title: siINTS11 RNA-seq Rep 3

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Untreated RNA-seq samples were mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
siNT and siINTS11 were first mapped to an ERCC spike genome, and reads not mappping to spike were subsequently mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
bigWigs output from STAR were used for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: bigWigs representing coverage (no normalization for untreated; DEseq-normalized for siNT and siINTS11)

treatment_protocol: Cells were either not treated or treated with siRNA (siNT or siINTS11) for 48 hours.

value: WT


title: PT6_late_CD3

status: Public on Oct 28 2022

type: SRA

city: Heidelberg

first: Michael

last: Kilian

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: PT6_late, sort CD3, T & NK cell subset bmref

extract_protocol:
Serial blood samples and BM aspirates were collected from patients treated with anti-BCMA TCE at variable time points, prior and post initiation of therapy and at relapse. Bone marrow mononuclear fractions were isolated through Ficoll density gradients coupled with magnetic sorting of CD3+ or CD45+ T cells.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
5' scRNA/TCR-seq

tag: tissue

value: human bone marrow mononuclear cells

tag: cell type

value: T and NK cells

tag: genotype

tag: treatment

value: relapsed-refractory multiple myeloma


title: PT5_late_CD3

source_name: PT5_late, sort CD3, T & NK cell subset bmref


title: PT5_early_CD3

source_name: PT5_early, sort CD3, T & NK cell subset bmref


title: siINTS11 RNA-seq Rep 2

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Embryonic stem cell

growth_protocol: INTS11Halo cells were maintained in SFES+2i/LIF.

extract_protocol:
RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.

value: Embryonic stem cell

tag: cell line


title: PT4_pre_CD3

source_name: PT4_pre, sort CD3, T & NK cell subset bmref


title: siNT RNA-seq Rep 3

value: siNT


title: PT4_late_CD3

source_name: PT4_late, sort CD3, T & NK cell subset bmref


title: siINTS11 RNA-seq Rep 1


title: PT3_pre_CD3

source_name: PT3_pre, sort CD3, T & NK cell subset bmref


title: PT3_late_CD3

source_name: PT3_late, sort CD3, T & NK cell subset bmref


title: siNT RNA-seq Rep 2


title: siNT RNA-seq Rep 1


title: PROTAC PRO-seq Rep 1

data_processing:
FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the mm10 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
Data was normalized to spike-in reads and  adjusted to account for variability in sequencing and spike batch.
Assembly: mm10
Supplementary files format and content: bigWigs representing 3' ends of RNA in 25 nt bins

extract_protocol:
Cells were permeabilized as in Reimer et al. 2021; run-ons were performed with biotinylated NTPs and then purified.
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

treatment_protocol: Cells were treated with DMSO or 500 nM PROTAC for 4 hours.

value: 500 nM PROTAC


title: DMSO TT-seq Rep 3

description: Other: 4sU RNA

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Samples were mapped to the Drosophila dm3 (spike) genome, and nonmapping reads subsequently mapped to mm10 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: mm10
Supplementary files format and content: bigWigs representing DEseq-normalized read coverage
Library strategy: TT-seq

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded totl RNA kit using the manufacturer's protocol.

treatment_protocol: Cells were treated with DMSO or 500 nM PROTAC for 4 hours and labled with 4sU for the final 20 minutes.

value: DMSO


title: PROTAC PRO-seq Rep 2


title: DMSO PRO-seq Rep 1


title: PT7_late_CD3

source_name: PT7_late, sort CD3, T & NK cell subset bmref


title: PT2_late_CD3

source_name: PT2_late, sort CD3, T & NK cell subset bmref


title: PT6_pre_CD3

source_name: PT6_pre, sort CD3, T & NK cell subset bmref


title: PROTAC INTS3 ChIP-seq Rep 2

library_source: genomic

data_processing:
Sequencing reads were filtered (requiring a mean quality score over 20) and trimmed to 50 bp.
Data from WT cells were mapped to a genome representing mm10 rRNA genes. Reads not mapping here were mapped to mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Data from INTS11Halo cells were first mapped to the Drosophila dm3 genome (spike) and reads not mapping here were subsequently mapped mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Mapped reads were converted to bedGraphs representing deduplicated fragment midpoints using extract_fragments.pl (DOI 10.5281/zenodo.5519914), which were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: INTS11Halo bigWigs represent deduplicated, background-subtracted, normalized fragment centers. WT bigWigs represent deduplicated fragment centers.

