SSR1 RNA-Seq in HepG2

General Information


RBP	SSR1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SSR1-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	SSR1-BGHcLV45-67
Rep2	SSR1-BGHcLV45-68
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	57.0
Rep2_WB	60.9
Antibody Cat#	A304-978A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1630

Experiment Information (Status: Submitting)

	BGHcLV45-67	BGHcLV45-68
idx	1217	1217
TRCN#_or_BGC#	BGC#0001219	BGC#0001219
shRNA_or_gRNA_sequence	AGTGGCACAAGATCTTACAG	AGTGGCACAAGATCTTACAG
PAM	AGG	AGG
Name	SSR1_81	SSR1_81
Sample_ID	BGHcLV45-67	BGHcLV45-68
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	SSR1	SSR1
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3008	2853
WB_result	57.0	60.9
Ave_WB
WB_DONE_date	11/1/24
MW	32kd
IP
antibody_Cat#	A304-978A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9757	9758

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV45-67	BGHcLV45-68
Sample_ID	BGHcLV45-67	BGHcLV45-68
Sample Name
Sample Name	SSR1-BGHcLV45-67	SSR1-BGHcLV45-68
RBP	SSR1	SSR1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13718	13719

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-67	BGHcLV45-68
Sample #	33	34
Sample Name	SSR1-BGHcLV45-67	SSR1-BGHcLV45-68
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	311	294
Peak_Molarity	61.20	77.30
libSampleQC_DNA_Well	DNA_Library_set76/set1/A11.png	DNA_Library_set76/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/A5.png	RNA_Library_set76/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-67	BGHcLV45-68
RBP	SSR1	SSR1
Batch_ID	BGHcLV45	BGHcLV45
WB_result	57.000	60.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4642	4643

Sequencing Information

	BGHcLV45-67	BGHcLV45-68
Sample_ID	BGHcLV45-67	BGHcLV45-68
Sample Name	SSR1-BGHcLV45-67	SSR1-BGHcLV45-68
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	41,126,301	34,154,259
total_aligned_reads	37,859,768	30,671,379
unique_aligned_reads	35,874,073	28,900,213
percent_uniqueAligned	0.87229	0.84617
correlation_replicates	0.971763	0.971763
spikein_reads	60,232	29,008
percent_spikeins	0.00146	0.00085
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3353	3354

Data Submission Information DCC submission information was not avaliable

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
SSR1-BGHcLV45-67_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3353	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31844
SSR1-BGHcLV45-67_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3353	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31886
SSR1-BGHcLV45-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGHcLV45-67_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31928
SSR1-BGHcLV45-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_Aligned.sortedByCoord.out.bam		ENCORE2	31970
SSR1-BGHcLV45-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_Aligned.sortedByCoord.out.bam		ENCORE2	32012
SSR1-BGHcLV45-67_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_Aligned.sortedByCoord.out.bam		ENCORE2	32054
SSR1-BGHcLV45-67_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_Aligned.sortedByCoord.out.bam		ENCORE2	32096
SSR1-BGHcLV45-67_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3353					GRCh38	V40	SSR1-BGHcLV45-67_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGHcLV45-67_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32138
SSR1-BGHcLV45-68_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3354	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31845
SSR1-BGHcLV45-68_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3354	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31887
SSR1-BGHcLV45-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGHcLV45-68_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31929
SSR1-BGHcLV45-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_Aligned.sortedByCoord.out.bam		ENCORE2	31971
SSR1-BGHcLV45-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_Aligned.sortedByCoord.out.bam		ENCORE2	32013
SSR1-BGHcLV45-68_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_Aligned.sortedByCoord.out.bam		ENCORE2	32055
SSR1-BGHcLV45-68_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_Aligned.sortedByCoord.out.bam		ENCORE2	32097
SSR1-BGHcLV45-68_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3354					GRCh38	V40	SSR1-BGHcLV45-68_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,SSR1-BGHcLV45-68_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32139