CDC5L RNA-Seq in K562

General Information


RBP	CDC5L
Cell_Line	K562
Method	CRISPR
Exp_Name	CDC5L-BGKcLV28-K562
ENCODE_series_ID	ENCSR608EQY
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR544ZMX
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CDC5L-BGKcLV28-11
Rep2	CDC5L-BGKcLV28-12
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	55.5
Rep2_WB	59.1
Antibody Cat#	A301-681A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB386CPV
Status	Released
Project	ENCODE4
ID	822

Experiment Information (Status: Released)

	BGKcLV28-11	BGKcLV28-12
idx	945	946
TRCN#_or_BGC#	BGC#0000688	BGC#0000688
shRNA_or_gRNA_sequence	GCCCGCTTGGCTAATACTCA	GCCCGCTTGGCTAATACTCA
PAM	GGG	GGG
Name	CDC5L_93	CDC5L_93
Sample_ID	BGKcLV28-11	BGKcLV28-12
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CDC5L	CDC5L
qPCR_result	16.0	33.0
Ave_qPCR	24.5
RT-qPCR_primer-F	atgggaccaaattgaacagg
RT-qPCR_primer-R	tttcttgttgtcgctgaacg
protein_conc	1536	2052
WB_result	55.5	59.1
Ave_WB	57.3
WB_DONE_date	6/22/21	JESS
MW	92kd
IP
antibody_Cat#	A301-681A	LOT #1
Antibody DCC ID	ENCAB386CPV	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	5079	5080

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDC5L	Product_ID: A301-681A Lot_ID: 1 Source: Bethyl Labs Target Name: CDC5L-human

Experiment Status

	BGKcLV28-11	BGKcLV28-12
Sample_ID	BGKcLV28-11	BGKcLV28-12
Sample Name
Sample Name	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-12
RBP	CDC5L	CDC5L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9903	9904

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-11	BGKcLV28-12
Sample #	11	12
Sample Name	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-12
Sample_Name_Alias
Index Well Position	C06	D06
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	322	331
Peak_Molarity	132.00	113.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C2.png	DNA_Library_set48-49/set3/D2.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/C2.png	RNA_Library_set48-49/set2/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-11	BGKcLV28-12
RBP	CDC5L	CDC5L
Batch_ID	BGKcLV28	BGKcLV28
WB_result	55.500	59.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2072	2073

Sequencing Information

	BGKcLV28-11	BGKcLV28-12
Sample_ID	BGKcLV28-11	BGKcLV28-12
Sample Name	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-12
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	111,236,712	101,235,080
total_aligned_reads	106,538,542	97,084,578
unique_aligned_reads	98,033,504	89,045,302
percent_uniqueAligned	0.88131	0.87959
correlation_replicates	0.997326	0.997326
spikein_reads	33,228	19,042
percent_spikeins	0.00030	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1823	1824

Data Submission Information

	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-12	BGKcLV28-12	BGKcLV28-12	BGKcLV28-12
ENCODE_alias	brenton-graveley:CDC5L-BGKcLV28	brenton-graveley:CDC5L-BGKcLV28-11	brenton-graveley:L-CDC5L-BGKcLV28-11	brenton-graveley:CDC5L-BGKcLV28-11_S93_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC5L-BGKcLV28-11_S93_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC5L-BGKcLV28-K562	brenton-graveley:CDC5L-BGKcLV28-12	brenton-graveley:L-CDC5L-BGKcLV28-12	brenton-graveley:CDC5L-BGKcLV28-12_S94_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDC5L-BGKcLV28-12_S94_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR544ZMX	ENCBS183DAH	ENCLB195GQV	ENCFF556UXJ	ENCFF395SWX	ENCSR608EQY	ENCBS607GSW	ENCLB102SLL	ENCFF254NFP	ENCFF338KFE
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	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-11	BGKcLV28-12	BGKcLV28-12	BGKcLV28-12	BGKcLV28-12
Sample Name	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-11	CDC5L-BGKcLV28-12	CDC5L-BGKcLV28-12	CDC5L-BGKcLV28-12	CDC5L-BGKcLV28-12
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		CDC5L-BGKcLV28-11.pdf	L-CDC5L-BGKcLV28-11.pdf				CDC5L-BGKcLV28-12.pdf	L-CDC5L-BGKcLV28-12.pdf
ID	3476	3586	3720	3854	3988	7129	3587	3721	3855	3989

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
CDC5L-BGKcLV28-11_S93_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1823	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	3940
CDC5L-BGKcLV28-11_S93_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1823	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	3998
CDC5L-BGKcLV28-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1823					GRCh38	V40	CDC5L-BGKcLV28-11_S93_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGKcLV28-11_S93_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19222
CDC5L-BGKcLV28-11_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	1823					GRCh38	V40	CDC5L-BGKcLV28-11/Aligned.sortedByCoord.out.bam		ENCORE2	19280
CDC5L-BGKcLV28-11_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	1823					GRCh38	V40	CDC5L-BGKcLV28-11/Aligned.sortedByCoord.out.bam		ENCORE2	19338
CDC5L-BGKcLV28-11_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	1823					GRCh38	V40	CDC5L-BGKcLV28-11/Aligned.sortedByCoord.out.bam		ENCORE2	19396
CDC5L-BGKcLV28-11_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	1823					GRCh38	V40	CDC5L-BGKcLV28-11/Aligned.sortedByCoord.out.bam		ENCORE2	19454
CDC5L-BGKcLV28-11_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1823					GRCh38	V40	CDC5L-BGKcLV28-11_S93_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGKcLV28-11_S93_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19512
CDC5L-BGKcLV28-12_S94_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1824	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	3941
CDC5L-BGKcLV28-12_S94_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1824	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	3999
CDC5L-BGKcLV28-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1824					GRCh38	V40	CDC5L-BGKcLV28-12_S94_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGKcLV28-12_S94_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19223
CDC5L-BGKcLV28-12_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	1824					GRCh38	V40	CDC5L-BGKcLV28-12/Aligned.sortedByCoord.out.bam		ENCORE2	19281
CDC5L-BGKcLV28-12_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	1824					GRCh38	V40	CDC5L-BGKcLV28-12/Aligned.sortedByCoord.out.bam		ENCORE2	19339
CDC5L-BGKcLV28-12_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	1824					GRCh38	V40	CDC5L-BGKcLV28-12/Aligned.sortedByCoord.out.bam		ENCORE2	19397
CDC5L-BGKcLV28-12_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	1824					GRCh38	V40	CDC5L-BGKcLV28-12/Aligned.sortedByCoord.out.bam		ENCORE2	19455
CDC5L-BGKcLV28-12_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1824					GRCh38	V40	CDC5L-BGKcLV28-12_S94_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDC5L-BGKcLV28-12_S94_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19513