molecule: genomic DNA

extract_protocol:
Cells were crosslinked with formaldehyde for 10 minutes and quenched with glycine. After washing, cell pellets were resuspended in sonication buffer and sonicated using the Qsonica Q800R3 system. Chromatin was pre-cleared with Protein A agarose and incubated with the indicated antibody overnight. Protein A agarose beads were added and allowed to bind antibody-epitope complexes. IPs were washed extensively and eluted twice. DNA was purified using phenol/chloroform.
INTS11Halo eluates were spiked with Drosophila DNA. All libraries were constructed with the NEB NEBNext Ultra II DNA Library kit .

treatment_protocol: WT cells were not treated. INTS11Halo cells were treated with DMSO or 500 nM PROTAC for 4 hours.

tag: chip antibody

value: INTS3 (Bethyl Labs, A302-051A)


title: PT19_pre_CD3

source_name: PT19_pre, sort CD3, T & NK cell subset bmref


title: PROTAC INTS3 ChIP-seq Rep 1


title: Day7_2

city: Beijing

first: Tao

last: Zou

address: 27, Taipingroad

country: China

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: NOT PROVIDED
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each sample

source_name: cranial dura

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: strain

tag: age

value: wild type

value: cranial dura


title: PT16_late_CD3

source_name: PT16_late, sort CD3, T & NK cell subset bmref


title: PT16_pre_CD3

source_name: PT16_pre, sort CD3, T & NK cell subset bmref


title: inducible Tet-TKO mESCs after tamoxifen treatment, rep2

city: La Jolla

first: Hugo

last: Sepulveda

state: California

address: 9420 Athena Circle

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

data_processing:
Paired reads were mapped with STAR using the parameters (--outFilterMultimapNmax 1 --outSAMattributes All --outSAMprimaryFlag OneBestScore –sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate).
Counts per gene were obtained from htseq-count (version 0.7.1.); Differential Gene Expression was done with R (version 3.5.2) using the DESEQ2 package (version 1.26.0).
A gene was considered DGE if both the absolute Log2FC was ≥ 0.5 and a adj.pvalue (FDR) ≤0.05 threshold was met.
Genome_build: Mus Musculus genome (version mm9)
Supplementary_files_format_and_content: Tab-Separated Files with Normalized expression per sample.

source_name: inducible Tet-TKO mESCs

growth_protocol: mESC were cultured under 2i-conditions (CHIR99021 and PD0325901) using Mouse Embryonic Fibroblasts (MEFs) as feeders.

extract_protocol:
CD326+/GFP+/Live/Thy1.2-/LiveDead dye- mESCs were sorted from Tamoxifen-treated mESCs (either Ctrl or TetiTKO). And  total RNA were extracted using Qiagen RNeasy plus micro kit
Libraries were constructed using the Smart2seq protocol.
50x50bp pair end sequencing.

treatment_protocol: mESCs were treated with tamoxifen (1µM) for 2.5 days and then cultured for 4 additional days.

value: CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki and CreERT2 wt/ki; Tet1/2/3fl/fl; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki

value: mESCs

value: 6.5 days after tamoxifen-treatment

value: tamoxifen (1µM) treatment for 2.5 days then 4 additional days in culture

value: Tet TKO


title: DMSO INTS11 ChIP-seq Rep 1

value: INTS11 (Sigma, HPA029025)


title: Ctrl mESCs after tamoxifen treatment, rep3

source_name: Control mESCs

value: CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki and CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki

