title: XX_D2_H3K4me1_sgFoxd3_R3

data_processing:
Sequencing adapters were removed using Trim Galore (v0.6.4) with option [--paired –nextera] (https://github.com/FelixKrueger/TrimGalore).
The trimmed reads were then aligned using bowtie2 (v2.3.5.1) with the options [--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000](Langmead and Salzberg 2012) and processed using samtools (v1.10) with options [view -f 2 -q 20] and [sort](Li et al. 2009).
Blacklisted regions for mm10 were removed using bedtools (v2.29.2) with options [intersect -v](Quinlan and Hall 2010; Amemiya et al. 2019).
Duplicates were marked and removed using Picard (v2.18.25) with options [MarkDuplicates VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = TRUE] (http://broadinstitute. github.io/picard).
BigWig tracks were created using deepTools (v2.0) with options [bamCoverage -e -bs 10 --normalizeUsing CPM -ignore chrX chrY] (Ramírez et al. 2016).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: TX1072 SP427 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with 2i and LIF (2iSL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). 500 mM dTAG-13 was added to the medium to degrade the CRISPRi system. The cells were cultured at a density of 4*104 cells/cm2 and passaged every second day.

extract_protocol:
Following dissociation with Accutase, 1*105 cells per antibody were collectedand quickly washed in Wash buffer (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 10 mM Sodium butyrate, Protease Inhibitor, and 1 mM PMSF).
10 μl Concanavalin A beads (Bangs Laboratories) were equilibrated with 100 μl binding buffer (20 mM HEPES-KOH, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and then concentrated in 10 μl binding buffer. The cells were bound to the Concanavalin A beads by incubating for 10 min at RT on a rotator. Following, the beads were separated using a magnet and resuspended in 100 μl chilled Antibody buffer (Wash buffer with 0.05% Digitonin and 2 mM EDTA). Subsequently, 1 μl of primary antibody (Supplemental Table S6) was added and incubated on a rotator for 3 hours at 4°C. After magnetic separation, the beads were resuspended in 100 μl chilled Dig-wash buffer (Wash buffer with 0.05% Digitonin) containing 1 μl secondary antibody and incubated for 1 hour at 4°C on a rotator. The beads were washed three times with chilled Dig-wash buffer and resuspended in chilled Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with 1:250 diluted 3xFLAG-pA-Tn5 preloaded with mosaic-end adapters. After incubation for 1 hour at 4°C on a rotator, the beads were washed four times with chilled Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer, 10 mM MgCl2). Tagmentation was performed for 1 hour at 37°C and stopped by adding 2.25 μl 0.5 M EDTA, 2.75 μl 10% SDS and 0.5 μl 20 mg/mL Proteinase K and vortexing for 5 s. DNA fragments were solubilized overnight at 55 °C followed by 30 min at 70 °C to inactivate residual Proteinase K. DNA fragments were purified with the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 25 μl elution buffer.10 μl Concanavalin A beads (Bangs Laboratories) were equilibrated with 100 μl binding buffer (20 mM HEPES-KOH, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and then concentrated in 10 μl binding buffer. The cells were bound to the Concanavalin A beads by incubating for 10 min at RT on a rotator. Following, the beads were separated using a magnet and resuspended in 100 μl chilled Antibody buffer (Wash buffer with 0.05% Digitonin and 2 mM EDTA). Subsequently, 1 μl of primary antibody (Supplemental Table S6) was added and incubated on a rotator for 3 hours at 4°C. After magnetic separation, the beads were resuspended in 100 μl chilled Dig-wash buffer (Wash buffer with 0.05% Digitonin) containing 1 μl secondary antibody and incubated for 1 hour at 4°C on a rotator. The beads were washed three times with chilled Dig-wash buffer and resuspended in chilled Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with 1:250 diluted 3xFLAG-pA-Tn5 preloaded with mosaic-end adapters. After incubation for 1 hour at 4°C on a rotator, the beads were washed four times with chilled Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer, 10 mM MgCl2). Tagmentation was performed for 1 hour at 37°C and stopped by adding 2.25 μl 0.5 M EDTA, 2.75 μl 10% SDS and 0.5 μl 20 mg/mL Proteinase K and vortexing for 5 s. DNA fragments were solubilized overnight at 55 °C followed by 30 min at 70 °C to inactivate residual Proteinase K. DNA fragments were purified with the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 25 μl elution buffer.

treatment_protocol: Differentiation was induced at a density of 2.1*104 cells/cm2 on 10 µg/ml fibronectin (Merck or Corning) via 2i/LIF withdrawal (-2iL conditions) (DMEM, 10% FBS (GIBCO), 0.1 mM b-mercaptoethanol). Knockdown was induced 2 days prior to differentiation via the removal of dTAG fom the medium.


title: KP ctrl #3

status: Public on May 21 2025

type: SRA

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

data_processing:
Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Assembly: Reads in fastq format were aligned to the mouse reference genome version GRCh38 with Gencode mV23 annotations using STAR aligner version 2.6.1a in 2-pass mode. Reads per gene were counted by STAR.
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN)
Sequencing libraries were be prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs).

tag: tissue

value: lung

tag: cell type

value: KP lung adenocarcinoma


title: XX_D2_H3K4me1_sgFoxd3_R2

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

library_source: genomic

molecule: genomic DNA

source_name: Embryonic stem cells

value: Embryonic stem cells

tag: cell line

tag: genotype

value: CAST / C57BL/6

tag: treatment


title: 31 div

city: Irvine

first: Edwin

middle: S

last: Monuki

state: CA

address: 845 Health Science Road

department: Experimental Pathology

country: USA

institute: University of California Irvine

description:
Library name: Sample 1
10X Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed and mapped to the reference genome GRCh38 through Cell Ranger. Briefly, genes expressed in <10 cells were excluded, and cells with 1000-6000 genes/cell and <12.5% mitochondrial gene expression were included. The four time points were tested for their batch effect through two batch correction methods; RPCA and SCTransform with the Seurat platform. Datasets post quality control were combined with the merge function in Seurat while the time point of origin was retained in the metadata. RPCA batch correction was done with default settings of features to consider (2000) and plotted as a UMAP with color coding by time point of origin showing similar display of cells to the non-corrected. SCTransform batch correction was done with default settings of features to consider (all) and plotted as a UMAP with color coding by time point of origin showing similar display of cells to the non-corrected. Due to the similar grouping of cells in batch and non-batch corrected data, non-batch corrected data was used for further processing with the SoptSC platform.
Assembly: Human
Assembly: GRCh38
Supplementary files format and content: Tab seperated value files and matirx files

organism: Homo sapiens

source_name: H1 derived cells

extract_protocol:
For each timepoint, two wells of a 4-well chamber slide were dissociated and pooled. The selected protocol involved dissociating with warm TrypLE (Thermo Fisher #12605010) for 25 minutes at 37C, resuspending in FACS buffer at RT (0.02% BSA in DPBS), then propidium iodine was added for 10 minutes (Thermo Fisher #P1304MP) before placing on ice. FACS for single live cells was performed by the UCI Flow Cytometry Core using a FACSAria II (BD Biosciences).
Single cell capture with the 10x Chromium platform, cDNA library preparation, and cDNA QC analysis (Qubit dsDNA HS Assay kit (Life Technologies Q32851) and high sensitivity DNA chips (Agilent. 5067-4626)) were performed by the UCI Genomics Research and Technology Hub (GRT Hub). Library generation was done with a V2 chemistry kit and an average capture of ~10,000 barcoded cells, per user guide (CG00052 Rev B). The cDNA libraries were sequenced using the HiSeq 4000 platform (Illumina) to achieve an average depth of 50,000 reads per cell and 2,500 genes per cell.

value: H1 derived cells

value: APOE 3/3


title: XX_D2_TFi_Unsorted_R2

description:
TFi.count.txt
TFi.count_normalized.txt

data_processing:
*library strategy: Pooled CRISPR screen
Count tables were generated using MAGeCK (v0.5.9.3) with [mageck count –norm-method control](Li et al. 2014).
Screen targets were enriched using MAGeCK (v0.5.9.3) with the normalized count tables and [mageck mle --permutation-round 10](Li et al. 2014).
Assembly: mm10
Supplementary files format and content: Count tables (.txt)
Supplementary files format and content: Normalized count tables (.txt)
Supplementary files format and content: Enrichment using mageck mle (.txt)

growth_protocol: TX1072 SP107/SP427 mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with LIF (SL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). The cells were cultured at a density of 4*104 cells/cm2 and passaged every second day.

extract_protocol:
Following cell sorting at the FACS, genomic DNA was isolated using phenol/chloroform extraction. First, cell pellets were incubated for 14 hours at 65 °C in de-crosslinking buffer (1% SDS (Invitrogen), 1.25 µl DTT (Roth) and 10 µl 5M NaCl (Sigma) in Tris-EDTA buffer (Sigma)). Next, 20 µl RNAse A (10 mg/ml, New England Biolabs) were added and the solution incubated for 1 hour at 37 °C. Following, 5 µl Proteinase K (20 mg/ml, Ambion) was added and the solution incubated for 1 hour at 50 °C. Subsequently, 275 µl of Phenol/Chloroform (Roth) were added and the mixture vortexed for 1 min. The samples were then centrifuged for 10 min at 13,000 rpm. The aqueous phase, containing the genomic DNA, was transferred to a new tube and the sample was cleaned using ethanol precipitation. The pellets were dried and resuspended in 50 µl water.
The guide cassette was amplified for 20 cycles using the KAPA HiFi PCR ReadyMix with primers OG115/OG116.  To keep 300x coverage, at least 20 µg (TFi screen) or 1.6 µg (TFiMini screen) of genomic DNA were amplified per sample. Following clean-up with the DNA Clean & Concentrator Kit, sequencing barcodes were added in a second PCR using the KAPA HiFi PCR ReadyMix for 11-12 cycles

treatment_protocol: A coverage of >300x was retained during all steps. Following transduction of the TFi Lib into the TX SP107 cell line under SL conditions, the cells were selected for three days using puromycin. Subsequently, the cells were transferred into 2iSL medium. At the same time, 1*10^7 cells were frozen (Selected population).  After three days, the split dCas9-KRAB system was induced via the addition of ABA. The cells were then differentiated for 48 hours via 2i/LIF-withdrawal. During the FlowFISH staining for Xist RNA, 1*10^7 cells were frozen (Unsorted population). Using flow cytometry, cells were according to Xist expression into Xist-high (top 15%), Xist-low (bottom 15% of the Xist-positive cells) and Xist-neg (bottom 15%) populations. At least 1.5*10^7 cells were recovered per population.   For the TFiMini screen, the TX SP427 cell line was transduced under SL conditions in the presence of dTAG-13. Following three days of puromycin selection, the cells were transferred to 2iSL conditions. At the same time, 1*10^7 cells were frozen (Selected population). After 8 days, the CasTuner system was induced via the removal of dTAG-13 from the medium. Two days later, the cells were differentiated via 2i/LIF-withdrawal. At the same time, 1*10^7  cells were frozen (2iSL population). After two days of 2i/LIF-withdrawal, the cells were stained via FlowFISH and sorted according to Xist expression into Xist-High (top 15%) and Xist-Neg (bottom 15%) populations using flow cytometry. At least 5*10^5 cells were recovered per population.

value: 2iL-withdrawal/Pooled CRISPRi screen


title: KP ctrl #1


title: 8dpf larvae, grwd1-del-2

city: Toronto

first: Aleixo

last: Muise

state: ON

address: 686 Bay Street, 19-9400 I-M PGCRL

department: Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
The raw sequence FASTQ files were assessed for quality control using FastQC, trimmed to remove adapters using Trimmomatic-v0.39, and aligned to the zebrafish reference genome GRCz11 using HISAT2. Reads in genes were counted using featureCounts, and differential expression analysis was carried out using the DESeq2 package in R
Assembly: zebrafish (GRCz11)
Supplementary files format and content: tab-delimited text files include the count values for each Sample

organism: Danio rerio

source_name: whole fish

growth_protocol: For wt and grwd1 crispants ,embryos were obtained via natural mating and cultured in embryo E3 buffer, raised in 10cm petridish with E3 embryonic buffer and incubated at 28.5 .

