title: EGFP gene targeted by SpCas9:sgRNA targeting TGGC2

description:
DC100
U2OS genomic DNA
no processed data file because fastq files were fed directly into CRISPResso

value: spcas9 in egfp gene -- indel formation:TGGC2


title: PR8;PB1-UFO_SYN_1

status: Public on Jun 25 2020

type: SRA

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: transcriptomic

data_processing:
Raw sequencing reads were aligned to the mouse GRCm38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples

molecule: total RNA

organism: Mus musculus

extract_protocol:
Mouse lungs were homogenized in liquid nitrogen. 1 ml Trizol was added per 50-100 mg of tissue and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: infection

value: IAV

tag: pb1 mutation site

tag: genotype

value: Control

tag: time

value: 6 days post-inoculation

tag: tissue

value: lung


title: EGFP gene targeted by SpCas9:sgRNA targeting CCGGG

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description:
DC64
U2OS genomic DNA
no processed data file because fastq files were fed directly into CRISPResso

library_source: genomic

data_processing:
for samples "SpyPre", "SpyDbl", "SpyNoIPTG", "Spy105" were subjected to command line data processing. The grep function was used isolate the sequences making up the PAM library and discard the rest of the reads. The code requires that the neighboring 12nt of the protospacer match the reference sequence. The remaining sequences were sorted alphabetically and the code counts the number of times each sequence occurs in a given sample. A tab-delimited .txt file is then output.
sequencing reads were demuxed with trimmed adapters by the sequencing core facility for samples:  "DC64", "DC65", "DC67", "DC68", "DC69", "DC92", "DC93", "DC94", "DC97", "DC98", "DC99", and "DC100". The fastq files were input directly to the CRISPResso
Supplementary_files_format_and_content: "presed.txt" is a tab-delimited file containing the PAM sequences and corresponding read counts for the pre-sorted library. These PAM sequences were isolated from the fastq files meeting the sorting requirements (12nt matching the reference sequence upstream of the PAM)
Supplementary_files_format_and_content: "dblsed.txt" is a tab-delimited file containing the PAM sequences and corresponding read counts for the post-sorted library with two growth cycles. These PAM sequences were isolated from the fastq files meeting the sorting requirements (12nt matching the reference sequence upstream of the PAM)
Supplementary_files_format_and_content: "nosed.txt" is a tab-delimited file containing the PAM sequences and corresponding read counts for the post-sorted library grown in the presence of 0mM IPTG. These PAM sequences were isolated from the fastq files meeting the sorting requirements (12nt matching the reference sequence upstream of the PAM)
Supplementary_files_format_and_content: "105sed.txt" is a tab-delimited file containing the PAM sequences and corresponding read counts for the post-sorted library grown in the presence of 10mM IPTG. These PAM sequences were isolated from the fastq files meeting the sorting requirements (12nt matching the reference sequence upstream of the PAM)

molecule: genomic DNA

organism: Homo sapiens

source_name: U2OS gDNA

growth_protocol:
growth protocol for "SpyPre" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 base media. DNA was then isolated from a fraction of cells and saved for sequencing to determine the pre-selection library diversity.
growth protocol for "SpyDbl" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 base media. Following a growth cycles in M9 base media, the cells were then grown for two growth cycles in the selection media (M9 media with 0.002% glycerol, 0.02% cas amino acids,  0.2% xylose, and 0mM IPTG). The cells were then used for sequencing.
growth protocol for "SpyNoIPTG" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 base media. Following one growth cycle in M9 base media, the cells were then grown in the selection media (M9 media with 0.002% glycerol, 0.02% cas amino acids,  0.2% xylose, and 0mM IPTG). The cells were then used for sequencing.
growth protocol for "Spy105" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 base media. Following one growth cycle in M9 base media, the cells were then grown in the selection media (M9 media with 0.002% glycerol, 0.02% cas amino acids,  0.2% xylose, and 10mM IPTG). The cells were then used for sequencing.
growth protocol for "DC64", "DC65", "DC67", "DC68", "DC69", "DC92", "DC93", "DC94", "DC97", "DC98", "DC99", and "DC100": U2OS.EGFP cells were maintained in DMEM high glucose, 10% fetal bovine serum, and 1% penicillin and streptomycin, incubated at 37C with 5% CO2 using standard tissue culture techniques.

extract_protocol:
The reporter plasmid was isolated from pre- and post-xylose cultures (for samples "SpyPre", "SpyDbl", "SpyNoIPTG", and "Spy105") and DNA was amplified from this region with oligos containing the necessary Illumina adapters.
U2OS gDNA was extracted using the GeneJET Genomic DNA Extraction kit 72 hours after transfection. (Thermo Scientific Cat no K0721) following manufacturer's instruction. for "DC64", "DC65", "DC67", "DC68", "DC69", "DC92", "DC93", "DC94", "DC97", "DC98", "DC99", and "DC100"
The five nucleotide PAM library was inserted into the target plasmid backbone using Q5 mutagenesis.

treatment_protocol: treatment protocol for "DC64", "DC65", "DC67", "DC68", "DC69", "DC92", "DC93", "DC94", "DC97", "DC98", "DC99", and "DC100": Plasmid encoding the SpCas9 and sgRNA were prepped using Qiagen Endo-free Plasmid Maxi-Prep kit and transfected with the GenJet transfection reagent for U2OS cells version II (SignaGen). Cells were seeded at 200,000 cells / well in a 12 well dish one day prior to transfection. Cells were transfected for 72 hours.

tag: selection stage of 5n pam library -- pam screen

tag: number of growth cycles in d-xylose -- pam screen

tag: concentration of iptg in growth medium -- pam screen

tag: pam targeted by sgrna

value: spcas9 in egfp gene -- indel formation:CCGGG


title: EGFP gene targeted by SpCas9:sgRNA targeting GTGGC1

description:
DC65
U2OS genomic DNA
no processed data file because fastq files were fed directly into CRISPResso

value: spcas9 in egfp gene -- indel formation:GTGGC1


title: Adult_CTX_VIPcre_Dnmt3aKO_Sun1IP_H3K27ac_rep1

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Reads were trimmed with Trimmomatic (Bolger et al., 2014) using SLIDINGWINDOW:5:30. Reads were then mapped to the mm9 genome with default parameters using Bowtie2 (Langmead et al., 2009) only retaining uniquely mapping reads with samtools (Li et al., 2009) using parameters -h -b -F 3844 -q 10. For the allele-specific mapping of C57BL6/J and SPRET/EiJ reads, the SPRET/EiJ pseudogenome was assembled as detailed in Vierbuchen et al., 2017. Briefly, SNPs in the SPRET/EiJ relative to the mm10 reference genome were annotated with VCFtools, only high-confidence SNPs were retained, and these SNPs were used to construct the SPRET/EiJ pseudogenome with Modtools. Reads were trimmed with Trimmomatic (Bolger et al., 2014) using SLIDINGWINDOW:5:30. Paired-end trimmed reads were re-paired with the repair.sh utility from bbmap (Bushnell 2014). Each read was mapped in parallel to both the mm10 reference genome or the generated SPRET/EiJ pseudogenome. Reads initially mapped to the SPRET/EiJ pseudogenome were converted back to mm10 reference genome coordinates with Lapels (Huang et al., 2014). BAM files with mapped reads of reads that overlapped at least one SPRET/EiJ SNP were retained for downstream analysis. These reads converted back into FASTQ files wherein every possible allelic combination of SNPs for each read was represented (up to 2^20 reads). The original reads were only retained if and only if all possible allelic combinations mapped to the same coordinates on the alternate genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

growth_protocol: Brain tissue was taken from wild-type mice or transgenic mice maintained under standard housing conditions.

extract_protocol:
INTACT-purified nuclei were crosslinked in 1% formaldehyde, followed by the addition of 0.125M glycine to stop crosslinking activity. The nuclei were washed with cold 1XPBS, then lysed once with L1 buffer (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors, sodium butyrate), followed by an incubation in L2 buffer (10mM Tris-HCl pH8.0, 200mM NaCl, protease inhibitors, sodium butyrate). The nuclei were resuspended in L3 buffer (1M Tris-HCl pH8.0, 5M NaCl, 0.5 M EDTA, 0.5 M EGTA, 10% Na-Deoxycholate, 20% N-lauroylsarcosine, protease inhibitors, sodium butyrate) and sonicated with a Bioruptor (Diagenode) for 40 cycles of 30 seconds “on” and 45 seconds “off.” Sonicated chromatin were centrifuged at 13,000 rpm for 10 minutes at 4°C to remove insoluble pellet, and then pre-cleared by incubating with Protein A Dynabeads (Thermofisher) for 2 hours at 4°C. Pre-cleared chromatin were incubated with Dynabeads conjugated to H3K27ac (Abcam ab4729) or H3K4me1 (Abcam ab8895) antibodies overnight at 4°C. Beads were washed twice each with Low Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 150mM NaCl, 2mM EDTA), High Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 500mM NaCl, 2mM EDTA) and LiCl buffer (250mM LiCl, 1% NP40, 1mM EDTA, 10mM TrisHCl pH8.0, 1% Sodium Deoxycholate) at 4°C, and washed once with 1XTE buffer at room temperature. Immunoprecipitated chromatin were first eluted off the beads with 1XTE+1%SDS at 65°C with shaking for 30 minutes, and then were de-crosslinked overnight at 65°C. RNAseA was added to each sample, followed by an incubation at room temperature for 30 minutes. The samples were incubated with proteinase K for two to three hours at 55°C with shaking. Immunoprecipitated DNA were purified using phenol-chloroform-isoamyl alcohol followed by Qiagen MinElute columns.
Libraries were constructed by using Ovation Ultralow Library Systems (Nugen) following manufacturer instructions.

tag: background

value: Vip-cre; Sun1; Dnmt3a fl/fl

value: Cortex

tag: antibodies

value: Rabbit anti-H3K27ac, Abcam, Cat# ab4729


title: Adult_CTX_SSTcre_Dnmt3aWT_Sun1IP_H3K4me1_rep2

value: Sst-cre; Sun1; Dnmt3a +/+

value: Rabbit anti-H3K4me1, Abcam, Cat # ab8895


title: 35S:MiEFF18_3

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq preprocessing included the trimming of library adapters and quality controls with Trimmomatic. Paired-end reads with a Phred Quality Score Qscore > 20 and a read length > 30 bases were retained, and ribosomal RNA sequences were removed with SortMeRNA. Processed reads were aligned using Tophat2 with the following arguments: --max-multihits 1 -i 20 --min-segment-intron 20 --min-coverage-intron 20 --library-type fr-firststrand --microexon-search -I 1000 --max-segment-intron 1000 --max-coverage-intron 1000 --b2-very-sensitive.
Reads overlapping exons were counted per gene with the FeatureCounts function of the Rsubreads package, using the GTF annotation files from the Araport11 repository (https://www.araport.org/downloads/Araport11_Release_201606/annotation/Araport11_GFF3_genes_transposons.201606.gff.gz). Read counts were normalized with DESeq2
Genome_build: tair10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized counts