value: control


title: Ctrl mESCs after tamoxifen treatment, rep2


title: PT14_late_CD3

source_name: PT14_late, sort CD3, T & NK cell subset bmref

value: human bone marrow mononuclear cells

value: T and NK cells


title: PT18_pre_CD3

source_name: PT18_pre, sort CD3, T & NK cell subset bmref

value: relapsed-refractory multiple myeloma


title: PROTAC INTS11 ChIP-seq Rep 2

value: Embryonic stem cell


title: PT17_late_CD3

source_name: PT17_late, sort CD3, T & NK cell subset bmref


title: PT8_late_CD3

source_name: PT8_late, sort CD3, T & NK cell subset bmref


title: PT2_pre_CD3

source_name: PT2_pre, sort CD3, T & NK cell subset bmref


title: PT2_early_CD3

source_name: PT2_early, sort CD3, T & NK cell subset bmref


title: DMSO INTS3 ChIP-seq Rep 2

source_name: Embryonic stem cell


title: PT19_late_CD3

source_name: PT19_late, sort CD3, T & NK cell subset bmref


title: PROTAC INTS11 ChIP-seq Rep 1

value: 500 nM PROTAC


title: PT3_early_CD3

source_name: PT3_early, sort CD3, T & NK cell subset bmref


title: DMSO PRO-seq Rep 2

value: DMSO


title: PT17_pre_CD3

source_name: PT17_pre, sort CD3, T & NK cell subset bmref


title: DMSO INTS3 ChIP-seq Rep 1

value: INTS3 (Bethyl Labs, A302-051A)


title: DMSO INTS11 ChIP-seq Rep 2


title: PT18_late_CD3

source_name: PT18_late, sort CD3, T & NK cell subset bmref


title: inducible Tet-TKO mESCs after tamoxifen treatment, rep3


title: RNA_Epiblast_IVC_rep1

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
RNA-sequencing data
SM2_Epiblast_IVC_counts.csv

data_processing:
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
RNA-seq: For Smart-seq2 data, raw sequencing data were processed as our previously reported (Gu et al., 2019). Briefly, the raw reads were trimmed by using Cutadapt (v1.15). The sequences for adapters, oligo-dT, TSO sequences were trimmed from raw reads. The trimmed reads were further aligned to the mm9 mouse transcriptome by using STAR (v2.6.0a). Raw counts for genes expression were quantified by using HTSeq (v0.10.0). For bulk RNA-seq, raw sequencing data was processed by Trim Galore (v0.6.6) and was further aligned to the mouse transcriptome by using STAR (v2.6.0a). The 33  featureCounts (v2.0.1) was used for raw counts of genes expression. In this study, for comparing among different datasets, gene expression levels were defined as log2(TPM+1).
scBS-seq: Adaptor sequences, random primers and low-quality bases were removed by Trim Galore (v0.6.6). Reads shorter than 50 bp after trimming were excluded. The retained reads were then mapped to the mouse reference genome mm9 by Bismark (v0.23.0) in paired-end mode, and unmapped reads were re-mapped to the reference genome in single-end mode. SAMtools (v0.1.18) were adopted to remove PCR duplicates. The methylation level of CpG and CH sites were quantified by MethylDackel (v0.5.0).
scCOOL-seq: The pipeline of data processing of single-cell COOL-seq data was basically the same as the pipeline of processing single-cell bisulfite sequencing data which has been described (Gu et al., 2019; Yan et al., 2021). After determination of CpG and CH methylation level by MethylDackel, the WCG (W=A or T) and GCH (H= A,T or C) sites were summed from each single cell.
Genome_build: mm9
Supplementary_files_format_and_content: *bw: bigwig files; *.xls.gz: Count matrix in tab/comma-separated value files