extract_protocol:
Wt and grwd1 crispants at 8dpf  were euthanized by immersion in ice water for 10 minutes and then were collected for RNA extraction. N=15 larvae were pooled for each group.
RNA were extracted using RNAeasy mini kit(Qiagen). 600ng of total RNA were used for the construction of sequencing libraries.
RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo-Zero Plus protocol to generate polyA-enriched, rRNA-depleted libraries.
Illumina NovaSeq - S4 flowcell

treatment_protocol: CRISPR/Cas9 system was utilized to knockout grwd1. The targeting sequences are: grwd1 gRNA1: 5’- GATACATGCGGTAAGCGGAG-3’ and grwd1 gRNA2: 5’- ACTCCACCGACAGATCCCAT-3’ were designed by CHOPCHOP. 100pg of each gRNA and 150pg of Cas9 mRNA were injected into embryos at one cell stage. The F0 larvae were transferred to the nursery (n=96) at 5dpf and all of them died within 5dpf-15dpf.  Therefore, we used first-generation (F0) mosaic grwd1 mutant zebrafish by CRISPR.

value: whole fish

value: grwd1 crispants

tag: time


title: XX_D2_H3K4me1_sgFoxd3_R1


title: 8dpf larvae, wt-2

value: wildtype


title: lung tissue-CONTROL-CTRL1_r62.81a

type: genomic

city: Hamilton

first: John

middle: Edward

last: McDonough

address: 50 Charlton Ave E

institute: McMaster University

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
IDAT files were processed with R package minfi, preserving control probe data. Quality control steps were performed to exclude failed samples with low-quality reads as well as any probes that failed in one or more samples (i.e. detection p-value > 0.01, representing the probability that the signal differs from the background signal due to chance as estimated from negative controls). MethylToSNP was used to eliminate CpG probes at single nucleotide polymorphisms (SNPs), while reducing data loss by considering SNPs specific only to the studied participants, based on the similarity of site-specific methylation patterns to expected SNPs. Probes in the array that showed cross-reactivity were excluded using a list(3) and in total, 47,138 probes were removed, leaving 819,618 probes for further analysis. Data were normalized using the normal-exponential using out-of-band probes (Noob) normalization method, to account for technical variation in the background fluorescence signal, and through the Beta-mixture quantile normalization (BMIQ) method in package watermelon to adjust the beta-values of type-II design probes to the statistical characteristics of type-I probes. However, 𝞫-values have significant heteroscedasticity in the low and high methylation ranges and were therefore logit-transformed to M-values for statistical analysis for a more constant standard deviation across the methylation range.
processed value definition: Average beta

label: Cy5 and Cy3

source_name: lung tissue sample

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extract from lung tissue samples using Qiagen DNeasy DNA extraction kits.

tag: disease

value: CONTROL

tag: Stage

tag: subject

tag: Sex

value: M

tag: age

value: lung tissue sample


title: XX_D2_H3K4me1_sgOtx2_R3


title: XX_D2_TFi_Negative_R2

description:
TFi.count.txt
TFi.count_normalized.txt
TFi_mle_HighvsNeg.txt
TFi_mle_LowvsNeg.txt


title: lung tissue-CONTROL-CTRL2_r94.78a


title: XX_D2_H3K4me1_sgOtx2_R2


title: 8dpf larvae, wt-1


title: XX_D2_TFi_Low_R2

description:
TFi.count.txt
TFi.count_normalized.txt
TFi_mle_LowvsNeg.txt


title: CD34+ HSC, _DMSO, donor 2

city: Cambridge

first: Samuel

last: Lessard

state: Massachusetts

address: 350 Water street

institute: Sanofi

description:
Erythroid differentiation
Day 14

data_processing:
Performed by Genewiz, NJ.
Adapter sequences and nucleotides with poor quality were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to the GRCh38 human reference genome using STAR v.2.5.2b.
Gene level reads counts were estimated using the R Subread package v.1.5.2, including only unique reads falling within exons.
DESeq2 was used to identify differentially expressed genes between DMSO and compound treated cells.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene read counts for each sample

molecule: polyA RNA

source_name: Hematopoietic stem cells

growth_protocol: We cultured mobilized CD34+ human stem / progenitor cells (HSPC) from healthy individuals for 3 days in a maintenance media consisting of X-VIVO 10 (VWR cat#12002-004), 100 U/mL penicillin-streptomycin (ThermoFisher, cat#15140122), 2mM L-glutamine (Fisher Scientific, cat#25030-081), 100ng/mL Recombinant Human Stem Cell Factor (Thermofisher, cat#CTP2113), 100ng/mL Recombinant Human Thrombopoietin (Thermofisher, cat#PHC9513) and 100ng/mL Recombinant Human Flt-3 Ligand (Thermofisher, cat#CTP9413).

extract_protocol:
RNA was harvested using a Trizol reagent kit (Invitrogen)
Poly-A selection and paired-end 2x150bp library preparation (Illumina) was performed by Genewiz, NJ.

treatment_protocol: We differentiated CD34+ cells into erythroid cells using a three-step differentiation protocol (Giarratana, M.C., et al). In brief, we cultured CD34+ cells for 7 days in Step 1 media, consisting of Iscove’s modified Dulbecco’s medium (IMDM) (Invitrogen, cat#31980-030) supplemented with 1X GlutaMAX, 100U/mL penicillin-streptomycin, 5% human AB+ plasma (Stemcell Technologies, cat#70039.6), 330ug/mL human holo-transferrin (Sigma, cat#T0665), 10ug/mL human insulin (Sigma, cat#I9278), 2U/mL heparin (Sigma, cat#H3149), 1uM/mL hydrocortisone (Sigma, cat#H6909), 3U/mL recombinant human erythropoietin (EPO) (Invitrogen, cat#PHC2054), 100ng/mL SCF and 5ng/mL interleukin 3 (IL-3) (Sigma, cat#H7166). On day 7, we transferred cells to Step 2 media, a Step 1 media without hydrocortisone and IL-3, and cultured them for 3 to 4 days. We then transferred cells to a Step 3, which has the same composition as Step 2 media without SCF. We cultured cells in Step 3 media for 8 to 9 days

value: DMSO

value: Hematopoietic stem cells

value: CD34+ Hematopoietic stem cells


title: XX_D2_H3K4me1_sgOtx2_R1


title: XX_D2_TFi_High_R2

description:
TFi.count.txt
TFi.count_normalized.txt
TFi_mle_HighvsNeg.txt


title: 8dpf larvae, grwd1-del-1


title: lung tissue-IPF-IPF5_r110.16

value: IPF


title: XX_D2_H3K4me1_sgNfrkb_R3


title: lung tissue-IPF-IPF1_r3.10


title: CD34+ HSC, _DMSO, donor 3

description:
Erythroid differentiation
Day 14


title: XX_D2_TFi_Unsorted_R1

description:
TFi.count.txt
TFi.count_normalized.txt


title: lung tissue-IPF-IPF9_r162.15


title: XX_D2_H3K4me1_sgNfrkb_R2


title: lung tissue-IPF-IPF8_r147.69


title: XX_D2_TFi_Selected_R1

description:
TFi.count.txt
TFi.count_normalized.txt


title: CD34+ HSC, compound B, donor 3

description:
Erythroid differentiation
Day 14

value: coupound B


title: XX_D2_TFi_Selected_R2

description:
TFi.count.txt
TFi.count_normalized.txt


title: lung tissue-CONTROL-CTRL4_r146.13


title: CD34+ HSC, compound B, donor 2

description:
Erythroid differentiation
Day 14


title: lung tissue-IPF-IPF2_r11.11


title: XX_D2_TFi_Negative_R1


title: XX_D2_H3K4me1_sgNfrkb_R1


title: XX_D2_TFi_Low_R1


title: XX_D2_H3K4me1_sgZic3_R3


title: XX_D2_H3K4me1_sgZic3_R2


title: CD34+ HSC, compound B, donor 1

description:
Erythroid differentiation
Day 14


title: CD34+ HSC, --DMSO, donor 3

description:
Erythroid differentiation
Day 14


title: lung tissue-IPF-IPF2_r11.30


title: XX_D2_TFi_High_R1


title: XX_D2_H3K4me1_sgZic3_R1


title: lung tissue-IPF-IPF5_r110.58


title: CD34+ HSC, _DMSO, donor 1

description:
Erythroid differentiation
Day 14


title: testes DicerTG 28Y35338 i

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed in two rounds using fastx-toolkit version 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit) and cutadapt version 1.8.3 (31). First, 4 random bases were trimmed from left side: fastx_trimmer -f 5 -i {INP}.fastq -o {TMP}.fastq
Next, NEXTflex adapters were trimmed. Additionally, the N-nucleotides on ends of reads were trimmed and reads containing more than 10% of the N-nucleotides were discarded: cutadapt --format="fastq" --front=”GTTCAGAGTTCTACAGTCCGACGATCNNNN” --adapter=”NNNNTGGAATTCTCGGGTGCCAAGG” --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output=”${TRIMMED}.fastq" --trim-n --match-read-wildcards ${TMP}.fastq
Trimmed reads were mapped to the mouse (mm10) genome with following parameters: STAR --readFilesIn ${TRIMMED}.fastq.gz --runThreadN 4 --genomeDir ${GENOME_INDEX} --genomeLoad LoadAndRemove --readFilesCommand unpigz -c --readStrand Unstranded --limitBAMsortRAM 20000000000 --outFileNamePrefix ${FILENAME} --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 99999 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v4 from UCSC: genomeCoverageBed -ibam ${FILENAME}.bam -bg -split > ${FILENAME}.bedGraph wigToBigWig ${FILENAME}.bedGraph chrNameLength.txt ${FILENAME}.bw
Assembly: mm10
Supplementary files format and content: .bigWig
Supplementary files format and content: coverage genome browser tracks files: - bigWig format - generated in a non-stranded mode - not normalized for library size

source_name: testes

extract_protocol:
Organs from adult mice (9-13 w) were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by phenol–chloroform extraction according to the manufacturer's protocol.
Small-RNA libraries were prepared using the NextFlex Small-RNA-seq v3 kit (Amplicon) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15-18 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 140-160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform

value: testes

value: DicerTg(O-HA)

value: LCMV infected


title: testes WT 28Y35292 i

value: Dicerwt/wt


title: lung tissue-IPF-IPF6_r120.31


title: XX_D2_H3K4me1_sgNT_R2

value: Embryonic stem cells

value: CAST / C57BL/6


title: XX_D2_H3K4me1_sgNT_R3


title: CD34+ HSC, oxindole, donor 3

description:
Erythroid differentiation
Day 14

value: oxindole


title: CD34+ HSC, --DMSO, donor 1

description:
Erythroid differentiation
Day 14


title: testes DicerDHEL1het 28Y35293 i


title: lung tissue-CONTROL-CTRL1_r62.79


title: XX_D2_H3K4me3_sgFoxd3_R3


title: CD34+ HSC, oxindole, donor 1

description:
Erythroid differentiation
Day 14


title: spleen DicerTG 28Y35338 i

source_name: spleen

value: spleen


title: lung tissue-IPF-IPF7_r127.4


title: lung tissue-IPF-IPF4_r50.16


title: XX_D2_H3K4me1_sgNT_R1


title: spleen WT 28Y35286 i


title: XX_D2_H3K4me3_sgFoxd3_R2


title: lung tissue-CONTROL-CTRL2_r94.136


title: L02 cells,PNK treated linear pre-gRNA,rep3

city: Hong Kong

first: yicen

last: zhou

address: Block 2, To Yuen Building, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
L02_linear_pre_gRNA_PNK_rep3
L02_RNAseq_raw_counts.txt.gz

data_processing:
The quality of raw data were evaluated by FastQC (v0.12.1)
Sequence reads were aligned to the human reference genome hg19 by HISAT2 (2.1.0)
The reads(counts) for each gene were obtained using featureCounts (v2.0.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RNA-seq three biological replicates raw counts for each sample in HeLa, NCM460,HEK293T, HCT116 and L02 cells transfected with empty plasmid,circular or linear pcDNA3.1-neo plasmids and circular or linear pre-gRNA plasmids.