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: roots

extract_protocol:
Root were harveseted and flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: roots

tag: age

value: 14 days


title: smd1b_3


title: smd1b_2


title: smd1b_1


title: WT3

value: wildtype


title: Adult_CTX_SSTcre_Dnmt3aWT_Sun1IP_H3K27ac_rep2


title: Adult_CTX_SSTcre_Dnmt3aKO_Sun1IP_H3K4me1_rep2

value: Sst-cre; Sun1; Dnmt3a fl/fl


title: WT1


title: Adult_CTX_SSTcre_Dnmt3aKO_Sun1IP_H3K27ac_rep2


title: Adult_CTX_SSTcre_Dnmt3aWT_Sun1IP_Input_rep1


title: TS543_ICRF_2_ATAC-seq

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
ATAC-seq reads were processed using proatac package https://github.com/buenrostrolab/proatac
Genome_build: hg19
Supplementary_files_format_and_content: summits.bed files were generated using macs2.

source_name: TS543 glioma cells

extract_protocol: ATAC-seq was performed.

treatment_protocol: To investigate whether TOP2B contributed to maintenance of chromatin accessibility at the promoters where it is localized, in cell line TS543 we performed ATAC-seq following a 6 hrs. treatment with DMSO or ICRF-193 10 uM.

tag: agent

tag: cell type

value: glioma cells


title: Adult_CTX_SSTcre_Dnmt3aWT_Sun1IP_H3K27ac_rep1


title: Adult_CTX_SSTcre_Dnmt3aKO_Sun1IP_Input_rep1


title: TS543_ICRF_1_ATAC-seq


title: Adult_CTX_VIPcre_Dnmt3aKO_Sun1IP_H3K4me1_rep1


title: TS543_DMSO_2_ATAC-seq

value: DMSO


title: TS543_DMSO_1_ATAC-seq


title: Adult_CTX_SSTcre_Dnmt3aKO_Sun1IP_H3K4me1_rep1


title: TS543_WT_ATAC-seq


title: TOP2A_TS543_DMSO_chip-seq

description: TOP2A TS543 DMSO

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam, TOP2B Abcam) was incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

tag: chip antibody


title: 35S:MiEFF18_2


title: TOP2A_TS543_ETO_chip-seq

description: TOP2A TS543 ETO

value: ETO


title: Adult_CTX_SSTcre_Dnmt3aKO_Sun1IP_H3K27ac_rep1


title: 35S:MiEFF18_1


title: TOP2B_0777A_ETO_chip-seq

description: TOP2B 0777A ETO

source_name: 0777A glioma cells

tag: cell line


title: TOP2B_0777A_DMSO_chip-seq

description: TOP2B 0777A DMSO


title: 8wk_CTX_SSTcre_Sun1IP_Input

value: Sst-cre; Sun1


title: TOP2B_SNB19_DMSO_chip-seq

description: TOP2B SNB19 DMSO

source_name: SNB19 glioma cells


title: WT2


title: Aged_CTX_VIPcre_Sun1IP_H3K27ac_rep1

value: Vip-cre; Sun1


title: TOP2B_NU01482_DMSO_chip-seq

description: TOP2B NU01482 DMSO

source_name: Glioma cells


title: TOP2B_NU01482_ETO_chip-seq

description: TOP2B NU01482 ETO


title: Aged_CTX_VIPcre_Sun1IP_H3K27ac_rep2


title: Aged_CTX_SSTcre_Sun1IP_H3K27ac_rep2


title: TOP2B_NU01722_DMSO_chip-seq

description: TOP2B NU01722 DMSO


title: TOP2B_SNB19_ETO_chip-seq

description: TOP2B SNB19 ETO


title: Adult_CTX_SSTcre_Dnmt3aWT_Sun1IP_H3K4me1_rep1


title: TOP2B_NU01722_ETO_chip-seq

description: TOP2B NU01722 ETO


title: 8wk_CTX_Rorbcre_Sun1_H3K27ac_rep2

value: Rorb-cre; Sun1


title: Aged_CTX_SSTcre_Sun1IP_H3K27ac_rep1


title: TS543_ICRF_RNAseq_10

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: readcount files were generated using featureCounts.

extract_protocol: Total RNA was extracted from indicated cells with Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instuctions, and treated with DNaseI (Promega).

treatment_protocol: We treated cells with the TOP2 inhibitor ICRF193 10Um for 5hrs followed by RNA-seq, TOP2 inhibition performed with ICRF-193 and confirmed by decatenation assays(TOPOKIT).

tag: genotypes

tag: treatment

value: ICRF193 10Um for 5hrs


title: TS543_ICRF_RNAseq_9


title: TS543_ICRF_RNAseq_8


title: 1wk_CTX_Rorbcre_Sun1_H3K27ac_rep2

tag: genotype


title: 8wk_CTX_Rorbcre_Sun1_H3K27ac_rep1


title: TS543_ICRF_RNAseq_7


title: 8wk_CTX_VIPcre_Sun1IP_Input


title: TS543_ICRF_RNAseq_6


title: 1wk_CTX_Rorbcre_Sun1_H3K27ac_rep1


title: TS543_ICRF_RNAseq_5


title: 8wk_CTX_SSTcre_Sun1IP_H3K4me1_rep2


title: TS543_ICRF_RNAseq_4


title: 8wk_CTX_SSTcre_Sun1IP_H3K4me1_rep1


title: 3wk_CTX_SSTcre_Sun1IP_H3K4me1_rep2


title: TS543_ICRF_RNAseq_3


title: 1wk_CTX_SSTcre_Sun1IP_H3K4me1_rep2


title: 3wk_CTX_SSTcre_Sun1IP_H3K4me1_rep1


title: TS543_ICRF_RNAseq_2


title: TS543_DMSO_RNAseq_10


title: TS543_ICRF_RNAseq_1


title: 8wk_CTX_VIPcre_Sun1IP_H3K4me1_rep2


title: TS543_DMSO_RNAseq_9


title: TS543_DMSO_RNAseq_8


title: 8wk_CTX_VIPcre_Sun1IP_H3K4me1_rep1


title: 3wk_CTX_VIPcre_Sun1IP_H3K4me1_rep2


title: TS543_DMSO_RNAseq_7


title: TS543_DMSO_RNAseq_6


title: 21dMaleVNC3

city: Ann Arbor

first: Laura

last: Buttitta

state: MI

address: 1105 N.University Ave

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: Denoted in processed file as column Sample_72077

data_processing:
Sequencing was performed by the UM DNA Sequencing Core, using the Illumina HiSeq4000 platform
Files were concatenated those into a single .fastq file for each sample
The quality of the raw reads data for each sample was checked using FastQC (version v0.11.7) to identify features of the data that may indicate quality problems ,
Adaptors and poor quality bases were trimmed from reads using bbduk from the BBTools suite (v37.90)
Quality processed reads were aligned to the Ensembl Dm6 genome using STAR (v2.6.1a) with --quantMode GeneCounts flag option set to produce gene-level counts. MultiQC (v1.6a0) was run to summarize QC information for raw reads, QC processed reads, alignment, and gene-count information. Differential expression analyses were carried out using DESeq2 (v1.14.1). Data were pre-filtered to remove genes with 0 counts in all samples. Normalization and differential expression was performed with DESeq2, using a negative binomial generalized linear model.
Genome_build: BDGP6
Supplementary_files_format_and_content: Normalization and differential expression was performed with DESeq2, using a negative binomial generalized linear model. Depth normalised counts of the sequencing reads per annotated gene generated using DeSeq2 are contained in the Excel file. Each column is denotes a sample.

organism: Drosophila melanogaster

source_name: Canton-S

growth_protocol: Unmated animals collected at eclosion were separated into males and females reared 10 per vial at 25°C in 12h Light/12h dark conditions prior to dissection at ZT=2

extract_protocol:
10 brains from Canton-S females and males raised at 25°C on Cornmeal/Dextrose food under normal 12h L/D cycles at ZT = 2, were dissected into optic lobes, VNC and Central brain per sample. Tissues were directly dissolved into TRIZOL-LS. Samples were vortexed at speed 10 for 10 seconds. RNA extraction was performed with a chloroform phase separation and precipitated at -30°C overnight, centrifuged at 4°C for 20 minutes at 12000g. The RNA pellet obtained was resuspended in 20µl of RNAse-free water.
Using PolyA selection, the University of Michigan's Sequencing Core generated directional barcoded libraries for each sample and confirmed the quality via the Bioanalyzer and qPCR.

treatment_protocol: Animals were aged to 0, 2, 7 or 21 days post eclosion

value: adult central nerve cord

tag: gender

value: male

value: 21 day old

tag: strain

value: Canton-S


title: 3wk_CTX_VIPcre_Sun1IP_H3K4me1_rep1

value: Cortex


title: hAESCs_ Day 10_Control 2

type: RNA

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: Gene expression data from untreated control hAESCs on day 10

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) [https://www.gsea-msigdb.org/gsea/index.jsp]. We prepared heat maps in online visualization tool Morpheus (https://software.broadinstitute.org/morpheus/).
Signal intensity of all the samples derived from Expression Console using RMA algorithm. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files).

label: biotin

source_name: Untreated control hAESCs on day10, biological rep 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AESCs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with 20 μM of Isorhamnetin every 48 hours for the treatment samples. Control samples were maintained in Placental basal medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from 10- and 20-day cultures. Day 0 control samples were collected after the initial treatment.

