title: Sarm1 -/- mouse, neuron, stroke, biol rep 4


title: Sarm1 -/- mouse, neuron, stroke, biol rep 3

status: Public on May 01 2025

type: SRA

city: Los Angeles

first: Yutaro

last: Komuro

state: CA

address: 635 Charles E Young Dr S

department: Neurology

country: USA

institute: University of California Los Angeles

library_source: transcriptomic

data_processing:
Quality of sequencing was assessed using FastQC, followed by read alignment with STAR aligner.
The mm10 reference genome was used.
Following alignment, counts were read using htseq-count.
Differential gene expression was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was extracted using the Rneasy conventional RNA preparation kit from Qiagen.
RNA libraries were prepared using the NuGEN Ovation Ultralow system with KAPA HyperPrep.

tag: tissue

value: Brain

tag: cell type

value: neuron

tag: genotype

value: Sarm1 -/-

tag: treatment

value: stroke


title: SARS-CoV-2 spike pseudotyped virus selected replicate 1

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
Library name: SARS2_r1
Supp_table_1_kozak_sortseq_and_infection.csv

library_source: genomic

data_processing:
For short-read sequencing generated by the Illumina NextSeq, the forward and reverse reads were paired using PEAR (Zhang et al. 2014). Kozak sequences were counted from the paired reads using Enrich2 (Rubin et al. 2017), and filtered to exclude reads possessing nucleotides with quality scores less than 20. For longer-read sequencing generated by the Illumina MiSeq, generated through submission to the Amplicon-EZ service offered by Genewiz / Azenta, the reads were paired as above, except the paired reads were subsequently processed with a custom Python script “Extract_Kozak.py”, which identified true Kozak library reads from template molecule reads, and for each Kozak read, extracted the Kozak sequence found in that read. All subsequent analyses of the sequencing outputs were performed in R version 4.3.1 (2023-06-16). An R markdown file with code to recreate the analysis (Kozak.Rmd), along with the relevant data files and the various python scripts for the initial processing of FASTQ files, can be found in the MatreyekLab Github repository under “MatreyekLab/Kozak”. A table of the fastq files generated and analyzed for this work is included as Supplementary Table 4. The Kozak sort-seq scores were calculated similarly to previous work (Matreyek et al, 2018, 2021), with some minor changes. For samples sequenced to sufficient read depth, a density-plot of sequence counts normally yields a bimodal distribution, with one peak stemming from a log-normal distribution of counts with a median of 10 or greater, largely reflecting sequences of physical molecules amplified and sequenced from the sample, and a separate peak with a count of 1, largely reflecting sequences derived from sequencing error. We harnessed this property to computationally remove erroneous sequence counts. For each bin, we identified the local minima between these two peaks, and removed sequence counts below this sample-specific threshold value, to yield a dataset of filtered counts. For each sequenced sample, the filtered count of each variant was divided by the sum of counts recorded in that sample to obtain variant-specific frequencies (Fv,bin). For replicates 1 and 2, which both included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the technical replicate frequencies were averaged to yield an average frequency for each variant, which was used as the Fv,bin value. These frequencies were used to calculate a weighted average for each variant for each replicate (Wv,rep), using the following formula.  Wv,rep =(Fv,bin1 0) + (Fv,bin2 (1/3)) + (Fv,bin3 (2/3)) + (Fv,bin4 1)Fv,bin1 + Fv,bin2 + Fv,bin3 + Fv,bin4   Thus, all weighted average values ranged from a value of 0 to 1. Pairwise comparisons of variant-specific weighted averages are shown in Supplementary Fig 2. Once the weighted average values were calculated for each variant for each replicate, they were log10 transformed, averaged, and the base-10 exponential calculated to yield the geometric mean weighted average value. Correspondingly, the standard deviation of the log10 transformed values were calculated and used to calculate the upper and lower 95% confidence intervals, which were later transformed as a base-10 exponential to accompany the geometric mean weighted averages.  To calibrate these weighted averages to MFI equivalent values, we generated cells recombined with ACE2-miRFP670 constructs encoding 16 different Kozak sequences, which were measured for miRFP670 fluorescence intensity using analytical flow cytometry. A linear model was first generated to establish the conversion factor enabling scaling of our weighted average scores to MFI-equivalent values. While accurate for values between 1% and 100% of the consensus Kozak, the linear model performed poorly for extremely high or low values, with the minimum and maximum scaled values being 0.0003 and 3.89; both of these values were outside of the range physically observed with this assay. We thus used logistic regression to approximate the linear model, but furthermore bound all scaled values between 0.004 and 1.34. These resulting values are referred to as the calibrated scores.  Enrichment values for infection experiments were initially filtered similarly to the sort-seq scores, wherein we identified the local minima between the two peaks observed in a density plot representation of sequence counts, and removed sequence counts below his sample-specific threshold value, to yield a dataset of filtered counts. The counts for each variant were divided by the total counts for that sequence sample, to yield sample-specific variant frequencies. For infection samples that included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the geometric means of the technical replicate frequencies were used. Each hygromycin-selected infected sample had a corresponding unselected sample. For each pair, we divided variant-specific frequencies following selection by those prior to selection, obtaining an enrichment ratio. The STIM1 survival scores were calculated similarly, with the exception that the ratio was the quotient of each Kozak variant frequency recombined into cells divided by the frequency of that variant in the sequenced plasmid library.
Assembly: Custom synthetic amplicon
Supplementary files format and content: csv file with calibrated sort-seq scores and infection scores
Supplementary files format and content: csv file with ACE2 variant-specific infection scores

molecule: genomic DNA

organism: synthetic construct

source_name: HEK 293T

extract_protocol:
Genomic DNA was isolated from each sample using the JetFlex™ Genomic DNA purification kit (Thermo Fisher, A30700).
ACE2 amplicon generation and high throughput sequencing A section of DNA spanning the recombination junction, and including the Kozak sequence preceding the ACE2 open reading frame, was amplified from the genomic DNA extracts using PCR. For each 50 µL PCR reaction, the following components were used: 2 µg genomic DNA (quantified by nanodrop), 0.25 µM  forward primer containing i7 index barcode and 0.25 µM  reverse primer containing i5 index barcode, and 25 µL of Phusion plus high fidelity PCR mix (Thermo Fisher, F548L). A total of five PCR reactions were performed per condition, which each tube initially incubated at 95 °C for 3 minutes, followed by 25 cycles of 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, followed by a final 72 °C incubation for 1 minute. PCR products were mixed with 6x DNA loading dye (NEB, B7024S) and separated on 1.5% agarose TAE gel. Bands corresponding to the expected 293 bp amplicon size were excised and extracted using the Freeze and Squeeze kit according to the manufacturer’s instructions (Bio-Rad, 7326166). Eluted PCR products were purified using a Zymo clean and concentrator kit (Zymo Research, D4003). Amplicon concentrations were measured using Qubit dsDNA BR assay kit (Life technologies, Q32853). Amplicons from all the experimental conditions were pooled in equimolar ratios and sequenced on an Illumina NextSeq550 with a 75-cycle high output kit. Oligonucleotide sequences for PCR and custom Illumina primers for sequencing are listed in Supplementary Table 3.

tag: cell line

value: HEK 293T

value: G542Ac3 landing pad


title: ChIP-seq_RAW264.7_macroH2A_SPT16_rep2

city: beijing

first: ji

last: dengyu

address: 10 Xitoutiao, Youanmen, Fengtai District

country: China

institute: Capital Medical Universit

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus (mm10) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters.
Assembly: mm10
Supplementary files format and content: WIG

growth_protocol: MDA-MB-231 cells were infected with lentivirus, and stable cell lines were generated by puromycin (1 μg/mL) selection

extract_protocol:
The cells were crosslinked in adherent conditions with 1% formaldehyde for 15 min at room temperature and quenched with glycine to a final concentration of 125 nM. Fixed cells were lysed in nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, protease inhibitors) to extract nuclei and sheared by sonication to 200-500-bp-sized fragments. Sheared chromatin was incubated with rabbit anti-HA antibodies (Abcam, ab9110, 3 μg) and protein A/G-Dynabeads (Life Technology, 10 μl) for 12 hours at 4 ℃. The beads were washed with RIPA150 (50 mMTris-HCl, pH 8.0,150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), RIPA500 (50 mM Tris-HCl, pH 8.0, 0.5 M NaCl,1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), RIPA-LiCl (50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate, 0.5 M LiCl) and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), respectively. The beads were resuspended with NLB buffer (10 mM Tris-HCl, pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS). After de-crosslinked at 65 ℃ for 6 hours, DNA fragments were digested with RNase A and proteinase K. Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.

value: macrophage

tag: antibody


title: E17.5_BMI1_GFP_3

city: Portland

first: Guanming

last: Wu

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: OHSU

data_processing:
Reads were aligned using bwa-mem
Aligned reads were deduplicated using samtools rmdup
Bam files were generated for merged replicates
Peaks were called on merged replicates as well as individual replicates
All called peaks were merged to generate the all_peaks master peak set
Assembly: mm10
Supplementary files format and content: bed files containing called peaks

source_name: Murine intestinal epithelial cells

extract_protocol:
Nuclei were extracted using nuclei isolaiton buffer (NIB)
Tagmentation on isolated nuclei was performed using Illumina Nextera reagents

value: Murine intestinal epithelial cells


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 8

description:
Library name: SARS2_r8_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Sarm1 -/- mouse, neuron, stroke, biol rep 2


title: ChIP-seq_RAW264.7_macroH2A_SPT16_rep1


title: ChIP-seq_RAW264.7_macroH2A_LPS_HA_rep2

value: HA


title: ChIP-seq_RAW264.7_macroH2AS139A.siFACT_HA_rep2


title: E17.5_BMI1_GFP_2


title: Sarm1 -/- mouse, neuron, stroke, biol rep 1


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 7

description:
Library name: SARS2_r7_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: E17.5_BMI1_GFP_1


title: ChIP-seq_RAW264.7_macroH2AS139A.siFACT_HA_rep1


title: ChIP-seq_RAW264.7_macroH2A.siFACT_HA_rep2


title: 4907

first: Craig

last: Dorrell

address: 3181 SW Sam Jackson Park Rd.