growth_protocol: Plate HEK293T and HCT116 and HeLa and L02 and NCM460 cells were transfected circular or linear plasmid  for 24 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the LM-seq protocol.

value: human liver cell

value: WT

value: transfected with PNK treated linear pre-gRNA plasmid


title: XX_D2_H3K4me3_sgFoxd3_R1


title: L02 cells,PNK treated linear pre-gRNA,rep2

description:
L02_linear_pre_gRNA_PNK_rep2
L02_RNAseq_raw_counts.txt.gz


title: CD34+ HSC, --DMSO, donor 2

description:
Erythroid differentiation
Day 14


title: liver WT 28Y35286 i

source_name: liver

value: liver


title: XX_D2_H3K4me3_sgOtx2_R3


title: lung tissue-IPF-IPF3_r25.22

value: M

value: lung tissue sample


title: CD34+ HSC, oxindole, donor 2

description:
Erythroid differentiation
Day 14

value: Hematopoietic stem cells

value: CD34+ Hematopoietic stem cells


title: MOLM-13, Assay 1, rep 5

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Combined compounds for replicate 5
Assay_1_rep5

library_source: other

data_processing:
Demultiplex reads, trim with Cutadapt, extract UMI, align with STAR, sort and index, deduplicate with UMI-tools, concatenate counts, remove batch effects with ComBat, normalize CLR.
Assembly: NA
Supplementary files format and content: Processed data files are matrices of raw read counts for all the features (cell surface proteins) for each compound treatment and replicate
Library strategy: Surface-plex, a new high-throughput technology for amplification of antibody-oligo conjugates from plates.

molecule: other

growth_protocol: MOLM-13 cultured in compound and RPMI media (with 10% FBS and 1% P/S) at 37C and 5% atmospheric CO2

extract_protocol:
Oligos from antibody-oligo conjugates were directly amplified from cells bound with Total-Seq B antibodies.
Illumina sequencing libraries were constructed directly from the antibody-oligos with two rounds of PCR, adding TruSeq adapters.

value: acute myeloid leukemia


title: MOLM-13, Assay 1, rep 4

description:
Combined compounds for replicate 4
Assay_1_rep4


title: spleen DicerDHEL1het 28Y35291 i


title: L02 cells,PNK treated linear pre-gRNA,rep1

description:
L02_linear_pre_gRNA_PNK_rep1
L02_RNAseq_raw_counts.txt.gz


title: L02 cells,AP treated linear pre-gRNA,rep3

description:
L02_linear_pre_gRNA_AP_rep3
L02_RNAseq_raw_counts.txt.gz

value: transfected with AP treated linear pre-gRNA plasmid


title: liver DicerDHEL1het 28Y35291 i


title: L02 cells,AP treated linear pre-gRNA,rep2

description:
L02_linear_pre_gRNA_AP_rep2
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K4me3_sgOtx2_R2


title: MOLM-13, Assay 1, rep 2

description:
Combined compounds for replicate 2
Assay_1_rep2


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,RNA-seq rep1

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

data_processing:
The quality of the raw reads was assessed using FastQC.
We returned 245,960,792 total tags for the G. mellonella larvae samples.
The G. mellonella larvae reads were mapped against G. mellonella assembly ASM364042v2.
We used STAR Aligner version 2.7.1a with default settings.
G. mellonella larvae libraries on average 49.1 million reads mapped. To quantify the mapped reads from RNA-Seq libraries, Rsubread FeatureCount function was utilized using same parameters as used for RNA-Seq quantification
Assembly: GCA_003640425.2
Supplementary files format and content: tab-seperated valuess file include raw count values for each Sample

organism: Galleria mellonella

source_name: SA.GI.P. BigBig

extract_protocol: RNA-Seq libraries were prepared using 1 ug of total RNA with TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer's instructions.

tag: development stage

value: larvae

tag: time point

tag: strain

value: SA.GI.P. BigBig

value: Infected with Madurella mycetomatis


title: L02 cells,linear pre-gRNA,rep3

description:
L02_linear_pre_gRNA_rep3
L02_RNAseq_raw_counts.txt.gz

value: transfected with linear pre-gRNA plasmid


title: XX_D2_H3K4me3_sgNfrkb_R3

value: Embryonic stem cells

value: CAST / C57BL/6


title: XX_D2_H3K4me3_sgNfrkb_R2


title: MOLM-13, Assay 1, rep 1

description:
Combined compounds for replicate 1
Assay_1_rep1


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,RNA-seq rep3


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,RNA-seq rep2


title: L02 cells,AP treated linear pre-gRNA,rep1

description:
L02_linear_pre_gRNA_AP_rep1
L02_RNAseq_raw_counts.txt.gz


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,RNA-seq rep1


title: L02 cells,linear pre-gRNA,rep2

description:
L02_linear_pre_gRNA_rep2
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K4me3_sgZic3_R3


title: L02 cells,linear pre-gRNA,rep1

description:
L02_linear_pre_gRNA_rep1
L02_RNAseq_raw_counts.txt.gz


title: PBMC, after therapy, week 24, sample 9_2

city: Moscow

first: Sergey

last: Ivanov

address: 10, Pogodinskaya street

country: Russia

institute: Institute of Biomedical Chemistry

description:
Library name: s9_2
Column name in read_counts.txt: s9_2

data_processing:
Mapping reads to the genome was performed using STAR 2.7.9a software (parameters: outFilterMismatchNmax 3, GRCh38 genome, Ensembl annotation).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

extract_protocol:
The blood was centrifuged within two hours of collection. Blood samples were centrifuged at room temperature for 25 minutes at 1,600 RCF. PBMC isolation was started immediately after centrifugation. As a result of PBMC isolation about 150 µl of PBMC were obtained from each patient. After addition of 900 µl of TRIzol™ (Thermo Fisher Scientific) to each 80 µl of isolated PBMC the frozen cells (-196 ⁰) were used for RNA sequencing. Total RNA was isolated from cells using TRIzol™ (Thermo Fisher Scientific) according to the standard protocol. The total RNA was then used to obtain the polyA fraction using Dynabeads® mRNAPurificationKit oligoT magnetic beads (Ambion) according to the instructions.
Libraries were prepared from polyA RNA for mass parallel sequencing using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) according to the kit instructions. Library concentration was determined using the Qubit dsDNA HS Assay Kit - (Thermo Fisher Scientific) on a Qbit 2.0 instrument. Library fragment length distribution was performed using the Agilent High Sensitivity DNA Kit (Agilent).

value: blood

value: peripheral blood mononuclear cells

tag: patient id

value: after therapy

value: week 24

tag: cd4 count

tag: cd8 count

tag: viral load


title: PBMC, after therapy, week 24, sample 8_2

description:
Library name: s8_2
Column name in read_counts.txt: s8_2

tag: tissue

tag: cell type


title: PBMC, after therapy, week 24, sample 7_2

description:
Library name: s7_2
Column name in read_counts.txt: s7_2


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,RNA-seq rep3


title: XX_D2_H3K4me3_sgZic3_R2

tag: cell line

tag: genotype


title: MOLM-13, Assay 1, rep 3

description:
Combined compounds for replicate 3
Assay_1_rep3


title: XX_D2_H3K4me3_sgOtx2_R1

tag: treatment


title: L02 cells,pre-gRNA,rep3

description:
L02_pre_gRNA_rep3
L02_RNAseq_raw_counts.txt.gz

value: human liver cell

value: WT

value: transfected with pre-gRNA plasmid


title: PBMC, after therapy, week 24, sample 6_2

description:
Library name: s6_2
Column name in read_counts.txt: s6_2

tag: time


title: XX_D2_H3K4me3_sgZic3_R1


title: PBMC, after therapy, week 24, sample 5_2

description:
Library name: s5_2
Column name in read_counts.txt: s5_2


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,RNA-seq rep1


title: XX_D2_H3K4me3_sgNT_R3


title: L02 cells,pre-gRNA,rep1

description:
L02_pre_gRNA_rep1
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K4me3_sgNfrkb_R1


title: PBMC, after therapy, week 24, sample 4_2

description:
Library name: s4_2
Column name in read_counts.txt: s4_2


title: PBMC, after therapy, week 24, sample 3_2

description:
Library name: s3_2
Column name in read_counts.txt: s3_2


title: XX_D2_H3K4me3_sgNT_R1


title: L02 cells,PNK treated linear pcDNA3.1-neo,rep3

description:
L02_linear_pcDNA3.1_neo_PNK_rep3
L02_RNAseq_raw_counts.txt.gz

value: transfected with PNK treated linear pcDNA3.1-neo plasmid


title: liver DicerTG 28Y35338 i

value: liver

value: DicerTg(O-HA)

value: LCMV infected


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,RNA-seq rep2

value: larvae


title: PBMC, after therapy, week 24, sample 2_2

description:
Library name: s2_2
Column name in read_counts.txt: s2_2


title: L02 cells,PNK treated linear pcDNA3.1-neo,rep2

description:
L02_linear_pcDNA3.1_neo_PNK_rep2
L02_RNAseq_raw_counts.txt.gz


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,RNA-seq rep2

value: SA.GI.P. BigBig


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,RNA-seq rep1

value: Infected with Madurella mycetomatis


title: PBMC, after therapy, week 24, sample 1_2

description:
Library name: s1_2
Column name in read_counts.txt: s1_2


title: Healthy Galleria mellonella larvae,RNA-seq rep3

value: No treatment


title: XX_D2_H3K27ac_sgFoxd3_R3

value: Embryonic stem cells


title: L02 cells,PNK treated linear pcDNA3.1-neo,rep1

description:
L02_linear_pcDNA3.1_neo_PNK_rep1
L02_RNAseq_raw_counts.txt.gz


title: L02 cells,pre-gRNA,rep2

description:
L02_pre_gRNA_rep2
L02_RNAseq_raw_counts.txt.gz


title: L02 cells,AP treated linear pcDNA3.1-neo,rep3

description:
L02_linear_pcDNA3.1_neo_AP_rep3
L02_RNAseq_raw_counts.txt.gz

value: transfected with AP treated linear pcDNA3.1-neo plasmid


title: XX_D2_H3K27ac_sgFoxd3_R1

value: CAST / C57BL/6


title: XX_D2_H3K27ac_sgFoxd3_R2


title: PBMC, before therapy, week 0, sample 10

description:
Library name: s10
Column name in read_counts.txt: s10

value: blood

value: peripheral blood mononuclear cells

value: before therapy

value: week 0


title: PBMC, before therapy, week 0, sample 11

description:
Library name: s11
Column name in read_counts.txt: s11


title: Healthy Galleria mellonella larvae,RNA-seq rep2


title: L02 cells,AP treated linear pcDNA3.1-neo,rep2

description:
L02_linear_pcDNA3.1_neo_AP_rep2
L02_RNAseq_raw_counts.txt.gz

value: human liver cell

value: WT


title: Healthy Galleria mellonella larvae, RNA-seq rep1


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,LQ-ssCAGE rep3 T7d

data_processing:
After performing base calling for all samples, we returned 251,856,022 total tags for the G. mellonella larvae samples
G. mellonella larvae libraries on average 14.5 million reads mapped, of these on average 47.0% uniquely mapped against ASM364042v2
The G. mellonella larvae reads were mapped against G. mellonella assembly ASM364042v2.
We used STAR Aligner version 2.7.1a with default settings.
Using LQ-ssCAGE  a genome wide map of Transcription start site (TSS) was established for both the Galleria mellonella larvae
Assembly: GCA_003640425.2
Supplementary files format and content: tab-seperated valuess file include TSS gene expression level values for each Sample


