title: L0000

tag: disease

value: Asymptomatic/Mild


title: mb1_CTRL.1

status: Public on Dec 19 2020

type: SRA

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed. Reads were aligned to mouse genome build mm10 using HISAT2, v2.0.3beta aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR(3.28.0) TMM method and log2 transformed with voom (limma3.42.0).
Batch effect was removed using ComBat (sva3.34.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID.

molecule: total RNA

organism: Mus musculus

source_name: CLL splenocytes (CD19+B220-)

extract_protocol:
Cells were isolated from sorted CLL spenocytes (CD19+B220-) and RNA was harvested using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) according to manufacturer’s instructions
We performed cDNA library prep starting from 5 ng RNA (CD19 samples) or 8 ng RNA (mb1 samples) per sample with the "SMART-seq v4 Ultra Low Input RNA Kit for Sequencing", according to Clontech protocol (mb1 samples). For CD19 samples, we applied the modification recommended by Clontech in the SMART-seq v4 protocol: starting Nextera XT with an input of 150pg instead of the 1ng indicated by Illumina. Final AMPure bead purification with 0.9x ratio, to enrich for longer fragments.
We then performed a Nextera XT library prep according to Illumina protocol 15031942 Rev. E. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation 4200. We performed paired-end 2x79nt (CD19 samples) or single end 75nt (mb1 samples) sequencings on NextSeq 500.

tag: strain

tag: gender

value: female

tag: transgene

value: IgH.TEμ;RNIC lox/+

tag: cre

tag: group

value: CTRL

tag: replicate

tag: batch


title: CD19_CTRL.1

value: male


title: L8205

city: Dubai

first: Ruchi

last: Jain

address: Al jaddaf

department: Genomics

country: United Arab Emirates

institute: Al jalila Children's Specialty Hospital

data_processing:
High quality reads (Q ≥ 30) were first mapped to rRNA sequences to remove potential rRNA reads using hisat v2-2.1.0.
fastq files were then aligned to GRCh37 (hg19) of Human reference genome
The unmapped reads were then mapped to the SARS-CoV-2 genome (GenBank Accession number: NC_045512.2) using BWA v0.7.17
PCR duplicates were removed with Picard MarkDuplicates program v2.18.17
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm in the SubReads package v2.0.1
Differentially expressed genes (1.5-fold and 5% false discovery rate) were identified by DeSeq2 v1.28.1
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

organism: Homo sapiens

source_name: Nasopharyngeal swabs

extract_protocol:
RNA was extracted from nasopharyngeal swabs using the QIAamp Viral RNA Mini or the 213 EZ1 DSP Virus Kits (Qiagen, Hilden, Germany)  according to the manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA Library kit from Illumina (San Diego, CA, USA) , according to the manufacturer’s instructions.
RNA-seq NovaSeq SP Reagent kit (2 X 150 cycles) from Illumina (San Diego, CA, USA)

tag: disease severity


title: L8497


title: REH_RUNX1_rep1

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19)
The .sam files were converted to .bam files using SAMtools
The .bam files were then processed to yield .wig files using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wig

molecule: genomic DNA

growth_protocol: REH cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min. Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

tag: cell line

value: REH

tag: cell type

value: Pre-B lymphoblast cells

tag: tissue

value: Peripheral blood

tag: chip antibody

value: RUNX1 (ab23980, Abcam)


title: L8156


title: L7356


title: REH_input


title: L8480


title: WT H2O2 treated, Stat3-IP rep1 [WT-H2O2_1]

status: Public on Dec 18 2020

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Raw reads were trimmed against adaptors first, and then were quality trimmed by skewer with default settings.
Trimmed reads were mapped onto the mouse genome (mm10, Ensembl Release 95) by hisat2 with the following options, --no-spliced-alignment -I 100 -X 800.
The uniquely and correctly aligned reads were extracted according to the mapping tags, and the duplicated reads were marked and filtered out by picard-tools.
The binding sites of transcript factor (peaks) were identified by MACS2, and the parameter --keep-dup was set to 1. The blacklisted genomic regions in the mouse were applied (https://github.com/Boyle-Lab/Blacklist)  to avoid the artificial peaks.
The annotations of binding sites were conducted by ChIPpeakAnno using the Ensembl R database (build version 79). The flanking sequences were extracted for each binding site, which were used to identify the binding motifs using MEME Suite.
Genome_build: mm10, Ensembl Release 95
Supplementary_files_format_and_content: peak files in bed format

source_name: WT H2O2 treated, Stat3-IP

growth_protocol: WT-Stat3 and Stat3-C3S MEFs were plated with a confluence of 1.5X10^6 cells per 10cm dishes in full medium. The day after, full medium was replaced with starving medium (0,5% FBS) and cells were incubated overnight under normal growth conditions (37°C, 5% CO2).

extract_protocol:
Frozen cell pellets were lysed and sonicated in ice to produce DNA fragments of 300-400 base pairs. Residual insoluble chromatin was sedimented by centrifugation at 14,000 rpm for 10 minutes at 4°C. 10% of each supernatant was set aside as the input fraction. For immunoprecipitations, samples were pre-cleared with agarose beads (2h at 4°C), diluted and divided into 2 fractions to which were added either a-Stat3 antibody (124H6 Cell Signalling) or mouse IgG (MFCD00212351, Sigma) as negative control, and incubated on a wheel at 4°C over night. Immune complexes were collected by incubation with protein-A sepharose beads (GE Healthcare) for 1 h and centrifugation. Beads were washed serially in buffers of increasing ionic strength and detergent concentration, complexes were eluted from the beads in bicarbonate and incubated at 65°C for 6 h to reverse crosslinks. Samples were treated with proteinase K and DNA was purified using a GeneJet purification kit.
ChIP-Seq libraries were prepared using the NEBNext Ultra DNA library Prep Kit for Illumina (NEB; E7370S) and NEBNext Multiplex Oligos for Illumina (NEB; E7335, E7710, E7730), following instructions in the application note: Low input ChIP-Seq using the NEBNext Ultra Library Prep Kit for Illumina (https://international.neb.com/-/media/catalog/application-notes/low-input-chipseq-using-the-nebnext-ultra-library-prep-kit-for-illumina-e7442.pdf?rev=91023778031446d88ebc26b53d3b8b83). Libraries were sequenced on the Illumina NextSeq 500 using a NextSeq 500 High Output v2.5 150 cycle kit (Illumina; 20024907).

treatment_protocol: Cells were treated with LIF (10ng/ml) for 45 minutes or 100mM hydrogen peroxide for 1 hour (plus relative controls) and cross-linked for 10 minutes by adding formaldehyde in the culture medium to a final concentration of 1%. Cross-linking reaction was stopped by addition of glycine 125mM. Cell were harvested, centrifuged at 2.600 rpm for 10 minutes and the cell pellets were stored at -80°C.

tag: genotype/variation

value: wild type

value: murine embryonic fibroblasts (MEFs)

tag: treatment


title: WT H2O2 treated, Stat3-IP rep2 [WT-H2O2_2]

value: a-Stat3 antibody (124H6 Cell Signalling)


title: WT IgG-IP [WT-neg]

source_name: WT IgG-IP

value: mouse IgG (MFCD00212351, Sigma)


title: Patient 1 replicate 1

city: Seattle

first: Robert

middle: K.

last: Bradley

state: Washington

address: 1100 Fairview Ave N

department: Public Health Sciences/Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Mutations were introduced into the endogenous UPF1 locus using CRISPR/Cas9

data_processing:
Gene annotations from UCSC knownGene track, Ensembl71, and MISO v2.0 were merged.
RNA-seq reads were mapped to the transcriptome with RSEM v1.2.4, modified to invoke Bowtie v1.0.0 with the ‘-v 2’ option.
Remaining unaligned reads were mapped to the genome as well as a database of possible splice junctions, consisting of all possible combinations of 5' and 3' splice sites annotated for each gene, using TopHat v2.0.8b.
Isoform ratios were quantified with MISO v2.0.
The abundance of NMD(+) isoforms was determined for each sample.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel files containing differentially spliced isoforms for HEK 293T cell lines carrying mutations for Patient 1 and Patient 9.

molecule: polyA RNA

source_name: Human embryonic kidney

growth_protocol: HEK 293T cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, and 100 mg/mL Streptomycin (PenStrep, GIBCO). Cells were cultured at 37°C and 5% CO2. Cells were split at a ratio of 1:10 once they reached 90-100% confluency as needed.

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was Poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol.

treatment_protocol: Ultramers for homology directed repair (HDR) were designed using previously described strategies (Richardson, Ray, DeWitt, Curie, & Corn, 2016) and synthesized by IDT, Inc. HEK 293T cells were transiently transfected with 1 μg/mL sgRNA/pX459 Cas9 expression plasmid and 20 nM HDR Ultramer using Lipofectamine 2000 that was diluted in Opti-MEM Reduced Serum Medium (ThermoFisher). Cells were incubated at 37°C for 24 hours, at which time the transfection medium was replaced with DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, 100 mg/mL Streptomycin (PenStrep, GIBCO), and 2 mg/mL puromycin. Cells were then incubated for 48-72 hours in DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, 100 mg/mL Streptomycin (PenStrep, GIBCO), and 2 mg/mL puromycin, at which time genomic DNA was extracted and regions of interest were amplified using the appropriate oligos. Monoclonal cell lines carrying the desired mutations were obtained via flow cytometry.