department: Pediatrics

data_processing:
Genewiz/Azenta platform
Assembly: GRCm39
Supplementary files format and content: RPKM values, tab delimited

source_name: liver

extract_protocol:
Qiagen RNEasy
Genewiz standard library

value: liver

value: oxm


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 6

description:
Library name: SARS2_r6_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: E15.5_Epcam_3


title: 4906


title: E15.5_Epcam_2


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 5

description:
Library name: SARS2_r5_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 4

description:
Library name: SARS2_r4_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: 4669


title: ChIP-seq_RAW264.7_macroH2AS139A_HA_rep2


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 3

description:
Library name: SARS2_r3_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: ChIP-seq_RAW264.7_macroH2A.siFACT_HA_rep1


title: 4657


title: E14.5_Epcam_3


title: ChIP-seq_RAW264.7_macroH2AS139A_HA_rep1


title: E14.5_Epcam_2


title: E15.5_Epcam_1


title: 4648

value: met


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 1

description:
Library name: SARS2_r1_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: E14.5_Epcam_1


title: VSVG pseudotyped virus selected replicate 4

description:
Library name: VSVG_r4_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: ChIP-seq_RAW264.7_macroH2A_HA_rep1


title: E12.5_Epcam_3


title: 4647


title: 4632

value: wt


title: ChIP-seq_RAW264.7_macroH2A_HA_rep2


title: VSVG pseudotyped virus selected replicate 3

description:
Library name: VSVG_r3_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: Adult murine lung immune cells,replicate 2, scRNA-seq

city: Shanghai

first: Guilin

last: Yang

address: Yueyang road 320

institute: Center for Excellence in Molecular Cell Science

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adult murine lung immune cells treated with influenza PR8 rep2

extract_protocol:
Left lung lobes from wild type adult mice infected influenza PR8 14 days were digested by gentle shaking at 37℃ in lysis buffer containing Dispase II and Collagenase type I. Tissue were dissociated to single cells and the following antibodies were used to sort immune cells: Rat anti-FITC CD45, Rat anti-FITC CD31, Rat anti- APC Epcam.  The cells were subjected to fluorescence activated cell sorting (FACS) to select all Epcam-CD31-CD45+cells. Sorted dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar     Fluorescence Cell Analyzer (Aber Instruments).
Exposure cells to lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA  synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3. 1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo  Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing was performed by Majorbio Co., Ltd (Shanghai, China).

value: Lung

value: Immune cell

value: wild type

value: infected with influenza PR8


title: E12.5_Epcam_2


title: Adult murine lung immune cells,replicate 1, scRNA-seq

description: 10x Genomics

source_name: Adult murine lung immune cells treated with influenza PR8 rep1


title: VSVG pseudotyped virus selected replicate 2

description:
Library name: VSVG_r2_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: E12.5_Epcam_1


title: 4602


title: 4779

value: met+oxm


title: VSVG pseudotyped virus selected replicate 1

description:
Library name: VSVG_r1_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV-2 spike pseudotyped virus unselected replicate 2

description:
Library name: SARS2_r2_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: 4579


title: Adult_Igr5_GFP_ISC_3


title: Pancreas, Day 21, PBS treated, Sox4 wild-type, Kras G12D background, mouse 1

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

description:
K_WT_D21_1
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt

data_processing:
Mapping to the mouse genome was performed using hisat2 software 2.0.5
Reads with adapter contamination were removed. Reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) were removed. Reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read were removed.
Assembly performed using Stringtie 1.3.3b
Quantifications perfomed using Featurecounts 1.5.0-p3
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes fpkm values for each sample

source_name: Pancreas

growth_protocol: All animal experiments described were approved by the University of Copenhagen’s ethical committee. All animal experiments were performed in accordance with the Danish Animal Welfare Act and FELASA. Attention has been paid to the ARRIVE guidelines, recommendations, and policy. Genetically engineered mouse models and C57Bl/6J mice used in this project were purchased from Janvier Labs (Le Genest-Saint-Isle, France), and animals were fed a laboratory chow diet and had free access to water. Mice were maintained on a genetically mixed background. Mice were genotyped at weaning.

extract_protocol:
Based on the commercial protocol, the pancreatic tissue’s RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Pancreatic tissue is added to 2 mL of RLT buffer (with 2-Mercaptoethanol, 1:100) and homogenised using a homogeniser (IKA, T10 basic). Homogenizer was washed between the samples with MilliQ water and 70% ethanol to avoid cross-contamination. After tissues were homogenised, 1 volume (2 mL) of 70% ethanol was added. Next, RNeasy Spin columns were loaded with 700μL of the sample and centrifuged for 30 seconds at maximum speed (>13.000rpm). All collected flow-through was discarded. This step was repeated several times. From here, the instructors´ protocol was followed.  The extracted RNA’s concentration and sample quality were measured using a spectrophotometer (DeNovix, DS-11).
For RNA library preparation the mRNA is enriched by poly(A) capture. RNA is then fragmented by enzyme digestion (or Covaris). cDNA reverse transcription is followed by RNA library preparation. After a library quality control, sequencing is performed using the Illumina NovaSeq 6000 platform, pair-end 150 bp sequencing strategy (short-reads), with a depth of the recommended 20 million read pair per sample. Following data quality control, bioinformatic analysis is performed. Gene set enrichment analysis was performed using the open source GSEA software46

treatment_protocol: To induce recombination of the alleles, tamoxifen (T5648; Sigma-Aldrich) was administered through intraperitoneal injections every other day for 5 days (e.g., Monday, Wednesday, Friday) at a dose of 3mg per injection. Tamoxifen was dissolved in corn oil (C8267; Sigma-Aldrich) at a stock concentration of 30mg/ml (100ul/injection). A standard wash-out of 2 weeks was performed. To inducetissue injury in the pancreas, the cholecystokinin analogue caerulein (C9026; Sigma-Aldrich) was administered through intraperitoneal injections every hour for 7 hours (8 injections/day) on 2 consecutive days at a concentration of 125ug/kg body weight as described elsewhere43. Control mice were injected with equivalent volume of PBS following the same protocol.

value: Pancreas

value: Ptf1aCreER; Sox4+/+; YFP+/+; KrasG12D/+

value: Ptf1aCreER; Sox4WT; KrasG12D; YFP

value: Caerulein day 21


title: Pancreas, Day 21, PBS treated, Sox4 wild-type, Kras G12D background, mouse 2

description:
K_WT_D21_2
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt


title: VSVG pseudotyped virus unselected replicate 4

description:
Library name: VSVG_r4_neg
Supp_table_1_kozak_sortseq_and_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: VSVG pseudotyped virus unselected replicate 3

description:
Library name: VSVG_r3_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Pancreas, Day 21, Caeruelein treated, Sox4 conditional knock-out, Kras G12D background, mouse 3

description:
K_KO_D21_3
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt

value: Ptf1aCreER; Sox4-/-; YFP+/+; KrasG12D/+

value: Ptf1aCreER; Sox4KO; KrasG12D; YFP


title: Adult_Igr5_GFP_ISC_1

value: Murine intestinal epithelial cells


title: VSVG pseudotyped virus unselected replicate 2

description:
Library name: VSVG_r2_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: 4563

value: liver


title: Pancreas, Day 21, Caeruelein treated, Sox4 conditional knock-out, Kras G12D background, mouse 2

description:
K_KO_D21_2
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt


title: VSVG pseudotyped virus unselected replicate 1

description:
Library name: VSVG_r1_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Adult_BMI1_GFP_48hrIR_3


title: 4562


title: Adult_BMI1_GFP_48hrIR_2


title: Pancreas, Day 21, Caeruelein treated, Sox4 conditional knock-out, Kras G12D background, mouse 1

description:
K_KO_D21_1
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt


title: 4548

value: met


title: SARS-CoV spike pseudotyped virus selected replicate 7

description:
Library name: SARS1_r7_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: Pancreas, Day 21, PBS treated, Sox4 wild-type, Kras G12D background, mouse 3

description:
K_WT_D21_3
K_KO_D21vsK_WT_D21_deg
gene_count.txt
gene_fpkm.txt


title: 4593


title: Adult_BMI1_GFP_3


title: 4585

value: wt


title: Pancreas, Day 2, PBS treated, Sox4 wild-type, Kras WT background, mouse 2

description:
WT_D2_2
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt

value: Ptf1aCreER; Sox4+/+; YFP+/+

value: Ptf1aCreER; Sox4WT; YFP

value: Caerulein day 2


title: 4428

value: oxm


title: Adult_BMI1_GFP_48hrIR_1


title: Adult_Igr5_GFP_ISC_2


title: SARS-CoV spike pseudotyped virus selected replicate 5

description:
Library name: SARS1_r5_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: 4524


title: Adult_BMI1_GFP_2


title: 4406

value: met+oxm


title: Adult_BMI1_GFP_1


title: 4403


title: SARS-CoV spike pseudotyped virus selected replicate 4

description:
Library name: SARS1_r4_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: Pancreas, Day 2, Caeruelein treated, Sox4 conditional knock-out, Kras WT background, mouse 2

description:
KO_D2_2
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt

value: Pancreas

value: Ptf1aCreER; Sox4-/-; YFP+/+

value: Ptf1aCreER; Sox4KO; YFP


title: SARS-CoV spike pseudotyped virus selected replicate 1

description:
Library name: SARS1_r1_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: KPC-Cdh11+/- non-immune

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

extract_protocol:
KPC-Cdh11+/+, KPC-Cdh11+/- and Cdh11+/+ cohorts (n>=4) were euthanized at 4-5 months of age. Pancreases were excised and single cell suspensions were prepared using a collagenase digestion solution (3 mg/ml Collagenase I (ThermoFisher Scientific Catalog #17018029), 100 µg/mL DNase I (Roche Catalog #11284932001), Dispase II (Roche Catalog #4942078001) in RPMI1640 media supplemented with 10% FBS (ThermoFisher Scientific, Catalog #11875101) for 1 hour with shaking at 37°C.  Digests were filtered through a 100 µm cell strainer and depleted of red blood cells using ACK lysis buffer, per manufacturer guidelines (Gibco, Catalog #A1049201). Remaining cells were analyzed for viability and CD45 expression. CD45-/7-AAD-  (non-immune) and CD45+/7-AAD- (immune) cells populations were sorted via fluorescently activated cell sorting (FACS) and collected for scRNA-seq preparation.
Both immune (CD45+) and non-immune (CD45-) cell populations were independently sequenced using a Chromium Single Cell 3' Reagent Kit and Chomium instrument (10X Genomice, Pleasanton, CA). Library preparation was performed according to manufacturer’s protocol.