value: amnion epithelial stem cells


title: hAESCs_ Day 0_Control 2

description: Gene expression data from untreated control hAESCs on day 0

source_name: Untreated control hAESCs on day0, biological rep 2


title: 21dMaleCB3

description: Denoted in processed file as column Sample_72074

tag: tissue

value: adult central brain


title: 21dMaleVNC2

description: Denoted in processed file as column Sample_72076


title: hAESCs_ Day 10_isorhamnetin 3

description: Gene expression data from isorhamnetin treated hAESCs on day 10

source_name: hAESCs treated with isorhamnetin for 10 days, biological rep 3


title: 21dMaleVNC1

description: Denoted in processed file as column Sample_72075


title: hAESCs_ Day 10_Isorhamnetin 1

source_name: hAESCs treated with isorhamnetin for 10 days, biological rep 1


title: hAESCs_ Day 10_Control 3

source_name: Untreated control hAESCs on day10, biological rep 3


title: hAESCs_ Day 10_Control 1

source_name: Untreated control hAESCs on day10, biological rep 1


title: hAESCs_ Day 0_Control 1

source_name: Untreated control hAESCs on day0, biological rep 1


title: hAESCs_ Day 10_isorhamnetin 2

source_name: hAESCs treated with isorhamnetin for 10 days, biological rep 2


title: 1wk_CTX_VIPcre_Sun1IP_H3K4me1_rep2

value: Rabbit anti-H3K4me1, Abcam, Cat # ab8895


title: 21dMaleCB2

description: Denoted in processed file as column Sample_72073


title: TS543_DMSO_RNAseq_4


title: 1wk_CTX_SSTcre_Sun1IP_H3K4me1_rep1


title: TS543_DMSO_RNAseq_3


title: 1wk_CTX_VIPcre_Sun1IP_H3K4me1_rep1


title: 21dMaleCB1

description: Denoted in processed file as column Sample_72072


title: 21dMaleOL3

description: Denoted in processed file as column Sample_72071

value: Adult brain optic lobe


title: TS543_DMSO_RNAseq_2


title: 21dMaleOL2

description: Denoted in processed file as column Sample_72070


title: TS543_DMSO_RNAseq_1


title: TS543_DMSO_RNAseq_5


title: 8wk_CTX_SSTcre_Sun1IP_H3K27ac_rep1

value: Rabbit anti-H3K27ac, Abcam, Cat# ab4729


title: 3wk_CTX_SSTcre_Sun1IP_H3K27ac_rep2


title: BT142_ICRF_RNAseq_7

source_name: BT142 glioma cells


title: BT142_ICRF_RNAseq_6


title: BT142_ICRF_RNAseq_5


title: 1wk_CTX_SSTcre_Sun1IP_H3K27ac_rep2


title: BT142_ICRF_RNAseq_4


title: 3wk_CTX_SSTcre_Sun1IP_H3K27ac_rep1


title: BT142_ICRF_RNAseq_3


title: 8wk_CTX_VIPcre_Sun1IP_H3K27ac_rep2


title: 7dMaleCB3

description: Denoted in processed file as column Sample_72065

value: 7 day old


title: BT142_ICRF_RNAseq_2


title: 7dMaleVNC2

description: Denoted in processed file as column Sample_72067


title: 1wk_CTX_SSTcre_Sun1IP_H3K27ac_rep1


title: 7dMaleVNC1

description: Denoted in processed file as column Sample_72066


title: 7dMaleCB2

description: Denoted in processed file as column Sample_72064


title: 7dMaleVNC3

description: Denoted in processed file as column Sample_72068


title: 8wk_CTX_VIPcre_Sun1IP_H3K27ac_rep1


title: 7dMaleCB1

description: Denoted in processed file as column Sample_72063


title: BT142_ICRF_RNAseq_1


title: 3wk_CTX_VIPcre_Sun1IP_H3K27ac_rep1


title: 3wk_CTX_VIPcre_Sun1IP_H3K27ac_rep2


title: BT142_DMSO_RNAseq_5

value: DMSO


title: 21dMaleOL1

description: Denoted in processed file as column Sample_72069


title: 7dMaleOL3

description: Denoted in processed file as column Sample_72062


title: 7dmaleOL2

description: Denoted in processed file as column Sample_72061


title: BT142_DMSO_RNAseq_3


title: BT142_DMSO_RNAseq_4


title: 1wk_CTX_VIPcre_Sun1IP_H3K27ac_rep1


title: BT142_DMSO_RNAseq_2


title: 2dMaleVNC2

description: Denoted in processed file as column Sample_72058

value: 2 day old


title: BT142_DMSO_RNAseq_1


title: TOP2B_BT142_ETO_chip-seq

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

value: ETO

value: glioma cells


title: 2dMaleCB1

description: Denoted in processed file as column Sample_72054


title: TOP2B_BT142_DMSO_chip-seq


title: TOP2B_TS543_ETO_chip-seq


title: 2dMaleCB3

description: Denoted in processed file as column Sample_72056


title: 2dMaleCB2

description: Denoted in processed file as column Sample_72055


title: 2dMaleVNC1

description: Denoted in processed file as column Sample_72057


title: 0dMaleVNC3

description: Denoted in processed file as column Sample_72050

value: 0 day old


title: 2dMaleOL3

description: Denoted in processed file as column Sample_72053


title: 0dMaleVNC2

description: Denoted in processed file as column Sample_72049


title: 2dMaleOL1

description: Denoted in processed file as column Sample_72051


title: TOP2B_TS543_DMSO_chip-seq


title: 7dMaleOL1

description: Denoted in processed file as column Sample_72060


title: 0dMaleVNC1

description: Denoted in processed file as column Sample_72048


title: 1wk_CTX_VIPcre_Sun1IP_H3K27ac_rep2

value: Vip-cre; Sun1


title: 2dMaleVNC3

description: Denoted in processed file as column Sample_72059

value: adult central nerve cord


title: 60weeks_2

city: Tokyo

first: Shuji

last: Hibiya

address: 1-5-45, Yushima, Bunkyo-ku

department: Gastroenterology and Hepatology

institute: Tokyo Medical and Dental University

description: 60 weeks treatment with inflammatory reagents

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by air-drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting (Scan resolution 3um, TIFF file dynamic range 20bit).

data_processing: Agilent Feature Extraction was used to quantify each spot. The output RAW data was imported into GeneSpring (Agilent) and normalized with 75th percentile shift.

source_name: Mouse colon organoids treated with inflammatory reagents for 60 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin columns purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with Agilent 2100 BioAnalyzer and the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop 1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: colon organoid

value: inflammatory reagents for 60 weeks


title: 0dMaleCB3

description: Denoted in processed file as column Sample_72047

value: male

value: Canton-S


title: Tsix +/- differentiationday 3 (replicate 1)

city: Boston

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

data_processing:
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using bowtie2 and novoalign
allele specific reads were called by custom script (Pinter et al., 2012)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million with deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (fwd:watson, rev:crick strand) and RPKM normalized

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium or differentiated accordingly

extract_protocol:
Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016); Strand-specific RNA sequencing, multiplexed

treatment_protocol: Nuclei were isolated, permeabilized for nuclear run-on. Nascent transcripts were labeled with Biotin-11-ATP, Biotin-11-CTP, Biotin-11-GTP, Biotin-11-UTP

value: Tsix +/-

tag: developmental stage

value: differentiation day 3

tag: Sex

value: female

value: C57BL/6J x CAST/EiJ hybrid


title: 0dMaleCB2

description: Denoted in processed file as column Sample_72046

value: adult central brain


title: 12weeks_3

description: 12 weeks treatment with inflammatory reagents

source_name: Mouse colon organoids treated with inflammatory reagents for 12 weeks

value: inflammatory reagents for 12 weeks


title: 60weeks_1


title: 12weeks_2


title: 2dMaleOL2

description: Denoted in processed file as column Sample_72052

value: Adult brain optic lobe


title: 60weeks_3


title: DCs, stimulated with vesicles from the commensal EcoR12, replicate 3

city: Barcelona

last: Baldoma

address: Joan XXIII, 27-31

department: Bioquímica i Fisiologia

country: Spain

institute: Universitat de Barcelona

data_processing:
Illumina bcl2fastq version 2.17.1.14: basecalling
Skewer (v0.2.2): adapter trimming
bowtie (v 1.2.2): read alignment (--non-deterministic)
htseq-count (v0.9.1.): read assignment to miRNAs (using version 22 of mirBase annotation)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Text files output of htseq-count: count of reads assigned to each miRNA

source_name: dendritic cells

growth_protocol: Bacterial strains were grown aerobically at 37 °C in Luria-Bertani broth (LB). Growth was monitored by measuring the optical density at 600 nm.

extract_protocol:
RNA was isolated from mo-DCs by using Qiagen RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen)
Illumina TruSeq small RNA Sample Prep Kit (ref. RS-200-0012) was used according to the manufacturer's protocol, using about 500ng of total RNA per sample.

treatment_protocol: Membrane vesicles were isolated as previously described (Aguilera et al., 2014)

value: dendritic cells

value: Stimulated with vesicles from a commensal strain


title: DCs, stimulated with vesicles from the commensal EcoR12, replicate 2


title: Parental cell line (replicate 2) PRO-seq

description:
Library strategy: PRO-seq
PROseq-WT.c.bw
PROseq-WT.w.bw

data_processing:
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using TopHat2 (Kim et al., 2013)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (w:watson, c:crick strand) and fpm normalized

growth_protocol: Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium

extract_protocol:
Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016)

value: undifferentiated ES cells

tag: genotype/variation

value: wild type


title: 0dMaleOL3

description: Denoted in processed file as column Sample_72044

value: 0 day old


title: 0dMaleCB1

description: Denoted in processed file as column Sample_72045


title: DCs, stimulated with vesicles from the commensal EcoR12, replicate 1


title: 0dMaleOL2

description: Denoted in processed file as column Sample_72043


title: DCs, stimulated with vesicles from the probiotic EcN, replicate 3

value: Stimulated with probiotic vesicles


title: 12weeks_1

value: colon organoid


title: 0weeks_3

description: untreated organoids

source_name: Mouse colon organoid at 0 weeks

value: untreated


title: DCs, stimulated with vesicles from the probiotic EcN, replicate 1


title: Tsix +/- differentiation day 3 (replicate 2)


title: HT-29 APCsh_I_RNASeq

city: Munich

first: Peter

last: Jung

address: Thalkirchner Street 36

department: DKTK at LMU Munich

country: Germany

institute: DKFZ Heidelberg

data_processing:
base calling was done with bcl2fastq 2.19.0.316. For all samples, low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90 percent of the read needing a quality phred score > 20
Homertools 4.7 4 were used for PolyA-tail trimming, and reads with a length < 17 were removed
Count data were generated by mapping the filtered reads directly against the human union genes (Ensembl release 85, http://www.ensembl.org) with bowtie25 and counting the read number per gene
For the comparison with DESeq2, the input tables containing the replicates for the groups to compare were created by a custom perl script. DESeq2 (version 1.4.1) was run with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: The counting files (.txt) provide ENSEMBL IDs of transcripts and RPKM value: reads per kilobase of target per million bps, and have been generated with the FastRNAMapper tool (https://www.dkfz.de/gpcf/root/menu-left/analysis-pipelines/fastrnamapper) from filtered reads
Supplementary_files_format_and_content: HT29_APCsh_vs_NonS_annotated.txt contains DeSeq2 output data from the comparison of the duplicate pTZ APCsh versus pTZ NonS samples. The table contains ENSEMBL Ids, Gene Symbol, Base Count, Log2 fold change, fold change, and adjusted p-value information

source_name: colorectal cancer cell line

growth_protocol: HT-29 cells were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% FBS and 100U/mL Penicillin / 0.1 mg/mL Streptomycin (all from Gibco, Thermofisher Scientific)

extract_protocol:
Cells were washed with ice-cold PBS and RNA was extracted with the PureLink RNA purification kit in combination with PureLink DNase (both Invitrogen/ThermoFisher) according to the manufacturer`s protocol
Sequencing libraries were prepared using the TrueSeq Stranded mRNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions

treatment_protocol: For shRNA induction, cells were treated with 500 ng/ml Doxycycline (stock concentration 1 mg/ml dissolved in ethanol) for 72 hours

