A follow-up plasmid MPRA tested 30 constructs formed from six synthetic 4-mer TF-binding-site arrangements and five spacer variants, including the original spacer. Each construct was designed with five barcodes and was mixed with a small portion of the SYN library.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CVCL:6442
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The mini-spacer constructs were 80 bp synthetic four-site elements upstream of the same minimal Pou5f1/dsRed reporter backbone. Supplementary file 1L provides barcode-level normalized activities for three replicates; this table aggregates rows labeled miniSpacer and reports activity changes relative to the matching original-spacer construct.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (26 of 26)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
Page 1 · 30 rows · End of results
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 26 definitions
element_id
Unique synthetic 4-mer construct identifier from Supplementary file 1K.
base_construct_id
Identifier of the same six-site-order construct with the original spacer.
spacer_variant
Original spacer or one of four replacement spacer variants.
spacer_pattern
Spacer pattern from Supplementary file 1J; [TFBS] marks the embedded binding-site block.
sequence
5-prime-to-3-prime sequence of the 80 bp synthetic insert.
sequence_length_bp
Length of the tested synthetic insert in base pairs.
tfbs_order
Order/orientation token string for the four binding sites.
tfbs_orientation
Comma-separated forward/reverse orientation for each site.
tfbs_count
Number of consensus pluripotency TF-binding sites; four for every mini-spacer construct.
tfbs_factors
Comma-separated factor names corresponding to tfbs_order.
barcode_count_design
Number of designed barcodes per construct, nominally five.
barcode_count_summary_rows
Number of miniSpacer rows available in Supplementary file 1L before complete-replicate filtering.
barcode_count_qc
Number of barcode-level summary rows with finite values in all three RNA replicates retained for aggregation.
activity_rep1
Mean normalized barcode activity across retained barcodes in RNA replicate 1, as reported at barcode level in Supplementary file 1L.
activity_rep2
Mean normalized barcode activity across retained barcodes in RNA replicate 2.
activity_rep3
Mean normalized barcode activity across retained barcodes in RNA replicate 3.
activity_sem_barcode_rep1
Standard error across retained barcode-level activities in RNA replicate 1.
activity_sem_barcode_rep2
Standard error across retained barcode-level activities in RNA replicate 2.
activity_sem_barcode_rep3
Standard error across retained barcode-level activities in RNA replicate 3.
activity_mean
Mean of the three construct-level replicate activities.
activity_sem_replicates
Standard error of the three replicate activities.
log2_activity_mean
Base-2 logarithm of activity_mean.
original_activity_mean
Activity mean of the matching original-spacer construct.
delta_vs_original
Activity mean minus the matching original-spacer activity mean.
fold_vs_original
Activity mean divided by the matching original-spacer activity mean.
effect_percent_vs_original
Percent activity change relative to the matching original-spacer construct.
Quality control
The authors used five barcodes per mini-spacer construct and performed the assay with three biological replicates. Package QC retained 30/30 constructs; barcode-level rows with a missing value in any of the three replicate activity columns were excluded from aggregation, leaving 28 constructs with 5/5 complete rows and 2 constructs with 4/5 complete rows.
Curation notes
Mini-spacer data were not part of the eight-sample GEO series; they are included in the eLife supplementary workbook. The workbook’s 1M sheet mixes the mini-spacer pool with a small SYN subset and several unmapped NA_NA rows, so the package uses the intended 30 constructs from 1K and only the 1L rows explicitly labeled miniSpacer.