tag: strain

tag: cancer

value: Tumor

value: CD45- cells

tag: age

value: 4-5 months


title: Pancreas, Day 2, Caeruelein treated, Sox4 conditional knock-out, Kras WT background, mouse 1

description:
KO_D2_1
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt


title: Cdh11+/+

value: Normal

value: All cells


title: 4398


title: SARS-CoV spike pseudotyped virus selected replicate 2

description:
Library name: SARS1_r2_sel
Supp_table_1_kozak_sortseq_and_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: 3T3NgBR cells-3

city: Mineola

first: Qing

middle: Robert

last: Miao

state: NY

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

data_processing:
First, the raw data in fastq format was processed using fastq software, resulting in the extraction of clean reads. This was achieved by removing adapter-containing reads, reads with ploy-N, and low-quality reads. All further analyses were conducted on this high-quality, clean data. The reference genome and gene model annotation files were directly downloaded from a genome website. The reference genome index was constructed using Hisat2 v2.0.5, and the paired-end clean reads were aligned to the reference genome using the same version of Hisat2. Hisat2 was chosen for mapping due to its ability to create a splice junction database from the gene model annotation file, providing superior mapping results compared to other non-splice mapping tools.
Finally, featureCounts v1.5.0-p3 was employed to quantify the number of reads mapped to each gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (4.3.1).
Assembly: mm10
Supplementary files format and content: Rawcounts_NIH3T3_Ng3T3BR.csv

growth_protocol: NIH3T3 and 3T3NgBR cells  were cultured in DMEM medium with penicillin, streptomycin and 10% (v/v) calf serum (Invitrogen)

extract_protocol:
RNA was harvaested using Rneasy mini plus-ki (Qiagen).1.5 ug of total RNA was used for construction of sequencing libraries
RNA libraries fro RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufacturer's protocols.

treatment_protocol: NIH3T3 cell were infected with lentivirus carrying non-silencing shRNAi (NS) or shRNAi targeting NgBR (shNgBR), stable NS or shNgBR cell lines were established by puromycin selection. NIH-3T3 cells were transfected pIRES-NgBR with HA tag plasmid, stable NIH-3T3 with NgBR-HA cells were established by G418 selection.

value: mouse embryo fibroblasts

value: NgBR overexpression


title: KPC-Cdh11+/+ non-immune


title: SARS-CoV spike pseudotyped virus selected replicate 6

description:
Library name: SARS1_r6_sel
Supp_table_1_kozak_sortseq_and_infection.csv


title: Pancreas, Day 2, PBS treated, Sox4 wild-type, Kras WT background, mouse 3

description:
WT_D2_3
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt

value: Ptf1aCreER; Sox4+/+; YFP+/+


title: 3T3NgBR cells-2


title: placenta, Zfp202 KO, E12.5, rep2

city: Guangzhou

first: Bo

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Approximately 16 - 20 million Q30 >90% trimmed and filtered high-quality 150 bp paired-end reads per sample were mapped to the mouse (mm10) using HISAT2 (Kim et al. 2015) with default parameters.
Expression visualized tracks were generated with bigwig files generated by bamCoverage
Assembly: mm10
Supplementary files format and content: bigwig

molecule: polyA RNA

source_name: placenta

extract_protocol:
RNA was prepared from cells or embryos using the Eastep Super RNA extraction kit (Promega).
RNA-seq libraries were prepared from total RNA from cells or embryos using the TruSeq stranded mRNA sample preparation kit (Illumina)

value: placenta

tag: developmental stage

value: embyro

value: Zfp202 KO

value: embyro day 12.5


title: KPC-Cdh11+/- immune

value: CD45+ cells


title: placenta, Zfp202 KO, E12.5, rep1


title: Pancreas, Day 2, PBS treated, Sox4 wild-type, Kras WT background, mouse 1

description:
WT_D2_1
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt

value: Pancreas

value: Ptf1aCreER; Sox4WT; YFP

value: Caerulein day 2


title: 3T3NgBR cells-1


title: SARS-CoV spike pseudotyped virus unselected replicate 7

description:
Library name: SARS1_r7_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: NIH3T3 cells-3

value: Wildtype


title: placenta, wildtype, E12.5, rep2

value: wildtype


title: SARS-CoV spike pseudotyped virus unselected replicate 6

description:
Library name: SARS1_r6_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Pancreas, Day 2, Caeruelein treated, Sox4 conditional knock-out, Kras WT background, mouse 3

description:
KO_D2_3
KO_D2vsWT_D2_deg
gene_count.txt
gene_fpkm.txt

value: Ptf1aCreER; Sox4-/-; YFP+/+

value: Ptf1aCreER; Sox4KO; YFP


title: SARS-CoV spike pseudotyped virus selected replicate 3

description:
Library name: SARS1_r3_sel
Supp_table_1_kozak_sortseq_and_infection.csv

value: HEK 293T


title: SARS-CoV spike pseudotyped virus unselected replicate 5

description:
Library name: SARS1_r5_neg
Supp_table_1_kozak_sortseq_and_infection.csv

value: G542Ac3 landing pad


title: placenta, wildtype, E12.5, rep1


title: NIH3T3 cells-2

value: mouse embryo fibroblasts


title: SARS-CoV spike pseudotyped virus unselected replicate 4

description:
Library name: SARS1_r4_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Zfp202 KO, placenta, RRBS

data_processing:
RRBS data were trimmed and then analyzed by bismark (https://github.com/FelixKrueger/Bismark).
Assembly: mm10
Supplementary files format and content: bedGraph

extract_protocol:
5 μg genomic DNA was digested by adding 2.5 μl of 20 U/μl MspI enzyme (R0106S, NEB), 2 μl NEB buffer2 and 12 μl H2O at 37 °C overnight.
The 3′ terminal of digested DNA was end-repaired and an extra A (required by adapter ligation) was added on both strands in a single reaction (KAPA Hyper Prep Kit (Roche)). DNA was then ligated to methylated adaptor (NEB). Ligated DNA was digested by USER enzyme (NEB) and then purified purified using a QIAquick MinElute kit (Qiagen). Sequencing index were added by PCR. Sequencing was performed on a Novaseq6000 (Illumina).

value: MspI


title: KPC-Cdh11+/+ immune

value: Tumor

value: 4-5 months


title: NIH3T3 cells-1


title: Skin WT T cells-Exp3

city: New York

first: Ashley

middle: Stephen

last: Doane

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
complete processing pipeline avaialble at https://github.com/DoaneAS/atacflow
Read adapter trimming using ngtrim
Alignment to mm10 using bowtie2
PCR duplicate removeal by piccard tools and removal of mitochondrial reads
bigWig files generated by DeepTools
Peak calling using genrich
Assembly: mm10
Supplementary files format and content: Bam file: aligned and filtered ATAC-seq reads
Supplementary files format and content: narrowPeak (bed) file: ATAC-seq peaks
Supplementary files format and content: Bw file: BigWig of ATAC-seq insertion sites

source_name: CD8+ OT1-donor Skin Tissue Resident Memory T cell (TRM)

extract_protocol:
Omni-ATAC-seq https://www.nature.com/articles/nmeth.4396
illumina nextera
paired-end 50bp reads

value: C57Bl6/J mice

value: CD8+ Tissue resident memory T cell

value: Wild type

value: Day 14 post VACV infection


title: Skin PD1KO T cells-Exp3

value: CD8+ OT1-donor Skin Tissue Resident Memory T cell (TRM)

value: PD1 KO


title: SARS-CoV spike pseudotyped virus unselected replicate 2

description:
Library name: SARS1_r2_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV spike pseudotyped virus unselected replicate 3

description:
Library name: SARS1_r3_neg
Supp_table_1_kozak_sortseq_and_infection.csv


title: Zfp202 WT, placenta, RRBS

value: placenta

value: embyro day 12.5

value: Zfp202 WT


title: Zfp202 KO, testis, RRBS

source_name: testis

value: testis

value: adult

value: Zfp202 KO


title: TFO Compartmentalized Self-Replication, GuSCN, BioReplicate 3

city: Seattle

first: Nicholas

middle: Anthony

last: Popp

email: poppn@uw.edu, poppn13@gmail.com

state: Washington

address: 3720 15th Avenue NE, S-320

department: Genome Sciences

institute: University of Washington School of Medicine

library_source: other

data_processing:
Libraries were sequenced on a NextSeq 2000 instrument (Illumina) and base called using the instrument's Real Time Analysis software.
Barcode sequencing reads were first converted to FASTQ format and demultiplexed using bcl2fastq (v2.20). Forward and reverse barcode reads were paired using PEAR (v0.9.11). Unique barcodes were counted.
To reduce counting noise error, we removed variants with a frequency lower than 10-6 and variants that were present in less than two experimental replicates.
Barcodes were pooled by variant to create a total read count for each variant in each library. Variants were then scored with the same formula used by Enrich2 for two-timepoint selections. A pseudo-count of 0.5 reads per variant was added to prevent divide-by-zero errors. Variants were then scored by dividing variant counts by wild-type counts to generate a WT-normalized variant frequency, calculating enrichment of this frequency by dividing the post-selection value by the pre-selection value, taking the natural logarithm of this enrichment, and then averaging the resulting log-transformed enrichment across experimental replicates
Library growth and expression prior to CSR imposed a large selective pressure that enriched certain nonsense and missense variants relative to the original library. To avoid artifacts from barcodes with abnormal growth profiles, we removed all barcodes with >2-fold enrichment during growth from analysis.
Assembly: None
Supplementary files format and content: scored_variants_TFO.csv processed data file is a comma-separated text file containing the functional scores for each variant in each experimental condition
Supplementary files format and content: final_barcode_variant_map_single.csv processed data file is a comma-separated text file containing the barcode-variant map determined by PacBio long-read sequencing.
Library strategy: Targeted self-amplification of barcoded plasmid DNA

molecule: other

organism: Escherichia coli

source_name: T7 Express LysY/Iq

growth_protocol: 100ng of barcoded TFO library (or, for mock selection, 1ng of barcoded TFO-WT and 100ng of barcoded TFO-XX) was transformed into 50µL T7 Express LysY/Iq cells using the manufacturer’s recommended high-efficiency protocol. The transformed cells were outgrown in 1mL SOC medium at 37C 250rpm for one hour, then inoculated into 10mL 2x YT broth with 100µg/mL carbenicillin in 50mL sterile conical tubes covered with AirPore sheets (Qiagen). Cultures were incubated overnight at 30°C, 200rpm. The following morning, 100µL of each culture was subcultured into 10mL fresh media and grown at 37°C 250rpm until exponential phase was reached (OD600 = 0.4-0.6). Cultures were induced with 0.4mM IPTG and allowed to express for 2 hours. Culture OD600 measurements were taken and an equivalent of 0.5mL of culture at OD600=1.0 was aliquoted to a new microcentrifuge tube for further processing.To determine pre-CSR variant frequencies in this “grown” library, two 1mL samples of culture (post-expression, as it existed immediately before CSR) were also saved and pelleted at 16,000g for 1 minute, after which supernatant was removed and pellets were stored at -20C. These pellets were later processed using a Monarch Plasmid Miniprep Kit (New England BioLabs T1010).