value: HEK 293T

tag: clonality

value: monoclonal

tag: mutated gene

tag: mutation

tag: method mutagenesis

value: CRISPR/Cas9 homology directed repair


title: WT input DNA [WT-input]

source_name: WT input DNA


title: WT control, Stat3-IP rep2 [WT-C2]

source_name: WT control, Stat3-IP

value: control


title: WT control, Stat3-IP rep1 [WT-C1]


title: WT LIF treated, Stat3-IP rep2 [Lif2_S5]

source_name: WT LIF treated, Stat3-IP

value: LIF


title: C3S H2O2 treated, Stat3-IP rep2 [C3S_H2O2_C2]

source_name: C3S H2O2 treated, Stat3-IP

value: redox-insensitive mutant of Stat3 (Stat3-C3S)


title: C3S H2O2 treated, Stat3-IP rep1 [C3S_H2O2_C1]


title: spleen_ND_CX3CR1neg_Replicate5

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited text file include sequence read counts of each sample

extract_protocol:
Samples for RNA-seq were directly sorted in semi-skirted 96-well PCR plate including lysis buffer (2xTCL buffer (Qiagen, #1070498) + RNase-free water + beta-mercaptoethanol (1% total volume)).
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

tag: strain

tag: age

value: 13 months

tag: diet

value: ND

value: spleen

value: splenic CD8 T cells


title: C3S control, Stat3-IP rep1 [C3S_C1]

source_name: C3S control, Stat3-IP


title: spleen_ND_CX3CR1neg_Replicate2


title: spleen_ND_CX3CR1neg_Replicate1


title: spleen_ND_CX3CR1neg_Replicate4


title: spleen_CDHFD_CX3CR1neg_Replicate6

value: CD-HFD


title: spleen_ND_CX3CR1neg_Replicate3


title: C3S control, Stat3-IP rep2 [C3S_C2]


title: spleen_ND_CX3CR1neg_Replicate6


title: spleen_CDHFD_CX3CR1neg_Replicate4


title: spleen_CDHFD_CX3CR1neg_Replicate3


title: spleen_CDHFD_CX3CR1neg_Replicate2


title: liver_ND_CXCR6pos_Replicate5

value: liver

value: hepatic CD8 T cells


title: liver_ND_CXCR6pos_Replicate6


title: liver_ND_CXCR6pos_Replicate4


title: liver_ND_CXCR6pos_Replicate3


title: liver_ND_CXCR6pos_Replicate1


title: liver_ND_CXCR6neg_Replicate5


title: WT LIF treated, Stat3-IP rep1 [Lif1_S6]

value: wild type


title: liver_ND_CXCR6neg_Replicate4


title: liver_ND_CXCR6neg_Replicate3


title: liver_CDHFD_CXCR6pos_Replicate6


title: liver_CDHFD_CXCR6pos_Replicate5


title: liver_CDHFD_CXCR6pos_Replicate3


title: liver_ND_CXCR6neg_Replicate1


title: spleen_CDHFD_CX3CR1neg_Replicate5


title: liver_CDHFD_CXCR6pos_Replicate4


title: liver_CDHFD_CXCR6neg_Replicate6


title: liver_CDHFD_CXCR6neg_Replicate4


title: liver_CDHFD_CXCR6neg_Replicate3


title: liver_CDHFD_CXCR6neg_Replicate1


title: liver_CDHFD_CXCR6neg_Replicate5


title: liver_CDHFD_CXCR6pos_Replicate2


title: liver_CDHFD_CXCR6pos_Replicate1


title: liver_CDHFD_CXCR6neg_Replicate2


title: spleen_CDHFD_CX3CR1neg_Replicate1


title: liver_ND_CXCR6neg_Replicate2


title: glioblastoma cells-NC_1

city: Xi'an

first: Xiangyu

last: Gao

address: changle xi

country: China

institute: Forth military medical university

data_processing: analyzed by custom service provided by Gene Denovo Biotechnology Co.(Guangzhou,China)

source_name: glioblastoma cells

growth_protocol: glioblastoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/F12 (1:1) supplemented with 10% fetal bovine serum  and 1% penicillin–streptomycin solution.

extract_protocol:
RNA was extracted using the Trizol reagent and rRNA was removed. RNA samples were fragmented into appropriate short fragments. RNA fragments of 18–30 nucleotides in length were enriched by polyacrylamide gel electrophoresis (PAGE). After adding 3’ and 5’ adapters, samples were subjected to RT-PCR, and PCR products with 140-160 bp size were enriched to generate a cDNA library
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: glioblastoma cells were treated with HMGB1 or control PBS for 48 h

value: brain

value: glioblastoma

value: glioblastoma cells treated with PBS for 48 h


title: glioblastoma cells-NC_2


title: glioblastoma cells-NC_3


title: glioblastoma cells-HMGB1_1

value: glioblastoma cells treated with HMGB1 for 48 h


title: glioblastoma cells-HMGB1_3


title: Sample28_Dis_HEK_PK_veryhigh

city: Heidelberg

first: Kai

last: Fenzl

address: Meyerhofstraße 1

institute: EMBL

data_processing:
library strategy: Ribosome Profiling
Raw NextSeq550 sequencing files were converted with bcl2fastq2 conversion software (v2.20) to obtain single fastq files per indexed sample using following command: bcl2fastq -p16 -r4 -w4 --no-lane-splitting -R <path_to_input_folder> -o <path_to_output_folder>. Only samples 5-8 were sequenced by the DKFZ Sequencing Facility on a HighSeq2000 machine and converted to fastq files.
3' adaptor sequences were trimmed with Cutadapt (v1.13) with the following command:  cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a ATCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz For samples sequenced on HiSeq2000 following command was used:  cutadapt --cores=4 -q20 -m23 --discard-untrimmed -O6 -a CTGTAGGCACCATCAATTCGTATGCCGTCTTCTGCTTG -o <path_to_output>.fastq.gz <path_to_input>.fastq.gz
Unique molecular identifiers (UMIs) were extracted from each read for the downstream analysis using a custom Julia script (available as supplement information of this study) with the following command: julia <path_to_script>/Script1.jl <path_to_input>.fastq.gz <path_to_output>.fastq.gz --umi3 5 --umi5 2. Only samples 5-8 did not contain UMI sequences in the adaptors, therefore this step was not included for U2OS samples.
For removal of human rRNA contaminants, sequenced libraries were aligned to rRNA sequences including: RNA45SN1 - RNA45SN5 (human 28S, 18S, 5.8S), RNA5S1 (human 5S), MTRNR2L10 (Mito 16S), MT-RNR1 (Mito 12S), MT-RNR2U1 (Mito 16S), 22 mito tRNAs, 631 nuclear human tRNAs. The E. coli rRNA file included: 5S rRNA (rrfA -  rrfH), 16S rRNA (rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, and rrsH), 23S rRNA (rrlA, rrlB, rrlC, rrlD, rrlE, rrlG, and rrlH). All rRNA contaminations were removed by Bowtie2 (v.2.3.5.1) with the following command: bowtie2 -p4 -t -x <path_to_folder_with_Bowtie-indexed_rRNA_contamination> -q <path_to_input_file>.fastq.gz' --un <path_to_output_file>.fastq -S /dev/null
Reads that did not align to rRNA were aligned to the human genome (GRCh38p10) or E.coli genome (GCA_000022665.2, E. coli BL21(DE3), including additional chromosome files containing custom plasmid sequences, see the corresponding sample description field) using STAR (v2.7.1a) with the following command: STAR --runThreadN 24 --genomeDir <path_to_indexed_genome> --readFilesIn <path_to_input>.fastq --outFilterMultimapNmax 1 --outFilterType BySJout --alignIntronMin 5 --outFileNamePrefix <path_to_output> --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All XS --quantMode GeneCounts --twopassMode Basic
All reads aligning to the coding sequence (CDS) were assigned (a-, p-, e-site) via a custom Julia script (available as supplement information of this study). p-site assigned reads were used for all downstream analysis.This script accounts for soft-clipping via the '-c 1' option: the integer indicates the bases at the 5' end that often arise from untemplated addition by the reverse transcriptase during library preparation by using the following command: julia <path_to_script>/Script2.jl -c 1 -g <path_to_genome_annotation>.gff' -u -o <path_to_output> <path_to_input>.bam
Genome_build: Human genome (GRCh38p10), E.coli genome (GCF_000009565.1, E. coli BL21(DE3))
Supplementary_files_format_and_content: Processed data are stored in HDF5 files. Each HDF5 file contains one data set per gene. Each data set consists of a 2-row matrix, with the first row containing the 1-based position within the CDS, and the second row the number of detected P-site reads at this position. Additional information is stored in the data set attributes, including: gene and protein names, transcript isoform used for position assignment, length of the coding sequence, chromosome and strand location of the gene. In this study the p-side assignments stored in such HDF5 files were further analyzed using RiboSeqTools (available at: https://github.com/ilia-kats/RiboSeqTools).

growth_protocol: Human cells were cultivated in the indicated temperature and growth medium (as indicated in the corresponding sample "characteristics: growth conditions" field). Cells were passaged regularly through trypsinization. For all experiments cells were seeded 18-24 hours before lysis in 15 cm2 dishes (3.5 million U2OS and 6 million HEK293-T cells) to reach 70-90% confluency at the time of harvesting. E. coli cells were cultivated in the indicated temperature and growth medium (as indicated in the corresponding sample "characteristics: growth conditions") with shaking at 120 rpm. For all experiments 200 ml of EZ-RDM were inoculated with an overnight culture to an initial OD600 of 0.05 and grown untill a cell density of OD600 = 0.4 - 0.6 was reached for harvest.

extract_protocol:
RNA from frozen ribosome fractions was extracted using the hot acid phenol method as described in Galmozzi and Merker et al. 2019
Libraries from isolated ribosome footprints were prepared following the previously published protocol (Galmozzi and Merker et al. 2019)

treatment_protocol: General information on treatments is indicated in the corresponding sample characteristics field. For detailed information, please refer to the Material and Methods of the original publication.

tag: cell line/strain

tag: tissue source

value: Embrionic Kidney

tag: genotype

value: wild-type

tag: sample type

value: Footprints from disome fraction

tag: growth condition

value: DMEM with GlutaMAX, pyruvate, 10% FCS, pen/strep, 37°C, 5% CO2, humidified

value: lysates treated with PK in a 1:200 ratio (PK to total protein amount)


title: Sample27_Mono_HEK_PK_veryhigh

value: Footprints from monosome fraction


title: Sample26_Dis_HEK_PK_high

value: lysates treated with PK in a 1:2000 ratio (PK to total protein amount)


title: Sample24_Dis_HEK_PK_mid

value: lysates treated with PK in a 1:6000 ratio (PK to total protein amount)


title: Sample23_Mono_HEK_PK_mid


title: Sample21_Mono_HEK_PK_low

value: lysates treated with PK in a 1:20000 ratio (PK to total protein amount)


title: Sample19_Mono_HEK_no_PK

value: no PK treatment


title: Sample22_Dis_HEK_PK_low


title: Sample20_Dis_HEK_no_PK


title: liver_ND_CXCR6pos_Replicate2

value: 13 months

value: ND

value: liver

tag: cell type


title: Sample15_Mono_HEK_no_puro_Rep2

value: no puromycin treatment, lysate crosslinked with PFA


title: Sample13_Mono_HEK_puro_Rep1

value: lysate treated with 2mM puromycin, lysate crosslinked with PFA


title: Sample14_Dis_HEK_puro_Rep1


title: Sample16_Dis_HEK_no_puro_Rep2


title: Sample17_Mono_HEK_puro_Rep2


title: Sample9_Total_HEK_Rep1

value: Footprints from cushion-isolated ribosomes


title: Sample11_Mono_HEK_no_puro_Rep1


title: Sample 3_Mono_HEK_Rep2


title: Sample4_Dis_HEK_Rep2


title: Sample12_Dis_HEK_no_puro_Rep1


title: Sample10_Total_HEK_Rep2


title: Sample2_Dis_HEK_Rep1


title: Sample1_Mono_HEK_Rep1


title: Sample25_Mono_HEK_PK_high


title: Sample18_Dis_HEK_puro_Rep2


title: MDA-MB-231 - SGI-110 rep. 2

city: Odense C

first: morten

last: gjerstorff

state: FYN

address: J.B. Winslows Vej 25, 3.