source_name: Mouse IVC Epiblast

extract_protocol:
To collect preimplantation embryos, 6-8week old females (C57BL/6) were super-ovulated by injection of PMSG and hCG. MII oocytes were collected at 14-15 hours after hCG injection. As to preimplantation embryos, superovulated female mice were mated with either C57BL/6 or PWK males. Embryos were collected at 25-26 h (zygotes), 42-43 h (2-cell), 56-57 h (4-cell), 70-71 h (8-cell), and 94-96 h (blastocysts) after hCG injection. To isolate pronuclei, mouse zygotes at PN3- PN4 stages were collected and pronucleus were isolated as previously described (Guo et al., 2014). Zygotes which were maternally deficient in Tet3 were obtained through Zp3-Cre mediated conditional knockout in oocytes as previously described (Guo et al., 2014). To inhibit DNA replication, zygotes were treated with aphidicolin until the collection of pronuclei (Guo et al., 2014). The inhibition of DNA replication in mouse zygotes was validated by EdU incorporation assay.
ACE-seq: The construction of ACE-seq libraries followed the published protocol (Schutsky et al., 2018), with minor modifications. Fragmented gDNA was first modified using UDP- glucose and T4 Phage β-glucosyltransferase at 37 °C for 1 h. Then 0.1 N NaOH was added to the modified gDNA for denaturation at 55 °C for 10 min. APOBEC enzyme was used to deaminate gDNA at 37°C for 3 hrs. After deamination, gDNA was purified using Ampure XP beads before library construction according to the TAILS procedure (Gu et al., 2019; Yan et al., 2021). Finally, the ACE-seq libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. scBS-seq: The zona pellucida of MII oocytes and 2-cell embryos were firstly removed by Tyrode's Solution. Construction of the scBS-seq or scCOOL-seq libraries were performed as previously described (Guo et al., 2017a; Smallwood et al., 2014). DNA libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. Single-cell RNA-seq: Single-cell RNA-seq of 2-cell embryos were conducted by using smart-seq2 protocol (Picelli et al., 2014). In brief, single cell was picked into lysis buffer and Poly(A)+ RNA was captured by Oligo(dT) primer. The first strand of cDNA was synthesized by reverse transcription, then amplified, purified and fragmented. Fragmented cDNA was processed to construct RNA-seq library by NEBNext UltraII DNA Library Prep Kit for Illumina.
ACE-seq, scBS-seq and scRNA-seq

value: C57BL/6(mother) x C57BL/6(father)

value: WT


title: RNA_Epiblast_IVC_rep2


title: inducible Tet-TKO mESCs after tamoxifen treatment, rep1

value: CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki and CreERT2 wt/ki; Tet1/2/3fl/fl; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki


title: PT15_late_CD3

source_name: PT15_late, sort CD3, T & NK cell subset bmref


title: PT14_pre_CD3

source_name: PT14_pre, sort CD3, T & NK cell subset bmref


title: PT11_late_CD3

source_name: PT11_late, sort CD3, T & NK cell subset bmref


title: Ctrl mESCs after tamoxifen treatment, rep1

value: mESCs


title: PT13_late_CD3

source_name: PT13_late, sort CD3, T & NK cell subset bmref


title: PT15_pre_CD3

source_name: PT15_pre, sort CD3, T & NK cell subset bmref


title: PT13_pre_CD3

source_name: PT13_pre, sort CD3, T & NK cell subset bmref


title: RNA_Epiblast_E6.5_ND_rep1

description:
RNA-sequencing data
SM2_Epiblast_PGC_counts.csv

source_name: Mouse Epiblast E6.5


title: RNA_Epiblast_E6.5_ND_rep2


title: WGBS_Epiblast_IVC_rep2

description: Bisulfite-sequencing data profiled by bisulfite sequencing


title: PT10_late_CD3

source_name: PT10_late, sort CD3, T & NK cell subset bmref


title: ACE_PGC_E12.5_rep2

description: ACE-Seq sequencing data profiled by ACE-Seq

source_name: Mouse PGCs E12.5

value: C57BL/6(mother) x PWK(father)