tag: crc type

value: MSS, BRAF-V600E, APC-mutant, colorectal cancer

tag: passage

value: 3-5 after lentiviral transduction

tag: mycoplasma tested

value: regularly tested as negative

value: shRNA-mediated silencing of APC


title: Parental cell line (replicate 1) PRO-seq

value: female


title: HT-29 APCsh_II_RNASeq


title: DCs, stimulated with vesicles from the probiotic EcN, replicate 2


title: DCP1A KO clone J15 (replicate 1) PRO-seq

description:
Library strategy: PRO-seq
PROseq-DCP1aKO2.c.bw
PROseq-DCP1aKO2.w.bw

value: C57BL/6J x CAST/EiJ hybrid

value: DCP1A KO


title: 0weeks_1

description: untreated organoids


title: DCP1A KO cloneJ15 (replicate 2) PRO-seq


title: 0dMaleOL1

description: Denoted in processed file as column Sample_72042

value: male

tag: age

value: Canton-S


title: 21dFemaleVNC3

description: Denoted in processed file as column Sample_72041

value: adult central nerve cord

value: 21 day old


title: DCs, Unstimulated, replicate 3

value: dendritic cells

value: Unstimulated


title: DCs, Unstimulated, replicate 2


title: DCP1A KO clone C17 (replicate 2) PRO-seq

description:
Library strategy: PRO-seq
PROseq-DCP1aKO1.c.bw
PROseq-DCP1aKO1.w.bw

value: undifferentiated ES cells


title: HT-29 NonS_I_RNASeq

value: control


title: 21dFemaleVNC1

description: Denoted in processed file as column Sample_72039


title: DCs, Unstimulated, replicate 1


title: DCP1A KO clone C17 (replicate 1) PRO-seq


title: 21dFemaleCB3

description: Denoted in processed file as column Sample_72038

value: adult central brain


title: human unselected 40S 2

city: Canberra

first: Susan

last: Wagner

state: ACT

address: 131 Garran Road

department: The John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Library strategy: TCP-seq
Illumina CASAVA 1.8 for base calling
adapter trimming (fastx_clipper of FASTX Toolkit 0.0.13), filtering by alignment to rRNA (bowtie 1.2.2) and ncRNA, tRNA (bowtie2 2.2.6)
alignment to transcriptome Ensembl GRCh38.80 and genome GRCh38 with TopHat 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: human_metagene_FP5end_AUG_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the AUG start codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_FP5end_STOP_-80+30_FPlength.ods; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the STOP codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: human_metagene_coverage_CAP_-40+40.csv; footprint coverage from -40 nt to +40 nt relative to the transcript start
Supplementary_files_format_and_content: human_genewise_FPcount_transcript_area.csv; footprint count per transcript area
Supplementary_files_format_and_content: human_genewise_mean_CI_FP5end_FP3end_AUG_-50+50.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints without 5’extension (footprint 5’end from -12 to -14 nt)
Supplementary_files_format_and_content: human_coverage_ATF4_ENST00000396680_-50.csv; coverage for the 5’UTR and the beginning of the CDS for ATF4 (starting at -50 nt from the transcript start)

source_name: HEK293T cells

growth_protocol: 3.5 Mio cell seeded into one Ø 15 cm dish, 48 h growth, around 80 % confluency at harvest; growth at 37ºC, 5 % CO2, in DMEM + 10% FBS (20 ml per dish)

extract_protocol:
in-plate cell lysis with detergent, RNase I digestion to generate ribosomal footprints, 40S/80S separation (followed by Co-IP if indicated), hot acid phenol RNA extraction
according to Ingolia et al., 2010, Methods Enzymol (different RNA fragment size selection, different set of rRNA depletion oligos)

treatment_protocol: incubation of the cell culture with 0.3 % w/v formaldehyde for 5 min in a cold room

tag: antibody

value: no

tag: protocol

value: RNA 40S footprint


title: NoIPTGinductionRep2

description: only one of the paired end reads shown because target region was covered by both pairs

data_processing:
for samples "NoIPTGinductionRep1", "IPTGinductionRep1", "NoIPTGinductionRep2", and "IPTGinductionRep2" were subjected to command line data processing. The grep function was used isolate the sequences making up the PAM library and discard the rest of the reads. The code requires that the neighboring sequence from the PAM matched the reference sequence. The remaining sequences were sorted alphabetically and the code counts the number of times each sequence occurs in a given sample. A tab-delimited .txt file is then output.
Supplementary_files_format_and_content: "NR1bioreptest1r2.txt" is a tab-deliminted file containing the PAM sequences and corresponding read counts for the 1st replicate of the library grown in M9 xylose without IPTG induction.
Supplementary_files_format_and_content: "NR2biorepIPTG1r2.txt" is a tab-deliminted file containing the PAM sequences and corresponding read counts for the 1st replicate of the library grown in M9 xylose with 1mM IPTG induction.
Supplementary_files_format_and_content: "NR3bioreptest2r2.txt" is a tab-deliminted file containing the PAM sequences and corresponding read counts for the 2nd replicate of the library grown in M9 xylose without IPTG induction.
Supplementary_files_format_and_content: "NR4biorepIPTG2r2.txt" is a tab-deliminted file containing the PAM sequences and corresponding read counts for the 2nd replicate of the library grown in M9 xylose with 1mM IPTG induction.

organism: Escherichia coli

source_name: 5N PAM library for SpyCas9 in selective medium with no IPTG induction

growth_protocol: growth protocol for "NoIPTGinductionRep1" and "NoIPTGinductionRep2" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 xylose  medium. After 15.5 hours of incubation, the culture was split into two flasks. These samples were maintained in the same culture medium for the remaining 30 minutes of incubation. The cells were then spun down, washed in PBS three times, and then back diluted into M9 xylose medium without IPTG induction. The following day, the plasmid DNA was extracted from the cells.

extract_protocol:
The reporter plasmid was isolated from IPTG induced and uninduced cultures and DNA was amplified from this region with oligos containing the necessary Illumina adapters.
The five nucleotide PAM library was inserted inot the target plasmid backbone using Q5 mutagenesis.

treatment_protocol: growth protocol for "IPTGinductionRep1" and "IPTGinductionRep2" samples: The PAM nucleotide library was freshly transformed into the host strain (already expressing dCas9 and the sgRNA) and recovered in LB media with antibiotics. The cells were grown, spun down, and washed in PBS three times prior to the next overnight growth in M9 xylose  medium. After 15.5 hours of incubation, the culture was split into two flasks. These samples were maintained in the M9 glycerol medium and 1mM IPTG was added to the culture for the remaining 30 minutes of incubation. The cells were then spun down, washed in PBS three times, and then back diluted into M9 xylose medium with 1mM IPTG induction. The following day, the plasmid DNA was extracted from the cells.

value: Library amplified from plasmid

tag: concentration of iptg (mm)

tag: molecule subtype

value: plasmid DNA


title: Parental cell line (replicate 2) RNA-seq

description:
RNAseq-WT.c.bw
RNAseq-WT.w.bw

data_processing:
Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using TopHat2 (Kim et al., 2013)
Mapped reads were further analyzed by Homer(ver 4.8) (Heinz et al., 2010) to generate a raw read count table
DESeq2 package (Love et al. 2014) was used for downstream RNA-seq analysis
Strand-specific coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (w:watson, c:crick strand) and fpm normalized

extract_protocol:
Total RNA was isolated using TRIzol extraction, rRNA was depleted and RNA fragmented by heating in presence of Mg2+, CDNA 1st strand was produced using random primers
NEBNext Ultra Directional RNA Second Strand Synthesis Module (E7550S) was used as described with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240L) for multiplexed library preparation

value: wild type


title: 21dFemaleCB2

description: Denoted in processed file as column Sample_72037

source_name: Canton-S

value: female


title: 0weeks_2

description: untreated organoids

value: colon organoid

value: untreated


title: IPTGinductionRep1

source_name: 5N PAM library for SpyCas9 in selective medium with 1mM IPTG induction


title: 21dFemaleCB1

description: Denoted in processed file as column Sample_72036


title: Parental cell line (replicate 1) RNA-seq

description:
RNAseq-WT.c.bw
RNAseq-WT.w.bw

value: C57BL/6J x CAST/EiJ hybrid


title: NoIPTGinductionRep1


title: siKLF11-2 ATAC_2

city: Nanjing

first: Le

last: Qu

address: 305 East Zhongshan Road

country: China

institute: Jinling Hospital, Clinical School of Medical College, Nanjing University

data_processing:
We used a publically available ATAC-Seq pipeline based on the official pipeline specification of ENCODE (https://github.com/kundajelab/atac-seq-pipeline).
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 was used to call peaks and an initial threshold q-value of 0.1 was set as cutoff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Normalized (per million reads) bigWig files were generated using the pipelines' MACS2 output.

source_name: osteosarcoma cell line (MG63) cells

growth_protocol: The osteosarcoma cell line MG63 cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
50,000 cells were used per reaction. Nuclei were isolated after resuspension and centrifugation in Lysis buffer. The 50 μl transposase reaction with isolated nuclei was incubated at 37 °C for 30 min. DNA was purified using a MinElutePCR purification column (Qiagen).
The transposed DNA fragments were preamplified by a first PCR reaction with 5 cycles containing barcoded Nextera PCR primers. The optimal number of cycles was determined by a SybrGreen qPCR reaction containing a 5 µl aliquot from the first PCR. The second PCR was then carried out with 8 cycles and the libraries were first purified by MinElutePCR purification column (Qiagen) and then further size-selected by AMPure XP beads to obtain libraries with a size distribution between 150-1000 base pairs.

treatment_protocol: MG63 cells were transfected with KLF11 or control siRNA and cultured for 96h.

tag: cell type

value: osteosarcoma cell line (MG63) cells


title: DCP1A KO cloneJ15 (replicate 2) RNA-seq

description:
RNAseq-DCP1aKO2.c.bw
RNAseq-DCP1aKO2.w.bw

value: DCP1A KO


title: 21dFemaleOL3

description: Denoted in processed file as column Sample_72035

value: Adult brain optic lobe

value: 21 day old

value: Canton-S


title: DCP1A KO clone J15 (replicate 1) RNA-seq

value: undifferentiated ES cells


title: HT-29 NonS_II_RNASeq

tag: cell line

value: MSS, BRAF-V600E, APC-mutant, colorectal cancer

value: 3-5 after lentiviral transduction

value: regularly tested as negative

tag: treatment

value: control


title: 21dFemaleVNC2

description: Denoted in processed file as column Sample_72040

value: adult central nerve cord

tag: gender


title: siKLF11-2 ATAC_1

tag: genotype


title: siKLF11-1 ATAC_2


title: DCP1A KO clone C17 (replicate 2) RNA-seq

description:
RNAseq-DCP1aKO1.c.bw
RNAseq-DCP1aKO1.w.bw

tag: strain


title: 21dFemaleOL2

description: Denoted in processed file as column Sample_72034

tag: tissue


title: 21dFemaleOL1

description: Denoted in processed file as column Sample_72033


title: DCP1A KO clone C17 (replicate 1) RNA-seq

tag: developmental stage

tag: Sex


title: siKLF11-1 ATAC_1


title: IPTGinductionRep2

value: Library amplified from plasmid

value: plasmid DNA


title: 7dFemaleVNC3

description: Denoted in processed file as column Sample_72032

value: female

value: 7 day old


title: human unselected 80S 2

value: no

value: RNA 80S footprint


title: siNC-2 ATAC_2

description: siNC-ATAC.merged.nodup.sort.bw

value: osteosarcoma cell line (MG63) cells


title: Lp4_3_7.6 (L002)

city: Philadelphia

first: Amanda

last: Glazier

state: PA

department: Biology

institute: Temple University

data_processing:
Quality check with Fastqc
Cutadapt v1.15 with an overlap of 10and a minimum length of 60 and Trimmomatic v0.36 with a Phred threshold of 30, leading and trailing score threshold of 3, and length minimum of 50 were used to trim adapters and quality filter
Bowtie2v2.3.4 was used to align reads to the transcriptome
DESeq2 was used for analyses, including abundance normalization

organism: Desmophyllum pertusum

source_name: Polyp from experimental tissue

growth_protocol: Fragments were maintained at the respective pH regimes and sampled at 2, 4.5, and 8.5 weeks

extract_protocol:
Qiagen RNAeasy kit
single-end Illumina HiSeq 2500

tag: colony

value: Colony 4

tag: time point

value: time point 3

tag: ph treatment

value: polyp


title: 7dFemaleVNC2

description: Denoted in processed file as column Sample_72031

tag: age

value: Canton-S


title: siNC-2 ATAC_1

description: siNC-ATAC.merged.nodup.sort.bw


title: Lp4_3_7.6 (L001)


title: 7dFemaleVNC1

description: Denoted in processed file as column Sample_72030


title: Lp4_2_7.6 (L001)

value: time point 2


title: eiF4E Selective 80S Ribosome FPs Hela Cells [7_80S_4E_Xl]

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

institute: DKFZ

description:
80S_eIF4E_2
processed data file: Master_Data_Table.xlsx

data_processing:
Library strategy: Ribo-seq
Adapter sequences and randomized nucleotides (Nextflex) or polyA stretches (Clonentech) were trimmed from raw reads using cutadapt.
Nuclear and mitochondrial Ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
The remaining reads were separately aligned to the human transcriptome (Ensemble transcript assembly 94) and human genome using BBmap.  Multiple mappings were allowed.
Genome_build: human transcriptome (Ensemble transcript assembly 94)
Supplementary_files_format_and_content: Master_Data_Table1.xlsx: Excel file includes values that are normalized to sequencing depth (divided by number of mappings and multiplied by a scaling factor).