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequenced reads were trimmed for adaptor sequence and then mapped to the hg19 genome using STAR 2.3.1z_r395 with standard parameters.
Reads in exons were counted using the iRNA-seq pipeline from Madsen et al., Nucleic Acids Research, 2015.
Diferential gene expression analysis was performed using DeSeq2 (Love et al., Genome Biology, 2014).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for every sample and DeSeq2 output

source_name: Breast adenocarcinoma

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich) supplemented with 10 % fetal bovine serum (FBS, Sigma-Aldrich) and 1 % penicillin-streptomycin. The cells were kept at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using guanidiumthiocyanate
Purified RNA was prepared for sequencing using the TruSeq RNA sample preparation kit according to manufacturer’s instructions (Illumina) and sequenced using the Illumina HiSeq 1500 system.

treatment_protocol: MDA-MB-231 cells were treated for 96 hours with 1 µM guadecitabine and then left untreated for another 24 hours before harvest

tag: cell line

tag: tissue

value: Breast adenocarcinoma


title: SK-N-AS_14

first: Frank

last: Westermann

address: Im Neuenheimer Feld 280

institute: Hopp Children's Cancer Center (KiTZ) and German Cancer Research Center (DKFZ)

description: single-cell RNA-seq (MARS-seq)

data_processing:
read 2 contains the 7 bp cell barcode followed by the 8 bp UMI.
Pool barcode, cell-specific tags and UMIs were extracted and reads with ambiguous plate/cell-specific tags were filtered
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome combined with ERCC spike-in pseudo-assembly using Bowtie2 v2.1.0  and the standard parameters “-m 1 -t --best --chunkmbs 64 –strata”
Sequence reads were filtered for reads mapping to a range of -1000 to +200 bp from a known transcription termination site
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated values file with gene counts for every gene and cell

source_name: Neuroblastoma cell line

growth_protocol: SK-N-AS cells were cultured in RPMI1640 medium supplemented with 10% fetal calf serum and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene and single-cells were sorted into 384-well plates.
Libraries were prepared as described previously (Jaitin et al., 2014)

treatment_protocol: Cells were not treated.

value: Neuroblastoma cell line

value: SK-N-AS


title: SK-N-AS_15

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_8

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_9

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_10

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_13

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_11

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_7

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_6

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_3

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_16

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_12

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_1

description: single-cell RNA-seq (MARS-seq)


title: SUM159 DMSO Sample 1

city: Houston

first: Jarey

middle: Hao

last: Wang

state: Texas

address: 1 Baylor Plaza, 304B, Anderson Building

institute: Baylor College of Medicine

data_processing:
Raw read of fastq format were obtained after adapter removal in BaseSpace. Index of the mm10 mouse or hg38 human genome was built using hisat2-v2.0.4.
Proper paired-end reads were aligned to the reference genome using hisat2-v2.0.4.
Expression was quantified and FPKM normalized using Cufflinks (Cuffquant and Cuffnorm).
Genome_build: hg38
Supplementary_files_format_and_content: Abundance files from Cufflinks

growth_protocol: SUM159 cells grown in media as described in manuscript.

extract_protocol:
RNA isolated using the RNeasy kit (Qiagen).
~300 bp insert strand specific library with polyA selection (TruSeq Stranded mRNA kit, Illumina).

treatment_protocol: Cells treated with SD6 or DMSO for 72h prior to collection in RNA lysis buffer.

value: Immortalized cell line

value: Vehicle Control


title: SUM159 SD6 Sample 2

value: Drug Treated


title: SUM159 SD6 Sample 3


title: SUM159 DMSO Sample 3


title: SUM159 SD6 Sample 1


title: SUM159 DMSO Sample 2


title: SK-N-AS_4

description: single-cell RNA-seq (MARS-seq)


title: SK-N-AS_5

description: single-cell RNA-seq (MARS-seq)


title: LM2 SD6 Sample 2

growth_protocol: LM2 cells grown in media as described in manuscript.


title: LM2 DMSO Sample 3


title: LM2 DMSO Sample 1


title: LM2 SD6 Sample 3


title: LM2 DMSO Sample 2


title: SK-N-AS_2

description: single-cell RNA-seq (MARS-seq)


title: LM2 SD6 Sample 1


title: SMARCA4 mutated ATRT Case 03 [SMARCA4d]

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Fastq files were aligned to hg19 human genome using STAR aligner (v2.5.2a). Reads counts were obtained from the STAR generated BAM files with featureCounts (v2.0.0) using hg19 gene annotation (Ensembl release 87). The count matrix was used to obtain normalized reads via variance stabilizing transformation applied through DESeq2 R package (v1.26.0) and then batch corrected using removeBatchEffect function of R package limma (v3.42.2).
Genome_build: hg19
Supplementary_files_format_and_content: normalized counts (VST)

source_name: SMARCA4 mutated ATRT

extract_protocol:
For RNA isolation from FFPE tissue, 10 x 10 µm sections were cut and RNA isolated using the Maxwell® RSC RNA FFPE Kit (Promega). The RNA integrity was analyzed with the RNA 6000 Nano Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). From total RNA, the ribosomal RNA was depleted with the help of the RiboCop rRNA Depletion Kit (Lexogen).
The RNA sequencing library was generated using the CORALL Total RNA-Seq Library Prep Kit (Lexogen). Concentrations of all samples were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and fragment lengths distribution of the final libraries was analyzed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples were normalized to 2 nM and pooled at equimolar concentrations. The library pool was sequenced on the NextSeq500 (Illumina) with 1 x 75 bp, with 24.5 to 35.1 million reads per sample.

tag: Sex

value: female

value: primary atypical teratoid rhabdoid tumor (ATRT)

tag: genotype/variation

value: SMARCA4 mutated

tag: location

value: supratentorial


title: SMARCA4 mutated ATRT Case 02 [SMARCA4c]

value: male


title: SMARCB1 mutated ATRT-MYC Case 29 [kkfz261]

source_name: SMARCB1 mutated ATRT-MYC

value: SMARCB1 mutated


title: SMARCA4 mutated ATRT Case 12 [SMARCA4f]

value: infratentorial


title: SMARCA4 mutated ATRT Case 01 [SMARCA4a]


title: SMARCB1 mutated ATRT-TYR Case 39 [kkfz222]

source_name: SMARCB1 mutated ATRT-TYR


title: glioblastoma cells-HMGB1_2

value: brain

value: glioblastoma

tag: treatment

value: glioblastoma cells treated with HMGB1 for 48 h


title: SMARCA4 mutated ATRT Case 14 [SMARCA4j]


title: SMARCB1 mutated ATRT-MYC Case 32 [kkfz262]


title: SMARCA4 mutated ATRT Case 13 [SMARCA4g]


title: BaumsDatabaseID_12812 [16S]

city: University Park

first: Iliana

middle: B

last: Baums

state: PA

address: 212 Mueller Laboratory, Penn State University

department: Biology

institute: The Pennsylvania State University

data_processing:
Paired-end sample data with quality scores were imported and then reads were joined using vsearch join-pairs and quality filtered using quality-filter q-score-joined within Qiime2 (Bolyen et al. 2018; Caporaso et al. 2010). Chimeras were removed and sequences denoised using deblur with p-trim-length parameter of 230 which truncates the read at this position. Illumina runs were analyzed separately in Qiime2 and combined after the deblur analysis. The Naive Bayes classifier was trained on only the region of the target sequences that was sequenced and taxonomy assigned using Silva 132 reference sequences clustered at 99% sequence similarity. The output  was a table containing operational taxonomic units (OTU). OTUs were normalized using the QIIME2 plugin, q2-perc-norm (Gibbons et al. 2018), a model-free approach that corrects batch effects in case-control microbiome studies, with condition of bleaching (Normal color/slightly pale (Not bleached) vs bleached/very pale (Bleached)) as the case-control. Correction for batch effects was necessary because genet was confounded with Miseq run.
Supplementary_files_format_and_content: Genus-table_norm.csv
Supplementary_files_format_and_content: Order-table_norm.csv

organism: Acropora palmata

source_name: Whole tissue extract

extract_protocol: The hypervariable V1 and V2 regions of the 16S rRNA gene were amplified using a general bacterial primer pair with Illumina CS1 and CS2 Fluidigm adapters. [27F 5’-TCGTCGGCAGCGT CAGATGTGTATAAGAGACAGAGAGTTTGATCMTGGCTCAG-3’ and 355R 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTGCCTCCCGTAGGAGT-3’] (Rodriguez-Lanetty et al. 2013). Polymerase chain reactions were performed using 0.1 U µL-1  Gotaq (Promega), 1X Gotaq buffer (Promega), 0.25 mM dNTPs (Bioline), 2.5 mM MgCl2, and 0.25 µM of each primer.   Initial denaturation was performed at 95°C for 5 min followed by 30 cycles of 95°C for 30 sec, 51°C for 1 min, and 72°C for 1 min.  Final extension was performed at 72°C for 7 min.  PCR products were checked on a 1% agarose gel for a band near 450bp.  Libraries were prepared at the DNA services facility at the University of Illinois, Chicago and sequenced on a MISEQ2500 platform. Genets P1034, P2138, P1002, and P2151 were run on one chip, and Genets P2656 and P2598 were run together on the second Miseq chip.

tag: peak bleaching status

value: Normal Color

tag: reef

value: Sand Island

tag: location of within colony sampling

value: Not a Branch

tag: coral genet id


title: BaumsDatabaseID_12813 [16S]

value: Bleached


title: CD19_NICD.3

source_name: CLL splenocytes (CD19+B220-)

tag: strain

tag: gender

tag: transgene

value: IgH.TEμ;RNIC lox/+ CD19-Cre

tag: cre

tag: group

value: NICD

tag: replicate

tag: batch


title: SMARCB1 mutated ATRT-SHH Case 36 [kkfz260]

source_name: SMARCB1 mutated ATRT-SHH


title: BaumsDatabaseID_12810 [16S]

value: Branch


title: BaumsDatabaseID_12808 [16S]


title: BaumsDatabaseID_12789 [16S]

value: Molasses


title: BaumsDatabaseID_12787 [16S]

value: Very Pale


title: BaumsDatabaseID_12811 [16S]


title: Reference strain Snf1 on high glucose_biological rep3

type: RNA

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

institute: Technical University of Denmark

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.6. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

label: Biotin

organism: Saccharomyces cerevisiae

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: strains were grown in 1 liter bioreactor at 30°C, pH 5.0 and aerobically, 40 g/L glucose initially