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,RNA-seq rep3


title: L02 cells,AP treated linear pcDNA3.1-neo,rep1

description:
L02_linear_pcDNA3.1_neo_AP_rep1
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K27ac_sgOtx2_R3


title: XX_D2_H3K4me3_sgNT_R2


title: PBMC, before therapy, week 0, sample 8

description:
Library name: s8
Column name in read_counts.txt: s8


title: PBMC, before therapy, week 0, sample 9

description:
Library name: s9
Column name in read_counts.txt: s9


title: L02 cells,linear pcDNA3.1-neo,rep2

description:
L02_linear_pcDNA3.1_neo_rep2
L02_RNAseq_raw_counts.txt.gz

value: transfected with linear pcDNA3.1-neo plasmid


title: XX_D2_H3K27ac_sgOtx2_R2


title: PBMC, before therapy, week 0, sample 7

description:
Library name: s7
Column name in read_counts.txt: s7


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,LQ-ssCAGE rep2 T7d


title: L02 cells,linear pcDNA3.1-neo,rep3

description:
L02_linear_pcDNA3.1_neo_rep3
L02_RNAseq_raw_counts.txt.gz


title: PBMC, before therapy, week 0, sample 6

description:
Library name: s6
Column name in read_counts.txt: s6


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,LQ-ssCAGE rep3 T72


title: L02 cells,pcDNA3.1-neo,rep3

description:
L02_pcDNA3.1_neo_rep3
L02_RNAseq_raw_counts.txt.gz

value: transfected with pcDNA3.1-neo plasmid


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,LQ-ssCAGE rep2 T72


title: XX_D2_H3K27ac_sgNfrkb_R1


title: PBMC, before therapy, week 0, sample 4

description:
Library name: s4
Column name in read_counts.txt: s4


title: XX_D2_H3K27ac_sgOtx2_R1


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,LQ-ssCAGE rep1 T7d


title: L02 cells,pcDNA3.1-neo,rep1

description:
L02_pcDNA3.1_neo_rep1
L02_RNAseq_raw_counts.txt.gz


title: L02 cells,linear pcDNA3.1-neo,rep1

description:
L02_linear_pcDNA3.1_neo_rep1
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K27ac_sgNfrkb_R3


title: L02 cells,pcDNA3.1-neo,rep2

description:
L02_pcDNA3.1_neo_rep2
L02_RNAseq_raw_counts.txt.gz


title: L02 cells,control,rep3

description:
L02_control_rep3
L02_RNAseq_raw_counts.txt.gz

value: control


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 72h,LQ-ssCAGE rep1 T72


title: XX_D2_H3K27ac_sgZic3_R2


title: XX_D2_H3K27ac_sgNfrkb_R2


title: PBMC, before therapy, week 0, sample 3

description:
Library name: s3
Column name in read_counts.txt: s3


title: L02 cells,control,rep2

description:
L02_control_rep2
L02_RNAseq_raw_counts.txt.gz


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,LQ-ssCAGE rep3 T24


title: PBMC, before therapy, week 0, sample 2

description:
Library name: s2
Column name in read_counts.txt: s2


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,LQ-ssCAGE rep2 T24


title: XX_D2_H3K27ac_sgNT_R3


title: PBMC, before therapy, week 0, sample 5

description:
Library name: s5
Column name in read_counts.txt: s5


title: PBMC, before therapy, week 0, sample 1

description:
Library name: s1
Column name in read_counts.txt: s1


title: XX_D2_H3K27ac_sgZic3_R1


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 24h,LQ-ssCAGE rep1 T24


title: HCT116 cells,PNK treated linear pre-gRNA,rep3

description:
HCT116_linear_pre_gRNA_PNK_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: human colorectal adenocarcinoma cell

value: transfected with PNK treated linear pre-gRNA plasmid


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,LQ-ssCAGE rep1 T4

value: larvae

value: SA.GI.P. BigBig


title: Biological replicate of SE-3

city: Bengaluru

first: Varsha

middle: N

last: Tamilkumar

state: Karnataka

address: Bellary road

department: Genetics and Development

country: India

institute: NCBS

description:
Library name: SE_C
1x50bp sequencing read length

data_processing:
The data was processed using the usegalaxy web server. The quality of the sequencing was checked using the FastQC module. The adaptor sequences was trimmed using Trimmomatic. The reads were mapped on to the genome sequence using HISAT2. The total number of reads per gene was counted using feature counts. The output of this step was used in Limma voom for differential gene expression analysis.
Assembly: galGal6.refGene.gtf
Supplementary files format and content: tab-delimited tabular file includes raw counts for each sample

organism: Gallus gallus

source_name: Surface ectoderm adjacent to the otic vesicle in stage HH17

growth_protocol: Kaveri eggs were incubated at 37C in a humidified incubator for 60 hours

extract_protocol:
Total RNA was isolated using Tri reagent (Sigma- Aldrich catalogue no:T9424) as per the manufacturer’s protocol. Total RNA was resuspended in 12uL of DEPC treated water. 1uL of the sample was used for analysing the quality using bioanalyser and 1uL was used to check the concentration using Qubit.
NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L

treatment_protocol: All the tissue was WT. To remove contamination of mesenchymal cells in the sample, the otic vesicle and surface ectoderm was subjected to 15mins of dispase (2.4U/ml) treatment at RT. The tissue was placed in 20uL droplet of dispase.

value: epithelial cells-embryonic

value: Wild type

tag: breed

value: Kaveri

tag: batch


title: Biological replicate of SE-4

description:
Library name: SE_D
1x50bp sequencing read length

value: Surface ectoderm adjacent to the otic vesicle in stage HH17


title: L02 cells,control,rep1

description:
L02_control_rep1
L02_RNAseq_raw_counts.txt.gz


title: XX_D2_H3K27ac_sgNT_R2

value: Embryonic stem cells

value: CAST / C57BL/6


title: XX_D2_H3K27ac_sgZic3_R3


title: HCT116 cells,PNK treated linear pre-gRNA,rep2

description:
HCT116_linear_pre_gRNA_PNK_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,LQ-ssCAGE rep3 T4

description: Two replicates (columns) are filtered from the downstream analysis due to low mapping ratio.

value: Infected with Madurella mycetomatis


title: Biological replicate of SE-1

description:
Library name: SE_A
1x50bp sequencing read length


title: n3_IgG-coIP

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

data_processing:
Sequencing data was processed on usegalaxy.eu platform.
Fastq Quality Control using FastQC  (v. 0.11.9). Adapter trimming and quality filtering was done using Trim Galore! (v. 0.6.7)
Trimmed and quality filtered reads were aligned to mm10 genome assembly using RNAStar (2.7.10b).
FOXG1-coIP reads were normalized to IgG-coIP reads using bamcompare (v. 3.5.4) and the average calculated using bigwigAverage (v. 3.5.4).
Differently immunoprecipitated RNA were calculated using Deseq2 (v. 2.11.4.0.8) after counting (featurecount, v. 2.0.3).
Assembly: mm10
Supplementary files format and content: bigwig, featurecounts.tabular, deseq2_results.tabular

source_name: whole brain

growth_protocol: Each replicate (n) came from independent mice.

extract_protocol:
Co-Immunoprecipitation (Co-IP) was performed as previously described . In brief, P0 whole brain tissue was lysed in lysis buffer (300mM NaCl, 20mM Tris, 1mM EDTA, 0.5% Nonidet-40 (NP-40), pH 7.4) supplemented with protease inhibitor (Sigma-Aldrich/Merck, Germany) and incubated for 30min on ice, triturating every 10min 20 times. After a 10min centrifugation at 13000rpm, the supernatant was collected. The samples were diluted dropwise to reach a salt concentration of 100 mM and NP-40 concentration of 0.15% using equilibration buffer (20mM Tris, 1mM EDTA, pH 7.4). Protein concentrations were determined with Bradford reagent (Bio-Rad, United Kingdom). 10% input was saved and equal amounts of protein were used for all Co-IPs. Protein G Dynabeads (10004D, Thermo Scientific, USA) were washed with Co-IP buffer (100mM NaCl, 20mM Tris, 1mM EDTA, 0.15% NP-40 pH 7.4), and incubated with Co-IP antibodies at 4°C overnight. The following antibodies were used: anti-FOXG1 (#61211, Active Motif, USA), IgG (#C15410206, Diagenode, Belgium). Antibody-coupled beads were washed once with Co-IP buffer before Co-IP. Cell lysates were precleared with Protein G Dynabeads for 1h at 4°C, subsequently transferred to antibody-coupled beads, and incubated overnight at 4°C in rotation. In FOXG1-coIP_RNAse samples, RNAse A (1:400, R4642, Sigma-Aldrich/Merck) was added to this overnight step. Antibody-coupled beads were washed 3 times with Co-IP buffer. The washed beads were resuspended in RLT buffer of the RNA isolation kit and purified according the manufacturer’s instructions (RNAeasy Mini Kit, Qiagen, Germany).
Total RNA extract of FOXG1- and IgG-coIP respectively were used for RIPseq. The cDNA libraries were constructed using TruSeq total RNA sample preparation kit (Illumina, USA), following the manufacturer’s instructions and sequenced on Illumina NovaSeq as paired-end 101bp reads.

value: whole brain

value: wildtype

value: IgG-coIP


title: HCT116 cells,PNK treated linear pre-gRNA,rep1

description:
HCT116_linear_pre_gRNA_PNK_rep1
HCT116_RNAseq_raw_counts.txt.gz

value: WT


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 4h,LQ-ssCAGE rep2 T4


title: XX_D2_H3K27ac_sgNT_R1


title: Healthy Galleria mellonella larvae, LQ-ssCAGE rep3 T0

value: No treatment


title: n3_FOXG1-coIP


title: n3_Input

value: no treatment


title: Biological replicate of SE-2

description:
Library name: SE_B
1x50bp sequencing read length


title: HCT116 cells,AP treated linear pre-gRNA,rep3

description:
HCT116_linear_pre_gRNA_AP_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: human colorectal adenocarcinoma cell

value: transfected with AP treated linear pre-gRNA plasmid


title: Biological replicate of OV-3

description:
Library name: OV_C
1x50bp sequencing read length

source_name: Otic vesicle without the opening in stage HH17


title: HCT116 cells,linear pre-gRNA,rep3

description:
HCT116_linear_pre_gRNA_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with linear pre-gRNA plasmid


title: Healthy Galleria mellonella larvae, LQ-ssCAGE rep2 T0

value: larvae

value: SA.GI.P. BigBig


title: HCT116 cells,AP treated linear pre-gRNA,rep2

description:
HCT116_linear_pre_gRNA_AP_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: Healthy Galleria mellonella  larvae, LQ-ssCAGE rep1 T0


title: n2_IgG-coIP


title: Biological replicate of OV-4

description:
Library name: OV_D
1x50bp sequencing read length

value: Otic vesicle without the opening in stage HH17

value: epithelial cells-embryonic

value: Wild type


title: HCT116 cells,AP treated linear pre-gRNA,rep1

description:
HCT116_linear_pre_gRNA_AP_rep1
HCT116_RNAseq_raw_counts.txt.gz


title: TFi_PlasmidLibrary

description:
Plasmid
TFi.count.txt
TFi.count_normalized.txt

organism: synthetic construct


title: HCT116 cells,linear pre-gRNA,rep2

description:
HCT116_linear_pre_gRNA_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: n2_FOXG1-coIP


