CLTC RNA-Seq in K562

General Information


RBP	CLTC
Cell_Line	K562
Method	CRISPR
Exp_Name	CLTC-BGKcLV28-K562
ENCODE_series_ID	ENCSR037JLU
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR899RVY
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CLTC-BGKcLV28-23
Rep2	CLTC-BGKcLV28-24
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	83.0
Rep2_qPCR	70.7
Rep1_WB	54.8
Rep2_WB	60.216034
Antibody Cat#	A304-743A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB019OFH
Status	Released
Project	ENCODE4
ID	828

Experiment Information (Status: Released)

	BGKcLV28-23	BGKcLV28-24
idx	957	958
TRCN#_or_BGC#	BGC#0000700	BGC#0000700
shRNA_or_gRNA_sequence	ATCGCCATTCTAGCCTTGCA	ATCGCCATTCTAGCCTTGCA
PAM	GGG	GGG
Name	CLTC_90	CLTC_90
Sample_ID	BGKcLV28-23	BGKcLV28-24
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CLTC	CLTC
qPCR_result	83.0	70.7
Ave_qPCR	76.9
RT-qPCR_primer-F	acttagccggtgctgaagaa
RT-qPCR_primer-R	aaccgacggatagtgtctgg
protein_conc	2073	2442
WB_result	54.8	60.216034
Ave_WB	57.5
WB_DONE_date	6/29/21	JESS
MW	192k
IP
antibody_Cat#	A304-743A	LOT #1
Antibody DCC ID	ENCAB019OFH	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	5091	5092

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CLTC	Product_ID: A304-743A Lot_ID: 1 Source: Bethyl Labs Target Name: CLTC-human

Experiment Status

	BGKcLV28-23	BGKcLV28-24
Sample_ID	BGKcLV28-23	BGKcLV28-24
Sample Name
Sample Name	CLTC-BGKcLV28-23	CLTC-BGKcLV28-24
RBP	CLTC	CLTC
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9915	9916

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-23	BGKcLV28-24
Sample #	23	24
Sample Name	CLTC-BGKcLV28-23	CLTC-BGKcLV28-24
Sample_Name_Alias
Index Well Position	G07	H07
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	369	336
Peak_Molarity	82.00	102.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G3.png	DNA_Library_set48-49/set3/H3.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set48-49/set3/C8.png	RNA_Library_set48-49/set2/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-23	BGKcLV28-24
RBP	CLTC	CLTC
Batch_ID	BGKcLV28	BGKcLV28
WB_result	54.800	60.216
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2084	2085

Sequencing Information

	BGKcLV28-23	BGKcLV28-24
Sample_ID	BGKcLV28-23	BGKcLV28-24
Sample Name	CLTC-BGKcLV28-23	CLTC-BGKcLV28-24
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	77,135,904	72,965,832
total_aligned_reads	72,486,862	67,497,954
unique_aligned_reads	66,863,600	61,861,686
percent_uniqueAligned	0.86683	0.84782
correlation_replicates	0.955592	0.955592
spikein_reads	17,836	12,194
percent_spikeins	0.00023	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1835	1836

Data Submission Information

	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-24	BGKcLV28-24	BGKcLV28-24	BGKcLV28-24
ENCODE_alias	brenton-graveley:CLTC-BGKcLV28	brenton-graveley:CLTC-BGKcLV28-23	brenton-graveley:L-CLTC-BGKcLV28-23	brenton-graveley:CLTC-BGKcLV28-23_S105_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGKcLV28-23_S105_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGKcLV28-K562	brenton-graveley:CLTC-BGKcLV28-24	brenton-graveley:L-CLTC-BGKcLV28-24	brenton-graveley:CLTC-BGKcLV28-24_S106_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CLTC-BGKcLV28-24_S106_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR899RVY	ENCBS043OMI	ENCLB126DIU	ENCFF351WEO	ENCFF476FDB	ENCSR037JLU	ENCBS645RJM	ENCLB316XAN	ENCFF552OHC	ENCFF316TUC
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	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-23	BGKcLV28-24	BGKcLV28-24	BGKcLV28-24	BGKcLV28-24
Sample Name	CLTC-BGKcLV28-23	CLTC-BGKcLV28-23	CLTC-BGKcLV28-23	CLTC-BGKcLV28-23	CLTC-BGKcLV28-23	CLTC-BGKcLV28-23	CLTC-BGKcLV28-24	CLTC-BGKcLV28-24	CLTC-BGKcLV28-24	CLTC-BGKcLV28-24
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		CLTC-BGKcLV28-23.pdf	L-CLTC-BGKcLV28-23.pdf				CLTC-BGKcLV28-24.pdf	L-CLTC-BGKcLV28-24.pdf
ID	3482	3598	3732	3866	4000	7144	3599	3733	3867	4001

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
CLTC-BGKcLV28-23_S105_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1835	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	3952
CLTC-BGKcLV28-23_S105_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1835	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	4010
CLTC-BGKcLV28-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1835					GRCh38	V40	CLTC-BGKcLV28-23_S105_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGKcLV28-23_S105_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19234
CLTC-BGKcLV28-23_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	1835					GRCh38	V40	CLTC-BGKcLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	19292
CLTC-BGKcLV28-23_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	1835					GRCh38	V40	CLTC-BGKcLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	19350
CLTC-BGKcLV28-23_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	1835					GRCh38	V40	CLTC-BGKcLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	19408
CLTC-BGKcLV28-23_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	1835					GRCh38	V40	CLTC-BGKcLV28-23/Aligned.sortedByCoord.out.bam		ENCORE2	19466
CLTC-BGKcLV28-23_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1835					GRCh38	V40	CLTC-BGKcLV28-23_S105_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGKcLV28-23_S105_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19524
CLTC-BGKcLV28-24_S106_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1836	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	3953
CLTC-BGKcLV28-24_S106_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1836	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	4011
CLTC-BGKcLV28-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1836					GRCh38	V40	CLTC-BGKcLV28-24_S106_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGKcLV28-24_S106_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19235
CLTC-BGKcLV28-24_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	1836					GRCh38	V40	CLTC-BGKcLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	19293
CLTC-BGKcLV28-24_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	1836					GRCh38	V40	CLTC-BGKcLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	19351
CLTC-BGKcLV28-24_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	1836					GRCh38	V40	CLTC-BGKcLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	19409
CLTC-BGKcLV28-24_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	1836					GRCh38	V40	CLTC-BGKcLV28-24/Aligned.sortedByCoord.out.bam		ENCORE2	19467
CLTC-BGKcLV28-24_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1836					GRCh38	V40	CLTC-BGKcLV28-24_S106_L004_R1_001.filtered.trimmed.paired.fastq.gz,CLTC-BGKcLV28-24_S106_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19525