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA)

treatment_protocol: biomass samples were taken at steadystate, cooled down immediately and centrifuged with cooling, The cell pellets were frozen in liquid nitrogen

tag: genotype

tag: glucose concentration


title: Reference strain Snf1 on low glucose_biological rep2

value: 5 g/L


title: Mutant strain T210A on low glucose_biological rep3


title: Reference strain Snf1 on low glucose_biological rep1


title: Reference strain Snf1 on high glucose_biological rep1


title: CD19_CTRL.3

value: female

value: IgH.TEμ;RNIC lox/+

value: CTRL


title: Reference strain Snf1 on low glucose_biological rep3


title: Mutant strain T210A on low glucose_biological rep2


title: BaumsDatabaseID_12785 [16S]


title: Mutant strain T210A on low glucose_biological rep1


title: Mutant strain T210A on high glucose_biological rep3


title: BaumsDatabaseID_12784 [16S]


title: BaumsDatabaseID_12782 [16S]


title: Mutant strain Alpha1 on low glucose_biological rep2


title: BaumsDatabaseID_12793 [16S]


title: Reference strain Snf1 on high glucose_biological rep2


title: Mutant strain T210A on high glucose_biological rep2


title: BaumsDatabaseID_12814 [16S]


title: BaumsDatabaseID_12720 [16S]

value: Key Largo


title: BaumsDatabaseID_12721 [16S]


title: BaumsDatabaseID_12718 [16S]


title: Mutant strain Alpha1 on high glucose_biological rep3


title: BaumsDatabaseID_12715 [16S]


title: BaumsDatabaseID_12717 [16S]


title: Mutant strain Alpha1 on low glucose_biological rep1


title: BaumsDatabaseID_12724 [16S]


title: BaumsDatabaseID_12712 [16S]


title: Mutant strain Alpha1 on high glucose_biological rep1


title: Mutant strain T210A on high glucose_biological rep1


title: BaumsDatabaseID_12723 [16S]


title: Mutant strain Alpha1 on low glucose_biological rep3


title: BaumsDatabaseID_12711 [16S]


title: Primary CRPC, VP

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

department: Biological Sciences

institute: University of Notre Dame

description: Gene expression data from ventral  prostate (VP) of CRPC-bearing PB-Cre/Pten/Smad4/mTmG mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 2.0 Software (Thermo Fisher)

label: biotin

source_name: ventral prostate of mice with castration-resistant prostate cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PB-Cre/Pten/Smad4 mice were maintained in SPF animal facility with standard chow diet

extract_protocol: Total RNA from fresh tissues was extracted using Direct-zol RNA Miniprep Kit (Zymo Research). The quantity and quality of each sample were measured using an Agilent 2100 Bioanalyzer.

treatment_protocol: PB-Cre/Pten/Smad4 males with established prostate cancer were treated with surgical castration followed by enzalutamide-admixed diet.

tag: tissue

value: prostate tumor

tag: type

value: castration-resistant prostate cancer

tag: age

value: 4-6 months old


title: DLP, CRPC, rep2

description: Gene expression data from dorsolateral prostate (DLP) of CRPC-bearing PB-Cre/Pten/Smad4 mice

source_name: dorsolateral prostate of mice with castration-resistant prostate cancer


title: BaumsDatabaseID_12710 [16S]

value: Normal Color


title: Primary CRPC, AP

description: Gene expression data from anterior prostate (AP) of CRPC-bearing PB-Cre/Pten/Smad4/mTmG mice

source_name: anterior prostate of mice with castration-resistant prostate cancer


title: Primary CRPC, DLP

description: Gene expression data from dorsolateral  prostate (DLP) of CRPC-bearing PB-Cre/Pten/Smad4/mTmG mice


title: Lung metastasis CRPC

description: Gene expression data from lung metastasis nodule of CRPC-bearing PB-Cre/Pten/Smad4/mTmG mice

source_name: lung metastasis of mice with castration-resistant prostate cancer

value: prostate tumor (lung metastasis)


title: DLP, CRPC, rep3


title: DLP, treatment-naïve, rep1

description: Gene expression data from dorsolateral prostate (DLP) of treatment-naïve  PB-Cre/Pten/Smad4 mice

source_name: dorsolateral prostate of treatment-naïve mice

value: treatment naïve


title: DLP, CRPC, rep1


title: BaumsDatabaseID_12681 [16S]

value: Bleached

value: Grecian Rocks


title: BaumsDatabaseID_12719 [16S]


title: BaumsDatabaseID_12709 [16S]


title: BaumsDatabaseID_12676 [16S]

value: Slightly Pale


title: Mutant strain Alpha1 on high glucose_biological rep2


title: BaumsDatabaseID_12669 [16S]

value: Not a Branch


title: BaumsDatabaseID_12667 [16S]


title: BaumsDatabaseID_12670 [16S]

value: Branch


title: SK-N-BE(2)C_ctrl2

data_processing:
STAR aligner v2.5.2b was used to align fastq files. Default alignment call parameters were used except for the following modifications:  --sjdbOverhang 200 --outSAMtype BAM Unsorted SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --twopassMode Basic --twopass1readsN -1 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20
Sambamba v0.6.5 was used for alignment file sorting, duplicate marking and BAM index generation using 12 threads.
Quality control analysis was performed using the sambamba flagstat command and the rnaseqc tool v1.1.8.
Gene specific gene counting over exon features was performed using Featurecounts v1.5.1.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated values file with raw gene counts for every gene and sample

growth_protocol: Cells were cultured in RPMI1640 medium supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO2 and subcultured every 3-4 days.

extract_protocol:
Cells were harvested using versene and total RNA was isolated using the Qiagen miRNeasy Mini Kit. Total RNA was depleted from ribosomal RNA using the Illumina Ribo-Zero rRNA Removal Kit
Libraries were prepared according to the New England Biolabs NEBNext Ultra Directional RNA Library Prep Kit protocol.

treatment_protocol: Cells were treated with 10 µM ATRA or solvent control (ethanol) for 144 hours.

value: Neuroblastoma cell line

tag: cell line

tag: treatment

value: ethanol


title: SK-N-BE(2)C_ctrl


title: BaumsDatabaseID_12664 [16S]

tag: peak bleaching status

tag: reef


title: SK-N-BE(2)C_ATRA2

value: 10 uM ATRA


title: BaumsDatabaseID_12659 [16S]

tag: location of within colony sampling

tag: coral genet id


title: CTRL_Tregs_alone_rep1

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

institute: INSERM

description: Control - Tregs alone - Paired biological replicate 1

hyb_protocol: Paired biological replicates (3 for each group) were hybridized to the Sentrix BeadChips Array mouse WG-6 v2 (Illumina) according to the manufacter's protocol.

scan_protocol: Gene expression analysis was performed using GeneChip Mouse Genome 430 2.0 arrays (Affymetrix), as recommended by the manufacturer.

data_processing:
Fluorescence values corresponding to raw expression data were extracted from CEL files using the R oligo package with the corresponding platform definitions (pd.mouse430.2). Internal controls and ambiguous probes were removed.
Raw expression values  (no log2) extracted with RMA with no normalization and no background or technical correction as parameters.

source_name: Tregs alone, activated by anti-CD3 and anti-CD28

label_protocol: Total RNA was amplified and converted to biotinylated cRNA according to the manufacturer’s protocol (Illumina TotalPrep RNA Amplification Kit; Ambion).

growth_protocol: Female C57BL/6J mice were purchased from Janvier Labs (Le Genest-Saint-Isle, France). All procedures were performed in accordance with Paris Descartes University Ethical Committee for Animal Experimentation and the French Ministry of Research and Higher Education, (authorization N°APAFIS#3846). The animals were maintained on a strict 12-h light-dark cycle and were housed at 22–23°C, in cages containing a maximum of 5 animals, with ad libitum access to food and water. 3 mice at 12 weeks of age were sacrificed to harvest the spleen to obtain steady state Tregs. Mobilized progenitor cells (MPPs) were prepared as follows : Wild type C57BL/6J (12-week-old) were injected subcutaneously for 4 consecutive days with human recombinant G-CSF (200 μg/kg/day) (Zarzio 48MU/0.5ml, Sandoz) and recombinant murine Flt3-L (20 μg/kg/day) (Immunotools, Friesoythe, Germany). Total splenocytes were magnetically sorted for c-kit+ cells with an automated magnetic cell sorter (Robosep, StemCell Technologies, Vancouver, BC, Canada), further stained with the mAbs directed against Sca-1, CD34 and CD11b and electronically sorted into c-kithighSca-1highCD34+CD11b-/low cells with the FACS Aria II cell sorter (BD Biosciences).

extract_protocol: Tregs were cultivated for 3 days with anti-CD3 and anti-CD28 alone or together with freshly purified MPPs. After 3 days, CD4+ cells (Treg) were sorted for extraction of RNA using RNeasy Micro kit (QIAGEN). ). Its quality was verified in an Agilent Bioanalyzer.

treatment_protocol: Spleen Tregs of each mouse were characterized and FACS sorted in three independant sample (FACS Aria II, BD Bioscience) after staining with CD4+ and CD25 high markers. Purity was checked by flow cytometry and was above 99%. Non-specific Treg activation was performed in a 96 round bottom plate coated with 10µg/mL anti-CD3 mAb (clone 145 2C11) and 10µg/mL anti-CD28 mAb (Biolegend) for 2 hours before the addition of Tregs (50000/well). Each sample of sorted Tregs was plated and incubated alone or with mobilized MPP for 4 days, in custom RPMI 1640 containing physiologic levels of L-arginine (150M) supplemented with 10% fetal calf serum, 50µM 2-mercaptoethanol, 10mM N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid buffer, 1mM sodium pyruvate, and 100 U/mL penicillin-streptomycin (Life Technologies). Mobilized MPPs were plated at 5 x 104/well (1:1 ).