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,RNA-seq rep3


title: n2_Input


title: Biological replicate of OV-2

description:
Library name: OV_B
1x50bp sequencing read length

value: Kaveri


title: n1_Input


title: Biological replicate of OV-1

description:
Library name: OV_A
1x50bp sequencing read length


title: HCT116 cells,pre-gRNA,rep3

description:
HCT116_pre_gRNA_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with pre-gRNA plasmid


title: HCT116 cells,linear pre-gRNA,rep1

description:
HCT116_linear_pre_gRNA_rep1
HCT116_RNAseq_raw_counts.txt.gz


title: n1_IgG-coIP


title: Biological replicate of OE-3

description:
Library name: OE_C
1x50bp sequencing read length

source_name: Opening of the otic vesicle in stage HH17


title: Biological replicate of OE-4

description:
Library name: OE_D
1x50bp sequencing read length

value: Opening of the otic vesicle in stage HH17


title: HCT116 cells,pre-gRNA,rep2

description:
HCT116_pre_gRNA_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: n1_FOXG1-coIP

value: whole brain


title: Biological replicate of OE-2

description:
Library name: OE_B
1x50bp sequencing read length


title: Patient 11

type: RNA

city: Ulm

first: Linda

last: Hofmann

state: Deutschland

address: Frauensteige 14a, Haus 18

institute: University of Ulm

description:
miRNA
HAE11

hyb_protocol: Samples were denatured at 85°C for 5 min and then hybridized at 65°C for 12 h.

scan_protocol: Fluorescent reporter tags were scanned by an automated multi-channel epifluorescence scanner, generating the raw counts, using the SPRINT profiler and software.

data_processing: Raw counts were normalized using the positive ligation and negative controls present on the chip, using nSolver Analysis software.

label: not applicable

source_name: Plasma exosomes

label_protocol: not applicable

extract_protocol: Exosomes were isolated from plasma by differential ultracentrifugation and RNA was isolated from exosomes using miRNeasy micro Kit (Qiagen).

value: Plasma exosomes

tag: Sex

value: female

tag: age [years]

tag: hae type

value: Type II


title: Control_pooled_Input

data_processing:
Sequencing data was processed in usegalaxy.eu platform.
Fastq Quality Control using FastQC  (v. 0.11.9). high quality and uniquely mapping reads were retained (mapq > 5), Adapter trimming and quality filtering was done using Trim Galore! (v. 0.6.7)
Trimmed and quality filtered reads were aligned to mm10 genome assembly using Bowtie 2(v 2.5.0)
Peaks were called using MACS2 (v. 2.2.7.1) using default parameters from filtered BAM files.
Differently bound regions were analyzed using Diffbind (v. 2.5.0) with a FDR of 0.1.
Assembly: mm10
Supplementary files format and content: bigwig, narrowpeaks.bed, diffbind.bed

source_name: hippocampus

growth_protocol: Primary hippocampal tissue isolation and culture was done following a protocol modified after Brewer et al., 1993. Hippocampal tissue was isolated from E18.5 mouse embryos and dissociated by trypsinisation and trituration. Cells were counted and seeded 200,000/well in 24 well-plates and were grown in Neurobasal medium with B27 supplement (DIV0). Half-volume medium change was done every 48 hours.

extract_protocol:
virally transduced (shPantr1 or shLuciferase) primary hippocampal neurons were fixed and collected for subsequent ChIP-seq experiments according to the instructions of the servicing company (Active Motif). Briefly, cells were fixed by adding 1/10 volume formaldehyde solution (11% Formaldehyde, 0.1 M NaCl, 1 mM EDTA pH=8.0, 50 mM HEPES pH=7.9) directly to the medium and incubated at room temperature (RT) with agitation. Fixation was stopped by adding 1/20 volume 2.5 M Glycine solution (Roth, Germany) and incubating for 5 min at RT. Cells were scraped from the plates and transferred into conical tubes, and centrifuged at 800 rpm at 4°C for 10 min. Cells were resuspended and washed twice in chilled PBS-Igepal solution (0.5% Igepal CA-360 (Sigma) in 1X PBS pH 7.4 (Gibco)), and a third time in PBS-Igepal-PMSF (phenylmethylsulfonyl fluoride) solution (0.5% Igepal, 1 mM PMSF (Sigma) in 1X PBS pH 7.4). The supernatant was completely removed and cell pellets were snap frozen in liquid nitrogen and stored at -80°C until following ChIP-seq experiments. ChIPseq was performed at active motif with their FOXG1 antibody (Catalog No. 61211)
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara)
ChIP-Seq libraries were sequenced on Illumina NovaSeq 6000 as 75-nt single end reads.

treatment_protocol: Lentiviral particles were prepared using plko.1-CMV.Puro-tGFP-shPantr1 or plko.1-CMV.Puro-tGFP-shLuciferase (Genescript) plasmids. Cells were transduced with lentiviral particles on day-in-vitro (DIV) 1. At DIV4, transduced cells were selected using 0.3 µg/ml puromycin (P9620, Sigma) and cell proliferation was inhibited by addition of 2 µM Arabinocytosine (AraC, C1768, Sigma), while performing a half-volume medium change. Medium was changed again at DIV6 including 0.3 µg/ml puromycin and 2 µM AraC.

value: hippocampus

value: Primary Hippocampal Neurons

value: wildtype

value: Input


title: Patient 9

description:
miRNA
HAE09

value: Type I


title: HCT116 cells,pre-gRNA,rep1

description:
HCT116_pre_gRNA_rep1
HCT116_RNAseq_raw_counts.txt.gz

value: human colorectal adenocarcinoma cell

value: WT


title: Biological replicate of OE-1

description:
Library name: OE_A
1x50bp sequencing read length


title: HCT116 cells,PNK treated linear pcDNA3.1-neo,rep3

description:
HCT116_linear_pcDNA3.1_neo_PNK_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with PNK treated linear pcDNA3.1-neo plasmid


title: Patient 8

description:
miRNA
HAE08


title: FOXG1_ChIP_control_n2

value: control


title: Infected Galleria mellonella larvae with Madurella mycetomatis  at 7d,RNA-seq rep2

tag: development stage

value: larvae

tag: time point

value: SA.GI.P. BigBig

value: Infected with Madurella mycetomatis


title: PA3

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

country: China

institute: Sun Yat-sen University

description: Library name: PA3

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: counts_all.xlsx

growth_protocol: The HOKs was cultured in Defined Keratinocyte-SFM basal medium (Gibco) supplemented with 0.2% Defined Keratinocyte-SFM Growth Supplement (Gibco) and 1% penicillin-streptomycin. The cells were cultured at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, USA), then enrichment of mRNA with polyA tails was achieved through Oligo(dT) magnetic beads.
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.

treatment_protocol: The cells were treated differently for 2 hours after starvation: ACh group: Treated with ACh (100 nM) Pg group: Stimulated with Pg (MOI = 50) PA group: Treated with Pg + ACh NC group: Control

value: Human Oral Keratinocytes

value: ACh + Pg co-treatment


title: HCT116 cells,PNK treated linear pcDNA3.1-neo,rep2

description:
HCT116_linear_pcDNA3.1_neo_PNK_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: Patient 7

description:
miRNA
HAE07

value: Plasma exosomes

value: male


title: PA2

description: Library name: PA2


title: HCT116 cells,PNK treated linear pcDNA3.1-neo,rep1

description:
HCT116_linear_pcDNA3.1_neo_PNK_rep1
HCT116_RNAseq_raw_counts.txt.gz


title: Patient 6

description:
miRNA
HAE06


title: PA1

description: Library name: PA1


title: Patient 5

description:
miRNA
HAE05

value: female


title: HCT116 cells,AP treated linear pcDNA3.1-neo,rep3

description:
HCT116_linear_pcDNA3.1_neo_AP_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with AP treated linear pcDNA3.1-neo plasmid


title: FOXG1_ChIP_Pantr1KD_n1

value: hippocampus

value: Primary Hippocampal Neurons


title: Patient 4

description:
miRNA
HAE04


title: FOXG1_ChIP_Pantr1KD_n2

value: wildtype


title: HCT116 cells,AP treated linear pcDNA3.1-neo,rep2

description:
HCT116_linear_pcDNA3.1_neo_AP_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: Pg2

description: Library name: Pg2

value: Pg infection


title: Patient 10

description:
miRNA
HAE10

value: Type I


title: Replicate 2 for P30 Basal Ganglia (Dlx6a-cre::INTACT) single-cell ATAC

first: Min

last: Dai

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute of MIT and Harvard

library_source: genomic single cell

data_processing:
Reads from scATAC-seq libraries (FASTQ files) were aligned to the mouse mm10 (GENCODE vM23/Ensembl98) reference genome provided by 10x Genomics and the the fragment file was produced with the Cell Ranger ATAC pipeline v2.1.0 (10x Genomics) with default parameters (cellranger-atac count).
Assembly: mm10
Supplementary files format and content: The "filtered_peak_bc_matrix.h5" files contain the cell x peak matrices ouput by CellRanger-ATAC. The "fragments.tsv.gz" files contain the fragment files generated by CellRanger-ATAC. The "fragments.tsv.gz.tbi" files are the index files for corresponding "fragments.tsv.gz" files.

source_name: basal ganglia

extract_protocol:
Two brains from postnatal day (P) 30 Dlx6a-cre::INTACT mice were harvested, sectioned coronally on a mouse brain slicer (Zivic Instruments), and the basal ganglia region was dissected in ice-cold artificial cerebrospinal fluid (ACSF). Tissue was then transferred to a Dounce homogenizer containing lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, and 0.01% IGEPAL CA-630, 0.001% digitonin). Tissue was homogenized with 10 strokes of pestle A and 10 strokes of pestle B, and incubated for 5 min on ice before being filtered through a 30-μm filter and centrifuged at 500g for 10 min at 4°C. The pellet was resuspended in 1% bovine serum albumin for sorting GFP+ nuclei on a Sony SH800S cell sorter.
Nuclei were sorted into diluted nuclei buffer (10x Genomics). The scATAC-seq library was prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit v.1.0 (PN-1000111), Chromium Chip E Single Cell kit (PN-1000156) and Chromium i7 Multiplex Kit N, Set A (PN-1000084) as per manufacturer’s instructions. Libraries were sequenced using a Nova-Seq S2 100 cycle kit (Illumina).

value: basal ganglia


title: Pg3

description: Library name: Pg3

value: WT


title: Pg1

description: Library name: Pg1


title: Patient 3

description:
miRNA
HAE03


title: Patient 2

description:
miRNA
HAE02


title: Pantr1KD_pooled_Input

value: Input


title: HCT116 cells,linear pcDNA3.1-neo,rep3

description:
HCT116_linear_pcDNA3.1_neo_rep3
HCT116_RNAseq_raw_counts.txt.gz

value: human colorectal adenocarcinoma cell

value: transfected with linear pcDNA3.1-neo plasmid


title: ACh3

description: Library name: ACh3

value: ACh treatment


title: Replicate 1 for P30 Basal Ganglia (Dlx6a-cre::INTACT) single-cell ATAC


title: HCT116 cells,linear pcDNA3.1-neo,rep2

description:
HCT116_linear_pcDNA3.1_neo_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: FOXG1_ChIP_control_n1

value: control


title: A11_XC01_M07_T018

city: Hangzhou

first: chen

last: Xue

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

description: MobiNova

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the MobiVision software (v2.1, Intron included)
Assembly: GRCm39
Supplementary files format and content: h5ad file

source_name: immune cells and tumor cells

extract_protocol:
Collect the pieces into a C tube and add digestive enzyme mix（Miltenyi Biotec-human/mouse Tumor Dissociation Kit,）, fill with cell culture medium up to 5 mL. Incubate the tissue soup in a shaking incubator at 37℃ for 1 hour. Filter the dissociated tissue through the 70 μm cell strainer. Collect the cells by centrifugation at 300 x g for 5 minutes at 2-8°C. Aspirate the supernatant and resuspend the cells in CSB and count cell number. The cells are ready for further staining
library was constructed accoding to the manufactor's  instructions (MobiCube 3' RNA v2.0).

