CARS RNA-Seq in K562

General Information


RBP	CARS
Cell_Line	K562
Method	CRISPR
Exp_Name	CARS-BGKcLV26-K562
ENCODE_series_ID	ENCSR200EXF
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR267SUE
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CARS-BGKcLV26-57
Rep2	CARS-BGKcLV26-58
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	74.3
Rep2_WB	75.9
Antibody Cat#	A302-409A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB833ALL
Status	Released
Project	ENCODE4
ID	802

Experiment Information (Status: Released)

	BGKcLV26-57	BGKcLV26-58
idx	920	921
TRCN#_or_BGC#	BGC#0000666	BGC#0000666
shRNA_or_gRNA_sequence	TGAGATGCGTCATAGACGGT	TGAGATGCGTCATAGACGGT
PAM	TGG	TGG
Name	CARS1_96	CARS1_96
Sample_ID	BGKcLV26-57	BGKcLV26-58
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	CARS	CARS
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4101	4510
WB_result	74.3	75.9
Ave_WB	75.1
WB_DONE_date	5/6/21	jess
MW	84kDa
IP	Rabbit / I
antibody_Cat#	A302-409A	LOT# 1
Antibody DCC ID	ENCAB833ALL
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	5052	5053

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CARS	Product_ID: A302-409A Lot_ID: 1 Source: Bethyl Labs Target Name: CARS-human

Experiment Status

	BGKcLV26-57	BGKcLV26-58
Sample_ID	BGKcLV26-57	BGKcLV26-58
Sample Name
Sample Name	CARS-BGKcLV26-57	CARS-BGKcLV26-58
RBP	CARS	CARS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9785	9786

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-57	BGKcLV26-58
Sample #	43	44
Sample Name	CARS-BGKcLV26-57	CARS-BGKcLV26-58
Sample_Name_Alias
Index Well Position	C06	D06
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	293	310
Peak_Molarity	117.00	91.20
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/C6.png	DNA_Library_set48-49/set1/D6.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/C6.png	RNA_Library_set48-49/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-57	BGKcLV26-58
RBP	CARS	CARS
Batch_ID	BGKcLV26	BGKcLV26
WB_result	74.300	75.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1602	1603

Sequencing Information

	BGKcLV26-57	BGKcLV26-58
Sample_ID	BGKcLV26-57	BGKcLV26-58
Sample Name	CARS-BGKcLV26-57	CARS-BGKcLV26-58
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	85,494,080	43,871,546
total_aligned_reads	78,309,670	32,204,572
unique_aligned_reads	71,905,744	29,626,146
percent_uniqueAligned	0.84106	0.67529
correlation_replicates	0.994682	0.994682
spikein_reads	29,234	10,496
percent_spikeins	0.00034	0.00024
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1779	1780

Data Submission Information

	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-58	BGKcLV26-58	BGKcLV26-58	BGKcLV26-58
ENCODE_alias	brenton-graveley:CARS-BGKcLV26	brenton-graveley:CARS-BGKcLV26-57	brenton-graveley:L-CARS-BGKcLV26-57	brenton-graveley:CARS-BGKcLV26-57_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGKcLV26-57_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGKcLV26-K562	brenton-graveley:CARS-BGKcLV26-58	brenton-graveley:L-CARS-BGKcLV26-58	brenton-graveley:CARS-BGKcLV26-58_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CARS-BGKcLV26-58_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR267SUE	ENCBS328HQA	ENCLB810LAP	ENCFF496VJY	ENCFF038IIL	ENCSR200EXF	ENCBS870SOW	ENCLB843NIU	ENCFF941CNV	ENCFF948IOB
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	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-57	BGKcLV26-58	BGKcLV26-58	BGKcLV26-58	BGKcLV26-58
Sample Name	CARS-BGKcLV26-57	CARS-BGKcLV26-57	CARS-BGKcLV26-57	CARS-BGKcLV26-57	CARS-BGKcLV26-57	CARS-BGKcLV26-57	CARS-BGKcLV26-58	CARS-BGKcLV26-58	CARS-BGKcLV26-58	CARS-BGKcLV26-58
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-19	2022-02-04	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2022-02-04	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		CARS-BGKcLV26-57.pdf	L-CARS-BGKcLV26-57.pdf				CARS-BGKcLV26-58.pdf	L-CARS-BGKcLV26-58.pdf
ID	3467	3568	3702	3836	3970	7116	3569	3703	3837	3971

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
CARS-BGKcLV26-57_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1779	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	3872
CARS-BGKcLV26-57_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1779	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	3922
CARS-BGKcLV26-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1779					GRCh38	V40	CARS-BGKcLV26-57_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGKcLV26-57_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25559
CARS-BGKcLV26-57_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1779					GRCh38	V40	CARS-BGKcLV26-57_S49_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGKcLV26-57_S49_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25609
CARS-BGKcLV26-57_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	1779					GRCh38	V40	CARS-BGKcLV26-57/Aligned.sortedByCoord.out.bam		ENCORE2	26575
CARS-BGKcLV26-57_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	1779					GRCh38	V40	CARS-BGKcLV26-57/Aligned.sortedByCoord.out.bam		ENCORE2	26625
CARS-BGKcLV26-57_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	1779					GRCh38	V40	CARS-BGKcLV26-57/Aligned.sortedByCoord.out.bam		ENCORE2	26675
CARS-BGKcLV26-57_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	1779					GRCh38	V40	CARS-BGKcLV26-57/Aligned.sortedByCoord.out.bam		ENCORE2	26725
CARS-BGKcLV26-58_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1780	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	3873
CARS-BGKcLV26-58_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1780	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	3923
CARS-BGKcLV26-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1780					GRCh38	V40	CARS-BGKcLV26-58_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGKcLV26-58_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25560
CARS-BGKcLV26-58_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1780					GRCh38	V40	CARS-BGKcLV26-58_S50_L003_R1_001.filtered.trimmed.paired.fastq.gz,CARS-BGKcLV26-58_S50_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25610
CARS-BGKcLV26-58_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	1780					GRCh38	V40	CARS-BGKcLV26-58/Aligned.sortedByCoord.out.bam		ENCORE2	26576
CARS-BGKcLV26-58_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	1780					GRCh38	V40	CARS-BGKcLV26-58/Aligned.sortedByCoord.out.bam		ENCORE2	26626
CARS-BGKcLV26-58_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	1780					GRCh38	V40	CARS-BGKcLV26-58/Aligned.sortedByCoord.out.bam		ENCORE2	26676
CARS-BGKcLV26-58_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	1780					GRCh38	V40	CARS-BGKcLV26-58/Aligned.sortedByCoord.out.bam		ENCORE2	26726