extract_protocol:
1.2mL of oil phase was prepared fresh for each condition: 54µL Span 80, 4.8µL Tween 80, 0.6µL Triton X-100, and 1140.6µL light mineral oil (all from Sigma Aldrich). Oil phase was aliquoted into 2mL tubes, to each of which a rubber stopper from a 1mL syringe was added, vortexed, and chilled on ice.0.3mL of aqueous phase was prepared fresh for each condition and chilled on ice: 30µL 10x ThermoPol buffer, 7.8µL of (10mM each) dNTPs, 15µL 10µM CSR-DMS forward primer, 15µL 10µM CSR-DMS reverse primer, 50µL 6x GuSCN (water for conditions with no GuSCN), and 182.2µL water.The previously aliquoted cells were pelleted at 1500g for 15 min. Supernatant was removed and cells were resuspended in 1mL tris-buffered saline (TBS). Cells were then pelleted and resuspended in 0.3mL of ice-cold aqueous phase. The cell-aqueous phase mixtures were then added to the 1.2mL oil phase aliquots and emulsified on a Qiagen TissueLyser LT at 42 Hz for 4 min at 4°C.
We ordered a library saturated with all possible single-residue mutants of Thin Fingers polymerase from Twist Bioscience. To synthesize this library, the vendor needed to codon-optimize the wild-type sequence, and provided us with the optimized sequence (which we are calling “TFO”, for “Thin Fingers Optimized”). We validated that TFO-WT can be expressed and purified at yields comparable to TF-WT. The TFO library was delivered dry in 96-well plates, with each well containing 50ng of DNA saturated at a single codon, for total of 540 wells. We resuspended each well in 20uL of IDTE buffer (10mM Tris, 0.1mM EDTA, pH 8.0) (Integrated DNA Technologies) for a final concentration of 2.5ng/µL. 10µL of each well was sampled and pooled to mix all variants. The pooled library was cloned into 2B-T plasmid (Addgene plasmid #29666) using NEBuilder HiFi DNA Assembly Master Mix (New England Biolabs E2621S) following the manufacturer-recommended protocol for assembling two dsDNA fragments (2:1 molar ratio of TFO library insert to 2B-T vector, 0.03pmol total fragments, 1x NEBuilder master mix in 20µL reactions incubated at 50°C for 60 minutes followed by a 4°C hold). 2µL of the chilled NEBuilder products were then transformed into NEB Stable cells following the manufacturer-recommended high efficiency transformation protocol. Following outgrowth, varying dilutions of cells in NEB Stable outgrowth medium (1µL cells plus 99µL outgrowth medium, 1µL previous dilution plus 99µL outgrowth medium) were plated on LB+carb agar plates and incubated at 30C overnight while the remaining 999µL of cells were added to 9mL LB+carb medium and incubated at 30C, 250rpm overnight. The following day, plasmid was purified from the liquid culture using a Monarch Plasmid Miniprep Kit (New England BioLabs T1010) (culture was split into eight replicate plasmid preps). Colony counts from plates were estimated using OpenCFU45 and the results were extrapolated to estimate a total transformation yield of roughly 7e5 colony-forming units in the liquid culture (well in excess of the total number of synthesized variants and therefore expected to maintain coverage for all but the least abundant variants). The TFO saturated variant library was barcoded in a similar manner to the mock selection TFO-WT and TFO-XX constructs, but with additional care taken to minimize the number of PCR cycles and the fraction of unbarcoded variants. The library was linearized by PCR at the desired barcode insertion site using barcoding primers, 10ng TFO library in 2B-T plasmid, and Q5 HotStart High-Fidelity DNA Polymerase (New England Biolabs M0493S), following the manufacturer-recommended recipe for 50µL reactions with 1x Q5 High GC Enhancer. The reaction was supplemented with 1x EvaGreen intercalating dye (Biotium), monitored during amplification on a Bio-Rad CFX96 real-time PCR thermal cycler, and stopped before the PCR plateau phase. Thermal cycling parameters were 98°C for 30 seconds, 18 cycles of (98°C for 10 seconds, 72°C for 5 minutes). PCR products were purified using an Invitrogen PureLink PCR Cleanup Kit (using B3 high-molecular-weight-cutoff binding buffer), digested with DpnI (New England Biolabs R0176S) in 1x rCutSmart buffer for 15 minutes at 37°C to remove carryover circular plasmid template, and purified once more with the PureLink PCR Cleanup Kit (B3 buffer). Barcode oligos (ordered as Ultramer ssDNA oligos from Integrated DNA Technologies) were then cloned into the linearized plasmid PCR products using NEBuilder HiFi DNA Assembly Master Mix (New England Biolabs E2621S) following the manufacturer-recommended protocol for bridging double-stranded DNA with a single-stranded DNA oligo (1pmol oligo, 0.005 pmol vector, 1x NEBuilder master mix in 20µL reactions incubated at 50°C for 60 minutes followed by a 4°C hold). 2µL of the chilled NEBuilder products were then transformed into NEB Stable cells following the manufacturer-recommended high efficiency transformation protocol. Following 1 hour of outgrowth, varying dilutions of cells in NEB Stable outgrowth medium (1µL cells plus 99µL outgrowth medium, or 100µL of (1µL cells plus 999µL outgrowth medium)) were plated on LB+carb agar plates and incubated at 30C overnight while the remaining 998µL of cells were added to 9mL LB+carb medium and incubated at 30C, 250rpm overnight. The following day, plasmid was purified from the liquid culture using a Monarch Plasmid Miniprep Kit (New England BioLabs T1010) (culture was split into eight replicate plasmid preps). Colony counts from plates were estimated using OpenCFU and the results were extrapolated to estimate a total transformation yield of roughly 1.1e5 barcoded variants in the liquid culture.

treatment_protocol: Following emulsification, 100µL aliquots of emulsions were distributed into 0.2mL PCR tubes (total twelve tubes per condition). Emulsions were placed onto a Bio-Rad T100 thermal cycler and incubated as follows: (CSR+heat condition only: 100°C for 10 minutes), 95°C for 3 minutes, 20 cycles of (95°C for 30 seconds, 62°C for 30 seconds, 68°C for 30 seconds), 68°C for 8 minutes. Emulsions were then kept at 4°C for up to one week before further processing.Emulsions were combined into a single 1.5mL tube per condition and centrifuged for 10 min at 12,000g. The top oil layer was removed and discarded. To the bottom emulsion layer, 300µL (approximately 1:1 v/v) of chloroform was added and vortexed for 10 to 20 seconds, until the bottom layer appeared dissolved. The entire mixture was added to a PhaseLock tube (VWR 10847-802) and centrifuged for 2 minutes at 16,000g. The top aqueous layer was transferred to a new 1.5mL tube and further purified using an Invitrogen PureLink PCR Purification Kit following the manufacturer’s recommended instructions.

value: T7 Express LysY/Iq


title: TFO Compartmentalized Self-Replication, GuSCN, BioReplicate 2


title: Skin PD1KO T_cells Exp1


title: SARS-CoV spike pseudotyped virus unselected replicate 1

description:
Library name: SARS1_r1_neg
Supp_table_1_kozak_sortseq_and_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: Naïve T cells WT set B

source_name: CD8+ OT1-donor Naïve T cells

value: CD8+ OT1-donor Naïve T cells

value: Naive T cell

value: Day 0


title: Zfp202 WT, testis, RRBS

value: MspI


title: miRFP670 sort-seq replicate 4 bin4

description:
Library name: sortseq_rep_4_bin4
Supp_table_1_kozak_sortseq_and_infection.csv


title: Naïve T cells WT set A

value: C57Bl6/J mice

value: Wild type


title: Zfp202 KO, brain, RRBS, rep2

source_name: whole brain

value: whole brain


title: miRFP670 sort-seq replicate 4 bin3

description:
Library name: sortseq_rep_4_bin3
Supp_table_1_kozak_sortseq_and_infection.csv


title: TFO Compartmentalized Self-Replication, 100C Heat Kill, BioReplicate 2

value: Compartmentalized Self-Replication, 100C heat kill


title: Zfp202 KO, brain, RRBS, rep1


title: Zfp202 WT, brain, RRBS, rep2


title: TFO Compartmentalized Self-Replication, 100C Heat Kill, BioReplicate 3


title: Skin WT T cells-Exp1

value: CD8+ OT1-donor Skin Tissue Resident Memory T cell (TRM)

value: CD8+ Tissue resident memory T cell

value: Day 14 post VACV infection


title: miRFP670 sort-seq replicate 4 bin2

description:
Library name: sortseq_rep_4_bin2
Supp_table_1_kozak_sortseq_and_infection.csv


title: miRFP670 sort-seq replicate 4 bin1

description:
Library name: sortseq_rep_4_bin1
Supp_table_1_kozak_sortseq_and_infection.csv


title: Zfp202 WT, brain, RRBS, rep1

value: embyro day 12.5

value: Zfp202 WT


title: R_KO

type: RNA

city: Fukuoka

first: Lixiang

last: Wang

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression after 24 weeks on the  high fat diet

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray 4x44K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: knockout, high-fat diet, Refed, liver

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: Liver

tag: gender

value: Male


title: TCDD 10nM HaCaT

city: Sonipat

first: Kasturi

last: Mitra

state: Haryana

address: RGEC Sonipat Delhi NCR

department: Biology

country: India

institute: Ashoka University

description:
Library name: G1_S2
10X Genomics

data_processing:
Count matrix files were generated using 10x genomics cellranger (v.4.0) using hg38 as reference.
The matrix files where analyzed using Seurat package (v4.3.3).
Filter the data using nFeature_RNA > 2000 and the data is integrated using IntegrateData function of Seurat.
The clustering of the data were performed using 20 dimensions with resolution varied from 0.1-0.8.
The final seurat objects are saved using saveRDS function in R.
Assembly: hg38
Supplementary files format and content: Seurat objects save using saveRDS function in R.

organism: Homo sapiens

source_name: HaCaT

growth_protocol: Parental HaCaT cells were grown in standard growth conditions in DMEM with 10% FBS.