value: immune cells and tumor cells

value: HB


title: ACh2

description: Library name: ACh2

value: Human Oral Keratinocytes


title: HCT116 cells,linear pcDNA3.1-neo,rep1

description:
HCT116_linear_pcDNA3.1_neo_rep1
HCT116_RNAseq_raw_counts.txt.gz


title: Patient 1

description:
miRNA
HAE01

value: Plasma exosomes

value: male


title: ACh1

description: Library name: ACh1


title: Healthy donor 11

description:
miRNA
HD11

value: female

value: not applicable


title: A11_XC01_M07_T017

description: MobiNova


title: HCT116 cells,AP treated linear pcDNA3.1-neo,rep1

description:
HCT116_linear_pcDNA3.1_neo_AP_rep1
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with AP treated linear pcDNA3.1-neo plasmid


title: NC3

description: Library name: NC3

value: Untreated control


title: A11_XC01_M07_T016

description: MobiNova


title: HCT116 cells,pcDNA3.1-neo,rep2

description:
HCT116_pcDNA3.1_neo_rep2
HCT116_RNAseq_raw_counts.txt.gz

value: transfected with pcDNA3.1-neo plasmid


title: A11_XC01_M07_T014

description: MobiNova


title: HCT116 cells,pcDNA3.1-neo,rep1

description:
HCT116_pcDNA3.1_neo_rep1
HCT116_RNAseq_raw_counts.txt.gz


title: NC1

description: Library name: NC1


title: A11_XC01_M07_T015

description: MobiNova


title: NC2

description: Library name: NC2


title: HCT116 cells,pcDNA3.1-neo,rep3

description:
HCT116_pcDNA3.1_neo_rep3
HCT116_RNAseq_raw_counts.txt.gz


title: Healthy donor 9

description:
miRNA
HD09


title: HCT116 cells,control,rep3

description:
HCT116_control_rep3
HCT116_RNAseq_raw_counts.txt.gz


title: Healthy donor 10

description:
miRNA
HD10


title: Healthy donor 8

description:
miRNA
HD08


title: A11_XC01_M07_T013

description: MobiNova


title: HCT116 cells,control,rep2

description:
HCT116_control_rep2
HCT116_RNAseq_raw_counts.txt.gz


title: A11_XC01_M07_T012

description: MobiNova

value: HC


title: Healthy donor 6

description:
miRNA
HD06


title: Healthy donor 5

description:
miRNA
HD05


title: A11_XC01_M07_T011

description: MobiNova


title: CaSki cells, sictrl exp2

city: Rome

first: Alessandra

last: Soriani

address: Viale Regina Elena 291

country: Italy

institute: Sapienza University of Rome

description: Library name: sample7

data_processing:
Post-sequencing Quality Control was performed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v.0.12.1.
Adapter sequences were trimmed, and low-quality reads removed using cutadapt v3.4.
Mapping of RNA and generation of gene counts was done using STAR (Dobin A, et al. Boinformatics 2013) aligner v.2.7.10b against human reference (GRCh38 build p13) and using feature annotation (v109) downloaded from Ensembl repository.
Assembly: GRCh38 build p13
Supplementary files format and content: raw_counts.txt

source_name: CaSki

extract_protocol:
RNA was extracted from SiHa and CaSki cells using Total RNA mini kit (Geneaid, RB100), and then RNAs were treated with DNase I (AMPD1, Sigma Aldrich).
RNA libraries for RNAseq were prepared using 1,5 micrograms of total RNA, according to the manufacturer's protocol. Samples of CaSki and SiHa cells were prepared with Kapa RNA HyperPrep with RiboErase (total RNA) and Kapa Globin Depletion Hybridization Oligos (Roche). Samples were sequenced by NovaSeq 6000 Sequencing System, RUN 2x101 bp, Illumina Instrument. The average number of reads obtained from each sample was 140 M.

value: CaSki

value: cervical cancer cells

value: wt

value: siRNA transfection


title: CaSki cells, siADAR1 exp2

description: Library name: sample8


title: HCT116 cells,control,rep1

description:
HCT116_control_rep1
HCT116_RNAseq_raw_counts.txt.gz

value: human colorectal adenocarcinoma cell

value: WT


title: CaSki cells, siADAR1 exp1

description: Library name: sample6


title: Healthy donor 4

description:
miRNA
HD04


title: HEK293T cells,linear pre-gRNA,rep3

description:
HEK293T_linear_pre_gRNA_rep3
HEK293T_RNAseq_raw_counts.txt.gz

value: human embryonic kidney cell

value: transfected with linear pre-gRNA plasmid


title: CaSki cells, sictrl exp1

description: Library name: sample5


title: A11_XC01_M07_T010

description: MobiNova

value: immune cells and tumor cells


title: Healthy donor 3

description:
miRNA
HD03

value: Plasma exosomes


title: A11_XC01_M07_T009

description: MobiNova


title: HEK293T cells,linear pre-gRNA,rep2

description:
HEK293T_linear_pre_gRNA_rep2
HEK293T_RNAseq_raw_counts.txt.gz


title: Healthy donor 2

description:
miRNA
HD02


title: Healthy donor 7

description:
miRNA
HD07

value: male


title: VCaP_GRO_DexDHT_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
*library strategy: GRO-seq
Basecalls performed using CASAVA, and read were quality controlled and trimmer with FASTX-toolkit and HOMER.
Reads were aligned against human genome hg38 with Bowtie software (0.12.7) allowing 2 mismatches and keeping only the best aligned read.
Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph from minus strand (HOMER makeUCSCfile command) from alignment file.
Supplementary files format and content: bedGraph from plus strand (HOMER makeUCSCfile command) from alignment file.

source_name: VCaP

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
Nuclei were extracted from 12.5 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and Br-UTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. Br-UTP-labeled run-on RNA was immunopurified with anti-BrdU-coated Protein G Dynabeads and precipitated overnight.
Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified with DNA purification kit. The recovered cDNA was circularized, linearized, amplified with 14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up with DNA purification kit.

treatment_protocol: VCaP cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) or 100 nM of dihydrotestosterone (DHT) or Dex and DHT  for 1 h before the start of nuclei extraction.

value: VCaP

value: Vertebral Cancer of the Prostate

tag: dex treatment

tag: dht treatment


title: A11_XC01_M07_T008

description: MobiNova


title: SiHa cells, sictrl exp2

description: Library name: sample3

source_name: SiHa

value: SiHa


title: HEK293T cells,pre-gRNA,rep3

description:
HEK293T_pre_gRNA_rep3
HEK293T_RNAseq_raw_counts.txt.gz

value: transfected with pre-gRNA plasmid


title: SiHa cells, siADAR1 exp1

description: Library name: sample2


title: SiHa cells, siADAR1 exp2

description: Library name: sample4


title: VCaP_GRO_DexDHT_rep1


title: HEK293T cells,pre-gRNA,rep2

description:
HEK293T_pre_gRNA_rep2
HEK293T_RNAseq_raw_counts.txt.gz


title: Healthy donor 1

description:
miRNA
HD01

value: not applicable


title: SiHa cells, sictrl exp1

description: Library name: sample1


title: A11_XC01_M07_T006

description: MobiNova

value: LB


title: VCaP_GRO_DHT_rep2


title: A11_XC01_M07_T005

description: MobiNova


title: HEK293T cells,linear pcDNA3.1-neo,rep3

description:
HEK293T_linear_pcDNA3.1_neo_rep3
HEK293T_RNAseq_raw_counts.txt.gz

value: transfected with linear pcDNA3.1-neo plasmid


title: HEK293T cells,pre-gRNA,rep1

description:
HEK293T_pre_gRNA_rep1
HEK293T_RNAseq_raw_counts.txt.gz


title: A11_XC01_M07_T004

description: MobiNova


title: FOXG1 deletion, rep 2, scRNA

description: 10X Genomics

data_processing:
Reads from single cell (sc)RNAseq were aligned to the GRCh38 human reference genome, and the cell-by-gene count matrices were produced using the RNA STARSolo on the Galaxy Platform. Data were analysed using the Seurat R package v.4.3.0 with R v.4.2.2. The following parameters were used for filtering cells: cut_nUMI <- 500; cut_nGene <- 250; max_nGene <- 8500; cut_log10GenesPerUMI <- 0.80; cut_mito.Ratio <- 0.2; cut_ribo.Ratio <- 0.2.
Assembly: hg38
Supplementary files format and content: genes.tsv, matrix, barcodes.tsv

source_name: cerebral organoid

growth_protocol: hiPSC cell lines were grown in mTESR1 medium (Stem Cell, Canada) on Matrigel (Corning, USA). Control hiPSCs (FiPS Core, University Medicine Freiburg, Germany) were generated from fibroblast of a healthy donor (Craig-Mueller N, Hammad R, Elling R, Alzubi J, Timm B, Kolter J, Knelangen N, Bednarski C, Glaser B, Ammann S, Ivics Z, Fischer J, Speckmann C, Schwarz K, Lachmann N, Ehl S, Moritz T, Henneke P, Cathomen T (2020) Modeling MyD88 Deficiency In Vitro Provides New Insights in Its Function. Front Immunol 11:608802. doi:10.3389/fimmu.2020.608802). Cerebral organoids were generated according to an adapted version of the standard protocol (Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA (2013) Cerebral organoids model human brain development and microcephaly. Nature 501 (7467):373-379. doi:10.1038/nature12517), as described (Gabriel E, Gopalakrishnan J (2017) Generation of iPSC-derived Human Brain Organoids to Model Early Neurodevelopmental Disorders. J Vis Exp (122). doi:10.3791/55372). Briefly, 35.000 cells per well of a v-shaped, non-coated 96 well plate were seeded, centrifuged and treated as described. The organoids were cultivated in organoid medium until day 105 counting from the day of transfer into the spinning bottles. Half of the medium was exchanged weekly until week 10 and twice a week afterwards. Two organoids of either control hiPSCs or FOXG1del cells were collected for scRNA-seq library preparation.

extract_protocol:
Two organoids of each line were collected at day 105 and single cells were obtained according to the protocol of the Papain Dissociation System (Worthington, Lakewood, USA), with centrifugation steps carried out at 4°C.
Library preparation was performed with the 10x Genomics kit according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1, 10X Genomics, CA, USA).

treatment_protocol: no treatment

value: cerebral organoid

value: FOXG1 deletion


title: VCaP_GRO_DHT_rep1


title: FOXG1 deletion, rep1, scRNA

description: 10X Genomics


title: HEK293T cells,linear pre-gRNA,rep1

description:
HEK293T_linear_pre_gRNA_rep1
HEK293T_RNAseq_raw_counts.txt.gz


title: control, rep 2, scRNA

description: 10X Genomics

value: healthy control


title: VCaP_GRO_Dex_rep2


title: VCaP_GRO_Dex_rep1


title: A11_XC01_M07_T002

description: MobiNova


title: HEK293T cells,linear pcDNA3.1-neo,rep1

description:
HEK293T_linear_pcDNA3.1_neo_rep1
HEK293T_RNAseq_raw_counts.txt.gz


title: A11_XC01_M07_T007

description: MobiNova

value: HC


title: control, rep 1,scRNA

description: 10X Genomics


title: VCaP_GRO_EtOH_rep2


title: HEK293T cells,pcDNA3.1-neo,rep3

description:
HEK293T_pcDNA3.1_neo_rep3
HEK293T_RNAseq_raw_counts.txt.gz

value: WT

value: transfected with pcDNA3.1-neo plasmid


title: organoid_FOXG1ChIP input

data_processing:
Sequencing data was processed in usegalaxy.eu platform.
Fastq Quality Control using FastQC  (v. 0.11.9). Adapter trimming and quality filtering was done using Trim Galore! (v. 0.6.7)
Trimmed and quality filtered reads were aligned to hg38 genome assembly using Bowtie 2 (v. 2.5.0) and normalized (log2) to the input using bamcompare (v. 3.5.4). ChIPseeker (v. 1.28.3) was used to annotate genes to the peaks using the Gencode annotation (evidence-based annotation of the human genome (GRCh38), version 45 (Ensembl 111)) on MACS (v. 2.2.7.1) called narrow peaks.
heatmap values were calculated with computeMatrix (v. 3.5.1.0.0) with a distance upstream and downstream of the TSS: 5000 bp (Gencode annotation (evidence-based annotation of the human genome (GRCh38), version 45 (Ensembl 111)) and clustered and visualized with plotHeatmap (v. 3.5.1.0.1, kmeans (k=4)).
Assembly: hg38
Supplementary files format and content: Bowtie2_on_hCO-ctr-FOXG1-ChIPseq_alignments.bam: mapped ChIPseq reads in bam format
Supplementary files format and content: Bowtie2_on_hCO-ctr-Input_alignments.bam: : mapped input reads in bam format
Supplementary files format and content: bamCompare_on_hCO-FOXG1-ChIPseq_hg38_LFC.bigwig:  comparison of mapped reads FOXG1-ChIPseq vs. Input, type of comparison: log2
Supplementary files format and content: MACS2_callpeak_on_hCO-FOXG1-ChIPseq_hg38.bed: called narrow peaks in bed format
Supplementary files format and content: ChIPseeker_on_hCO-FOXG1-ChIPseq_hg38_Annotated_Peaks.tabular: Annotated MACS called peaks in tabular format
Supplementary files format and content: plotHeatmap_on_hCO-FOXG1-ChIPseq_hg38_sorted_filtered_regions.bed: filtered and clustered regions around the TSSs