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM +10% fetal bovine serum +100 U/ml Penicillin/Streptomycin (Gibco 15140122).

extract_protocol:
For cell harvest, growth medium was poured off and cells were quickly washed with ice-cold  washing solution (1x PBS 10 mM MgCl2 800 µM Cycloheximide). Washing solution was immediately poured off and freshly prepared crosslinking solution (1x PBS, 10 mM MgCl2, 200 µM Cycloheximide, 0.025% PFA, 0.5 mM DSP) was added to the cells. Cells were incubated with crosslinking solution for 15 minutes at room temperature while slowly rocking. Crosslinking solution was then poured off and remaining crosslinker was inactivated for 5 minutes with ice-cold quenching solution (1x PBS, 10 mM MgCl2, 200 µM Cycloheximide, 300 mM Glycine). Quenching solution was poured off and 150 µl of lysis buffer (0,25 M HEPES pH 7.5, 50 mM MgCl2, 1 M KCl, 5% NP40, 1000 μM CHX) was added to each 15 cm dish, resulting in 750µL of lysate. Lysis was carried out at 4°C.
After RNA extraction from total and IP-purified fractions, RNA quality and integrity were determined on an Agilent Bioanalyzer using the total RNA Nano 6000 Chip. For size selection, RNA was run on 15% Urea-Polyacrylamide gels (Invitrogen) and fragments of size 20-60 nt (80S libraries) and 20-80 nt (40S libraries) were excised using the Agilent small RNA ladder as a reference. RNA was extracted from the gel pieces by smashing the gels into small pieces with gel smasher tubes and extracting the RNA in 0.5 ml of 10 mM Tris pH 7 at 70°C for 10 minutes. Gel pieces were removed and RNA was precipitated using Isopropanol.  Footprints were then dephosphorylated using T4 PNK (NEB) for 2 hours at 37°C in PNK buffer without ATP. Footprints were then again precipitated and purified using isopropanol. For 40S footprints, contaminating 18S rRNA fragments were depleted as follows. Prevalent 18S rRNA fragments from the first round of 40S footprinting were used to design complementary Biotin-TEG-DNA oligonucleotides (sequences listed in Supplemental Table 4, ordered from Sigma-Aldrich). 100ng of RNA footprints were then hybridized to a mixture (proportional to occurrence of the fragment, listed in Suppl. Table 4) of these DNA oligos (in 40x molar excess) in (0.5M NaCl, 20mM Tris pH7.0, 1mM EDTA, 0.05% Tween20) by denaturing for 90 sec at 95C and then annealing by reducing the temperature by -0.1C/sec down to 37°C, then incubating 15min at 37°C. Hybridized species were pulled out using Streptavidin magnetic beads (NEB) by incubating at room temperature for 15 minutes, and the remaining RNA was purified by isopropanol precipitation. Footprints were then assayed using an Agilent Bioanalyzer small RNA chip and Qubit smRNA kit. 25 ng or less of footprint RNA was used as input for library preparation with SMARTer smRNA-SeqKit for Illumina from Takara / Clontech Laboratories according to the manufacturer’s instructions. Deep-sequencing libraries were sequenced on the Illumina Next-Seq 550 system.

treatment_protocol: Cellular stress conditions were induced by treatment with Tunicamycin at 1 µg / ml or 250 ng / ml for 16 hours.

value: HeLa

tag: rrna depletion

tag: library preparation kit

value: Takara

tag: index name

tag: index sequence

value: AGCGATAG


title: Cells from WT mice, biological replicate 3

city: Valladolid

last: García-Posadas

address: Paseo de Belén 17

institute: IOBA-University of Valladolid

description: Gene expression data from cultured lacrimal gland myoepithelial cells

hyb_protocol: Labeled and fragmented single stranded cDNAs were hybridized to the GeneChip Mouse Gene 2.0 ST Array (41,345 transcripts) (Affymetrix). Thereafter, the arrays were rinsed and stained using a FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were measured with a Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).

data_processing:
Scanned images were processed by the Affymetrix GeneChip Command Console (AGCC). The CEL files were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). Robust microarray analysis (RMA) was applied for normalization.
Gene transcripts with a maximal signal value less than 5 (log2) across all arrays were removed to filter for low and non-expressed genes, reducing the number of gene transcripts to 20900.

source_name: Cultured lacrimal gland myoepithelial cells from wild type C57BL/6J mice

label_protocol: 150 ng of total RNA was processed with a GeneChip HT One-Cycle cDNA Synthesis Kit and a GeneChip HT IVT Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Myoepithelial cells (MECs) were culture from mouse exorbital lacrimal glands. The glands were minced and incubated at 37º C in collagenase III (5 mg/ml) dissolved in Krebs Ringer Bicarbonate buffer containing 0.5% BSA for three 10min cycles. After incubation cell suspension was filtered through a 50 um nylon mesh into a plastic centrifuge tube and centrifuged 2 min at 700 rpm.  The pellet was washed twice with KRB buffer containing 4% BSA. The pellet was resuspended in KRB buffer plus 0.5% BSA and cells were placed in cultured dishes. Cells were fed with RPMI 1640 culture medium + 10% FBS, 2 mM L-glutamine, 100 µg/mL penicillin/streptomycin, 1% 1 M HEPES, NEEA mixture, and 1% sodium pyruvate. Cells were maintained for about 2-3 weeks in standard conditions.

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

treatment_protocol: There was no special treatment.


title: Lp4_2_7.6 (L002)


title: 09_siKLF11-H3K27ac-ChIP

data_processing:
The raw sequencing reads from ChIP-seq were aligned to human reference genome (UCSC GRCh37, hg19) using Bowtie 2.
Peak calling was performed using MACS2 (version 2.1.1) using the following settings: B --nomodel --SPMR -g hs --extsize 147. The resulting normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.
Normalized read density (RPKM) was calculated from pooled replicates using bamCoverage function in Deeptools
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

extract_protocol:
Cross-linked chromatin was sheared by sonication and immunoprecipitated with indiacted antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MG63 cells were transfected with KLF11 or control siRNA and cultured for 48h. MG63 cells were transfected with YAP or control siRNA and cultured for 48h.

tag: cell type

tag: chip antibody

value: Abcam, Cat# ab4729


title: Lp4_1_7.6 (L002)

value: time point 1


title: Cells from WT mice, biological replicate 2


title: eiF4G1 Selective 80S Ribosome FPs Hela Cells [7_80S_4G1_Xl]

description:
80S_eIF4G1_2
processed data file: Master_Data_Table.xlsx

tag: cell line

value: TCTCGCGC


title: 08_siNC-H3K27ac-ChIP

value: control


title: Cells from WT mice, biological replicate 1

value: female


title: Total 80S Ribosome FPs Hela cells [7_80S_Total_Xl]

description:
5_80S_Total
processed data file: Master_Data_Table.xlsx

value: CGGCTATG


title: 7dFemaleCB2

description: Denoted in processed file as column Sample_72028

value: adult central brain

tag: gender

value: 7 day old


title: 07_siYAP-2-KLF11-ChIP

value: osteosarcoma cell line (MG63) cells

tag: genotype

value: YAP-knockdown

value: Abnova, Cat# ABIN4329109


title: 7dFemaleCB1

description: Denoted in processed file as column Sample_72027

tag: strain


title: Cells from TSP1-1 mice, biological replicate 3

source_name: Cultured lacrimal gland myoepithelial cells from TSP1 null mice

value: TSP1 null


title: 8wk_CTX_SSTcre_Sun1IP_H3K27ac_rep2

data_processing:
Reads were trimmed with Trimmomatic (Bolger et al., 2014) using SLIDINGWINDOW:5:30. Reads were then mapped to the mm9 genome with default parameters using Bowtie2 (Langmead et al., 2009) only retaining uniquely mapping reads with samtools (Li et al., 2009) using parameters -h -b -F 3844 -q 10. For the allele-specific mapping of C57BL6/J and SPRET/EiJ reads, the SPRET/EiJ pseudogenome was assembled as detailed in Vierbuchen et al., 2017. Briefly, SNPs in the SPRET/EiJ relative to the mm10 reference genome were annotated with VCFtools, only high-confidence SNPs were retained, and these SNPs were used to construct the SPRET/EiJ pseudogenome with Modtools. Reads were trimmed with Trimmomatic (Bolger et al., 2014) using SLIDINGWINDOW:5:30. Paired-end trimmed reads were re-paired with the repair.sh utility from bbmap (Bushnell 2014). Each read was mapped in parallel to both the mm10 reference genome or the generated SPRET/EiJ pseudogenome. Reads initially mapped to the SPRET/EiJ pseudogenome were converted back to mm10 reference genome coordinates with Lapels (Huang et al., 2014). BAM files with mapped reads of reads that overlapped at least one SPRET/EiJ SNP were retained for downstream analysis. These reads converted back into FASTQ files wherein every possible allelic combination of SNPs for each read was represented (up to 2^20 reads). The original reads were only retained if and only if all possible allelic combinations mapped to the same coordinates on the alternate genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
INTACT-purified nuclei were crosslinked in 1% formaldehyde, followed by the addition of 0.125M glycine to stop crosslinking activity. The nuclei were washed with cold 1XPBS, then lysed once with L1 buffer (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 1mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors, sodium butyrate), followed by an incubation in L2 buffer (10mM Tris-HCl pH8.0, 200mM NaCl, protease inhibitors, sodium butyrate). The nuclei were resuspended in L3 buffer (1M Tris-HCl pH8.0, 5M NaCl, 0.5 M EDTA, 0.5 M EGTA, 10% Na-Deoxycholate, 20% N-lauroylsarcosine, protease inhibitors, sodium butyrate) and sonicated with a Bioruptor (Diagenode) for 40 cycles of 30 seconds “on” and 45 seconds “off.” Sonicated chromatin were centrifuged at 13,000 rpm for 10 minutes at 4°C to remove insoluble pellet, and then pre-cleared by incubating with Protein A Dynabeads (Thermofisher) for 2 hours at 4°C. Pre-cleared chromatin were incubated with Dynabeads conjugated to H3K27ac (Abcam ab4729) or H3K4me1 (Abcam ab8895) antibodies overnight at 4°C. Beads were washed twice each with Low Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 150mM NaCl, 2mM EDTA), High Salt buffer (0.1% SDS, 1% Triton X-100, 20mM Tris HCl pH8.0, 500mM NaCl, 2mM EDTA) and LiCl buffer (250mM LiCl, 1% NP40, 1mM EDTA, 10mM TrisHCl pH8.0, 1% Sodium Deoxycholate) at 4°C, and washed once with 1XTE buffer at room temperature. Immunoprecipitated chromatin were first eluted off the beads with 1XTE+1%SDS at 65°C with shaking for 30 minutes, and then were de-crosslinked overnight at 65°C. RNAseA was added to each sample, followed by an incubation at room temperature for 30 minutes. The samples were incubated with proteinase K for two to three hours at 55°C with shaking. Immunoprecipitated DNA were purified using phenol-chloroform-isoamyl alcohol followed by Qiagen MinElute columns.
Libraries were constructed by using Ovation Ultralow Library Systems (Nugen) following manufacturer instructions.

