S122_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19541