source_name: iPSC derived cerebral organoid

growth_protocol: hiPSC cell lines were grown in mTESR1 medium (Stem Cell, Canada) on Matrigel (Corning, USA). Control hiPSCs (FiPS Core, University Medicine Freiburg, Germany) were generated from fibroblast of a healthy donor (Craig-Mueller N, Hammad R, Elling R, Alzubi J, Timm B, Kolter J, Knelangen N, Bednarski C, Glaser B, Ammann S, Ivics Z, Fischer J, Speckmann C, Schwarz K, Lachmann N, Ehl S, Moritz T, Henneke P, Cathomen T (2020) Modeling MyD88 Deficiency In Vitro Provides New Insights in Its Function. Front Immunol 11:608802. doi:10.3389/fimmu.2020.608802). Cerebral organoids were generated according to an adapted version of the standard protocol (Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA (2013) Cerebral organoids model human brain development and microcephaly. Nature 501 (7467):373-379. doi:10.1038/nature12517), as described (Gabriel E, Gopalakrishnan J (2017) Generation of iPSC-derived Human Brain Organoids to Model Early Neurodevelopmental Disorders. J Vis Exp (122). doi:10.3791/55372). Briefly, 35.000 cells per well of a v-shaped, non-coated 96 well plate were seeded, centrifuged and treated as described. The organoids were cultivated in organoid medium until day 105 counting from the day of transfer into the spinning bottles. Half of the medium was exchanged weekly until week 10 and twice a week afterwards. Two organoids of either control hiPSCs or FOXG1del cells were further analysed after 105 days of cultivation in organoid medium using FOXG1-ChIPseq by active motif.

extract_protocol:
Two organoids were fixed and collected for subsequent ChIP-seq experiments according to the instructions of the servicing company (Active Motif). Briefly, cells or tissue were fixed by adding 1/10 volume formaldehyde solution (11% Formaldehyde, 0.1 M NaCl, 1 mM EDTA pH=8.0, 50 mM HEPES pH=7.9) directly to the medium and incubated at room temperature (RT) with agitation. Fixation was stopped by adding 1/20 volume 2.5 M Glycine solution (Roth, Germany) and incubating for 5 min at RT. Cells were scraped from the plates and transferred into conical tubes, and centrifuged at 800 rpm at 4°C for 10 min. Cells were resuspended and washed twice in chilled PBS-Igepal solution (0.5% Igepal CA-360 (Sigma) in 1X PBS pH 7.4 (Gibco)), and a third time in PBS-Igepal-PMSF (phenylmethylsulfonyl fluoride) solution (0.5% Igepal, 1 mM PMSF (Sigma) in 1X PBS pH 7.4). The supernatant was completely removed and cell pellets were snap frozen in liquid nitrogen and stored at -80°C until following ChIP-seq experiments. ChIPseq was performed at active motif using FOXG1 antibody (abcam ab18259)
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara)
ChIP-Seq libraries were sequenced on Illumina NovaSeq 6000 as 75-nt single end reads.

value: iPSC derived cerebral organoid

tag: age

value: Day 105

value: neural progenitors and neurons

value: wildtype


title: A11_XC01_M07_T001

description: MobiNova

value: immune cells and tumor cells


title: HEK293T cells,pcDNA3.1-neo,rep2

description:
HEK293T_pcDNA3.1_neo_rep2
HEK293T_RNAseq_raw_counts.txt.gz

value: human embryonic kidney cell


title: organoid_FOXG1ChIP


title: MI

city: Chicago

first: Edward

last: Thorp

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were performed using CellRanger v7.0.1
Aligned reads were then filtered for valid barcodes and UMIs to generate gene-cell matrices used for downstream analysis. To filter low-quality cells from the dataset, gene-cell matrices were read into R using Seurat (v4.3.0) R toolkit
Cells that expressed less than 300 features, less than 1000 unique molecular identifiers, and greater than 30% mitochondrial gene content were removed. Additionally, features that were not detected in at least ten single cells were removed.
Next, we normalized for cell cycle variation and used sctransform (v0.3.5) based normalization to recover sharper biological distinctions compared to log-normalization. To mitigate potential batch effects that are common for scRNAseq data, each dataset for each sample was integrated using Seurat’s FindIntegrationAnchors and IntegrateData function.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Adult C57BL/6J females were subjected to Sham or MI surgery (n=5 per group). 7 days after surgery, brains were collected and processed into single cell solutions using a Neuronal Tissue Dissociation Kit (P) following manufacturer's instructions. Myelin debris was removed by density gradient centrifugation and biological replicates were pooled together by condition for processing in the 10X Genomics Chromium System. A targeted number of 10,000 cells were loaded for each experimental condition. Single cell mRNA sequencing libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit (v3.1) pipeline following manufacturer protocols.
Library was performed following manufacturer's instructions (Single cell 3' v3, 10X Genomics)

value: Brain

value: Sham


title: LI46

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description: Library name: LI46

data_processing:
Data were analysed using the Lexogen's proprietary sequence analysis platform. Trimming using Bbduk and quality control with FASTQC.
Assembly: Assembly: HGhg38
Supplementary files format and content: raw counts; .txt
Supplementary files format and content: lcpm; .txt

source_name: Retroperitoneal Sarcoma

extract_protocol:
Qiagen Rneasy microRNA kit with Dnase treatment
Libraries were prepared according to Lexogen's instructions accompanying the Kit (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina)

value: Retroperitoneal Sarcoma

tag: type of_material

value: FFPE


title: HEK293T cells,pcDNA3.1-neo,rep1

description:
HEK293T_pcDNA3.1_neo_rep1
HEK293T_RNAseq_raw_counts.txt.gz

data_processing:
The quality of raw data were evaluated by FastQC (v0.12.1)
Sequence reads were aligned to the human reference genome hg19 by HISAT2 (2.1.0)
The reads(counts) for each gene were obtained using featureCounts (v2.0.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RNA-seq three biological replicates raw counts for each sample in HeLa, NCM460,HEK293T, HCT116 and L02 cells transfected with empty plasmid,circular or linear pcDNA3.1-neo plasmids and circular or linear pre-gRNA plasmids.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the LM-seq protocol.


title: UPF3B_KO, NPC, Rep6

city: La Jolla

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106).
To detect genes expression, reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCh38 (Ensembl version 106). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. Differentially expressed genes (DEGs) were defined using the DESeq2 program with the following thresholds: |Log2FC|>1 and q-val<0.01.
To measure transcript (or isoforms) expression levels, we used the RSEM package. Differential expressed transcripts (DETs) were defined using the EBSeq program with the following thresholds: PPEE<0.01 and PostFC>2 or <0.5.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited txt file including raw counts for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen), following the manufacturer’s protocol. Ribosomal RNAs were removed using NEBNext® rRNA Depletion Kit v2 (New England Biolabs).
The enriched mRNA was then used to make the library using the SMART-Seq® v4 PLUS Kit (Takara Bio), as per manufacturer's instructions. Libraries were sequenced (pair-end reads) with an Illumina NovaSeq 6000 platform for 100 cycles at the UCSD institute for Genomic Medicine (IGM) core.

treatment_protocol: hESCs were harvested and seeded as single cells at 6x104 cells per cm2. Once 80% confluent, the hESCs were cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gemini), 5 μM Rock inhibitor, 1 μM Dorsomorphin and 10 μM SB431542 (STEMCELL Technologies) for 2 days. Colonies were then cut into a big chess pattern, and cultured in DMEM/F12 (Gibco) supplemented with N2 (1:100; Gibco), 1 μM Dorsomorphin and 10 μM SB431542 for 5 days under rotation (95 rpm) inside a 37°C incubator. Embryoid bodies were then replated on plates coated with hESC-qualified Matrigel (Corning) in DMEM/F12 media supplemented with N2 (1:200; Gemini), and Gem21 (1:100; Gemini) for 7 days. Neural rosettes were picked and dissociated with Accutase (Gibco) and plated on plates coated with poly-ornithine/Laminin in DMEM/F12 media supplemented with N2 (1:200; Gemini), Gem21 (1:100; Gemini), and 20 ng/mL bFGF (Sigma). Homogeneous populations of NPCs were achieved after 2-3 passages with accutase in the same condition.

value: human embryonic stem cells

value: Induced to form NPCs


title: Sham

description: 10X Genomics

tag: tissue

value: MI


title: A11_XC01_M07_T003

description: MobiNova

tag: cell type

value: LB


title: HEK293T cells,control,rep3

description:
HEK293T_control_rep3
HEK293T_RNAseq_raw_counts.txt.gz

tag: cell line

value: control


title: HEK293T cells,linear pcDNA3.1-neo,rep2

description:
HEK293T_linear_pcDNA3.1_neo_rep2
HEK293T_RNAseq_raw_counts.txt.gz

tag: genotype

value: WT

value: transfected with linear pcDNA3.1-neo plasmid


title: UPF3B_KO, NPC, Rep5

tag: treatment


title: Upf3b_KO, Cere, Rep3

description: Cerebellum.counts.matrix.txt

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCm39 (Ensembl version 105).
To detect genes expression, reads were filtered for quality and aligned with STAR (2.5.2b) against the GRCm39 (Ensembl version 105). The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts. Differentially expressed genes (DEGs) were defined using the DESeq2 program with the following thresholds: |Log2FC|>1 and q-val<0.01.
To measure transcript (or isoforms) expression levels, we used the RSEM package. Differential expressed transcripts (DETs) were defined using the EBSeq program with the following thresholds: PPEE<0.01 and PostFC>2 or <0.5.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt file including raw counts for each sample

source_name: Cerebellum

growth_protocol: This study was carried out in strict accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the University of California, San Diego. The protocol was approved by the IACUC at the University of California, San Diego (permit number: S09160). All mice were housed under a 12 hr light:12 hr dark cycle and provided with food and water ad libitum.