tag: background

value: Sst-cre; Sun1

value: Cortex

tag: antibodies

value: Rabbit anti-H3K27ac, Abcam, Cat# ab4729


title: 7dFemaleOL3

description: Denoted in processed file as column Sample_72026

extract_protocol:
10 brains from Canton-S females and males raised at 25°C on Cornmeal/Dextrose food under normal 12h L/D cycles at ZT = 2, were dissected into optic lobes, VNC and Central brain per sample. Tissues were directly dissolved into TRIZOL-LS. Samples were vortexed at speed 10 for 10 seconds. RNA extraction was performed with a chloroform phase separation and precipitated at -30°C overnight, centrifuged at 4°C for 20 minutes at 12000g. The RNA pellet obtained was resuspended in 20µl of RNAse-free water.
Using PolyA selection, the University of Michigan's Sequencing Core generated directional barcoded libraries for each sample and confirmed the quality via the Bioanalyzer and qPCR.

tag: tissue

value: Adult brain optic lobe

value: Canton-S


title: Lp4_3_7.9 (L002)

tag: colony

value: Colony 4

value: time point 3

value: polyp


title: Cells from TSP1-1 mice, biological replicate 1

tag: Sex


title: Cells from TSP1-1 mice, biological replicate 2


title: 7dFemaleOL2

description: Denoted in processed file as column Sample_72025


title: siNC-1 ATAC_2

description: siNC-ATAC.merged.nodup.sort.bw

value: control


title: 7dFemaleCB3

description: Denoted in processed file as column Sample_72029

value: female


title: Lp4_3_7.9 (L001)

tag: time point

tag: ph treatment


title: 7dFemaleOL1

description: Denoted in processed file as column Sample_72024

tag: age


title: 07_siYAP-1-KLF11-ChIP


title: siNC-1 ATAC_1

description: siNC-ATAC.merged.nodup.sort.bw


title: eiF4E Selective 40S Ribosome FPs Hela Cells [7_40S_Xl_4E_Bukau]

description:
40S_eIF4E_Bukau/Ingolia
processed data file: Master_Data_Table.xlsx

value: HeLa

tag: rrna depletion

value: Custom rRNA Depletion

tag: library preparation kit

value: Ingolia/Bukau

value: GATCAGAT


title: Lp4_2_7.9 (L002)

value: time point 2


title: 06_siNC-2-KLF11-ChIP

value: osteosarcoma cell line (MG63) cells

value: Abnova, Cat# ABIN4329109


title: eiF4E Selective 40S Ribosome FPs Hela Cells [7_40S_4E_Xl]

description:
40S_eIF4E_2
processed data file: Master_Data_Table.xlsx

value: Takara

tag: index name

tag: index sequence

value: AGCGATAG


title: Total 40S Ribosome FPs Hela cells [7_40S_X_Bukau]

description:
40S_Total_Bukau/Ingolia
processed data file: Master_Data_Table.xlsx

value: ACAGTGAT


title: 06_siNC-1-KLF11-ChIP

tag: cell type

tag: chip antibody


title: Lp4_1_7.6 (L001)

value: time point 1


title: 2dFemaleVNC2

description: Denoted in processed file as column Sample_72022

value: adult central nerve cord

tag: gender

value: 2 day old

value: Canton-S


title: Lp4_1_7.9 (L002)

value: Colony 4

value: polyp


title: Lp4_2_7.9 (L001)


title: 05_HDAC2-ChIP

value: Abcam, Cat# ab7029


title: eiF4G1 Selective 40S Ribosome FPs Hela Cells [7_40S_4G1_Xl]

description:
40S_eIF4G1_2
processed data file: Master_Data_Table.xlsx

tag: cell line

value: HeLa

value: TCTCGCGC


title: Lp4_1_7.9 (L001)


title: 04_SIN3A-ChIP

value: Abcam, Cat# ab3479


title: Total 80S Ribosome FPs Hela cells without crosslink [7_80S_Total_UT]

description:
80S_Total_Untreated(No Crosslink)
processed data file: Master_Data_Table.xlsx

value: TAATGCGC


title: 2dFemaleVNC1

description: Denoted in processed file as column Sample_72021

value: female

tag: strain


title: 03_TEAD1-ChIP

value: osteosarcoma cell line (MG63) cells

value: BD Bioscience, Cat# 610923


title: 2dFemaleCB3

description: Denoted in processed file as column Sample_72020

value: adult central brain


title: 02_YAP-ChIP

value: Abcam, Cat# ab52771


title: 2dFemaleCB2

description: Denoted in processed file as column Sample_72019


title: Lp3_3_7.6 (L001)

value: Colony 3

value: time point 3


title: Total 40S Ribosome FPs Hela cells [7_40S_Total_Xl]

description:
40S_Total_5
processed data file: Master_Data_Table.xlsx

value: Custom rRNA Depletion

value: Takara

value: CGGCTATG


title: Lp3_3_7.6 (L002)


title: 2dFemaleCB1

description: Denoted in processed file as column Sample_72018

value: 2 day old

value: Canton-S


title: 01_KLF11-ChIP

value: Abnova, Cat# ABIN4329109


title: 2dFemaleVNC3

description: Denoted in processed file as column Sample_72023

value: adult central nerve cord


title: Lp3_2_7.6 (L002)

value: time point 2

value: polyp


title: 2dFemaleOL3

description: Denoted in processed file as column Sample_72017

value: Adult brain optic lobe


title: Total 80S Ribosome FPs Hela cells 4 min Harringtonine [5_80S_Total_T4]

description:
80S_Total_T4
processed data file: Master_Data_Table.xlsx

data_processing:
Library strategy: Ribo-seq
Adapter sequences and randomized nucleotides (Nextflex) or polyA stretches (Clonentech) were trimmed from raw reads using cutadapt.
Nuclear and mitochondrial ribosomal RNA and tRNA reads were removed by alignment to human tRNA and rRNA sequences using bowtie2.
The remaining reads were separately aligned to the human transcriptome (Ensembl transcript assembly 94) and human genome using BBmap. Multiple mappings were allowed.
Genome_build: GRCh38; Ensembl transcript assembly 94
Supplementary_files_format_and_content: Master_Data_Table1.xlsx: Excel file includes values that are normalized to sequencing depth (divided by number of mappings and multiplied by a scaling factor).

source_name: HeLa Cells

value: HeLa

value: AGCGATAG


title: Total 40S Ribosome FPs Hela cells without crosslink [7_40S_Total_UT]

description:
40S_Total_Untreated(No Crosslink)
processed data file: Master_Data_Table.xlsx

value: TAATGCGC


title: siKLF11_Rep.2_RNA-seq

data_processing:
After removing the adapter sequences and reads with poor quality by Trim Galore (v0.5.0, www.bioinformatics.babraham.ac.uk/projects/trim_galore), the qualified reads were mapped to the reference genome (hg19) and the expression level of genes were measured by RSEM (v1.3.1) with the reference annotation file obtained from Ensemble GRCh37.
The expression level of genes was calculated in the form of Fragments per Kilobase of transcript per Million Mapped Reads (FPKM). Genes whose expression level was not detected in all samples (FPKM<1) were excluded in the following analysis.
Differentially expressed genes (DEGs) were defined as genes with fold change >2 or <0.5 and Benjamini and Hochberg (BH) adjusted p-value < 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RPKM values were determined using custom scripts.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and contaminant DNA was removed by the RNase-Free DNase Set (Qiagen). RNA integrity was verified with the Agilent 2100 Bioanalyzer automated electrophoresis system (Agilent Technologies). mRNA was isolated using the Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MG63 cells were transfected with KLF11 or control siRNA and cultured for 48h.

value: osteosarcoma cell line (MG63) cells

tag: genotype


title: Total 80S Ribosome FPs Hela cells 2 min Harringtonine [5_80S_Total_T2]

description:
80S_Total_T2
processed data file: Master_Data_Table.xlsx

value: TCTCGCGC


title: 2dFemaleOL2

description: Denoted in processed file as column Sample_72016

data_processing:
Sequencing was performed by the UM DNA Sequencing Core, using the Illumina HiSeq4000 platform
Files were concatenated those into a single .fastq file for each sample
The quality of the raw reads data for each sample was checked using FastQC (version v0.11.7) to identify features of the data that may indicate quality problems ,
Adaptors and poor quality bases were trimmed from reads using bbduk from the BBTools suite (v37.90)
Quality processed reads were aligned to the Ensembl Dm6 genome using STAR (v2.6.1a) with --quantMode GeneCounts flag option set to produce gene-level counts. MultiQC (v1.6a0) was run to summarize QC information for raw reads, QC processed reads, alignment, and gene-count information. Differential expression analyses were carried out using DESeq2 (v1.14.1). Data were pre-filtered to remove genes with 0 counts in all samples. Normalization and differential expression was performed with DESeq2, using a negative binomial generalized linear model.
Genome_build: BDGP6
Supplementary_files_format_and_content: Normalization and differential expression was performed with DESeq2, using a negative binomial generalized linear model. Depth normalised counts of the sequencing reads per annotated gene generated using DeSeq2 are contained in the Excel file. Each column is denotes a sample.