extract_protocol:
Trypsinized single cells were washed in PBS (without ca++ or Mg++) with 0.04% BSA and tested for >90% viability. Single cell analysis was performed on a 10xGenomics platform according to 3’ v3.1 NextGem Dual Index manual.
The 3’-biased cDNA libraries were constructed through the following steps: cDNA fragmentation, end repair & A-tailing, and size selection by SPRIselect beads, adaptor ligation, and sample index PCR amplification, and then SPRIselect beads size selection again. The final constructed 3’-biased single cell libraries were sequenced by Illumina Nextseq500 machine, targeting total reads per cell for 20,000 at minimum, and the sequencing cycles consisted of 28bp for read 1, 90 bp for read 2, and 10 bp for i7 index, and 10bp for i5 index.

treatment_protocol: TCDD treatment (1nM and 10 nM) with Tolune Vehicle control for 2.5 hours timepoint

value: HaCaT

value: Keratinocyte

value: TCDD


title: TFO Compartmentalized Self-Replication, BioReplicate 3

value: T7 Express LysY/Iq

value: Compartmentalized Self-Replication


title: miRFP670 sort-seq replicate 3 bin2

description:
Library name: sortseq_rep_3_bin2
Supp_table_1_kozak_sortseq_and_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: TFO Compartmentalized Self-Replication, BioReplicate 2


title: Zfp202 KO, placenta, MeDIP

data_processing:
150-bp paired-end reads per MeDIP-seq were mapped to the mouse (mm10) genome using Bowtie2 (Langmead et al. 2009) with default parameters. Visualized tracks were generated with bigwig files generated by bamCoverage (Ramírez et al. 2016) and tdf files from igvtools (IGV 2.8.6)
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: MeDIP-seq

extract_protocol:
Genomic DNA was harvest from tissues and cells and then sonicated by Covaris, yielding genomic DNA fragments with a bulk size of 100 – 300 bp. The sheared genomic DNA was then extracted using a DNA extraction kit (QIAGEN) according to the manufacturer’s recommendations. 500 ng to 2 μg digested DNA was diluted to 178 μl in 1×TE buffer (pH8.0), denatured for 10 min in boiling water and immediately cooled on ice for 10 min. Then, 20 μl 10×IP buffer (100 mM sodium phosphate pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 2 μl 5mC antibody (Active Motif) were added to each sample and followed by overnight incubation at 4°C. Dynabeads-ProteinA/G (Invitrogen) pre-blocked with 0.5% BSA in PBS were added to pull down the antibody-DNA complexes for 3 h at 4°C. Beads were washed three times with 1×IP buffer, resuspended in 125 μl protease K digestion solution (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS, 0.2 mg/ml protease K), and incubated in a 55°C shaker for 0.5 hours. Bead-antibody-DNA mixtures were extracted using a QIAquick MinElute kit (Qiagen) according to the manufacturer’s instructions.
Up to 100 ng of MeDIPed DNA was subjected to sequencing library preparation using VAHTS ssDNA Library Prep Kit for Illumina (Vazyme)

value: placenta

value: Zfp202 KO

tag: medip antibody


title: miRFP670 sort-seq replicate 3 bin4

description:
Library name: sortseq_rep_3_bin4
Supp_table_1_kozak_sortseq_and_infection.csv


title: TCDD 1nM HaCaT

description:
Library name: 1_S1
10X Genomics


title: Zfp202 WT, testis, MeDIP

value: testis

value: adult


title: TFO Compartmentalized Self-Replication, BioReplicate 1


title: miRFP670 sort-seq replicate 3 bin3

description:
Library name: sortseq_rep_3_bin3
Supp_table_1_kozak_sortseq_and_infection.csv


title: TFO Grown library plasmid, BioReplicate 3

value: Transformed plasmid


title: TFO Compartmentalized Self-Replication, GuSCN, BioReplicate 1


title: Toluene-VehicleControl HaCaT

description:
Library name: TO1_S3
10X Genomics


title: miRFP670 sort-seq replicate 3 bin1

description:
Library name: sortseq_rep_3_bin1
Supp_table_1_kozak_sortseq_and_infection.csv


title: TFO Compartmentalized Self-Replication, 100C Heat Kill, BioReplicate 1

value: Compartmentalized Self-Replication, 100C heat kill


title: Drp1_WT.

description:
Gene expression after 24 weeks on the high fat diet
same raw data as GSM1566541

source_name: wild type, high-fat diet, liver


title: Zfp202 KO, testis, MeDIP


title: Drp1_KO.

description:
Gene expression after 24 weeks on the high fat diet
same raw data as GSM1566542

source_name: knockout, high-fat diet, liver


title: TFO Grown library plasmid, BioReplicate 2


title: Zfp202 KO, brain, MeDIP

value: whole brain

value: embyro day 12.5


title: TFO Grown library plasmid, BioReplicate 1


title: miRFP670 sort-seq replicate 2 bin3

description:
Library name: sortseq_rep_2_bin3
Supp_table_1_kozak_sortseq_and_infection.csv


title: HaCaT-Ras-THG-1 (S264A)

city: Tsukuba City

first: Yasuhito

last: Okano

state: Ibaraki Prefecture

address: 1-1-1 Tennodai

department: Institute of Medicine

institute: University of Tsukuba

description: Library name: Sample 3

data_processing:
The raw data was analyzed by CLC Genomics Workbench (Qiagen). Normalization is performed by quantile method. Normalized numbers are Log2-converted after adding 0.01 to avoid 0.
Assembly: hg19
Supplementary files format and content: csv file includes RPKM values for each Sample

extract_protocol:
Total RNAs were extracted from HaCaT-HRasG12V cells using Trizol reagent (Thermo Fisher Scientific). RNA quality was evaluated using Agilent Bioanalyzer with RNA 6000 Pico kit (Agilent Technologies Japan).
The RNA sequencing library was prepared with Agilent Bioanalyzer, DNA High-sensitivity kit (Agilent Technologies Japan, Ltd.) and performed with Illumina NextSeq500 (Illumina K.K.).


title: miRFP670 sort-seq replicate 2 bin4

description:
Library name: sortseq_rep_2_bin4
Supp_table_1_kozak_sortseq_and_infection.csv


title: HaCaT-Ras-THG-1 (WT)

description: Library name: Sample 2


title: TFO Original library plasmid, BioReplicate 1

source_name: NEB Stable

value: NEB Stable

value: Untransformed plasmid


title: Zfp202 WT, placenta, MeDIP

value: Zfp202 WT


title: Zfp202 WT, brain, MeDIP


title: miRFP670 sort-seq replicate 2 bin2

description:
Library name: sortseq_rep_2_bin2
Supp_table_1_kozak_sortseq_and_infection.csv

source_name: HEK 293T


title: HaCaT-Ras (-)

description: Library name: Sample 1

value: HaCaT


title: R_WT

source_name: wild type, high-fat diet, Refed, liver

value: Liver

value: Male


title: miRFP670 sort-seq replicate 2 bin1

description:
Library name: sortseq_rep_2_bin1
Supp_table_1_kozak_sortseq_and_infection.csv


title: OPMHd3_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.7), Trimmomatic (ver. 0.39) and cutadapt (ver. 3.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.104) using STAR (ver. 2.7.10a).
The read count of gene features was performed with the featureCounts tool (ver. 2.0.1)
Assembly: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the QIAseq Stranded mRNA Lib Kit UDI (QIAGEN, 180440).

treatment_protocol: One-day-old worms were cultured for two days on mNGM plates covered with OP50 (control group) or Lactiplantibacillus sp. MH-1.

value: Whole

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50 +MH-1


title: MCF7, wild type nuclei, 6.25 nM Dam, rep 2

city: Bethesda

first: David

middle: J.

last: Clark

state: MD

address: 6 Center Drive

department: NICHD

institute: NIH

description: Library name: MCF7_H8_damM_200U

data_processing:
The pair-end reads aligned to the reference genome using bowtie2 (2.5.1), the read ends and occupancy is calculated using bedtools (2.31.1).
The end counts and occupancy is further processed to calculate the methylated fraction of GATC sites at each genome location using the snakemake workflow snakemakeMethylFrac, and the methylated fractions are stored in the bigwig files.
The snakemake protocol for data processing is avaiable at https://github.com/zhuweix/snakemakeMethylFrac.
Assembly: hg38 and T2T chm13v1.1, as shown in the file name of the processed files.
Supplementary files format and content: bigwig files of the methylated fraction of GATC sites in each genome location.

source_name: Breast; Mammary gland

extract_protocol:
Genomic DNA was purified from Human MCF7 cells or nuclei by using Purelink genomic DNA kit (K182002) from invitrogen.
Genomic DNA was digested with excess DpnI and sonicated to ~300 bp fragments. Paired-end libraries were prepared using the New England Biolabs kits and protocols.
qDA-seq (Prajapati et al. (2024) NSMB

value: Breast; Mammary gland

value: Epithelial cell


title: OPMHd3_rep1


title: MCF7, wild type nuclei, 3.12 nM Dam, rep 2

description: Library name: MCF7_H8_damM_100U


title: NIH-3T3, ZFP202, ChIP-seq, rep1

data_processing:
150-bp paired-end reads per ChIP-seq were mapped to the mouse (mm10) genome using Bowtie2 with default parameters. Peaks were called in MACS and calling p values smaller than 1e-6 significant. Consensus target motifs were derived from peak regions using MEME-ChIP (https://meme-suite.org/meme/tools/meme-chip). ZFP binding peak analysis was performed using BedTools, and the matrix between CHIP peaks and repeats was calculated using ComputeMatrix. Heatmaps and profile plots were then generated by plotHeatmap or plotProfile using the calculated matrix generated by ComputeMatrix.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
For ChIP experiments, 2–4x10^7 cells were cross-linked for 10 minutes at room temperature by the addition of formaldehyde solution at final concentration of 1% followed by quenching with glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was stored at −80°C. Pellets were then lysed, resuspended in 1 mL of LB1 on ice for 10 min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, and protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10 min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, cells were resuspended in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) for histone marks and SDS shearing buffer (10 mM Tris pH8, EDTA 1 mM, SDS 0.15% and protease inhibitors) for transcription factors and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 20 min), yielding genomic DNA fragments with a bulk size of 100 – 300 bp. Coating of beads with specific antibodies (GFP (Invitrogen A-6455) was carried out during the day at 4°C, then chromatin was added to the beads overnight at 4°C for histone marks while antibodies for transcription factors were first incubated with chromatin with 1% Triton and 150 mM NaCl. Subsequently, washes were performed with 2x Low Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 150 mM NaCl, 0.15% SDS), 1x High Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 0.15% SDS), 1x LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC) and 1 with TE buffer. Final DNA was purified with QIAGEN Elute Column. The ChIPed DNA was then subjected to NGS sequencing or qPCR analysis.
For ChIP-seq, up to 10 nanograms of ChIPed DNA was subjected to sequencing library preparation using the KAPA Hyper Prep Kit (Roche).