tag: strain

tag: Sex

value: Female

value: 12 weeks

value: spleen

tag: cell type

value: Tregs

tag: in vitro activation

value: anti-CD3 10µg/mL+ anti-CD28 10µg/mL

tag: duration of in vitro activation

value: 3 days


title: DLP, treatment-naïve, rep2

value: prostate tumor

value: 4-6 months old


title: CTRL_Tregs_alone_rep2

description: Control - Tregs alone - Paired biological replicate 2


title: Tregs_with_MPPs_rep3

description: Tregs co-cultured hematopoietic multipotent progenitor - biological replicate 3

source_name: Tregs activated by anti-CD3 and anti-CD28, co-cultured with MPPs

tag: cocultured with

value: hematopoietic multipotent progenitors (MPPs)


title: CTRL_Tregs_alone_rep3

description: Control - Tregs alone - Paired biological replicate 3


title: Tregs_with_MPPs_rep1

description: Tregs co-cultured hematopoietic multipotent progenitor - biological replicate 1

tag: co-cultured with


title: Tregs_with_MPPs_rep2

description: Tregs co-cultured hematopoietic multipotent progenitor - biological replicate 2


title: SK-N-BE(2)C_ATRA


title: Sample7_Mono_U2OS_Rep2

tag: cell line/strain

tag: tissue source

value: Osteosarcoma

tag: genotype

value: wild-type

tag: sample type

value: Footprints from monosome fraction

tag: growth condition

value: DMEM with GlutaMAX, pyruvate, 10% FCS, pen/strep, 37°C, 5% CO2, humidified


title: BaumsDatabaseID_12650 [16S]

value: Normal Color

value: Grecian Rocks

value: Branch


title: BaumsDatabaseID_12652 [16S]

value: Slightly Pale

value: Not a Branch


title: BaumsDatabaseID_12653 [16S]

value: Bleached


title: BaumsDatabaseID_12649 [16S]


title: Sample5_Mono_U2OS_Rep1


title: P493-6_m6A_seq_Tet_72h

city: He Fei

first: Shi-Ting

last: Li

state: An Hui

address: No.443, Huangshan Road

department: Innovation Center for Cell Biology

institute: University of Science and Technology of China

data_processing:
Trimmed reads were aligned to human genome hg19 by Bowtie software.
Clean reads were aligned to the reference genome using TopHat (version 2.0.9)
Motifs were analyzed by HOMER.
The m6A-enriched regions in each MeRIP sample were extracted using MACS2 software (version 2.0.10).
Genome_build: hg19
Supplementary_files_format_and_content: fastq for RNA-seq data

source_name: Human B lymphocyte P493-6 cells

growth_protocol: P493-6 B cells were cultured in RPMI-1640 with 10% Tet system approved FBS (Takara Bio). Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
Total RNAs were extracted with TRNzol (Invitrogen, 15596-018), then purified with the Dynabeads® mRNA purification kit (Ambion, 61006) for two rounds. To immunoprecipitated m6A, purified mRNAs were digested by DNase I and then incubated at 94 °C for 60 seconds in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0), to cut them into pieces of ~ 100-nt. The reaction was stopped with 0.05 M EDTA (Ambion, AM8740), and was followed by standard ethanol precipitation and collection. Anti-m6A polyclonal antibody (12 ug antibody for 6 ug mRNAs; Synaptic Systems, 202003) was incubated with 50 ul Protein A beads (Sigma, P9424) in IPP buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.4) for 1 hr at room temperature. The mRNAs (6 ug) were incubated with the prepared antibody-beads mixture for 4 hrs at 4 °C. After washing, bound RNAs were extracted by TRNzol.
For the RNA-seq, fragmented RNAs were re-suspended in H2O and used for library generation with mRNA sequencing kit (Illumina).

treatment_protocol: P493-6 B cells that were treated with Tet for 72 hours or 0 hour with 1 ug/ml Tetracycline.

value: Human B lymphocyte P493-6 cells

tag: rip antibody

value: m6A polyclonal antibody (Synaptic Systems, 202003)


title: P493-6_m6A_seq_Tet_0h


title: BaumsDatabaseID_12648 [16S]

tag: peak bleaching status


title: Sample8_Dis_U2OS_Rep2

value: Footprints from disome fraction


title: mRNA MEF Control gRNA A rep 3

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

institute: Whitehead Institute / MIT

description:
Lentiviral transduction of gRNA
ACAGTG-s_5_1

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Reads from these libraries were aligned to the human genome (hg38) or mouse genome (mm10) using STAR v2.7.1
Count files were merged to generate tables of counts for each cell line.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: hg38 or mm10.
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

source_name: mRNA MEF Control gRNA

extract_protocol:
Cells were washed with PBS, and RNA was extracted using TRI-Reagent.
mRNA sequencing libraries were prepared using the Bioo NextFlex Rapid Directional RNA-Seq kit from poly(A)-selected total RNA.

tag: cell line/type

value: Immortalized mouse embryonic fibroblasts (MEF)

tag: genotype/variation

value: transduced with Cas9 and a gRNA

tag: grna

value: Non-targeting control gRNA


title: mRNA MEF Control gRNA A rep 2

description:
Lentiviral transduction of gRNA
TGACCA-s_5_1


title: mRNA MEF Control gRNA A rep 1

description:
Lentiviral transduction of gRNA
CGATGT-s_5_1


title: mRNA HeLa Control gRNA C

description:
Lentiviral transduction of gRNA
ACTTGA-s_4_1

source_name: mRNA HeLa Control gRNA

value: HeLa


title: mRNA iN Control gRNA C

description:
Lentiviral transduction of gRNA
ACTTGA-s_5_1

source_name: mRNA iN Control gRNA

value: Mouse neurons induced from embryonic stem cells


title: Sample6_Dis_U2OS_Rep1

value: Osteosarcoma

value: wild-type


title: mRNA iN Control gRNA B

description:
Lentiviral transduction of gRNA
TTAGGC-s_5_1


title: mRNA HeLa Control gRNA B

description:
Lentiviral transduction of gRNA
TTAGGC-s_4_1


title: mRNA iN Control gRNA A

description:
Lentiviral transduction of gRNA
ATCACG-s_5_1


title: sRNA iN Zswim8 knockout gRNA B

description:
AGTCAA-s_2_1
Lentiviral transduction of gRNA
iNeuron_sRNA_DESeq2_output_Zswim8.txt

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences.  These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs.  These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: TargetScanHuman release 7.2 or TargetScanMouse release 7.2
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

source_name: sRNA iN Zswim8 knockout gRNA

extract_protocol:
Cells were washed with PBS, and RNA was harvested using TRI-Reagent.
Small-RNA sequencing libraries were prepared as described (Kingston and Bartel, 2019).  A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA extracted from cells.

value: ZSWIM8 gRNA B


title: mRNA HeLa Control gRNA A

description:
Lentiviral transduction of gRNA
ATCACG-s_4_1


title: sRNA iN Control knockout gRNA B

description:
TAGCTT-s_2_1
Lentiviral transduction of gRNA
iNeuron_sRNA_DESeq2_output_Zswim8.txt

source_name: sRNA iN Control knockout gRNA


title: sRNA iN Zswim8 knockout gRNA A

description:
CTTGTA-s_2_1
Lentiviral transduction of gRNA
iNeuron_sRNA_DESeq2_output_Zswim8.txt

value: ZSWIM8 gRNA A


title: mRNA BJAB EV Control gRNA B

description:
Lentiviral transduction of gRNA
TAGCTT-s_4_1

source_name: mRNA BJAB EV Control gRNA

value: BJAB


title: sRNA iN Control knockout gRNA C

description:
GGCTAC-s_2_1
Lentiviral transduction of gRNA
iNeuron_sRNA_DESeq2_output_Zswim8.txt


title: P493-6_Input_Tet_0h


title: sRNA iN Control knockout gRNA A

description:
GATCAG-s_2_1
Lentiviral transduction of gRNA
iNeuron_sRNA_DESeq2_output_Zswim8.txt


title: mRNA MCF-7 Control gRNA B

description:
Lentiviral transduction of gRNA
AGTTCC-s_4_1

source_name: mRNA MCF-7 Control gRNA


title: sRNA MEF Zswim8 knockout gRNA B rep 3

description:
GCCAAT-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt

source_name: sRNA MEF Zswim8 knockout gRNA


title: sRNA MEF Zswim8 knockout gRNA B rep 2

description:
ACAGTG-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt


title: mRNA A549 Control gRNA B

description:
Lentiviral transduction of gRNA
GTAGAG-s_6_1

source_name: mRNA A549 Control gRNA


title: mRNA A549 Control gRNA C

description:
Lentiviral transduction of gRNA
GTCCGC-s_6_1


title: sRNA MEF Zswim8 knockout gRNA B rep 1

description:
TGACCA-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt


title: mRNA BJAB EV Control gRNA A

description:
Lentiviral transduction of gRNA
GATCAG-s_4_1


title: mRNA K562i ZSWIM8 knockdown gRNA B rep3

description:
Lentiviral transduction of gRNA
GGCTAC-s_2_1

source_name: mRNA K562i ZSWIM8 knockdown gRNA

value: expressing inducible KRAB-dCas9 (K562i) and transduced with a gRNA

value: ZSWIM8 gRNA B (CRISPRi)


title: mRNA MCF-7 Control gRNA A

description:
Lentiviral transduction of gRNA
AGTCAA-s_4_1


title: mRNA K562i ZSWIM8 knockdown gRNA B rep2

description:
Lentiviral transduction of gRNA
TAGCTT-s_2_1


title: sRNA MEF Control knockout gRNA A rep 2

description:
CGATGT-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt

source_name: sRNA MEF Control knockout gRNA


title: mRNA A549 Control gRNA A

description:
Lentiviral transduction of gRNA
CCGTCC-s_6_1


title: sRNA MEF Control knockout gRNA A rep 3

description:
TTAGGC-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt


title: mRNA K562i ZSWIM8 knockdown gRNA B rep1

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8b.txt
GATCAG-s_2_1


title: sRNA MEF Control knockout gRNA A rep 1

description:
ATCACG-s_2_1
Lentiviral transduction of gRNA
MEF_sRNA_DESeq2_output_Zswim8.txt


title: mRNA K562i ZSWIM8 knockdown gRNA A rep3

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8b.txt
ACTTGA-s_2_1

value: ZSWIM8 gRNA A (CRISPRi)


title: Sample 4B: MEFs C3S-H2O2b

data_processing:
Single end reads were trimmed against the sequencing library adaptor sequences using Scythe and low quality bases were trimmed from the reads using Sickle.
Reads were aligned to the murine reference genome mm10 using Tophat2 v2.0.10 with the non-default setting "record secondary alignments-report secondary alignments".
Raw reads counts were normalised and differential expression analysis was performed using MATLAB’s RNAseq data analysis pipeline (https://uk.mathworks.com/help/bioinfo/ug/identifying-differentially-expressed-genes-from-rna-seq-data.html).
We inferred differential expression between two conditions for each comparison (-/-WT cells basal v oxidation treatments; -/- C3S cells basal v oxidation treatments; basal treatment -/-WT v -/-C3S and oxidation treatment -/-WT v -/-C3S) with a negative binomial model using ‘nbintest’ function with a null hypothesis that the two data samples come from distributions with equal means. The hypothesis testing was done by considering that the variance as the sum of shot noise term (mean) and a locally regressed non-parametric smooth function of the mean where counts are modelled according to the distribution proposed in S. Anders, W. Huber (2010) Differential expression analysis for sequence count data. Genome Biol 11, R106.
The generated p-values were used corrected for multiple testing using Benjamini-Hochberg (BH) method. Two-fold change (i.e. 1 logFC) and adjusted p-value < 0.05 cut-offs were used to obtain differentially expressed genes for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Excel (xlsx) file contains normalised data for expressed genes as rows per condition (cell type and treatment) in columns

source_name: Murine Embryonic Fibroblasts

growth_protocol: MEFs were cultured in DMEM (Sigma D5671) on 10 cm dishes (Corning) in a humidified, 5% CO2 incubator. Cells were passaged 1:40 every 3-4 days up to passage 20 and then discarded.