value: female


title: Lp3_1_7.6 (L002)

value: Colony 3

value: time point 1


title: siKLF11_Rep.1_RNA-seq


title: 2dFemaleOL1

description: Denoted in processed file as column Sample_72015


title: siNC_Rep.2_RNA-seq

value: control


title: Lp3_1_7.6 (L001)


title: Total 80S Ribosome FPs Hela cells [5_80S_Total_T0]

description:
80S_Total_T0
processed data file: Master_Data_Table.xlsx

value: Takara

value: CGGCTATG


title: Lp3_3_7.9 (L002)

value: time point 3


title: siNC_Rep.1_RNA-seq


title: Total 40S Ribosome FPs Hela cells 2 min Harringtonine [5_40S_Total_T2]

description:
40S_Total_T2
processed data file: Master_Data_Table.xlsx

value: CTGAAGCT


title: 0dFemaleVNC3

description: Denoted in processed file as column Sample_72014

value: adult central nerve cord

value: 0 day old

value: Canton-S


title: 0dFemaleVNC2

description: Denoted in processed file as column Sample_72013


title: Total 40S Ribosome FPs Hela cells 4 min Harringtonine [5_40S_Total_T4]

description:
40S_Total_T4
processed data file: Master_Data_Table.xlsx


title: Lp3_3_7.9 (L001)

value: polyp


title: Total 40S Ribosome FPs Hela cells 1 min Harringtonine [5_40S_Total_T1]

description:
40S_Total_T1
processed data file: Master_Data_Table.xlsx

value: HeLa

value: GAATTCGT


title: 0dFemaleVNC1

description: Denoted in processed file as column Sample_72012


title: Lp3_2_7.9 (L002)

value: time point 2


title: 0dFemaleCB3

description: Denoted in processed file as column Sample_72011

value: adult central brain


title: Lp3_2_7.6 (L001)


title: Total 80S Ribosome FPs Hela cells 1 min Harringtonine [5_80S_Total_T1]

description:
80S_Total_T1
processed data file: Master_Data_Table.xlsx

value: TCCGCGAA


title: 0dFemaleCB2

description: Denoted in processed file as column Sample_72010

value: female


title: Total 40S Ribosome FPs Hela cells [5_40S_Total_T0]

description:
40S_Total_T0
processed data file: Master_Data_Table.xlsx

value: ATTCAGAA


title: removal_3

description: 12 weeks after the removal of inflammatory reagents following the 45-week treatment with inflammatory reagents

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by air-drying.

data_processing: Agilent Feature Extraction was used to quantify each spot. The output RAW data was imported into GeneSpring (Agilent) and normalized with 75th percentile shift.

source_name: Mouse colon organoids after the removal of inflammatory reagents

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin columns purification (Qiagen).  Dye incorporation and cRNA yield were checked with Agilent 2100 BioAnalyzer and the NanoDrop ND-1000 Spectrophotometer.

value: colon organoid

tag: treatment

value: inflammatory reagents


title: RNA-seq Hela Cells, 1000ng/ml Tunicamycin [4_RNS_Total_TM1000]

description:
RNA_seq_4_TM
processed data file: Master_Data_Table.xlsx

value: Illumina TruSeq Stranded


title: RNA-seq Hela Cells, Untreated [4_RNS_Total_UT]

description:
RNA_seq_4
processed data file: Master_Data_Table.xlsx


title: removal_2

tag: tissue


title: Lp3_1_7.9 (L001)

tag: colony

value: Colony 3

value: time point 1


title: Lp3_1_7.9 (L002)


title: 0dFemaleCB1

description: Denoted in processed file as column Sample_72009


title: Lp1_3_7.6 (L002)

value: Colony 1

value: time point 3


title: removal_1


title: 0dFemaleOL3

description: Denoted in processed file as column Sample_72008

value: Adult brain optic lobe

value: 0 day old


title: untreated_2

description: untreated organoids

source_name: Mouse colon organoid without treatment

value: untreated


title: Sample 53_Noncotyledon_portion_Rep2_NextSeq_MethylC-Seq

city: Vienna

first: Ranjith

last: Papareddy

address: Dr Bohr Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Single-end 75 base read MethylC-seq data from Noncotyledon_portion Biological replicate2_NextSeq
Noncotyledon_portion_Rep2_NextSeq_MethylC-Seq

data_processing:
Small RNA-seq Analysis: Adaptor trimming with Cutadapt parameters "cutadapt -a AGATCGGAAGA  -m 18 -M 30 --trimmed-only". End to End alignment with zero mismatched and upto 100 multimappers  against TAIR10  Arabidopsis thaliana genome with STAR "STAR --outFilterMultimapNmax 100 --outSAMtype SAM --outFilterMismatchNmax 0 --alignEndsType EndToEnd --outReadsUnmapped Fastx --alignIntronMax 1 --outSAMprimaryFlag AllBestScore".  Multi mapping reads rescued with rich-get-richer algorithem " readmapIO.py  ". Resulting bedfiles sorted, collapsed and normalized to totoal genome matching reads.
MethylC-Seq Analysis: Adaptor trimming with  trimeGalore (a wraper up trimmerer from Cutadapt) along with quality trimming, 6nt from 3' and 5' end were remove to exclude random hexamers used in preamplification step of methylome library preperation. After quality filtering and adaptor trimming, bisulfite-converted reads were aligned against the TAIR10 genome  using Bismark (bismark --non_directional -q --score-min L,0,-0.4) and deduplicated with function deduplicate_bismark -s --bam. Aligned BAM files with unique mapping reads and clonal deduplated were used as  input for the Methylpy software (https://bitbucket.org/schultzmattd/methylpy) to extract weighted methylation rate at each covered Cytosine site. Bisulfite conversion rates were calculated using the unmethylated chloroplast genome or spiked-in unmethylated Lambda phage DNA controls (European Nucleotide Archive Accession Number J02459, Promega catalog number D1521)
Genome_build: TAIR10
Supplementary_files_format_and_content: sRNA-Seq: Bed files contain tab-separated values of chromosomes (column 1), start (column 2) and stop (column 3) coordinates of smallRNAs followed by normalize RPM score (column 4), strand (column 5), sequence (column 6) and small RNA size (column 7)
Supplementary_files_format_and_content: MethylC-seq:  All Cytosin containing tab-separated values of chromosomes (column 1), start position(column 2)  of cytosine followed by strand  (column 3), Trinucleotide context  (column 4), count of reads supporting methylation (column 5) and total reads  (column 6); In addition ,Bigwig files containing chromosomes (column 1), start (column 2) and stop (column 3) and weighted methylation rate (column 4)

growth_protocol: Controlled growth chamber at 20˚C-22˚C with a 16-h light/8-h dark cycle. Plants were four weeks old when tissue was harvested.

extract_protocol:
samples 1 to 28 : Total RNA extracted with TRIzol reagent (Thermo Fisher Scientific) and size selected for 18-30nt RNA molecules with denaturing urea gel; Samples 29 to 69 : genomic DNA extracted with Quick-DNATM Micro prep Kit (Zymo D3020)
Samples 1 to 28 : Size selected RNA was used to synthesise cDNA with NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (cat. no E7300; New England Biolabs) according to the manufacturer’s recommendations. Various numbers of PCR cycles were used to amplify cDNAs: 18, 20, 22, and 24 PCR cycles for globular; 14, 16, 18, and 20 PCR cycles for early heart and 3 weeks old leaf samples. Final PCR amplicons were initially run on a 90% (v/v) formamide/8% (w/v) acrylamide gel for 30 min at 5W, followed by 30W for ≥2 h, and stained with SYBR Gold (1:10,000; Thermo Fisher Scientific). Intensity of PCR amplicons between 137-bp and 147-bp  Fluorescence intensities of amplicons were examined across the PCR cycles, 137-bp to 149-bp corresponding to 18- nucleotide to 30- nucleotide sRNAs with adapters respectively was inspected under UV transilluminator. Amplicons with  non-saturated signals from PCR cycles were gel-purified. Gel purified small RNA libraries are resuspenden in 15 μL of Elution Buffer (Qiagen). Finally small RNA libraries quality checked for expected size range with Agilent High sensitivity NGS fragment Kit (DNF-474-1000) were sequenced on a HiSeq 2500 instrument (Illumina) in 50 base single-end mode.
Samples 29 to 69 : Genomic DNA subjected to genomic DNA  bisulfite treatment for 200 minutes with EZ DNA Methylation-DirectTM Kit (Zymo D5020).preamplified for two cycles with primers (5′-CCCTACACGACGCTCTTCCGATCTNNNNNN-3′) containing random hexamers and purified using the Zymo DNA Clean and Concentrator kit. Adaptor primers (5′-CAGACGTGTGCTCTTCCGATCTNNNNNN-3′) were added to preamplified products and then amplified for 12 PCR cycles with indexing primers for Illumina sequencing. Methylome libraries were purified using Beckman Coulter AMPureXP DNA beads.
samples 1 to 28 : smallRNA-seq; samples 29 to 69: MethylC-Seq

tag: genotype acronym

value: wild type

value: Non Cotyledon_portion (8DAP) of embryo

tag: treatment nucleic acids prior to library construction

value: Bisulfite treated

tag: amount of total rna used for library construction


title: Lp1_3_7.6 (L001)

tag: time point

tag: ph treatment

value: polyp


title: eiF2S1 selective 80S Ribosome FPs, 1000 ng/mlHela Cells [4_80S_eiF2_TM1000]

description:
80S_eIF2S1_TM_2
processed data file: Master_Data_Table.xlsx

value: HeLa

tag: rrna depletion

value: Ribo Zero Gold

tag: library preparation kit

value: Takara

value: CGGCTATG


title: eiF2S1 selective 80S Ribosome FPs, Untreated Hela Cells [4_80S_eiF2_UT]

description:
80S_eIF2S1_2
processed data file: Master_Data_Table.xlsx

tag: index name

tag: index sequence

value: TAATGCGC


title: Sample 37_Cotyledon_portion_Rep2_NextSeq_MethylC-Seq

description:
Single-end 75 base read MethylC-seq data from Cotyledon_portion Biological replicate2_NextSeq
Cotyledon_portion_Rep2_NextSeq_MethylC-Seq

value: Cotyledon_portion (8DAP) of embryo


title: untreated_3

description: untreated organoids

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. The protocol includes on-column DNase digestion. RNA was quantified using a NanoDrop 1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: colon organoid


title: 0dFemaleOL1

description: Denoted in processed file as column Sample_72006

value: female

tag: age

value: Canton-S


title: Lp1_2_7.6 (L002)

value: Colony 1

value: time point 2


title: Total 80S Ribosome FPs 1000 ng/ml Hela Cells [4_80S_Total_TM1000]

description:
80S_Total_TM_2
processed data file: Master_Data_Table.xlsx

value: CTGAAGCT


title: Lp3_2_7.9 (L001)

value: Colony 3


title: S2-DSRC DNaseI-seq

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Library strategy: DNaseI-seq
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Genome_build: dm6
Supplementary_files_format_and_content: 5% FDR hotspot calls as .bed file

source_name: S2-DSRC cells

growth_protocol: S2 cells were grown at room temerature to 90% confluency

extract_protocol:
Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with DNaseI conditions as above.
Short DNA fragments were isolated using AMPure beads and subjected to standard illumina library construction

value: S2-DSRC cells

tag: condition

value: 75 U/mL DNaseI for 3 min at 37C


title: Total 80S Ribosome FPs Hela cells [4_80S_Total_UT]

description:
4_80S_Total
processed data file: Master_Data_Table.xlsx

tag: cell line

value: GAATTCGT


title: S2-DSRC AdMTase-seq (2 U Hin1523)

data_processing:
Library strategy: AdMTase-seq
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: dm6
Supplementary_files_format_and_content: 5% FDR peak calls as .bed file

growth_protocol: S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL; Hela cells were grown at room temerature to 90% confluency

extract_protocol: Short DNA fragments were subjected to standard Illumina library construction

treatment_protocol: Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above.