value: Cerebellum


title: LH87

description: Library name: LH87


title: HEK293T cells,control,rep2

description:
HEK293T_control_rep2
HEK293T_RNAseq_raw_counts.txt.gz


title: Upf3b_KO, Cere, Rep4

description: Cerebellum.counts.matrix.txt


title: HEK293T cells,control,rep1

description:
HEK293T_control_rep1
HEK293T_RNAseq_raw_counts.txt.gz


title: UPF3B_KO, NPC, Rep4


title: LH85

description: Library name: LH85


title: UPF3B_KO, NPC, Rep3


title: LH83

description: Library name: LH83


title: VCaP_GRO_EtOH_rep1

value: VCaP

value: Vertebral Cancer of the Prostate


title: NCM460 cells,linear pre-gRNA,rep3

description:
NCM460_linear_pre_gRNA_rep3
NCM460_RNAseq_raw_counts.txt.gz

value: human normal adult colon mucosal epithelial cell

value: transfected with linear pre-gRNA plasmid


title: UPF3B_KO, NPC, Rep2


title: LH70

description: Library name: LH70


title: NCM460 cells,linear pre-gRNA,rep2

description:
NCM460_linear_pre_gRNA_rep2
NCM460_RNAseq_raw_counts.txt.gz


title: Ctrl, Cere, Rep4

description: Cerebellum.counts.matrix.txt

value: Ctrl


title: LH67

description: Library name: LH67


title: Ctrl, Cere, Rep3

description: Cerebellum.counts.matrix.txt


title: NCM460 cells,linear pre-gRNA,rep1

description:
NCM460_linear_pre_gRNA_rep1
NCM460_RNAseq_raw_counts.txt.gz


title: LI44

description: Library name: LI44


title: Ctrl_NPC_Rep6


title: LH64

description: Library name: LH64


title: Ctrl, Cere, Rep2

description: Cerebellum.counts.matrix.txt


title: NCM460 cells,pre-gRNA,rep3

description:
NCM460_pre_gRNA_rep3
NCM460_RNAseq_raw_counts.txt.gz

value: transfected with pre-gRNA plasmid


title: Ctrl, Cere, Rep1

description: Cerebellum.counts.matrix.txt


title: LH61

description: Library name: LH61


title: Ctrl_NPC_Rep5


title: Upf3b_KO, Cere, Rep2

description: Cerebellum.counts.matrix.txt


title: NCM460 cells,pre-gRNA,rep2

description:
NCM460_pre_gRNA_rep2
NCM460_RNAseq_raw_counts.txt.gz


title: Ctrl_NPC_Rep4


title: LH58

description: Library name: LH58


title: Upf3b_KO, FC, Rep4

description: FC.counts.matrix.txt

source_name: frontal cortex

value: frontal cortex


title: Ctrl_NPC_Rep3


title: NCM460 cells,linear pcDNA3.1-neo,rep3

description:
NCM460_linear_pcDNA3.1_neo_rep3
NCM460_RNAseq_raw_counts.txt.gz


title: Upf3b_KO, FC, Rep3

description: FC.counts.matrix.txt


title: Upf3b_KO, Cere, Rep1

description: Cerebellum.counts.matrix.txt


title: UPF3B_KO, NPC, Rep1


title: Ctrl_NPC_Rep2


title: LG39

description: Library name: LG39

value: Retroperitoneal Sarcoma


title: NCM460 cells,linear pcDNA3.1-neo,rep2

description:
NCM460_linear_pcDNA3.1_neo_rep2
NCM460_RNAseq_raw_counts.txt.gz


title: LG36

description: Library name: LG36

value: FFPE


title: Upf3b_KO, FC, Rep1

description: FC.counts.matrix.txt


title: Upf3b_KO, FC, Rep2

description: FC.counts.matrix.txt


title: Ctrl_NPC_Rep1

value: human embryonic stem cells


title: UPF3B_KO, ESC, Rep6

growth_protocol: Cells were cultured in StemFlexTM medium (Gibco) on plates coated with hESC-qualified Matrigel (Corning).


title: LG31

description: Library name: LG31


title: Ctrl, FC, Rep4

description: FC.counts.matrix.txt


title: NCM460 cells,pcDNA3.1-neo,rep3

description:
NCM460_pcDNA3.1_neo_rep3
NCM460_RNAseq_raw_counts.txt.gz

value: transfected with pcDNA3.1-neo plasmid


title: LG12

description: Library name: LG12


title: UPF3B_KO, ESC, Rep5


title: Ctrl, FC, Rep3

description: FC.counts.matrix.txt


title: NCM460 cells,pcDNA3.1-neo,rep2

description:
NCM460_pcDNA3.1_neo_rep2
NCM460_RNAseq_raw_counts.txt.gz


title: NCM460 cells,pre-gRNA,rep1

description:
NCM460_pre_gRNA_rep1
NCM460_RNAseq_raw_counts.txt.gz


title: Ctrl, FC, Rep2

description: FC.counts.matrix.txt


title: LG09

description: Library name: LG09


title: LG41

description: Library name: LG41


title: UPF3B_KO, ESC, Rep3


title: LG06

description: Library name: LG06


title: UPF3B_KO, ESC, Rep4


title: NCM460 cells,pcDNA3.1-neo,rep1

description:
NCM460_pcDNA3.1_neo_rep1
NCM460_RNAseq_raw_counts.txt.gz


title: 5LRV_Monocytes_Empty_ATGCGCAG_ATTAGACG

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The raw sequences are aligned to the GRCm38 reference genome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: tar gzipped kallisto quantification output.

growth_protocol: Mice. C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed in a conventional, pathogen-free facility at the Hale Building for Transformative Medicine under a standard 12h light/dark cycle at 20–23°C and 50% humidity with access to water and food ad libitum, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC). Transgenic mouse genotypes were confirmed by PCR (Transnetyx). When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement.

extract_protocol:
Cells were lysed in 350µL RLT buffer and stored at -80°C until extraction following manufacturer’s instructions. RNA was transcribed to cDNA using the High-Capacity cDNA Reverse Transcription Kit (Life Technologies, 4368813)
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: strain

value: Female

value: 8 week

value: Brain

value: Monocytes

value: TRAIL Knockdown by sgRNA


title: NCM460 cells,control,rep3

description:
NCM460_control_rep3
NCM460_RNAseq_raw_counts.txt.gz

value: WT

value: control


title: NCM460 cells,control,rep2

description:
NCM460_control_rep2
NCM460_RNAseq_raw_counts.txt.gz


title: LE36

description: Library name: LE36


title: NCM460 cells,control,rep1

description:
NCM460_control_rep1
NCM460_RNAseq_raw_counts.txt.gz


title: Ctrl, FC, Rep1

description: FC.counts.matrix.txt


title: LE34

description: Library name: LE34


title: LG00

description: Library name: LG00


title: HeLa cells,linear pre-gRNA,rep3

description:
HeLa_linear_pre_gRNA_rep3
HeLa_RNAseq_raw_counts.txt.gz

source_name: HeLa

value: HeLa

value: human cervical adenocarcinoma cell


title: UPF3B_KO, ESC, Rep1


title: 5LRV_Monocytes_Empty_CGGAGCCT_ATTAGACG


title: NCM460 cells,linear pcDNA3.1-neo,rep1

description:
NCM460_linear_pcDNA3.1_neo_rep1
NCM460_RNAseq_raw_counts.txt.gz

value: human normal adult colon mucosal epithelial cell

value: transfected with linear pcDNA3.1-neo plasmid


title: LE32

description: Library name: LE32


title: 5LRV_Monocytes_Empty_GGAGCTAC_ATTAGACG


title: HeLa cells,linear pre-gRNA,rep2

description:
HeLa_linear_pre_gRNA_rep2
HeLa_RNAseq_raw_counts.txt.gz

value: transfected with linear pre-gRNA plasmid


title: 5LRV_Monocytes_Empty_TACGCTGC_ATTAGACG


title: Ctrl_ESC_Rep4

value: Ctrl


title: 5LRV_Monocytes_anti-TRAIL_TCGACGTC_AGGCTTAG

value: Control


title: LE28

description: Library name: LE28

value: Retroperitoneal Sarcoma

value: FFPE


title: LE30

description: Library name: LE30


title: HeLa cells,linear pre-gRNA,rep1

description:
HeLa_linear_pre_gRNA_rep1
HeLa_RNAseq_raw_counts.txt.gz


title: Ctrl_ESC_Rep3

value: human embryonic stem cells


title: Ctrl_ESC_Rep2


title: UPF3B_KO, ESC, Rep2


title: LE25

description: Library name: LE25


title: 5LRV_Monocytes_anti-TRAIL_TGCAGCTA_AGGCTTAG

value: Female


title: HeLa cells,pre-gRNA,rep2

description:
HeLa_pre_gRNA_rep2
HeLa_RNAseq_raw_counts.txt.gz

value: transfected with pre-gRNA plasmid


title: HeLa cells,linear pcDNA3.1-neo,rep3

description:
HeLa_linear_pcDNA3.1_neo_rep3
HeLa_RNAseq_raw_counts.txt.gz


title: LE23

description: Library name: LE23


title: Ctrl_ESC_Rep6


title: Ctrl_ESC_Rep5


title: LD90

description: Library name: LD90


title: HeLa cells,linear pcDNA3.1-neo,rep2

description:
HeLa_linear_pcDNA3.1_neo_rep2
HeLa_RNAseq_raw_counts.txt.gz


title: HeLa cells,linear pcDNA3.1-neo,rep1

description:
HeLa_linear_pcDNA3.1_neo_rep1
HeLa_RNAseq_raw_counts.txt.gz


title: 5LRV_Microglia_Empty_ACTGAGCG_AGGCTTAG

value: 8 week

value: Brain

value: Microglia


title: 5LRV_Microglia_Empty_TAGCGCTC_AGGCTTAG

value: TRAIL Knockdown by sgRNA


title: UPF2_iKO_KD, NPC, Rep3

value: Induced to form NPCs


title: UPF2_iKO_KD, NPC, Rep6


title: LD80

description: Library name: LD80


title: LD84

description: Library name: LD84


title: HeLa cells,pre-gRNA,rep1

description:
HeLa_pre_gRNA_rep1
HeLa_RNAseq_raw_counts.txt.gz

value: HeLa

value: WT


title: 5LRV_Microglia_Empty_CCTAAGAC_AGGCTTAG


title: Ctrl_ESC_Rep1


title: 5LRV_Microglia_Empty_ATGCGCAG_AGGCTTAG


title: LD78

description: Library name: LD78


title: UPF2_iKO_KD, NPC, Rep2


title: 5LRV_Microglia_anti-TRAIL_CGGAGCCT_AGGCTTAG


title: UPF2_iKO_KD, NPC, Rep1


title: HeLa cells,pre-gRNA,rep3

description:
HeLa_pre_gRNA_rep3
HeLa_RNAseq_raw_counts.txt.gz

value: human cervical adenocarcinoma cell


title: 5LRV_Microglia_Empty_TACGCTGC_AGGCTTAG


title: HeLa cells,pcDNA3.1-neo,rep3

description:
HeLa_pcDNA3.1_neo_rep3
HeLa_RNAseq_raw_counts.txt.gz

value: transfected with pcDNA3.1-neo plasmid


title: 5LRV_Monocytes_anti-TRAIL_CGATCAGT_AGGCTTAG

value: Monocytes


title: UPF2_iKO_KD, NPC, Rep5


title: UPF2_iKO_KD, NPC, Rep4


title: LD82

description: Library name: LD82


title: LD72

description: Library name: LD72


title: HeLa cells,pcDNA3.1-neo,rep1

description:
HeLa_pcDNA3.1_neo_rep1
HeLa_RNAseq_raw_counts.txt.gz


title: 5LRV_Microglia_anti-TRAIL_GCGTAGTA_AGGCTTAG


title: 5LRV_Microglia_anti-TRAIL_ACTCGCTA_AGGCTTAG


title: HeLa cells,pcDNA3.1-neo,rep2

description:
HeLa_pcDNA3.1_neo_rep2
HeLa_RNAseq_raw_counts.txt.gz


title: LD69

description: Library name: LD69


title: 5LRV_Microglia_anti-TRAIL_GGAGCTAC_AGGCTTAG


title: UPF2_iKO, NPC, Rep6


title: LD67

description: Library name: LD67


title: LD65

description: Library name: LD65


title: UPF2_iKO, NPC, Rep3


title: HeLa cells,control,rep2

description:
HeLa_control_rep2
HeLa_RNAseq_raw_counts.txt.gz

value: control


title: HeLa cells,control,rep3

description:
HeLa_control_rep3
HeLa_RNAseq_raw_counts.txt.gz


title: UPF2_iKO, NPC, Rep4


title: HeLa cells,control,rep1

description:
HeLa_control_rep1
HeLa_RNAseq_raw_counts.txt.gz


title: UPF2_iKO, NPC, Rep2