extract_protocol:
Cells were removed from plates using trypsin and collected by centrifugation at 1000 rpm for 5 min at RT. Total RNA was isolated using Nucleospin RNA isolation kit in accordance with manufacturer's instructions.
cDNA was synthesised and 8 barcoded directional libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina sequencing. Samples were multiplexed into two lanes on a HiSeq 2500 instrument used in rapid run mode to generate 2.2e8 single-end 50 bp reads.

treatment_protocol: Untreated controls or 2h treatment with H2O2 (100 µM)

value: Murine Embryonic Fibroblasts

tag: passage

tag: treatment


title: Sample 4A: MEFs C3S-H2O2a

tag: cell type


title: mRNA K562i CYRANO knockdown rep2

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8a.txt
CAGATC-s_2_1

source_name: mRNA K562i CYRANO knockdown

value: CYRANO gRNA


title: mRNA K562i CYRANO knockdown rep3

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8a.txt
CTTGTA-s_2_1


title: Sample 2A: MEFs C3S-0a

value: control


title: Sample 3A: MEFs WT-H2O2a


title: Sample 1B: MEFs WT-0b


title: Sample 3B: MEFs WT-H2O2b


title: Sample 2B: MEFs C3S-0b


title: mRNA K562i ZSWIM8 knockdown gRNA A rep1

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8a.txt
ATCACG-s_2_1


title: mRNA K562i Control knockdown rep3

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_CYRANO.txt
ACAGTG-s_2_1

source_name: mRNA K562i Control knockdown


title: SAM24376340 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from primary mouse bone marrow derived macrophages (BMDMs)

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.

tag: samid

value: Bone Marrow

tag: gender

value: Pam3 stimulation


title: SAM24376336 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3


title: sRNA K562i ZSWIM8 knockout clone 2

description:
ACAGTG-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences.  These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs.  These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: TargetScanHuman release 7.2 or TargetScanFly release 7.2.
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

source_name: sRNA K562i ZSWIM8 knockout

value: Knockout


title: K562 CRISPRi v2 screen Bottom 5% mCherry:GFP

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
As according to Weissman lab screen-processing pipeline (https://github.com/mhorlbeck/ScreenProcessing).
Genome_build: Weissman Lab human CRISPRi v2 10 gRNA/gene dictionary.
Supplementary_files_format_and_content: Tab-delimited text files contain counts for each gRNA cassette recovered from libraries generated from sorted cell populations.

growth_protocol: 200 million reporter cells were transduced with 24 mL lentiviral library by spinfection with 10 μg/mL polybrene for 45 min at 2200 RPM at 37°C. After 16 h of culture, cells were diluted 10-fold with fresh RPMI/10% FBS, and after another 20 h, cells were collected, seeded at 200,000 cells/mL, and selected with 3 μg/mL puromycin for 72 h. Cells were then cultured in RPMI/10% FBS with 0.1 μg/mL puromycin for 10 days in a HYPERFlask M, passaging as necessary every one to two days to maintain a maximal cell count of ~500 million.

extract_protocol: As described in Adelmann et al., 2019.

tag: cell line

value: expressing a miR-7 fluorescent reporter and the human CRISPRi v2 library

tag: mcherry

value: gfp ratio:Bottom 5%


title: SAM24376334 Bone Marrow Male Pam3 stimulation WT_Pam3

value: Male

value: WT


title: mRNA K562i ZSWIM8 knockdown gRNA A rep2

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_ZSWIM8b.txt
TTAGGC-s_2_1


title: sRNA K562i ZSWIM8 knockout clone 1

description:
TGACCA-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt


title: mRNA K562i Control knockdown rep2

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_CYRANO.txt
TGACCA-s_2_1

value: Non-targeting control gRNA


title: mRNA K562i Control knockdown rep1

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_CYRANO.txt
CGATGT-s_2_1


title: SAM24376325 Bone Marrow Male Pam3 stimulation WT_Pam3


title: SAM24376320 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime

value: No Treatment - media only


title: Sample 1A: MEFs WT-0a


title: sRNA MCF-7 ZSWIM8 knockout gRNA B

description:
TAGCTT-s_3_1
Lentiviral transduction of gRNA
MCF7_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA MCF-7 ZSWIM8 knockout gRNA

value: transduced with Cas9 and a gRNA

value: ZSWIM8 gRNA B


title: sRNA K562i WT clone 2

description:
CGATGT-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt

source_name: sRNA K562i WT

value: Wild-type


title: SAM24376333 Bone Marrow Male Pam3 stimulation WT_Pam3


title: mRNA K562i CYRANO knockdown rep1

description:
Lentiviral transduction of gRNA
K562i_mRNA_DESEq2_output_CYRANO.txt
GCCAAT-s_2_1

value: expressing inducible KRAB-dCas9 (K562i) and transduced with a gRNA


title: sRNA MCF-7 Control knockout gRNA B

description:
ACTTGA-s_3_1
Lentiviral transduction of gRNA
MCF7_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA MCF-7 Control knockout gRNA


title: sRNA MCF-7 Control knockout gRNA A

description:
CAGATC-s_3_1
Lentiviral transduction of gRNA
MCF7_sRNA_DESeq2_output_ZSWIM8.txt


title: SAM24376308 Bone Marrow Male No Treatment - media only WT_NoPrime


title: K562 CRISPRi v2 screen Top 5% mCherry:GFP

value: gfp ratio:Top 5%


title: SAM24376322 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime


title: sRNA HeLa ZSWIM8 knockout gRNA C

description:
AGTCAA-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA HeLa ZSWIM8 knockout gRNA

value: HeLa

value: ZSWIM8 gRNA C


title: sRNA HeLa ZSWIM8 knockout gRNA B

description:
GGCTAC-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt


title: sRNA K562i ZSWIM8 knockout clone 3

description:
GCCAAT-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt


title: SAM24376324 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime


title: SAM24376338 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3


title: SAM24376312 Bone Marrow Male No Treatment - media only WT_NoPrime


title: SAM24376344 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3


title: SAM24376318 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime


title: sRNA HeLa ZSWIM8 knockout gRNA A

description:
TAGCTT-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt

value: ZSWIM8 gRNA A


title: sRNA HeLa Control knockout gRNA C

description:
GATCAG-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA HeLa Control knockout gRNA


title: SAM24376314 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime

value: Bone Marrow


title: SAM24376316 Bone Marrow NA No Treatment - media only Ninj1KO_NoPrime


title: SAM24376331 Bone Marrow Male Pam3 stimulation WT_Pam3

value: Pam3 stimulation


title: sRNA HeLa Control knockout gRNA B

description:
ACTTGA-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt


title: sRNA K562i WT clone 3

description:
TTAGGC-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt


title: SAM24376310 Bone Marrow Male No Treatment - media only WT_NoPrime


title: C2C12_GM_C/EBPβ_rep2

city: Ottawa

first: Nadine

last: Wiper-Bergeron

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
HISAT2 (v 2.0.4) was used to map the reads to the GRCm38 (mm10) genome, using the Gencode M12 transcript annotations to guide alignment to spliced transcripts, and mapping parameters appropriate for a stranded RNA-seq library
featureCounts (v 1.4.6) used to count the mapped reads associated with each GENCODE transcript
The differential analysis was run using the DESeq2 package, which uses the read count tables generated by featureCounts
All data processing were performed by the Ottawa Bioinformatics Core Facility (OBCF) by Christopher Porter
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCounts gene quantification: tab-delimited text file of raw read counts per gene.
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text table extracted from DESeqResults object

source_name: proliferating myoblasts

growth_protocol: Myoblast cell line (C2C12)  maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) at 37ºC with 5% CO2

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) sent to the McGill University Genome Quebec Innovation Centre for sequencing using Illumina HiSeq 2500 platform.
mRNASeq stranded library (NEB) by McGill University Genome Quebec Innovation Centre

treatment_protocol: C2C12s were retrovirally transduced with empty vector or to overexpress C/EBPβ. After 7 days of 1200 μg/ml G418 selection, pooled stable cells were allowed to proliferate for 48 hours.