title: ACE_Epiblast_IVC_rep2


title: PT1_early_CD3

source_name: PT1_early, sort CD3, T & NK cell subset bmref


title: ACE_PGC_E11.5_rep1

source_name: Mouse PGCs E11.5


title: ACE_PGC_E9.5_rep2

source_name: Mouse PGCs E9.5


title: ACE_Epiblast_IVC_rep1


title: PT11_pre_CD3

source_name: PT11_pre, sort CD3, T & NK cell subset bmref


title: PT1_late_CD3

source_name: PT1_late, sort CD3, T & NK cell subset bmref


title: WGBS_Epiblast_IVC_rep1


title: ACE_PGC_E11.5_rep2


title: ACE_PGC_E9.5_rep1


title: PT10_pre_CD3

source_name: PT10_pre, sort CD3, T & NK cell subset bmref


title: ACE_Neuron_Nuclei_rep1

source_name: Mouse neuron nuclei


title: ACE_mESC_TetTKO_rep2

source_name: Mouse ESCs


title: ACE_PGC_E12.5_rep1


title: ACE_mESC_Serum_rep2

source_name: Primed mouse ESCs


title: ACE_Neuron_Nuclei_rep2


title: ACE_PGC_E11.5_rep3


title: ACE_mESC_N2B27_rep2

source_name: Naïve Mouse ESCs


title: ACE_mESC_N2B27_rep1


title: ACE_M_Pronucleus_TetCKO_rep1

source_name: Mouse male pronucleus

value: Tet CKO


title: ACE_mESC_Serum_rep1


title: ACE_M_Pronucleus_rep2


title: ACE_M_Pronucleus_TetCKO_rep2


title: ACE_M_Pronucleus_rep1


title: ACE_M_Pronucleus_Aph_rep1

value: Aphidicolin


title: ACE_M_Pronucleus_Aph_rep2


title: ACE_mESC_TetTKO_rep1

value: Tet TKO


title: ACE_M_PGC_E16.5_rep1

source_name: Mouse male PGCs E16.5


title: ACE_M_PGC_E16.5_rep4


title: ACE_M_PGC_E13.5_rep4

source_name: Mouse male PGCs E13.5


title: ACE_M_PGC_E16.5_rep2


title: ACE_M_PGC_E16.5_rep3


title: ACE_F_Pronucleus_TetCKO_rep3

source_name: Mouse female pronucleus


title: ACE_F_Pronucleus_TetCKO_rep2


title: ACE_F_Pronucleus_TetCKO_rep1


title: ACE_M_PGC_E13.5_rep3


title: ACE_M_PGC_E13.5_rep1


title: ACE_M_PGC_E13.5_rep2


title: ACE_F_Pronucleus_Aph_rep3


title: ACE_F_Pronucleus_rep1


title: ACE_F_Pronucleus_Aph_rep2


title: ACE_F_Pronucleus_rep2


title: ACE_F_Pronucleus_Aph_rep4


title: ACE_F_Pronucleus_Aph_rep1


title: ACE_F_PGC_E16.5_rep4

source_name: Mouse female PGCs E16.5


title: ACE_F_PGC_E16.5_rep2


title: ACE_F_PGC_E13.5_rep4

source_name: Mouse female PGCs E13.5


title: ACE_F_PGC_E16.5_rep1


title: ACE_F_PGC_E16.5_rep3


title: ACE_Epiblast_E6.5_rep4

source_name: Mouse Epiblast E6.5


title: ACE_Epiblast_E6.5_rep2


title: ACE_Epiblast_E6.5_rep1


title: ACE_Blastocyst_E3.5_rep4

source_name: Mouse Blastocyst E3.5


title: ACE_Blastocyst_E3.5_rep5


title: ACE_Blastocyst_E3.5_rep3


title: ACE_4-Cell_rep2

source_name: Mouse 4-Cell


title: ACE_4-Cell_rep3


title: ACE_8-Cell_rep1

source_name: Mouse 8-Cell


title: ACE_Blastocyst_E3.5_rep1


title: ACE_2-Cell_rep1

source_name: Mouse 2-Cell


title: gd8

city: Cologne

first: Sven

last: Borchmann

address: Weyertal 115c

institute: University Of Cologne

data_processing:
FASTQ files of 3’ UTR RNA-sequencing were checked for quality using FastQC (version 0.11.4).
Reads were mapped to the mouse reference genome GRCm38 (p6) using the STAR aligner (version 2.7.0).
Expression was quantified prior to downstream analysis with RSEM (version 1.3.1).
Analyses were run on the computing cluster of the Regional Computing Center of the University of Cologne (RRZK).
Gene expression of specific genes was compared by comparing z-scores of counts per million (CPM).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated .txt files are provided. One processed data file is provided for each one of three experiments which each consist of multiple experimental groups. Within each experiment data has been z-score normalized. Each column contains processed data from one sample and can be identified with the same identifier as each sample's raw data