treatment_protocol: GFP-fused ZFP202 were cloned into a piggyBac transposon vector and nucleofected  into NIH3T3 cells with helper plasmids. GFP positive cells were FACS sorted and cultured for passages. Anti-GFP ChIP experiments were performed on these ZFP202-GFP overexpressed cells.

value: ZFP202-GFP overexpression

tag: chip antibody

value: GFP


title: LKO_10

city: St. Louis

first: Brian

middle: Jesse

last: DeBosch

state: MO

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Liver

growth_protocol: Age-matched Arg2fl/fl and Arg2LKO littermate mice were co-housed and grown to 22-month of age

extract_protocol:
Trizol reagent was used to isolate total RNA, performed exactly per manufacturer protocol on 50-100mg liver tissue homogenate
oligo-dT

treatment_protocol: Mice were fed a normal chow diet for the duration of the experiment


title: OPd3_rep2

value: feeding OP50


title: miRFP670 sort-seq replicate 1 bin4

first: Kenneth

address: 2103 Cornell Rd

description:
Library name: sortseq_rep_1_bin4
Supp_table_1_kozak_sortseq_and_infection.csv

data_processing:
For short-read sequencing generated by the Illumina NextSeq, the forward and reverse reads were paired using PEAR (Zhang et al. 2014). Kozak sequences were counted from the paired reads using Enrich2 (Rubin et al. 2017), and filtered to exclude reads possessing nucleotides with quality scores less than 20. For longer-read sequencing generated by the Illumina MiSeq, generated through submission to the Amplicon-EZ service offered by Genewiz / Azenta, the reads were paired as above, except the paired reads were subsequently processed with a custom Python script “Extract_Kozak.py”, which identified true Kozak library reads from template molecule reads, and for each Kozak read, extracted the Kozak sequence found in that read. All subsequent analyses of the sequencing outputs were performed in R version 4.3.1 (2023-06-16). An R markdown file with code to recreate the analysis (Kozak.Rmd), along with the relevant data files and the various python scripts for the initial processing of FASTQ files, can be found in the MatreyekLab Github repository under “MatreyekLab/Kozak”. A table of the fastq files generated and analyzed for this work is included as Supplementary Table 4. The Kozak sort-seq scores were calculated similarly to previous work (Matreyek et al, 2018, 2021), with some minor changes. For samples sequenced to sufficient read depth, a density-plot of sequence counts normally yields a bimodal distribution, with one peak stemming from a log-normal distribution of counts with a median of 10 or greater, largely reflecting sequences of physical molecules amplified and sequenced from the sample, and a separate peak with a count of 1, largely reflecting sequences derived from sequencing error. We harnessed this property to computationally remove erroneous sequence counts. For each bin, we identified the local minima between these two peaks, and removed sequence counts below this sample-specific threshold value, to yield a dataset of filtered counts. For each sequenced sample, the filtered count of each variant was divided by the sum of counts recorded in that sample to obtain variant-specific frequencies (Fv,bin). For replicates 1 and 2, which both included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the technical replicate frequencies were averaged to yield an average frequency for each variant, which was used as the Fv,bin value. These frequencies were used to calculate a weighted average for each variant for each replicate (Wv,rep), using the following formula.  Wv,rep =(Fv,bin1 0) + (Fv,bin2 (1/3)) + (Fv,bin3 (2/3)) + (Fv,bin4 1)Fv,bin1 + Fv,bin2 + Fv,bin3 + Fv,bin4   Thus, all weighted average values ranged from a value of 0 to 1. Pairwise comparisons of variant-specific weighted averages are shown in Supplementary Fig 2. Once the weighted average values were calculated for each variant for each replicate, they were log10 transformed, averaged, and the base-10 exponential calculated to yield the geometric mean weighted average value. Correspondingly, the standard deviation of the log10 transformed values were calculated and used to calculate the upper and lower 95% confidence intervals, which were later transformed as a base-10 exponential to accompany the geometric mean weighted averages.  To calibrate these weighted averages to MFI equivalent values, we generated cells recombined with ACE2-miRFP670 constructs encoding 16 different Kozak sequences, which were measured for miRFP670 fluorescence intensity using analytical flow cytometry. A linear model was first generated to establish the conversion factor enabling scaling of our weighted average scores to MFI-equivalent values. While accurate for values between 1% and 100% of the consensus Kozak, the linear model performed poorly for extremely high or low values, with the minimum and maximum scaled values being 0.0003 and 3.89; both of these values were outside of the range physically observed with this assay. We thus used logistic regression to approximate the linear model, but furthermore bound all scaled values between 0.004 and 1.34. These resulting values are referred to as the calibrated scores.  Enrichment values for infection experiments were initially filtered similarly to the sort-seq scores, wherein we identified the local minima between the two peaks observed in a density plot representation of sequence counts, and removed sequence counts below his sample-specific threshold value, to yield a dataset of filtered counts. The counts for each variant were divided by the total counts for that sequence sample, to yield sample-specific variant frequencies. For infection samples that included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the geometric means of the technical replicate frequencies were used. Each hygromycin-selected infected sample had a corresponding unselected sample. For each pair, we divided variant-specific frequencies following selection by those prior to selection, obtaining an enrichment ratio. The STIM1 survival scores were calculated similarly, with the exception that the ratio was the quotient of each Kozak variant frequency recombined into cells divided by the frequency of that variant in the sequenced plasmid library.
Assembly: Custom synthetic amplicon
Supplementary files format and content: csv file with calibrated sort-seq scores and infection scores
Supplementary files format and content: csv file with ACE2 variant-specific infection scores

extract_protocol:
Genomic DNA was isolated from each sample using the JetFlex™ Genomic DNA purification kit (Thermo Fisher, A30700).
ACE2 amplicon generation and high throughput sequencing A section of DNA spanning the recombination junction, and including the Kozak sequence preceding the ACE2 open reading frame, was amplified from the genomic DNA extracts using PCR. For each 50 µL PCR reaction, the following components were used: 2 µg genomic DNA (quantified by nanodrop), 0.25 µM  forward primer containing i7 index barcode and 0.25 µM  reverse primer containing i5 index barcode, and 25 µL of Phusion plus high fidelity PCR mix (Thermo Fisher, F548L). A total of five PCR reactions were performed per condition, which each tube initially incubated at 95 °C for 3 minutes, followed by 25 cycles of 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, followed by a final 72 °C incubation for 1 minute. PCR products were mixed with 6x DNA loading dye (NEB, B7024S) and separated on 1.5% agarose TAE gel. Bands corresponding to the expected 293 bp amplicon size were excised and extracted using the Freeze and Squeeze kit according to the manufacturer’s instructions (Bio-Rad, 7326166). Eluted PCR products were purified using a Zymo clean and concentrator kit (Zymo Research, D4003). Amplicon concentrations were measured using Qubit dsDNA BR assay kit (Life technologies, Q32853). Amplicons from all the experimental conditions were pooled in equimolar ratios and sequenced on an Illumina NextSeq550 with a 75-cycle high output kit. Oligonucleotide sequences for PCR and custom Illumina primers for sequencing are listed in Supplementary Table 3.

value: HEK 293T

value: G542Ac3 landing pad


title: miRFP670 sort-seq replicate 1 bin3

description:
Library name: sortseq_rep_1_bin3
Supp_table_1_kozak_sortseq_and_infection.csv


title: miRFP670 sort-seq replicate 1 bin2

description:
Library name: sortseq_rep_1_bin2
Supp_table_1_kozak_sortseq_and_infection.csv


title: MCF7, wild type nuclei, 1.56 nM Dam, rep 2

description: Library name: MCF7_H8_damM_50U


title: LKO_9


title: LKO_8


title: MCF7, wild type nuclei, 0.78 nM Dam, rep 2

description: Library name: MCF7_H8_damM_25U


title: expanded mice at time point PI-7, repeats 1

city: Baltimore

first: Sam

last: Lee

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Xenium in situ

scan_protocol: Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions.

data_processing: Raw sequencing data was processed using the 10X Genomics Ranger  and Vignette from Satija Lab for data analysis was followed. Cells from two repeated samples were combined.

extract_protocol: Skin tissue samples were fixed with 4% PFA and embedded in paraffin. Sectioned slides amounted to xenium slides for downstream analysis.

value: skin


title: LKO_7


title: expanded mice at time point PI-7, repeats 2

description: Xenium in situ


title: OPd3_rep1


title: miRFP670 sort-seq replicate 1 bin1

city: Cleveland

last: Matreyek

institute: Case Western Reserve University

description:
Library name: sortseq_rep_1_bin1
Supp_table_1_kozak_sortseq_and_infection.csv


title: local injuries of the knee joint

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
nf-core/scrnaseq for 10x
seeksoultools for seekone
Assembly: hg38
Supplementary files format and content: comma delimeted text files include raw gene count values for each Sample

source_name: cells from synovial fluid

extract_protocol:
Synovial fluid was mixed with phosphate buffered saline. Cells were pelleted by centrifugation and frozen in 90% fetal bovine serum and 10% dimethyl sulfoxide. On the day of the experiment, the cells were thawed, their viability was assessed, and a protocol for RNA extraction and library preparation was carried out.
Library preparation was carried out according to the Chromium Next GEM protocol using Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) CG000315 Rev E

treatment_protocol: The patient's knee was exposed for 10 days to the FiberLase CR infrared laser (980 nm) from IPG Photonics in standard mode.

