CAT RNA-Seq in K562

General Information


RBP	CAT
Cell_Line	K562
Method	CRISPR
Exp_Name	CAT-BGKcLV26-K562
ENCODE_series_ID	ENCSR630APK
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR667JRK
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CAT-BGKcLV26-61
Rep2	CAT-BGKcLV26-62
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	32.5
Rep2_qPCR	28.1
Rep1_WB	66.3
Rep2_WB	71.8
Antibody Cat#	A304-767A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB661IMU
Status	Released
Project	ENCODE4
ID	804

Experiment Information (Status: Released)

	BGKcLV26-61	BGKcLV26-62
idx	924	925
TRCN#_or_BGC#	BGC#0000669	BGC#0000669
shRNA_or_gRNA_sequence	TTATTACAGTAGGGCCCCGT	TTATTACAGTAGGGCCCCGT
PAM	GGG	GGG
Name	CAT_96	CAT_96
Sample_ID	BGKcLV26-61	BGKcLV26-62
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	CAT	CAT
qPCR_result	32.5	28.1
Ave_qPCR	30.3
RT-qPCR_primer-F	catcgccacatgaatggata
RT-qPCR_primer-R	tttttgatgccctggtcagt
protein_conc	4842	4809
WB_result	66.3	71.8
Ave_WB	69.0
WB_DONE_date	5/18/21
MW	60kDa
IP	Rabbit / I
antibody_Cat#	A304-767A	LOT# 1
Antibody DCC ID	ENCAB661IMU	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5056	5057

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAT	Product_ID: A304-767A Lot_ID: 1 Source: Bethyl Labs Target Name: CAT-human

Experiment Status

	BGKcLV26-61	BGKcLV26-62
Sample_ID	BGKcLV26-61	BGKcLV26-62
Sample Name
Sample Name	CAT-BGKcLV26-61	CAT-BGKcLV26-62
RBP	CAT	CAT
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9789	9790

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-61	BGKcLV26-62
Sample #	47	48
Sample Name	CAT-BGKcLV26-61	CAT-BGKcLV26-62
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	299	296
Peak_Molarity	120.00	132.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G6.png	DNA_Library_set48-49/set1/H6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/G6.png	RNA_Library_set48-49/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-61	BGKcLV26-62
RBP	CAT	CAT
Batch_ID	BGKcLV26	BGKcLV26
WB_result	66.300	71.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1606	1607

Sequencing Information

	BGKcLV26-61	BGKcLV26-62
Sample_ID	BGKcLV26-61	BGKcLV26-62
Sample Name	CAT-BGKcLV26-61	CAT-BGKcLV26-62
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	76,934,590	51,935,334
total_aligned_reads	71,240,172	48,624,004
unique_aligned_reads	65,380,278	44,683,686
percent_uniqueAligned	0.84982	0.86037
correlation_replicates	0.997719	0.997719
spikein_reads	27,868	15,222
percent_spikeins	0.00036	0.00029
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1783	1784

Data Submission Information

	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-62	BGKcLV26-62	BGKcLV26-62	BGKcLV26-62
ENCODE_alias	brenton-graveley:CAT-BGKcLV26	brenton-graveley:CAT-BGKcLV26-61	brenton-graveley:L-CAT-BGKcLV26-61	brenton-graveley:CAT-BGKcLV26-61_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGKcLV26-61_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGKcLV26-K562	brenton-graveley:CAT-BGKcLV26-62	brenton-graveley:L-CAT-BGKcLV26-62	brenton-graveley:CAT-BGKcLV26-62_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAT-BGKcLV26-62_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR667JRK	ENCBS137FIF	ENCLB528YBR	ENCFF916GGQ	ENCFF684XXM	ENCSR630APK	ENCBS456UIQ	ENCLB825DEN	ENCFF391INP	ENCFF656QWH
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	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-61	BGKcLV26-62	BGKcLV26-62	BGKcLV26-62	BGKcLV26-62
Sample Name	CAT-BGKcLV26-61	CAT-BGKcLV26-61	CAT-BGKcLV26-61	CAT-BGKcLV26-61	CAT-BGKcLV26-61	CAT-BGKcLV26-61	CAT-BGKcLV26-62	CAT-BGKcLV26-62	CAT-BGKcLV26-62	CAT-BGKcLV26-62
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		CAT-BGKcLV26-61.pdf	L-CAT-BGKcLV26-61.pdf				CAT-BGKcLV26-62.pdf	L-CAT-BGKcLV26-62.pdf
ID	3469	3572	3706	3840	3974	7119	3573	3707	3841	3975

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
CAT-BGKcLV26-61_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1783	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3876
CAT-BGKcLV26-61_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1783	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3926
CAT-BGKcLV26-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGKcLV26-61_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25563
CAT-BGKcLV26-61_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61_S53_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGKcLV26-61_S53_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25613
CAT-BGKcLV26-61_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61/Aligned.sortedByCoord.out.bam		ENCORE2	26579
CAT-BGKcLV26-61_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61/Aligned.sortedByCoord.out.bam		ENCORE2	26629
CAT-BGKcLV26-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61/Aligned.sortedByCoord.out.bam		ENCORE2	26679
CAT-BGKcLV26-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1783					GRCh38	V40	CAT-BGKcLV26-61/Aligned.sortedByCoord.out.bam		ENCORE2	26729
CAT-BGKcLV26-62_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1784	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3877
CAT-BGKcLV26-62_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1784	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3927
CAT-BGKcLV26-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGKcLV26-62_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25564
CAT-BGKcLV26-62_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62_S54_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAT-BGKcLV26-62_S54_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25614
CAT-BGKcLV26-62_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62/Aligned.sortedByCoord.out.bam		ENCORE2	26580
CAT-BGKcLV26-62_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62/Aligned.sortedByCoord.out.bam		ENCORE2	26630
CAT-BGKcLV26-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62/Aligned.sortedByCoord.out.bam		ENCORE2	26680
CAT-BGKcLV26-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1784					GRCh38	V40	CAT-BGKcLV26-62/Aligned.sortedByCoord.out.bam		ENCORE2	26730