CSE1L RNA-Seq in K562

General Information


RBP	CSE1L
Cell_Line	K562
Method	CRISPR
Exp_Name	CSE1L-BGKcLV28-K562
ENCODE_series_ID	ENCSR285JMR
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR877CJJ
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CSE1L-BGKcLV28-43
Rep2	CSE1L-BGKcLV28-44
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	59.2
Rep2_qPCR	59.9
Rep1_WB	73.9
Rep2_WB	78.9
Antibody Cat#	A300-473A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB024AVF
Status	Released
Project	ENCODE4
ID	834

Experiment Information (Status: Released)

	BGKcLV28-43	BGKcLV28-43	BGKcLV28-44	BGKcLV28-44
idx	983	985	984	986
TRCN#_or_BGC#	BGC#0000720	BGC#0000720	BGC#0000720	BGC#0000720
shRNA_or_gRNA_sequence	AATTTGTGAAGCCGATCGAG	AATTTGTGAAGCCGATCGAG	AATTTGTGAAGCCGATCGAG	AATTTGTGAAGCCGATCGAG
PAM	tgg	tgg	tgg	tgg
Name	CSE1L_96	CSE1L_96	CSE1L_96	CSE1L_96
Sample_ID	BGKcLV28-43	BGKcLV28-43	BGKcLV28-44	BGKcLV28-44
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CSE1L	CSE1L	CSE1L	CSE1L
qPCR_result	59.2	59.2	59.9	59.9
Ave_qPCR	59.6	59.6
RT-qPCR_primer-F	aaaaagatctgtgcggttgg	aaaaagatctgtgcggttgg
RT-qPCR_primer-R	tcgggtaactcaaaaagacca	tcgggtaactcaaaaagacca
protein_conc	2336	2336	2668	2668
WB_result	73.9	58.5	78.9	54.4259012
Ave_WB	76.4	56.5
WB_DONE_date	7/9/21	2/22/22	JESS
MW	110KD	110KD
IP
antibody_Cat#	A300-473A	A300-472A	LOT #2	LOT #2
Antibody DCC ID	ENCAB024AVF	ENCAB578YRG	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5117	5119	5118	5120

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSE1L	Product_ID: A300-473A Lot_ID: 2 Source: Bethyl Labs Target Name: CSE1L-human
CSE1L	Product_ID: A300-472A Lot_ID: 2 Source: Bethyl Labs Target Name: CSE1L-human

Experiment Status

	BGKcLV28-43	BGKcLV28-44
Sample_ID	BGKcLV28-43	BGKcLV28-44
Sample Name
Sample Name	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-44
RBP	CSE1L	CSE1L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9927	9928

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-43	BGKcLV28-44
Sample #	35	36
Sample Name	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-44
Sample_Name_Alias
Index Well Position	C09	D09
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	318	370
Peak_Molarity	127.00	120.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/C5.png	DNA_Library_set48-49/set3/D5.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/C5.png	RNA_Library_set48-49/set2/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-43	BGKcLV28-44
RBP	CSE1L	CSE1L
Batch_ID	BGKcLV28	BGKcLV28
WB_result	73.900	78.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2096	2097

Sequencing Information

	BGKcLV28-43	BGKcLV28-44
Sample_ID	BGKcLV28-43	BGKcLV28-44
Sample Name	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-44
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	145,954,096	99,754,830
total_aligned_reads	140,073,394	96,094,534
unique_aligned_reads	129,212,022	88,326,168
percent_uniqueAligned	0.88529	0.88543
correlation_replicates	0.978256	0.978256
spikein_reads	30,490	14,996
percent_spikeins	0.00021	0.00015
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1847	1848

Data Submission Information

	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-44	BGKcLV28-44	BGKcLV28-44	BGKcLV28-44
ENCODE_alias	brenton-graveley:CSE1L-BGKcLV28	brenton-graveley:CSE1L-BGKcLV28-43	brenton-graveley:L-CSE1L-BGKcLV28-43	brenton-graveley:CSE1L-BGKcLV28-43_S117_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSE1L-BGKcLV28-43_S117_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSE1L-BGKcLV28-K562	brenton-graveley:CSE1L-BGKcLV28-44	brenton-graveley:L-CSE1L-BGKcLV28-44	brenton-graveley:CSE1L-BGKcLV28-44_S118_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSE1L-BGKcLV28-44_S118_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR877CJJ	ENCBS543AIH	ENCLB314LIG	ENCFF395OOQ	ENCFF083TQT	ENCSR285JMR	ENCBS744PRW	ENCLB576CDH	ENCFF621HFB	ENCFF572LSW
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	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-43	BGKcLV28-44	BGKcLV28-44	BGKcLV28-44	BGKcLV28-44
Sample Name	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-43	CSE1L-BGKcLV28-44	CSE1L-BGKcLV28-44	CSE1L-BGKcLV28-44	CSE1L-BGKcLV28-44
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		CSE1L-BGKcLV28-43.pdf	L-CSE1L-BGKcLV28-43.pdf				CSE1L-BGKcLV28-44.pdf	L-CSE1L-BGKcLV28-44.pdf
ID	3488	3610	3744	3878	4012	7157	3611	3745	3879	4013

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
CSE1L-BGKcLV28-43_S117_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1847	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	3964
CSE1L-BGKcLV28-43_S117_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1847	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	4022
CSE1L-BGKcLV28-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1847					GRCh38	V40	CSE1L-BGKcLV28-43_S117_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGKcLV28-43_S117_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19246
CSE1L-BGKcLV28-43_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	1847					GRCh38	V40	CSE1L-BGKcLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	19304
CSE1L-BGKcLV28-43_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	1847					GRCh38	V40	CSE1L-BGKcLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	19362
CSE1L-BGKcLV28-43_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	1847					GRCh38	V40	CSE1L-BGKcLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	19420
CSE1L-BGKcLV28-43_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	1847					GRCh38	V40	CSE1L-BGKcLV28-43/Aligned.sortedByCoord.out.bam		ENCORE2	19478
CSE1L-BGKcLV28-43_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1847					GRCh38	V40	CSE1L-BGKcLV28-43_S117_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGKcLV28-43_S117_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19536
CSE1L-BGKcLV28-44_S118_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1848	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	3965
CSE1L-BGKcLV28-44_S118_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1848	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	4023
CSE1L-BGKcLV28-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1848					GRCh38	V40	CSE1L-BGKcLV28-44_S118_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGKcLV28-44_S118_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19247
CSE1L-BGKcLV28-44_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	1848					GRCh38	V40	CSE1L-BGKcLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	19305
CSE1L-BGKcLV28-44_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	1848					GRCh38	V40	CSE1L-BGKcLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	19363
CSE1L-BGKcLV28-44_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	1848					GRCh38	V40	CSE1L-BGKcLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	19421
CSE1L-BGKcLV28-44_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	1848					GRCh38	V40	CSE1L-BGKcLV28-44/Aligned.sortedByCoord.out.bam		ENCORE2	19479
CSE1L-BGKcLV28-44_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1848					GRCh38	V40	CSE1L-BGKcLV28-44_S118_L004_R1_001.filtered.trimmed.paired.fastq.gz,CSE1L-BGKcLV28-44_S118_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19537