CAST RNA-Seq in K562

General Information


RBP	CAST
Cell_Line	K562
Method	CRISPR
Exp_Name	CAST-BGKcLV26-K562
ENCODE_series_ID	ENCSR798UAK
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR159HPD
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CAST-BGKcLV26-59
Rep2	CAST-BGKcLV26-60
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	21.3
Rep2_qPCR	32.1
Rep1_WB	78.8
Rep2_WB	86.4
Antibody Cat#	A304-794A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB248JEG
Status	Released
Project	ENCODE4
ID	803

Experiment Information (Status: Released)

	BGKcLV26-59	BGKcLV26-60
idx	922	923
TRCN#_or_BGC#	BGC#0000668	BGC#0000668
shRNA_or_gRNA_sequence	CTGTGGCTAAAAATTTACCG	CTGTGGCTAAAAATTTACCG
PAM	TGG	TGG
Name	CAST_90	CAST_90
Sample_ID	BGKcLV26-59	BGKcLV26-60
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	CAST	CAST
qPCR_result	21.3	32.1
Ave_qPCR	26.7
RT-qPCR_primer-F	aacttgctgctgccatctct
RT-qPCR_primer-R	ggcatcatcgaggtctttgt
protein_conc	4996	5125
WB_result	78.8	86.4
Ave_WB	82.6
WB_DONE_date	5/18/21	jess
MW	77kDa
IP	Rabbit / I
antibody_Cat#	A304-794A	LOT# 1
Antibody DCC ID	ENCAB248JEG	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	5054	5055

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAST	Product_ID: A304-794A Lot_ID: 1 Source: Bethyl Labs Target Name: CAST-human

Experiment Status

	BGKcLV26-59	BGKcLV26-60
Sample_ID	BGKcLV26-59	BGKcLV26-60
Sample Name
Sample Name	CAST-BGKcLV26-59	CAST-BGKcLV26-60
RBP	CAST	CAST
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9787	9788

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-59	BGKcLV26-60
Sample #	45	46
Sample Name	CAST-BGKcLV26-59	CAST-BGKcLV26-60
Sample_Name_Alias
Index Well Position	E06	F06
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	297	297
Peak_Molarity	123.00	120.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E6.png	DNA_Library_set48-49/set1/F6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/E6.png	RNA_Library_set48-49/set1/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-59	BGKcLV26-60
RBP	CAST	CAST
Batch_ID	BGKcLV26	BGKcLV26
WB_result	78.800	86.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1604	1605

Sequencing Information

	BGKcLV26-59	BGKcLV26-60
Sample_ID	BGKcLV26-59	BGKcLV26-60
Sample Name	CAST-BGKcLV26-59	CAST-BGKcLV26-60
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	44,207,944	47,544,686
total_aligned_reads	34,253,910	39,069,710
unique_aligned_reads	31,529,228	35,926,192
percent_uniqueAligned	0.71320	0.75563
correlation_replicates	0.997671	0.997671
spikein_reads	18,536	19,740
percent_spikeins	0.00042	0.00042
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1781	1782

Data Submission Information

	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-60	BGKcLV26-60	BGKcLV26-60	BGKcLV26-60
ENCODE_alias	brenton-graveley:CAST-BGKcLV26	brenton-graveley:CAST-BGKcLV26-59	brenton-graveley:L-CAST-BGKcLV26-59	brenton-graveley:CAST-BGKcLV26-59_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAST-BGKcLV26-59_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAST-BGKcLV26-K562	brenton-graveley:CAST-BGKcLV26-60	brenton-graveley:L-CAST-BGKcLV26-60	brenton-graveley:CAST-BGKcLV26-60_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAST-BGKcLV26-60_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR159HPD	ENCBS676SDY	ENCLB328TSU	ENCFF968VXH	ENCFF793OAI	ENCSR798UAK	ENCBS336JAA	ENCLB282FGR	ENCFF599WCG	ENCFF197LOL
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	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-59	BGKcLV26-60	BGKcLV26-60	BGKcLV26-60	BGKcLV26-60
Sample Name	CAST-BGKcLV26-59	CAST-BGKcLV26-59	CAST-BGKcLV26-59	CAST-BGKcLV26-59	CAST-BGKcLV26-59	CAST-BGKcLV26-59	CAST-BGKcLV26-60	CAST-BGKcLV26-60	CAST-BGKcLV26-60	CAST-BGKcLV26-60
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		CAST-BGKcLV26-59.pdf	L-CAST-BGKcLV26-59.pdf				CAST-BGKcLV26-60.pdf	L-CAST-BGKcLV26-60.pdf
ID	3468	3570	3704	3838	3972	7117	3571	3705	3839	3973

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
CAST-BGKcLV26-59_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1781	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	3874
CAST-BGKcLV26-59_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1781	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	3924
CAST-BGKcLV26-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1781					GRCh38	V40	CAST-BGKcLV26-59_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAST-BGKcLV26-59_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25561
CAST-BGKcLV26-59_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1781					GRCh38	V40	CAST-BGKcLV26-59_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAST-BGKcLV26-59_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25611
CAST-BGKcLV26-59_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	1781					GRCh38	V40	CAST-BGKcLV26-59/Aligned.sortedByCoord.out.bam		ENCORE2	26577
CAST-BGKcLV26-59_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	1781					GRCh38	V40	CAST-BGKcLV26-59/Aligned.sortedByCoord.out.bam		ENCORE2	26627
CAST-BGKcLV26-59_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	1781					GRCh38	V40	CAST-BGKcLV26-59/Aligned.sortedByCoord.out.bam		ENCORE2	26677
CAST-BGKcLV26-59_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	1781					GRCh38	V40	CAST-BGKcLV26-59/Aligned.sortedByCoord.out.bam		ENCORE2	26727
CAST-BGKcLV26-60_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1782	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	3875
CAST-BGKcLV26-60_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1782	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	3925
CAST-BGKcLV26-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1782					GRCh38	V40	CAST-BGKcLV26-60_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAST-BGKcLV26-60_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25562
CAST-BGKcLV26-60_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1782					GRCh38	V40	CAST-BGKcLV26-60_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAST-BGKcLV26-60_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25612
CAST-BGKcLV26-60_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	1782					GRCh38	V40	CAST-BGKcLV26-60/Aligned.sortedByCoord.out.bam		ENCORE2	26578
CAST-BGKcLV26-60_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	1782					GRCh38	V40	CAST-BGKcLV26-60/Aligned.sortedByCoord.out.bam		ENCORE2	26628
CAST-BGKcLV26-60_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	1782					GRCh38	V40	CAST-BGKcLV26-60/Aligned.sortedByCoord.out.bam		ENCORE2	26678
CAST-BGKcLV26-60_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	1782					GRCh38	V40	CAST-BGKcLV26-60/Aligned.sortedByCoord.out.bam		ENCORE2	26728