CLNS1A RNA-Seq in K562

General Information


RBP	CLNS1A
Cell_Line	K562
Method	CRISPR
Exp_Name	CLNS1A-BGKcLV28-K562
ENCODE_series_ID	ENCSR545FZJ
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR950KYU
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CLNS1A-BGKcLV28-21
Rep2	CLNS1A-BGKcLV28-22
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	67.9
Rep2_qPCR	69.8
Rep1_WB	49.6
Rep2_WB	53.2
Antibody Cat#	A304-521A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB677WEY
Status	Released
Project	ENCODE4
ID	827

Experiment Information (Status: Released)

	BGKcLV28-21	BGKcLV28-22
idx	955	956
TRCN#_or_BGC#	BGC#0000697	BGC#0000697
shRNA_or_gRNA_sequence	TGTAAAGGGTACCAGTGCCG	TGTAAAGGGTACCAGTGCCG
PAM	AGG	AGG
Name	CLNS1A_82	CLNS1A_82
Sample_ID	BGKcLV28-21	BGKcLV28-22
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CLNS1A	CLNS1A
qPCR_result	67.9	69.8
Ave_qPCR	68.9
RT-qPCR_primer-F	tgttgctgatgaagaagaggaa
RT-qPCR_primer-R	ctcaggatctggatgcaagg
protein_conc	2078	2349
WB_result	49.6	53.2
Ave_WB	51.4
WB_DONE_date	8/26/21
MW	26kd
IP
antibody_Cat#	A304-521A	LOT #1
Antibody DCC ID	ENCAB677WEY	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	5089	5090

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CLNS1A	Product_ID: A304-521A Lot_ID: 1 Source: Bethyl Labs Target Name: CLNS1A-human

Experiment Status

	BGKcLV28-21	BGKcLV28-22
Sample_ID	BGKcLV28-21	BGKcLV28-22
Sample Name
Sample Name	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-22
RBP	CLNS1A	CLNS1A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9913	9914

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-21	BGKcLV28-22
Sample #	21	22
Sample Name	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-22
Sample_Name_Alias
Index Well Position	E07	F07
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	327	330
Peak_Molarity	107.00	102.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E3.png	DNA_Library_set48-49/set3/F3.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E3.png	RNA_Library_set48-49/set2/F3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-21	BGKcLV28-22
RBP	CLNS1A	CLNS1A
Batch_ID	BGKcLV28	BGKcLV28
WB_result	49.600	53.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2082	2083

Sequencing Information

	BGKcLV28-21	BGKcLV28-22
Sample_ID	BGKcLV28-21	BGKcLV28-22
Sample Name	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-22
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	105,364,560	114,038,754
total_aligned_reads	91,520,296	110,159,416
unique_aligned_reads	83,922,198	101,620,982
percent_uniqueAligned	0.79649	0.89111
correlation_replicates	0.989196	0.989196
spikein_reads	21,536	32,096
percent_spikeins	0.00020	0.00028
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1833	1834

Data Submission Information

	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-22	BGKcLV28-22	BGKcLV28-22	BGKcLV28-22
ENCODE_alias	brenton-graveley:CLNS1A-BGKcLV28	brenton-graveley:CLNS1A-BGKcLV28-21	brenton-graveley:L-CLNS1A-BGKcLV28-21	brenton-graveley:CLNS1A-BGKcLV28-21_S103_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGKcLV28-21_S103_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGKcLV28-K562	brenton-graveley:CLNS1A-BGKcLV28-22	brenton-graveley:L-CLNS1A-BGKcLV28-22	brenton-graveley:CLNS1A-BGKcLV28-22_S104_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLNS1A-BGKcLV28-22_S104_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR950KYU	ENCBS126MYE	ENCLB562WVR	ENCFF701UQZ	ENCFF880SMY	ENCSR545FZJ	ENCBS528FQJ	ENCLB679YSY	ENCFF430WQO	ENCFF616ZCF
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	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-21	BGKcLV28-22	BGKcLV28-22	BGKcLV28-22	BGKcLV28-22
Sample Name	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-21	CLNS1A-BGKcLV28-22	CLNS1A-BGKcLV28-22	CLNS1A-BGKcLV28-22	CLNS1A-BGKcLV28-22
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		CLNS1A-BGKcLV28-21.pdf	L-CLNS1A-BGKcLV28-21.pdf				CLNS1A-BGKcLV28-22.pdf	L-CLNS1A-BGKcLV28-22.pdf
ID	3481	3596	3730	3864	3998	7143	3597	3731	3865	3999

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
CLNS1A-BGKcLV28-21_S103_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1833	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	3950
CLNS1A-BGKcLV28-21_S103_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1833	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	4008
CLNS1A-BGKcLV28-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1833					GRCh38	V40	CLNS1A-BGKcLV28-21_S103_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGKcLV28-21_S103_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19232
CLNS1A-BGKcLV28-21_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	1833					GRCh38	V40	CLNS1A-BGKcLV28-21/Aligned.sortedByCoord.out.bam		ENCORE2	19290
CLNS1A-BGKcLV28-21_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	1833					GRCh38	V40	CLNS1A-BGKcLV28-21/Aligned.sortedByCoord.out.bam		ENCORE2	19348
CLNS1A-BGKcLV28-21_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	1833					GRCh38	V40	CLNS1A-BGKcLV28-21/Aligned.sortedByCoord.out.bam		ENCORE2	19406
CLNS1A-BGKcLV28-21_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	1833					GRCh38	V40	CLNS1A-BGKcLV28-21/Aligned.sortedByCoord.out.bam		ENCORE2	19464
CLNS1A-BGKcLV28-21_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1833					GRCh38	V40	CLNS1A-BGKcLV28-21_S103_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGKcLV28-21_S103_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19522
CLNS1A-BGKcLV28-22_S104_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1834	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	3951
CLNS1A-BGKcLV28-22_S104_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1834	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	4009
CLNS1A-BGKcLV28-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1834					GRCh38	V40	CLNS1A-BGKcLV28-22_S104_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGKcLV28-22_S104_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19233
CLNS1A-BGKcLV28-22_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	1834					GRCh38	V40	CLNS1A-BGKcLV28-22/Aligned.sortedByCoord.out.bam		ENCORE2	19291
CLNS1A-BGKcLV28-22_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	1834					GRCh38	V40	CLNS1A-BGKcLV28-22/Aligned.sortedByCoord.out.bam		ENCORE2	19349
CLNS1A-BGKcLV28-22_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	1834					GRCh38	V40	CLNS1A-BGKcLV28-22/Aligned.sortedByCoord.out.bam		ENCORE2	19407
CLNS1A-BGKcLV28-22_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	1834					GRCh38	V40	CLNS1A-BGKcLV28-22/Aligned.sortedByCoord.out.bam		ENCORE2	19465
CLNS1A-BGKcLV28-22_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1834					GRCh38	V40	CLNS1A-BGKcLV28-22_S104_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLNS1A-BGKcLV28-22_S104_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19523