tag: strain

tag: differentiation status

value: proliferating myoblasts

value: retrovirally transduced to overexpress C/EBPBeta


title: sRNA A549 Control knockout gRNA B

description:
CGATGT-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA A549 Control knockout gRNA


title: SAM24376342 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3

tag: genotype


title: sRNA A549 ZSWIM8 knockout gRNA A

description:
TGACCA-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt

source_name: sRNA A549 ZSWIM8 knockout gRNA


title: C2C12_GM_pLXSN_rep2

value: retrovirally transduced with empty vector


title: SAM24376327 Bone Marrow Male Pam3 stimulation WT_Pam3

value: Male


title: sRNA K562i WT clone 1

description:
ATCACG-s_6_1
K562i_sRNA_KO_DESeq2_output_ZSWIM8.txt


title: C2C12_GM_pLXSN_rep1


title: SAM24376309 Bone Marrow Male No Treatment - media only WT_NoPrime

value: WT


title: sRNA MCF-7 ZSWIM8 knockout gRNA A

description:
GATCAG-s_3_1
Lentiviral transduction of gRNA
MCF7_sRNA_DESeq2_output_ZSWIM8.txt


title: sRNA A549 Control knockout gRNA A

description:
ATCACG-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt

value: Non-targeting control gRNA


title: SAM24376329 Bone Marrow Male Pam3 stimulation WT_Pam3


title: sRNA MCF-7 ZSWIM8 knockout gRNA C

description:
GGCTAC-s_3_1
Lentiviral transduction of gRNA
MCF7_sRNA_DESeq2_output_ZSWIM8.txt


title: sRNA HeLa Control knockout gRNA A

description:
ATCACG-s_4_1
Lentiviral transduction of gRNA
HeLa_sRNA_DESeq2_output_ZSWIM8.txt


title: SAM24376311 Bone Marrow Male No Treatment - media only WT_NoPrime

value: No Treatment - media only


title: SAM24376313 Bone Marrow Male No Treatment - media only WT_NoPrime


title: SAM24376346 Bone Marrow NA Pam3 stimulation Ninj1KO_Pam3


title: sRNA A549 ZSWIM8 knockout gRNA C

description:
GCCAAT-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt

value: transduced with Cas9 and a gRNA


title: C2C12_GM_C/EBPβ_rep1


title: sRNA A549 ZSWIM8 knockout gRNA B

description:
ACAGTG-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt

value: ZSWIM8 gRNA B


title: sRNA A549 Control knockout gRNA C

description:
TTAGGC-s_1_1
Lentiviral transduction of gRNA
A549_sRNA_DESeq2_output_ZSWIM8.txt


title: m15672

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Low quality bases (Phred<20) were trimmed from the 3’ end using FastX-Trimmer
Reads were mapped to the mouse mm10 genome using STAR.
Uniquely mapped reads from STAR were used in downstream analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: msnelson_rna_gnames.mx This is a tab delimited matrix of expression counts.

source_name: renal cortex

growth_protocol: All animal experiments were performed in accordance with guidelines from the Alfred Medical Research and Education Precinct (AMREP) Animal Ethics Committee and the National Health and Medical Research Council of Australia. All rodents were housed in a temperature-controlled environment, with a 12-h light/dark cycle and access to food (see treatment protocol) and water ad libitum.

extract_protocol:
Total RNA was extracted from renal cortex using the DirectZol kit (Zymo, USA).
Robosomal RNA was depleted from 200 ng total RNA using the NEB rRNA depletion kit, following library prep with the NEB Ultra Stranded RNA library kit for Illumina.

treatment_protocol: Mice were randomly assigned into three diet groups. (1) a standard chow diet, (2) heat-treated diet, and (3) heat-treated with added resistant starch.

tag: diet

value: Heat treated diet with added resistant starch

tag: genotype (leprdb)

value: heterozygous

tag: genetic background


title: m15668

value: Heat treated diet


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day30_rep1

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

institute: Weill Cornell Medical College

data_processing:
Sequeced reads were filtered by quality filter and adapter sequences removed using Flexbar (v 2.2) [Dodt et al., 2012)
Reads were aligned to hg19 using STAR aligner (v. 2.4.2a & 2.5.0a) (Dobin et al., 2013)
Gene coverage was generated using FeatureCounts (v.1.4.2) (Liao et al. 2014) for "BOOST" and "BUMP" samples and HTSEQ (v 0.5.3) for all other samples using GENECODE annotation (v19).
Differentail gene expression was performed using DESeq2 (v. 1.12.4) (Love et al, 2014) and annotated using biomaRt package (v. 2.28) (Durinck et al. 2009)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts or htseq

growth_protocol: Human pluripotent stem cells (hPSC)s were grown onto Vitronectin coated dishes with Essential 8 media. hPSCs were passaged every 4-5 days by EDTA, and passage 35-55 hPSCs were used for the experiments. Direct differentiation of midbrain dopamine neurons from hPSCs were performed on Geltrax coated dish in Neurobasal (Life Technologies)/N2(Stem Cell Technologies)/B27(Life Technologies) media containing L-glutamine, SHH C25II (R&D systems), LDN  (Stemgent), SB431542  (R&D systems), 0.7µM CHIR99021 (R&D systems), and 10uM Rock inhibitor (Y-27632, R&D systems), which represents day 0 of differentiation and cultured until day 3. On day 4, cells were exposure to different concentration of CHIR 0.7, 3, 5, and 7.5 µM until day 10. On day 7, LDN, SB, and SHH were withdrawn. On day 10, media was changed to Neurobasal/B27/L-Glu supplemented with BDNF (R&D), ascorbic acid (Sigma), GDNF (Peprotech), TGFβ3 (R&D), dibutyryl cAMP (Sigma), and CHIR 3 μM. On day 11, cells were dissociated using Accutase and replated under high cell density (800K cells/cm2) on polyornithine / laminin / fibronectin coated dishes in mDA differentiation media [(NB/B27/L-Glu, BDNF, ascorbic acid, GDNF, dbcAMP, TGFβ3, and DAPT (R&D)] until day 16. On day 16, cells were dissociated and plated as same procedure of day 11 and cultured until day 30 using mDA differentiation media.

extract_protocol:
Total RNAs from samples were isolated with TRIzol (Qiagen) using the Direct-zol™ RNA MiniPrep kit (Zymo Research, #R2052).
RNA-seq library preparation was performed at the MSKCC Integrated Genomics Operation Core Facility.

value: hPSC-derived neuron

tag: time point

value: Day 30 of differentiation from hPSC

value: CHIR-boosting (7.5uM) at day30


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day16_rep2

value: hPSC-derived neural progenitors

value: Day 16 of differentiation from hPSC

value: CHIR-boosting (7.5uM) at day16


title: m15664

value: Standard diet


title: m15669


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day30_rep2


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day16_rep1


title: m15670


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day11_rep1

value: Day 11 of differentiation from hPSC

value: CHIR-boosting (7.5uM) at day11


title: m15657

value: homozygous


title: Dopamine differentiated cells with CHIR-boosting (7.5uM) at day11_rep2


title: m15671


title: m15667


title: Dopamine differentiated cells with CHIR-boosting (5uM) at day11_rep1

value: CHIR-boosting (5uM) at day11


title: m15662


title: Dopamine differentiated cells with CHIR-boosting (3uM) at day11_rep2

value: CHIR-boosting (3uM) at day11


title: Dopamine differentiated cells with CHIR-boosting (5uM) at day11_rep2


title: Dopamine differentiated cells with CHIR-boosting (3uM) at day11_rep1


title: m15656


title: Dopamine differentiated cells with Chir 0.7uM at day11_rep2

value: Chir 0.7uM at day11


title: m15654


title: Human pluripotent stem cell_rep2

source_name: Human pluripotent stem cell

value: hPSC

value: Day 0


title: Dopamine differentiated cells with Chir 0.7uM at day11_rep1


title: m15651


title: m15653

value: Heat treated diet with added resistant starch


title: m15644

value: Heat treated diet

value: heterozygous


title: mRNA BJAB EV Control gRNA C

description:
Lentiviral transduction of gRNA
GGCTAC-s_4_1

source_name: mRNA BJAB EV Control gRNA

tag: cell line/type

value: BJAB

value: transduced with Cas9 and a gRNA

value: Non-targeting control gRNA


title: m15632


title: m15634


title: m15636


title: Input for Boost-Chir ChIP

data_processing:
Adapter sequences were removed using cutadapt (v1.6)
Sequences were mapped to hg19 using bwa mem (v0.7.12)
After mappting sequences were sorted and read groups added using PICARD tools
Duplicate reads were marked using PICARD MarkDuplicates command
Peaks calling was performed using Mac2
Genome_build: hg19
Supplementary_files_format_and_content: bed file format 6 +4. First 6 fields are standard bed format and additional 4 narrowPeak fields: signalValue, pValue, qValue, peak position

source_name: Neural progenitor cells

extract_protocol:
Chromatin immune-precipitation (ChIP) for H3K27me3 and H3K4me3 from each sample were performed using SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell signaling Tech, #9005) according to the instructions of the manufacturer.
ChIP-sequencing library was generated at the MSKCC Integrated Genomics Operation Core Facility.

value: Neural progenitor cells

tag: condition

value: Boost-Chir (7.5uM)

tag: chip antibody

value: Input


title: m15623

value: Standard diet


title: Neural progenitor cells at day 11 in Low-Chir - H3K27me3

value: Day 11 of differentiation from hPSC

value: Low-Chir

value: H3K27me3 (Millipore, 07-449)


title: Input for Low-Chir ChIP


title: m15604

source_name: whole kidney

extract_protocol:
Total RNA was extracted from whole kidneys using the DirectZol kit (Zymo, USA).
Robosomal RNA was depleted from 200 ng total RNA using the NEB rRNA depletion kit, following library prep with the NEB Ultra Stranded RNA library kit for Illumina.


title: Neural progenitor cells at day 11 in Boost-Chir (7.5 uM) - H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: Neural progenitor cells at day11 in Low-Chir - H3K4me3


title: m15603


title: m15601


title: m15599


title: m15597


title: Human pluripotent stem cell_rep1


title: m15595

value: homozygous


title: K562_4xAP3_r2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: K562 Dam-4xAP3 replicate 2

data_processing:
Library strategy: DamID-seq
The full protocol is described in Leemans, 2019.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg38 plus ribosomal model) using bwa mem 0.7.17.
Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
Genome_build: GRCh38 v15 combined with a ribosomal model (GenBank: U13369.1)
Supplementary_files_format_and_content: BigWig files of normalized 4xAP3 nucleolus DamID scores for 50kb genomic bins

source_name: K562 cells

growth_protocol: Human K562 cells were grown according to ATCC growth protocol, where cells were culuted in IMDM with 10% fetal bovine serum and split every 2 or 3 days.

extract_protocol:
Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019. 500 ng of genomic DNA was digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. Following DpnII digestion of intact GATC sequences, DNA fragments were amplified with 22-26 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 9-12 PCR cycles with illumina index adapters.

treatment_protocol: 100.000 cells were plated in a 12-well plate in 1mL full medium, supplemented with 8 μg/mL polybrene to enhance viral transduction efficiency. Cells were transduced with either Dam-only lentivirus or Dam-4xAP3 lentivirus. The following day, medium was refreshed and cells placed in a 6-well plate. Three days after transduction, cells were harvested and genomic DNA was isolated.