value: cells from synovial fluid

value: Normal

value: before infrared laser exposure


title: MCF7, wild type nuclei, No Dam, rep 2

description: Library name: MCF7_H8_damM_0U


title: MCF7, wild type nuclei, 6.25 nM Dam, rep 1

description: Library name: MCF7_H6_damM_200U


title: NIH-3T3, ZFP202, ChIP-seq, rep2


title: LKO_6

value: Liver


title: post-traumatic arthrosis of the 2nd degree after laser exposure

value: Male

value: after infrared laser exposure


title: expanded mice treated with Yoda1 at time point PI-7, repeats 2

description: Xenium in situ


title: expanded mice treated with Yoda1 at time point PI-7, repeats 1

description: Xenium in situ


title: MCF7, wild type nuclei, 3.12 nM Dam, rep 1

description: Library name: MCF7_H6_damM_100U


title: Flox_4


title: Flox_3


title: MCF7, wild type nuclei, 1.56 nM Dam, rep 1

description: Library name: MCF7_H6_damM_50U


title: Control 2

description: 10X genomics

data_processing:
nf-core/scrnaseq
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC from umbilical cord blood

extract_protocol:
Blood-EDTA was mixed 1 to 1 with phosphate buffered saline. The mixture was layered onto Ficoll and centrifuged with 800 g for 20 min with break 0. The PBMC ring was collected and washed with phosphate buffered saline. Cells were pelleted by centrifugation and frozen in 90% fetal bovine serum and 10% dimethyl sulfoxide. On the day of the experiment, the cells were thawed, their viability was assessed, and a protocol for RNA extraction and library preparation was carried out.
Library preparation was carried out according to the Chromium Next GEM protocol using Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) CG000315 Rev E

treatment_protocol: The patients underwent a cesarean section due to increasing severity of preeclampsia, high myopia, and a clinically narrow pelvis.

value: PBMC from umbilical cord blood

value: 39 weeks of gestation

value: cord blood

value: cesarean section


title: nonexpanded mice at time point PI-14, repeats 2

description: Xenium in situ


title: MCF7, wild type nuclei, 0.78 nM Dam, rep 1

description: Library name: MCF7_H6_damM_25U

value: Breast; Mammary gland

value: Epithelial cell


title: MCF7, wild type nuclei, No Dam, rep 1

description: Library name: MCF7_H6_damM_0U


title: Flox_2


title: Preeclampsia 2

description: 10X genomics

value: 35 weeks of gestation


title: expanded mice at time point PI-14, repeats 2

description: Xenium in situ


title: Control 1

description: 10X genomics

value: 38 weeks of gestation


title: Flox_1


title: expanded mice at time point PI-14, repeats 1

description: Xenium in situ


title: Preeclampsia 1

description: 10X genomics

value: 34 weeks of gestation


title: Confluent wild type live cells, 36 h Dam adenoviral vector transduction , rep 2

description: Library name: MCF10A_P8_36h

extract_protocol:
Genomic DNA was purified from Human MCF10A cells by using Purelink genomic DNA kit (K182002) from invitrogen.
Genomic DNA was digested with excess DpnI and sonicated to ~300 bp fragments. Paired-end libraries were prepared using the New England Biolabs kits and protocols.
qDA-seq (Prajapati et al. (2024) NSMB


title: murine bone marrow sample (pool: 3 mice)_HTO

city: Hannover

first: Tobias

last: Maetzig

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
The BCL files were converted to FASTQ files by Novogene utilized 10X barcodes of the ‘master-samples’ and 'HTO-libraries'.
The proprietary 10x Genomics CellRanger pipeline (v3.1.0) was used to perform the following steps. Based on the fastq files the gene expression and feature barcoding data was processed using cellranger counts with default parameters except for the setting of expected cells (--expect-cells 18000). For this step the Feature Reference was build according to the specification of TotalSeq™-A antibodies. Cellranger was used to align read data to the reference genome provided by 10X Genomics (Mouse reference dataset 3.0.0; mm10) using the aligner STAR, counting aligned reads per gene, and calculating clustering and summary statistics for the ‘master-samples’.
The ‘master-samples’ were demultiplexed to get the ‘sub-samples’ by use of Seurat (v3.1.5) in R (v3.6.3) with a method based on the vignette “Demultiplexing with hashtag oligos (HTOs)” of Satjja Lab (https://satijalab.org/seurat/v3.1/hashing_vignette.html). Briefly described, the HTO data were log-normalized and clustered to end up in optimized separation of ‘sub-sample’ data based on HTO signals, finally receiving individual lists of cell barcodes of the distinct ‘sub-samples’
Assembly: Mouse reference dataset 3.0.0; mm10
Supplementary files format and content: Matrix (txt) file containing cell barcodes, genes and normalized read counts, representing demultiplexed 'sub-sample' data.

molecule: protein

source_name: murine bone marrow

extract_protocol:
The primary mouse cells were labeled with hashtag TotalSeq-A0304 anti-mouse Hashtag 4 Antibody from Biolgend (#155807), secondary bone marrow tranplanted with Lin- LSCs was labeled with TotalSeq-A0305 anti-mouse Hashtag 5 Antibody from Biolgend (#155809), and secondary bone marrow transplanted with Lym+ LSCs was labeled with TotalSeq-A0306 anti-mouse Hashtag 6 Antibody from Biolgend (#155811)
Library preparation for scRNA-seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). An excess of cells was loaded to the 10x controller in order to reach a target number of 18000 cells per ‘master sample’. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).

value: bone marrow

tag: disease state

value: murine HoxA9/Meis1 (H9M) AML model


title: Confluent wild type live cells, 24 h Dam adenoviral vector transduction , rep 2

description: Library name: MCF10A_P8_24h


title: PANC-1,  siRNA for ZIC5 3

city: Hachioji-city

first: Reiko

last: Satow

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. RNA-seq reads were aligned to reference human genome (hg38/GRCh38) via software Hisat2 (v2.0.1).
Genome_build: hg38
Supplementary_files_format_and_content: all.raw.count

source_name: PANC-1 cells

growth_protocol: Cells were maintained at 37C with a 5% CO2 humidified atmosphere in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated from cells using a ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI)
Total RNA were quantified and qualified by Qubit RNA Assay and TapeStation RNA ScreenTape. cDNA libraries for RNA sequencing were established from total RNA 500 ng using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The adapter sequences used in the library preparation are Forward: AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA; Reverse: AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG
The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction.

treatment_protocol: siRNA was transfected using RNAimax (Thermo) according to manufacturer's protocol.

value: pancreatic cancer

value: cultured cell

value: transfect siRNA for ZIC5


title: murine bone marrow sample (pool: 3 mice)_GEX


title: PANC-1,  siRNA for ZIC5 2


title: 4T1-Bortezmib+AMD3100 bio rep 2

city: Macau

first: Dongyang

last: Tang

address: Keyan Street

institute: University of Macau

description:
Library name: 4T1-Bortezomib+AMD3100-L026
NovaSeq PE150

data_processing:
A quality check was conducted via MultiQC (v1.11). The RNA reads were aligned to the human or mouse reference genome and counted via featureCounts (2.0.1).
Assembly: GRCh38 for human cell line. GRCm38 for mouse tumor.
Supplementary files format and content: tab-delimited txt file includes raw count for each sample

source_name: Mouse tumor

extract_protocol:
Cells were tissues were kept in Trizol and RNA was isolated by Novogene.
mRNA library preparation (poly A enrichment) according to the standard protocol

value: Mouse tumor

value: Breast cancer cell line


title: post-traumatic arthrosis of the 2nd degree before laser exposure

value: cells from synovial fluid

value: Male

value: Normal

value: before infrared laser exposure


title: miR_9_3p_transcriptome_3

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

data_processing:
RNA-sequencing reads were aligned to the mouse genome GRChM38 (mm10) using HISAT2 (Kim et al., 2015). The gene expression profile was generated by Cufflinks 2.2.1 (Trapnell et al., 2010). Low and non-expressed genes with less than an average of 10 fragments per kilobase of exon model per million mapped reads (FPKM) in all samples were omitted from the analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
Primary neurons infected with AAV-hsyn-miR-9-3p or AAV-hsyn-mCherry were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: primary neurons

value: WT


title: PANC-1,  siRNA for ZIC5 1


title: 4T1-Bortezmib+AMD3100 bio rep 1

description:
Library name: 4T1-Bortezomib+AMD3100-L025
NovaSeq PE150


title: 4T1-Bortezmib+TM bio rep 3

description:
Library name: 4T1-Bortezomib+TM-L024
NovaSeq PE150


title: Confluent wild type live cells, 0 h, rep 2

description: Library name: MCF10A_P8_0h

value: Breast; Mammary gland

value: Epithelial cell


title: Confluent wild type live cells, 48 h Dam adenoviral vector transduction , rep 1

description: Library name: MCF10A_P7_48h


title: PANC-1, negative control siRNA 3

value: transfect negative control siRNA


title: miR_9_3p_transcriptome_1


title: PANC-1, negative control siRNA 2


title: Confluent wild type live cells, 48 h Dam adenoviral vector transduction , rep 2

description: Library name: MCF10A_P8_48h


title: Confluent wild type live cells, 36 h Dam adenoviral vector transduction , rep 1

description: Library name: MCF10A_P7_36h


title: Scramble_transcriptome_3

value: AAV-scramble


title: 4T1-Bortezmib+TM bio rep 2

description:
Library name: 4T1-Bortezomib+TM-L023
NovaSeq PE150


title: 4T1-Bortezmib+TM bio rep 1

description:
Library name: 4T1-Bortezomib+TM-L022
NovaSeq PE150


title: 4T1-Bortezmib+AMD3100 bio rep 3

description:
Library name: 4T1-Bortezomib+AMD3100-L027
NovaSeq PE150


title: PANC-1, negative control siRNA 1


title: Confluent wild type live cells, 24 h Dam adenoviral vector transduction , rep 1

description: Library name: MCF10A_P7_24h


title: Confluent wild type live cells, 12 h Dam adenoviral vector transduction , rep 2

description: Library name: MCF10A_P8_12h


title: 4T1-vehicle bio rep 3

description:
Library name: 4T1-vehicle-L021
NovaSeq PE150


title: Scramble_transcriptome_2


title: Confluent wild type live cells, 12 h Dam adenoviral vector transduction , rep 1

description: Library name: MCF10A_P7_12h


title: Flox_5

value: Liver


title: Scramble_transcriptome_1


title: MDA-MB-231-Bortezmib+AMD3100 bio rep 3

description:
Library name: MDA-MB-231-Bortezomib+AMD3100-L018
NovaSeq PE150

source_name: Breast

value: Breast


title: 4T1-vehicle bio rep 2

description:
Library name: 4T1-vehicle-L020
NovaSeq PE150


title: HUASMC, siRNA, siDDX24

city: Zhuhai

first: Yujiao

last: Gong

address: No. 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
ZebraCallV2 1.0.8.208
The sequencing data was filtered with SOAPnuke (v1.5.2)
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Ericscript (v0.5.5) [4] and rMATS (V3.2.5)[5] were used to fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Normal healthy human umbilical artery

growth_protocol: HUVSMC/HUASMC were maintained in SMCM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: To delivery siRNA into VSMC, LipofectamineTM 3000 Transfection Reagent (Invitrogen) were used essentially following the manufacturer's protocol. After 48 hours VSMC were harvested to extract total RNA.

