CSDE1 RNA-Seq in HepG2

General Information


RBP	CSDE1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CSDE1-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR121AXF
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR435YKS
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CSDE1-BGHcLV29-41
Rep2	CSDE1-BGHcLV29-42
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	62.9
Rep2_qPCR	72.1
Rep1_WB	55.0
Rep2_WB	50.4
Antibody Cat#	A303-158A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB463WVX
Status	Submitted
Project	ENCODE4
ID	858

Experiment Information (Status: Released)

	BGHcLV29-41	BGHcLV29-41	BGHcLV29-42	BGHcLV29-42
idx	874	876	875	877
TRCN#_or_BGC#	BGC#0000718	BGC#0000718	BGC#0000718	BGC#0000718
shRNA_or_gRNA_sequence	GTGAATTCCACATCATCGCC	GTGAATTCCACATCATCGCC	GTGAATTCCACATCATCGCC	GTGAATTCCACATCATCGCC
PAM	AGG	AGG	AGG	AGG
Name	CSDE1_91	CSDE1_91	CSDE1_91	CSDE1_91
Sample_ID	BGHcLV29-41	BGHcLV29-41	BGHcLV29-42	BGHcLV29-42
transduction_Date	7/20	7/20	7/20	7/20
days	D6	D6	D6	D6
RBP_name	CSDE1	CSDE1	CSDE1	CSDE1
qPCR_result	62.9	62.9	72.1	72.1
Ave_qPCR	67.5	67.5
RT-qPCR_primer-F	gccacagtggaatgtgtgaa	gccacagtggaatgtgtgaa
RT-qPCR_primer-R	cctcatctcctgcctgtagc	cctcatctcctgcctgtagc
protein_conc	4928	4928	3822	3822
WB_result	55.0	51.8	50.4	51.4
Ave_WB	52.7	51.6
WB_DONE_date	10/26/21	6/2/22	jess
MW	89KD	89KD
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A303-158A	A303-160A	LOT #1	LOT #1
Antibody DCC ID	ENCAB463WVX	ENCAB259ZCR
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/5/21		11/5/21
repeat_library
Note
ID	7053	7055	7054	7056

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CSDE1	Product_ID: A303-158A Lot_ID: 1 Source: Bethyl Labs Target Name: CSDE1-human
CSDE1	Product_ID: A303-160A Lot_ID: 1 Source: Bethyl Labs Target Name: CSDE1-human

Experiment Status

	BGHcLV29-41	BGHcLV29-42
Sample_ID	BGHcLV29-41	BGHcLV29-42
Sample Name
Sample Name	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-42
RBP	CSDE1	CSDE1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10001	10002

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-41	BGHcLV29-42
Sample #	29	30
Sample Name	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-42
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	299	291
Peak_Molarity	33.50	11.90
libSampleQC_DNA_Well	DNA_Library_set50/set1/E4.png	DNA_Library_set50/set1/F4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set1/E10.png	RNA_Library_set50/set1/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-41	BGHcLV29-42
RBP	CSDE1	CSDE1
Batch_ID	BGHcLV29	BGHcLV29
WB_result	55.000	50.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3116	3117

Sequencing Information

	BGHcLV29-41	BGHcLV29-42
Sample_ID	BGHcLV29-41	BGHcLV29-42
Sample Name	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-42
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	76,227,722	211,626,524
total_aligned_reads	69,824,932	198,792,550
unique_aligned_reads	65,819,130	186,738,450
percent_uniqueAligned	0.86345	0.88240
correlation_replicates	0.998856	0.998856
spikein_reads	13,288	43,934
percent_spikeins	0.00017	0.00021
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1897	1898

Data Submission Information

	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-42	BGHcLV29-42	BGHcLV29-42	BGHcLV29-42
ENCODE_alias	brenton-graveley:CSDE1-BGHcLV29	brenton-graveley:CSDE1-BGHcLV29-41	brenton-graveley:L-CSDE1-BGHcLV29-41	brenton-graveley:CSDE1-BGHcLV29-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSDE1-BGHcLV29-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSDE1-BGHcLV29-HepG2	brenton-graveley:CSDE1-BGHcLV29-42	brenton-graveley:L-CSDE1-BGHcLV29-42	brenton-graveley:CSDE1-BGHcLV29-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CSDE1-BGHcLV29-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR435YKS	ENCBS204FBI	ENCLB166THM	ENCFF390KQT	ENCFF873LEX	ENCSR121AXF	ENCBS769ODW	ENCLB078VAM	ENCFF847DJB	ENCFF916TQO
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	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-41	BGHcLV29-42	BGHcLV29-42	BGHcLV29-42	BGHcLV29-42
Sample Name	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-41	CSDE1-BGHcLV29-42	CSDE1-BGHcLV29-42	CSDE1-BGHcLV29-42	CSDE1-BGHcLV29-42
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CSDE1-BGHcLV29-41.pdf	L-CSDE1-BGHcLV29-41.pdf				CSDE1-BGHcLV29-42.pdf	L-CSDE1-BGHcLV29-42.pdf
ID	5856	5905	5977	6049	6121	6179	5906	5978	6050	6122

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
CSDE1-BGHcLV29-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1897	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5785
CSDE1-BGHcLV29-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1897	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5827
CSDE1-BGHcLV29-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGHcLV29-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18952
CSDE1-BGHcLV29-41_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	19010
CSDE1-BGHcLV29-41_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	19056
CSDE1-BGHcLV29-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	19102
CSDE1-BGHcLV29-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41/Aligned.sortedByCoord.out.bam		ENCORE2	19148
CSDE1-BGHcLV29-41_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1897					GRCh38	V40	CSDE1-BGHcLV29-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGHcLV29-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19194
CSDE1-BGHcLV29-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1898	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5786
CSDE1-BGHcLV29-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1898	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5828
CSDE1-BGHcLV29-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGHcLV29-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18953
CSDE1-BGHcLV29-42_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	19011
CSDE1-BGHcLV29-42_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	19057
CSDE1-BGHcLV29-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	19103
CSDE1-BGHcLV29-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42/Aligned.sortedByCoord.out.bam		ENCORE2	19149
CSDE1-BGHcLV29-42_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1898					GRCh38	V40	CSDE1-BGHcLV29-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSDE1-BGHcLV29-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19195