title: Neural progenitor cells at day 11 in Boost-Chir (7.5 uM) - H3K27me3


title: K562_4xAP3_r1

description: K562 Dam-4xAP3 replicate 1


title: K562_Dam_r1

description: K562 Dam-only control replicate 1


title: K562_Dam_r2

description: K562 Dam-only control replicate 2


title: K562_Dam_r3

description: K562 Dam-only control replicate 3


title: m15631


title: K562_4xAP3_r4

description: K562 Dam-4xAP3 replicate 4


title: m15587


title: K562_Dam_r4

description: K562 Dam-only control replicate 4


title: sRNA S2 zswim8/Dora knockout clone 3 TUBE input

description:
GGCTAC-s_4_1
S2_sRNA_TUBE_counts.txt

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences.  These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs.  These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: TargetScanFly release 7.2.
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

organism: Drosophila melanogaster

source_name: sRNA S2 zswim8/Dora knockout TUBE input

extract_protocol:
Cells were washed with PBS and lysed in TBS-N buffer (10 mM Tris pH 7.5, 150 mM NaCl, 0.5% NP-40, supplemented with protease inhibitor). For input samples,RNA was extracted from lysates using TRI-Reagent.  For eluates, lysates were incubated with anti-FLAG magnetic beads.  Beads were washed with TBS-N, and RNA was eluted and isolated using TRI-Reagent.
Small-RNA sequencing libraries were prepared as described (Kingston and Bartel, 2019).  A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from RNA extracted as described.

tag: cell line background

value: Knockout

tag: tube


title: sRNA S2 zswim8/Dora knockout clone 2 TUBE eluate

description:
AGCGCT-s_2_1
S2_sRNA_TUBE_counts.txt

source_name: sRNA S2 zswim8/Dora knockout TUBE eluate

value: Eluate


title: Per2_TSS-Liver_WT-Batch3-ZT8-WT-S621 [4C-Seq]

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

institute: École Polytechnique Fédérale de Lausanne

description:
4CSeq of Liver_WT of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz;processed_4Cseq_log10_counts_around_the_clock_FourierTransformed.txt.gz;processed_4Cseq_log10_counts_around_the_clock_AvgOverTime.txt.gz

data_processing:
Library strategy: 4C-Seq
mm9
Mapping was done using HTS station (http://htsstation.epfl.ch). See Supplemental methods of paper for detailed processing methods. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Log10 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney

source_name: Crosslinked genomic DNA

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes.         In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature.         Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF)         and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

tag: tissue

tag: feeding

value: Ad libitum

tag: age

value: post-natal 8-12 weeks

value: WT

tag: bait

tag: batch

tag: zeitgeber time


title: m15592

value: Heat treated diet


title: sRNA S2 zswim8/Dora knockout clone 1 TUBE input

description:
GCCAAT-s_2_1
S2_sRNA_TUBE_counts.txt


title: sRNA S2 zswim8/Dora knockout clone 1 TUBE eluate

description:
AGTCAA-s_2_1
S2_sRNA_TUBE_counts.txt


title: m15586


title: m15585


title: sRNA S2 zswim8/Dora knockout clone 2 TUBE input

description:
CAGATC-s_2_1
S2_sRNA_TUBE_counts.txt


title: sRNA S2 WT clone 3 TUBE eluate

description:
ACTTGA-s_4_1
S2_sRNA_TUBE_counts.txt

source_name: sRNA S2 WT TUBE eluate

value: Wild-type


title: Per2_TSS-Liver_WT-Batch3-ZT4-WT-S614 [4C-Seq]

tag: strain


title: K562_4xAP3_r3

description: K562 Dam-4xAP3 replicate 3

tag: cell line


title: Per2_TSS-Liver_WT-Batch3-ZT20-WT-S624 [4C-Seq]

tag: genotype


title: Per2_TSS-Liver_WT-Batch3-ZT4-WT-S620 [4C-Seq]


title: m15591

tag: diet

tag: genotype (leprdb)


title: Per2_TSS-Liver_WT-Batch3-ZT8-WT-S615 [4C-Seq]


title: sRNA S2 WT clone 1 TUBE eluate

description:
GGCTAC-s_2_1
S2_sRNA_TUBE_counts.txt


title: sRNA S2 WT clone 2 TUBE eluate

description:
CTTGTA-s_2_1
S2_sRNA_TUBE_counts.txt


title: sRNA S2 zswim8/Dora knockout clone 3 TUBE eluate

description:
TAGCTT-s_4_1
S2_sRNA_TUBE_counts.txt


title: Per2_TSS-Liver_WT-Batch3-ZT20-WT-S618 [4C-Seq]


title: sRNA S2 WT clone 3 TUBE input

description:
CAGATC-s_4_1
S2_sRNA_TUBE_counts.txt

source_name: sRNA S2 WT TUBE input


title: sRNA S2 WT clone 1 TUBE input

description:
TGACCA-s_2_1
S2_sRNA_TUBE_counts.txt


title: Per2_TSS-Liver_WT-Batch3-ZT12-WT-S622 [4C-Seq]


title: Per2_TSS-Liver_WT-Batch3-ZT16-WT-S617 [4C-Seq]


title: sRNA S2 WT clone 2 TUBE input

description:
ACAGTG-s_2_1
S2_sRNA_TUBE_counts.txt


title: Per2_TSS-Liver_WT-Batch3-ZT12-WT-S616 [4C-Seq]


title: sRNA S2 zswim8/Dora knockout clone 2

description:
CGATGT-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt

source_name: sRNA S2 zswim8/Dora knockout

tag: cell type

value: Drosophila S2

tag: genotype/variation


title: Per2_TSS-Liver_WT-Batch3-ZT16-WT-S623 [4C-Seq]


title: Per2_TSS-Liver_WT-Batch3-ZT0-WT-S613 [4C-Seq]


title: sRNA S2 zswim8/Dora knockout clone 3

description:
TTAGGC-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt


title: sRNA S2 WT clone 3

description:
GCCAAT-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt

source_name: sRNA S2 WT


title: Per2_TSS-Liver_WT-Batch3-ZT0-WT-S619 [4C-Seq]


title: sRNA S2 zswim8/Dora knockout clone 1

description:
ATCACG-s_8_1
S2_sRNA_DESeq2_output_zswim8.txt


title: sRNA S2 WT clone 1

description:
TGACCA-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt


title: sRNA C. elegans adult N2 rep 3

description:
AGCGCT-s_4_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences.  These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs.  These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: C. elegans miRNA index (Jan et. al, 2011).
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

organism: Caenorhabditis elegans

source_name: sRNA C. elegans adult N2

extract_protocol:
Worms were homogenized using a TissueLyser II with glass beads.  RNA was harvested using TRI-Reagent.
Small-RNA sequencing libraries were prepared as described (Kingston and Bartel, 2019).  A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA extracted from worms.

value: Gravid adult animals


title: Per1_TSS-Liver_WT-Batch3-ZT8-WT-S609 [4C-Seq]


title: sRNA C. elegans adult ebax-1 rep 3

description:
CACGGT-s_4_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt

source_name: sRNA C. elegans adult ebax-1


title: Per1_TSS-Liver_WT-Batch3-ZT8-WT-S603 [4C-Seq]


title: sRNA C. elegans adult ebax-1 rep 2

description:
GCGTCA-s_4_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt


title: sRNA C. elegans adult ebax-1 rep 1

description:
ACTTGA-s_2_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt


title: sRNA C. elegans adult N2 rep 1

description:
CAGATC-s_2_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt


title: sRNA C. elegans adult N2 rep 2

description:
AGTCAA-s_4_1
C_elegans_sRNA_DESeq2_output_ebax-1.txt


title: Per1_TSS-Liver_WT-Batch3-ZT20-WT-S612 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT4-WT-S608 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT16-WT-S611 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT4-WT-S602 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT16-WT-S605 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT12-WT-S610 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT12-WT-S604 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT0-WT-S607 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT0-WT-S601 [4C-Seq]


title: E. coli K-12 MG1655, 1-day exposure of fluoxetine induced tetracycline resistant mutant biological replicate-2

city: Brisbane

first: Min

last: Jin

address: st lucia,QLD

institute: The University of Queensland

description:
Flu1d-Tetr-2
antibiotics resistant mutants

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli K-12 MG1655, 1-day exposure of fluoxetine induced tetracycline resistant mutant

growth_protocol: liquid LB culture at 37 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: resistant strains as well as the original strain E. coli K-12 MG1655 were cultured in  triplicate in 10 mL liquid LB with 100 mg/L fluoxetine at 37 °C for 8 h, shaken at 150 rpm.

tag: resistance

value: tetracycline resistant mutant

tag: agent

value: fluoxetine


title: E. coli K-12 MG1655, 1-day exposure of fluoxetine induced tetracycline resistant mutant biological replicate-1

description:
Flu1d-Tetr-1
antibiotics resistant mutants


title: sRNA S2 WT clone 2

description:
ACAGTG-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced tetracycline resistant mutant biological replicate-3

description:
Flu30d-Tetr-3
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 30-day exposure of fluoxetine induced tetracycline resistant mutant


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S223 [4C-Seq]


title: Per1_TSS-Liver_WT-Batch3-ZT20-WT-S606 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S213 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT8-WT-S235 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT4-WT-S233 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT4-WT-S221 [4C-Seq]


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S217 [4C-Seq]


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced tetracycline resistant mutant biological replicate-1

description:
Flu30d-Tetr-1
antibiotics resistant mutants


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced chloramphenicol resistant mutant biological replicate-2

description:
Flu30d-Chlr-2
antibiotics resistant mutants

source_name: Escherichia coli K-12 MG1655, 30-day exposure of fluoxetine induced chloramphenicol resistant mutant

value: chloramphenicol resistant mutant


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S241 [4C-Seq]

description:
4CSeq of Liver_WT of mice
processed_4Cseq_log10_counts_around_the_clock.txt.gz;processed_4Cseq_log10_counts_around_the_clock_FourierTransformed.txt.gz;processed_4Cseq_log10_counts_around_the_clock_AvgOverTime.txt.gz


title: Hoxd4-Liver_WT-Batch3-ZT16-WT-S239 [4C-Seq]


title: E. coli, wild-type K-12 MG1655 Biological replicate-3

description:
control-3
control

source_name: Escherichia coli, wild-type K-12 MG1655

value: wild-type

value: control


title: E. coli K-12 MG1655, 30-day exposure of fluoxetine induced chloramphenicol resistant mutant biological replicate-1

description:
Flu30d-Chlr-1
antibiotics resistant mutants


title: Hoxd4-Liver_WT-Batch3-ZT20-WT-S229 [4C-Seq]