value: Normal healthy human umbilical artery

value: HUASMC

value: vasuclar smooth muscle cells

value: DDX24 knockdown


title: Confluent wild type live cells, 0 h, rep 1

description: Library name: MCF10A_P7_0h


title: MDA-MB-231-Bortezmib+AMD3100 bio rep 2

description:
Library name: MDA-MB-231-Bortezomib+AMD3100-L017
NovaSeq PE150

value: Breast cancer cell line


title: 4T1-vehicle bio rep 1

description:
Library name: 4T1-vehicle-L019
NovaSeq PE150


title: MDA-MB-231-Bortezmib+AMD3100 bio rep 1

description:
Library name: MDA-MB-231-Bortezomib+AMD3100-L016
NovaSeq PE150


title: miR_9_3p_transcriptome_2


title: HUVSMC, siRNA, siDDX24

value: HUVSMC


title: MDA-MB-231-Bortezmib+TM bio rep 3

description:
Library name: MDA-MB-231-Bortezomib+TM-L015
NovaSeq PE150


title: T47DTR_MS8815N_2

city: Durham

first: Joshua

last: Corbin

state: NC

address: 3 Genome Ct

institute: Duke University

description: T47DTR_MS8815N_vs_DMSO_DGEcount_vsdDESeq.tsv

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed.
Raw read counts were used for differential gene expression analysis by DESeq.
Assembly: hg38
Supplementary files format and content: matrix of RNA-seq read counts

growth_protocol: T47D, T47D-TR and BT-549 breast cancer cells were grown in RPMI1640 base medium plus 10% of FBS, 1,000 U/ml penicillin and streptomycin and 8 ug/ml insulin.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used

value: Human breast cancer cell


title: HUVSMC, siRNA, negative control

value: negative control


title: MDA-MB-231-Bortezmib+TM bio rep 2

description:
Library name: MDA-MB-231-Bortezomib+TM-L014
NovaSeq PE150


title: T47DTR_EPZ6438_2

description: T47DTR_EPZ6438_vs_DMSO_DGEcount_vsdDESeq.tsv


title: CAGEseq_VCAP shNIPBL_#2 5D rep2

city: New York

first: Elissa

middle: WP

last: Wong

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
CAGE-seq reads were analyzed based on the Nextflow CAGE-seq analysis pipeline.
Index sequences, EcoP15I recognition site and the first G following the EcoP15I site at the 5’-end from reads were removed using Cutadapt (v2.6).
rRNA sequences were filtered out using SortMeRNA (v4.2.0) and filtered reads were aligned to the hg19 genome using STAR (v2.7.1a).
At this step, two sets of BAM files were created for each sample: one with uniquely mapped reads (adding --outFilterMultimapNmax 1 to STAR command) and one with multi-mapped reads (adding --outFilterMultimapNmax 10 to STAR command). Unmapped reads from BAM files were removed.
BAM files were converted to BED files with the summed up 1 bp unclustered CAGE tags using SAMtools (v1.9) and bamtobed (v.2.26.0). We pooled CAGE tags across samples, filtered them by TPM threshold of 0.5 and then clustered them with paraclu to generate a BED file with the clustered CAGE transcription start sites (CTSSs). CAGE tags were intersected with the clusters identified by paraclu and a raw count table with columns for each sample and rows for each tag cluster was generated. DESeq2 (v1.30.1) was used to perform differential CAGE expression using the raw count table. CTSS clusters were annotated using R/Bioconductor packages ChIPseeker (v1.26.2) and AnnotationDbi (v1.52) using GENCODE (v19) gene annotations.
Assembly: hg19
Supplementary files format and content: Differential expression analysis by DESeq2

source_name: Prostate

growth_protocol: All cells lines were cultured in media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were cultured at 37 ºC in 5% CO2.

extract_protocol:
Cells were lyzed directly on culture dish with TRIzol RNA isolation reagent (Thermo fisher scientific). Total RNA was extracted by thorough mixing with chloroform and isopropanol precipitation of upper aqueous phase. 5 µg total RNA was reverse transcripted using a primer that carried a 15-nt random region and EcoP15I recognition sequence and SuperScriptIII RNase H- reverse transcriptase (Thermo fisher scientific) in the presence of trehalose/sorbitol to increase efficiency of reverse transcription. Diol groups on RNA/cDNA duplex were oxidated and labelled with biotin hydrazide (Vector laboratories). RNase I (Promega) treatment was performed to cleave single-stranded RNA regions that were not hybridized with first-strand cDNA. tRNA-coated streptavidin beads (Thermo fisher scientific) were used to capture biotinylated RNA/cDNA duplex. Sample was washed three times with wash buffer A [4.5 M NaCl, 50 mM EDTA (pH 8.0) and 0.1 % Tween20], once with wash buffer B [10 mM Tris–HCl (pH 8.5), 1 mM EDTA (pH 8.0), 0.5 M NaOAc (pH 6.1) and 0.1 % Tween20] and once with wash buffer C [0.3 M NaCl, 1 mM EDTA (pH 8.0) and 0.1 % Tween20]. Single-stranded cDNAs were released from streptavidin beads by heating at 95 °C for 5 min. Released cDNA was treated with RNase H (Thermo fisher scientific) and RNase I (Promega) at 37 °C for 45 min and proceed for library construction.
Library was constructed with modified primers for compatible sequencing on Illumina NextSeq/NovaSeq sequencer. Ligation of bar-coded 5’ linker was performed. Second-strand cDNA was synthesized using Deep Vent (exo-) DNA polymerase (NEB) and biotinylated second-strand primer. cDNA was treated with shrimp alkaline phosphatase (Thermo fisher scientific) to remove phosphate group from 5’ linker. EcoP15I (NEB) was used to cleave 27 nt downstream of the recognition site at the 5’ linker. 3’ linker was ligated to the 27-nt-long tags, purified with tRNA-coated streptavidin beads and amplified with 2x Phusion high-fidelity PCR mix (NEB). CAGE libraries were treated with Exonuclease I (NEB) to degrade any single-stranded DNA before sequencing.
Libraries were sequenced on NextSeq/NovaSeq using SR50 to obtain around 40 M reads for each library.

treatment_protocol: Cells that were transduced with lentivirus carrying puromycin-resistant shRNA plasmids were treated with 0.5-2 µg/ml puromycin.

value: Prostate

value: VCAP

value: Prostate cancer


title: T47DTR_EPZ6438_1


title: T47DTR_MS8815N_1


title: MDA-MB-231-Bortezmib+TM bio rep 1

description:
Library name: MDA-MB-231-Bortezomib+TM-L013
NovaSeq PE150


title: CAGEseq_VCAP shNIPBL_#2 5D rep1


title: T47DTR_MS8815_2

description: T47DTR_MS8815_vs_DMSO_DGEcount_vsdDESeq.tsv


title: T47DTR_MS8815_1


title: MDA-MB-231-vehicle bio rep 2

description:
Library name: MDA-MB-231-vehicle-L011
NovaSeq PE150


title: T47DTR_DMSO_4

description:
T47DTR_EPZ6438_vs_DMSO_DGEcount_vsdDESeq.tsv
T47DTR_MS8815_vs_DMSO_DGEcount_vsdDESeq.tsv
T47DTR_MS8815N_vs_DMSO_DGEcount_vsdDESeq.tsv

value: 0.05% DMSO vehicle control


title: CAGEseq_VCAP shLuc 5D rep1

value: shLuc


title: HUASMC, siRNA, negative control


title: T47DTR_DMSO_3


title: MDA-MB-231-vehicle bio rep 1

description:
Library name: MDA-MB-231-vehicle-L010
NovaSeq PE150


title: HCC1937-AMD3100 bio rep 3

description:
Library name: HCC1937-AMD3100-L009
NovaSeq PE150


title: Gr7_6

city: Yangsan

first: Ju Young

last: Yoon

address: Geumo-ro 20

country: South Korea

institute: Pusan National University Children's Hospital

description: not PWS,obese

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human or Mouse 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station

scan_protocol: GeneChips were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

label: biotin

source_name: whole blood

label_protocol: biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: ID

tag: bmi

tag: bmi-sds


title: Gr7_7

description: not PWS,obese


title: Gr7_5

description: not PWS,obese


title: Gr7_8

description: not PWS,obese


title: Gr7_9

description: not PWS,obese


title: Gr7_3

description: not PWS,obese


title: Gr7_4

description: not PWS,obese


title: BT549_C24_2

description: BT549_C24_vs_DMSO_normalizedExpression.txt


title: Gr7_2

description: not PWS,obese


title: HCC1937-AMD3100 bio rep 2

description:
Library name: HCC1937-AMD3100-L008
NovaSeq PE150

tag: tissue


title: BT549_C24_1

tag: cell type


title: Daoy_ PELP1 shRNA_1

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: Daoy cells expressing PELP1 shRNA vector

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Daoy

growth_protocol: Daoy cells were cultured in DMEM media supplemented with 10% FBS

extract_protocol:
Daoy cells transduced with lentiviral particles expressing either control shRNA or PELP1 shRNA vector and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from Daoy cells stably expressing control shRNA or PELP1 shRNA and subjected to RNA-seq analysis

value: Medulloblastoma cell line

value: PELP1 shRNA

value: Daoy


title: CAGEseq_VCAP shLuc 5D rep2

tag: genotype


title: MDA-MB-231-vehicle bio rep 3

description:
Library name: MDA-MB-231-vehicle-L012
NovaSeq PE150

value: Breast


title: HCC1937-AMD3100 bio rep 1

description:
Library name: HCC1937-AMD3100-L007
NovaSeq PE150


title: Daoy_ control shRNA_2

description: Daoy cells expressing control shRNA vector

tag: treatment

value: Control


title: Daoy_ control shRNA_1

tag: cell line


title: Gr6_7

description: not PWS,not obese


title: HCC1937-TM bio rep 3

description:
Library name: HCC1937-TM-L006
NovaSeq PE150


title: BT549_MS177N2_1

description: BT549_MS177N2_vs_DMSO_normalizedExpression.txt


title: Gr7_1

description: not PWS,obese


title: Gr6_6

description: not PWS,not obese