tag: m6a-mtase conditions

value: 2 U Hin1523 for 20min at 37C

tag: antibody

value: Millipore Sigma ABE572


title: Lp1_1_7.6 (L002)

value: time point 1

value: polyp


title: Lp1_2_7.6 (L001)


title: eiF4E selective 40S Ribosome FPs, Untreated Hela Cells [4_40S_eiF4E]

description:
40S_eIF4E_1
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Custom rRNA Depletion

value: Takara

value: ATTCAGAA


title: S2-DSRC AdMTase-seq (0.6 U EcoGII)

value: 0.6 U EcoGII for 20min at 37C


title: array 1-menstrual blood pool 1

city: Chengdu

first: Weibo

last: Liang

state: Sichuan

address: Forensic Medicine Building, No.17, Renmin South Road Third Section

institute: Sichuan University

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using an Axon GenePix 4000 B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Data were extracted using GenePix 6.0 software (Axon, USA). Expressed data were normalized using median normalization.

source_name: menstrual blood

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Life technologies, USA) and purified with the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Equal quantities of total RNA from three or two donors were combined to produce pooled samples.

treatment_protocol: The samples were collected from unrelated and healthy people wihout treatment.

tag: the number of samples

tag: gender

value: female

value: day 2 of the menstrual cycle

value: menstrual blood


title: array 2-vaginal secretion pool 2

source_name: vaginal secretion

value: 41, 42 years

tag: tissue

value: vaginal secretion


title: array 2-menstrual blood pool 2

value: day 3 of the menstrual cycle


title: eiF4E selective 80S Ribosome FPs, Untreated Hela Cells [4_80S_eiF4E]

description:
80S_eIF4E_1
processed data file: Master_Data_Table.xlsx

value: Ribo Zero Gold

value: TCCGCGAA


title: 0dFemaleOL2

description: Denoted in processed file as column Sample_72007

value: Adult brain optic lobe

value: 0 day old

tag: strain

value: Canton-S


title: eiF2S1 selective 40S Ribosome FPs, 1000 ng/mlHela Cells [4_40S_eiF2_TM1000]

description:
40S_eIF2S1_TM_2
processed data file: Master_Data_Table.xlsx

value: GAGATTCC


title: S2-DSRC AdMTase-seq (2 U EcoGII)

value: S2-DSRC cells

value: 2 U EcoGII for 20min at 37C

value: Millipore Sigma ABE572


title: eiF2S1 selective 40S Ribosome FPs, Untreated Hela Cells [4_40S_eiF2_UT]

description:
40S_eIF2S1_2
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Custom rRNA Depletion

value: Takara

value: CGCTCATT


title: Lp1_3_7.9 (L002)

tag: colony

value: Colony 1

value: time point 3

value: polyp


title: Lp1_1_7.6 (L001)

value: time point 1


title: array 2-semen pool 2

source_name: semen

value: male

value: 41, 50years

value: semen


title: S2-DSRC AdMTase-seq (6 U EcoGII)

value: 6 U EcoGII for 20min at 37C


title: Lp1_3_7.9 (L001)


title: untreated_1

description: untreated organoids

value: colon organoid

tag: treatment

value: untreated


title: Total 40S Ribosome FPs 1000 ng/ml Hela Cells [4_40S_Total_TM1000]

description:
40S_TM 2
processed data file: Master_Data_Table.xlsx

value: TCCGGAGA


title: S2-DSRC AdMTase-seq (0.6 U EcoGI)

value: S2-DSRC cells

value: 0.6 U EcoGI for 20min at 37C


title: Lp1_2_7.9 (L002)

tag: time point

value: time point 2


title: array 2-peripheral blood pool 2

source_name: peripheral blood

value: female

value: 38, 40 years

value: peripheral blood


title: Total 40S Ribosome FPs Hela cells [4_40S_Total_UT]

description:
40S_Total_4
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Custom rRNA Depletion

value: Takara

value: ATTACTCG


title: S2-DSRC AdMTase-seq (2 U EcoGI)

value: 2 U EcoGI for 20min at 37C

value: Millipore Sigma ABE572


title: RNA-seq Hela Cells, 250ng/ml Tunicamycin [3_RNS_Total_TM250]

description:
RNA_seq_3_TM
processed data file: Master_Data_Table.xlsx

value: Illumina TruSeq Stranded


title: array 1-peripheral blood pool 1

value: male


title: Lp1_1_7.9 (L002)

value: Colony 1

value: time point 1

tag: ph treatment

value: polyp


title: array 2-saliva pool 2

source_name: saliva

value: 22, 26years

value: saliva


title: RNA-seq Hela Cells, Untreated [3_RNS_Total_UT]

description:
RNA_seq_3
processed data file: Master_Data_Table.xlsx

tag: rrna depletion


title: S2-DSRC AdMTase-seq (2 U Btr192IV)

value: S2-DSRC cells

value: 2 U Btr192IV for 20min at 37C


title: array 1-vaginal secretion pool 1

value: female

value: vaginal secretion


title: array 1-saliva pool 1


title: S2-DSRC AdMTase-seq (6 U Btr192IV)

value: 6 U Btr192IV for 20min at 37C


title: Lp1_2_7.9 (L001)

value: time point 2


title: eiF2S1 selective 80S Ribosome FPs, Untreated Hela Cells [3_80S_eiF2_UT]

description:
80S_eIF2S1_1
processed data file: Master_Data_Table.xlsx

value: HeLa

value: Ribo Zero Gold

tag: library preparation kit

value: Takara

value: CTGAAGCT


title: S2-DSRC genomic DNA control

data_processing:
Library strategy: DNA-seq
Pacbio software pbalign, bamSieve, ipdSummary from smrtlink-release_8.0.0.79519
Subreads were aligned using pbalign --concordant --hitPolicy=randombest --minAccuracy 70 --minLength 50
bamSieve was used to extract single-molecule-coverage subsets of the aligned data for analysis with ipdSummary --pvalue 0.001 --identify m6A
Genome_build: dm6
Supplementary_files_format_and_content: bed formatted mapped molecule locations with ZMW ID in column 4

growth_protocol: S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL.

extract_protocol:
PCR-free PacBio libraries were constructed using standard protocol.
Long-read PacBio HiFi/CCS sequencing

treatment_protocol: Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above and genomic DNA was extracted then subjected to shearing and then PacBio library construction.


title: S2-DSRC AdMTase-seq (0.6 U Hia5)

value: 0.6 U Hia5 for 20min at 37C

value: Millipore Sigma ABE572


title: S2-DSRC deproteinized Hia5 control

value: 500 U Hia5 for 10min at 37C


title: S2-DSRC AdMTase-seq (0.6 U Btr192IV)

value: 0.6 U Btr192IV for 20min at 37C


title: S2-DSRC Fiber-seq (20 U Hia5)

value: 20 U Hia5 for 10min at 37C


title: S2-DSRC Fiber-seq (500 U Hia5)


title: Total 80S Ribosome FPs Hela cells [3_80S_Total_UT]

description:
3_80S_Total
processed data file: Master_Data_Table.xlsx

tag: index name

value: ATTCAGAA


title: S2-DSRC AdMTase-seq (2 U Hia5) - rep2

value: 2 U Hia5 for 20min at 37C


title: Total 80S Ribosome FPs 250 ng/ml Hela Cells [3_80S_Total_TM250]

description:
80S_Total_TM_1
processed data file: Master_Data_Table.xlsx

tag: index sequence

value: GAATTCGT


title: S2-DSRC AdMTase-seq (6 U Hia5) - rep2

value: S2-DSRC cells

value: 6 U Hia5 for 20min at 37C


title: array 1-semen pool 1

value: male

tag: age

value: semen


title: Ades2_tRH

city: Woods Hole

first: Elena

last: Lopez Peredo

state: MA

address: 7 MBL St

institute: Marine Biological Laboratory

description: Gene expression during desiccation in Acutodesmus deserticola

data_processing:
Basecalls performed using CASAVA version 1.4
Trimmomatic 0.35
assembly was subjected to a three-step refinement by removal of contigs (a) with <10 accumulated aligned reads across all time points and replicates, (b) corresponding to rRNA and (c) encoding bacterial transcripts. Non-algal transcripts were identified using blastx as implemented in BLAST+ against nr NCBI database with a cut-off e-value of 10-5. Taxonomical information for filtering bacterial transcripts was obtained using the flag -outfmt “6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sskingdoms sscinames sblastnames stitle”
Libraries were individually aligned to their respective reference transcriptomes using Bowtie 2 v.2.2 . Transcript abundance was estimated using RSEM v.1.2.28 . Expression matrices including read counts matrix, normalized ‘transcripts per million transcripts’ (TPM), and standardized ‘trimmed mean of M-values’ (TMM) were generated using Trinity script abundance_estimates_to_matrix.pl.
Differential expression analysis was performed on count data generated with RSEM using DESeq2. A gene was classified as a DEG if the change in its expression exceeded 4-fold (Log2 2-FC) in pairwise comparisons with a significance level <0.001 (adjusted p-value after Benjamini-Hochberg (BH) correction for multiple testing.
Assembly file has been submitted to the TSA.  TSA submission number: SUB5854543.
Genome_build: Trinity v2.1, jaccard clip option
Supplementary_files_format_and_content: Sdes_RSEM_plant_genes.counts.matrix (Read counts from expression analysis)
Sdes_RSEM_plant_genes.TMM.EXPR.matrix (Normalized expression data from DESeq2)

organism: Tetradesmus deserticola

source_name: algal cells in culture

growth_protocol: grown for six weeks in 250 mL Erlenmeyer flasks containing 150 mL of autoclaved BBM+WH medium

extract_protocol:
ZR Plant RNA MiniPrep™ (Zymo, Irvine, USA) followed by RNA Clean & Concentrator™-5 (Zymo, Irvine, USA)
Ovation Arabidopsis RNA-seq Systems (NuGEN, San Carlos, CA, USA). Nuclear, chloroplast, mitochondrial and bacterial ribosomic RNA (rRNA) was removed during the InDA-C adaptor cleavage step using a combination of commercially available oligos targeting prokaryote and green plant rRNA genes (Arabidopsis kit; NuGEN S02070, S02076, R01758, F01278) supplemented with 105 custom-made oligos

treatment_protocol: “Hydrated” stage were collected immediately after transferring 40 µL of algal cultures to a round cover glass. “Early” and “Late” desiccation stages corresponded to a volume-loss of 25% and 60% respectively and were collected 2.5 h and 7.5 h into the desiccation time course. The “Dry” stage corresponded to fully flattened dots (Fig. S1E). Dry algal dots remained in the drying chamber 11 additional hours until collection (circa 24 h after the beginning of the experiment). Finally, the “Rehydrated” stage corresponded to algal dots collected one hour after rehydration.

tag: Stage

value: Rehydrated


title: Ades1_tRH


title: S2-DSRC DNA Input Control

tag: cell line

value: Untreated