extract_protocol:
RNA was extracted from fresh frozen (FF) tissue with the RNeasy Mini Kit (Qiagen) and from FFPE tissue with the RSC RNA FFPE Kit (Maxwell, San Diego, CA). Both where used according to manufacturer’s instructions.
Only FF or FFPE samples were compared among each other. 3´mRNA libraries were generated from total RNA using the Lexogen QuantSeq kit according to the standard protocol. After validation (2200 TapeStation, Agilent Technologies, Santa Clara, CA) and quantification (Qubit System, Invitrogen, Carlsbad, California) pools of cDNA libraries were generated.  The pools were quantified using the KAPA Library Quantification kit (Peqlab, Radnor, PA) and the 7900HT Sequence Detection System (Applied Biosystems, Foster City, PA) and subsequently sequenced on an Illumina HiSeq4000 or NovaSeq6000 sequencer .

value: Tumor tissue

value: gamma-delta T cells only

tag: tumor model

value: subcutanous injection of B16F10 melanoma


title: ACE_F_PGC_E13.5_rep1


title: gd2


title: gd5


title: gd6


title: gd3


title: gd1


title: ACE_F_PGC_E13.5_rep3


title: ACE_8-Cell_rep2


title: gd4


title: ACE_Blastocyst_E3.5_rep2


title: LAK4

value: lymphokine activated killer cells only


title: LAK3


title: ACE_4-Cell_rep1


title: LAK2


title: KP_Triple_26

value: Triple combination (TRI-IT without lymphodepletion)

value: subcutanous injection of KP lung tumors


title: KP_Triple_27


title: KP_Triple_108


title: KP_Triple_25


title: KP_Triple_103


title: KP_TriIT_99

value: TRI-IT combination treatment


title: LAK1


title: KP_Triple_92


title: KP_TriIT_40


title: KP_TriIT_91


title: KP_TriIT_98


title: KP_TriIT_97


title: KP_TLR_ACT_14

value: TLR agonist mix + ACT


title: KP_TLR_ACT_15


title: KP_TriIT_100


title: KP_TriIT_41


title: KP_TLR_ACT_13


title: KP_TriIT_39


title: KP_TriIT_90


title: KP_Triple_109


title: KP_TLR_ACT_16


title: KP_TLR_ACT_11


title: KP_TLR_ACT_10


title: KP_TLR_ACT_12


title: KP_TLR_82

value: TLR agonist mix


title: KP_TLR_81


title: KP_TLR_75


title: KP_TLR_76


title: KP_PD1_TLR_87

value: aPD1 antibody + TLR agonist mix


title: KP_TriIT_38


title: KP_PD1_TLR_45


title: KP_PD1_TLR_44


title: KP_PD1_TLR_86


title: KP_PD1_TLR_43


title: KP_PD1_TLR_42


title: KP_PD1_TLR_114


title: KP_PD1_TLR_101


title: KP_PD1_113

value: aPD1 antibody


title: KP_PD1_106


title: KP_PD1_107


title: KP_PD1_TLR_102


title: KP_LD_89

value: lymphodepletion only group


title: KP_LD_94


title: KP_LD_93


title: KP_LD_88


title: KP_Ctrl_78

value: Control group


title: KP_Ctrl_80


title: KP_LD_104


title: KP_Ctrl_79


title: KP_Ctrl_77


title: KP_PD1_112


title: KP_Ctrl_33


title: KP_Ctrl_32


title: KP_Ctrl_31


title: KP_Ctrl_30


title: KP_LD_105


title: KP_Ctrl_28


title: KP_Ctrl_21


title: KP_Ctrl_23


title: KP_Ctrl_2


title: KP_Ctrl_22


title: KP_ACT_96

value: adoptive cellular therapy (ACT)


title: KP_Ctrl_110


title: KP_Ctrl_29


title: KP_Ctrl_111


title: KP_ACT_85


title: KP_Ctrl_1


title: KP_ACT_84


title: KP_Ctrl_24


title: ACE_F_Pronucleus_TetCKO_rep4

value: C57BL/6(mother) x C57BL/6(father)

value: Tet CKO


title: ACE_F_PGC_E13.5_rep2

value: WT


title: KP_ACT_83

value: Tumor tissue


title: KP-83

value: subcutanous TRI-IT

value: KrasLSL-G12D p53fl/fl (KP) mice

value: viral tumor induction with Ad5mSPC-Cre


title: ACE_Epiblast_E6.5_rep3

value: C57BL/6(mother) x PWK(father)


title: KP-77


title: KP-78


title: KP-81


title: KP-75


title: KP-74


title: KP-73


title: KP-71


title: KP-68


title: KP-147

value: inhalative TRI-IT


title: KP-144


title: KP-82


title: KP-135


title: KP-136


title: KP-129


title: KP-116


title: KP-125


title: KP-130


title: KP-60


title: Combi4

value: combined ACT treatment

value: subcutanous injection of B16F10 melanoma


title: KP-126


title: Combi3


title: CTL3

value: only CTLs


title: CTL2


title: Combi2


title: Combi1


title: CIK2

value: only cytokine induced killer cells


title: CTL1


title: CIK1


title: B16_Triple_64

value: Triple combination (TRI-IT without lymphodepletion)


title: LNCaP cells, Enzalutamide treatment, 7 days

city: West Lafayette

first: Changdeng

last: Hu

state: IN

address: 575 Stadium Mall Drive

department: Dept. of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
CellRanger 6.0.1 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.The FASTQ files were then aligned to the human reference genome hg38 with RNAseq aligner STAR [PMID: 23104886]. The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfification.
The CCA function from Seurat was used for integrative analysis of the samples.
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: prostate

growth_protocol: LNCaP cell line was purchased from ATCC. Cells were stored as frozen stock in vapor phase of LN2 and thawed prior to use. Cell lines were cultured 3 passages after thawing prior to experimentation and maintained for no longer than 30 total passages. LNCaP cells were cultured in RPMI 1640 (Corning), and All media were supplemented with 10% FBS (Atlanta Biologicals), 1 mM sodium pyruvate (Corning), penicillin (100 units/mL) and streptomycin (100 μg/mL) combination (Gibco), and 2 mM/L L-glutamine (Corning).

extract_protocol:
The 15 cm cell culture dishes were removed from the 37 °C incubator, medium was removed via aspiration, and cells were immediately washed once with 10 mL of 37 °C phosphate buffered saline (PBS), pH 7.4. PBS was removed via aspiration and 3 mL 0.25% trypsin (Corning) was added to the dishes. Dishes were rotated for complete coverage of the trypsin and incubated on the benchtop for 30 seconds. Roughly 2 mL of the trypsin was removed via aspiration, and dishes were transferred to a 37 °C incubator for exactly 4 minutes. 10 mL of 4 °C RPMI supplemented with 10% FBS was used for resuspension of the trypsinized cell suspension. Viability was checked on Countess II FL automated cell counter to ensure >90% viability. Cells were then centrifuged 4 minutes at 400x g at 4 °C to pellet the cells. Supernatant was aspirated and discarded, then cells were washed  with 1 mL 4 °C complete RPMI three times. Final resuspension of cells in 400 μL 4 °C complete RPMI was performed, and cell homogeneity and viability were checked to ensure singlet cells at >90% viability would be delivered to Indiana University School of Medicine Chemical Genomics Facility for 10X library preparation.
The single cell gene expression analysis was conducted using a 10X Chromium single cell system (10X Genomics, Inc) and a NovaSeq 6000 sequencer (Illumina, Inc). To maximize quality of cell suspension, cell harvest was optimized to retain >95% viability at time of harvest following three washes in RPMI/10%FBS. Following storage on ice for delivery of cells to 10X sequencing facility, the single cell suspension was subsequently washed a fourth time with RPMI/10% FBS, recentrifuged, and cell debris, dead cells and cell aggregates were removed by discarding supernatant and resuspending cells. Each clean single cell suspension was then be counted with hemocytometer under microscope for cell number and cell viability. The single cell suspension viability was over >90% and minimal cell debris and aggregation were ensured prior to loading. A target of 10,000 cells was used for loading; in practice, following final analysis, between 6,890 and 11,620 individual cells were identified per sample after all processing steps were completed. The cells were applied to a single cell master mix with lysis buffer and reverse transcription reagents, following the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide, CG000204 Rev D (10X Genomics, Inc). Along with the single cell gel beads and partitioning oil, the single cell master mixture containing the single cell suspension was dispensed onto a Single Cell Chip G in separate wells, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was be examined by Bioanalyzer and Qubit. The resulting library was sequenced in a custom program for 28b plus 91b paired-end sequencing on Illumina NovaSeq 6000. Depending on targeted cell recovery, roughly 33,000 – 82,000 reads per cell were generated and 91% of the sequencing reads reached Q30 (99.9% base call accuracy). A Phred quality score (Q score) was used to measure the quality of sequencing.

treatment_protocol: Cells were seeded at 450,000 cells per 15 cm culture dish and allowed to attach to the dish overnight. The following day, enzalutamide was added at 5 μM concentration diluted from 100 mM stock in DMSO. Dilutions were prepared such that DMSO content in culture plates, including DMSO control, was always 0.1%. Enzalutamide treatment was performed for 4, 7, or 14 days at 5 μM treatment. Media was refreshed and enzalutamide was re-applied to cell culture dishes every 72 h. DMSO cells were seeded at the same density and treated at same schedule as enzalutamide treatment groups but harvested at 70-80% confluency.

value: prostate

value: LNCaP

value: prostate adenocarcinoma cells

value: Enzalutamide induction, 7 days


title: B16_Triple_62


title: LNCaP cells, Enzalutamide treatment, 14 days

value: Enzalutamide induction, 14 days


title: LNCaP cells, DMSO treatment

value: WT

value: DMSO (negative control)


title: B16_Triple_61

value: Tumor tissue


title: B16_TriIT_7

value: TRI-IT combination treatment


title: LNCaP cells, Enzalutamide treatment, 4 days

value: Enzalutamide induction, 4 days


title: B16_TriIT_9


title: B16_TriIT_4


title: B16_TriIT_8


title: KP_ACT_95

value: adoptive cellular therapy (ACT)

value: subcutanous injection of KP lung tumors


title: ACE_2-Cell_rep2

value: C57BL/6(mother) x C57BL/6(father)


title: gd7

value: gamma-delta T cells only

value: subcutanous injection of B16F10 melanoma


title: B16_TriIT_36


title: B16_TriIT_37


title: monocyte, Mav, UWID085

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

data_processing:
Sequences were quality-assessed with FastQC and filtered with AdapterRemoval to remove adapters and poor-quality sequences (score < 30, length < 15, ambiguous > 1).
Sequences were aligned to the human genome (GRCh38 release 102) with STAR and quality-assessed with samtools flagstat and Picard. Alignments were filtered with samtools to remove PCR duplicates, unmapped, non-primary, and poor-quality alignments (MAPQ < 30).
High-quality alignments were quantified in gene exons using Subread featureCounts.
Assembly: hg38
Supplementary files format and content: comma-delimited text file with unnormalized counts for each library

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll gradient separation, resuspended in RPMI/10 containing M-CSF, and enriched for CD14+ monocytes using negative selection magnetic beads.

extract_protocol:
Cells were lysed in Trizol, and RNA was isolated by chloroform extraction followed by miRNeasy mini columns.
Total RNA (Ribo-depleted) Library prep. NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Monocytes were stimulated with M. avium (MOI 5) or media for 6 hours.

value: blood

value: monocyte

value: Mav

tag: disease

value: MACDZ


title: monocyte, Media, UWID084

value: Media


title: monocyte, Media, UWID085


title: B16_Triple_63

value: Triple combination (TRI-IT without lymphodepletion)


title: monocyte, Mav, UWID084


title: LNCaP cells, Enzalutamide treatment, 14 days, 2

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Assembly: hg38
Supplementary files format and content: differential analysis and raw counts

source_name: LNCaP

extract_protocol:
Following treatment (or control), cells were removed from 37C incubator and washed with cold PBS after removal of media. Cells were then harvested with Trizol reagent (Ambion) at 3 mL per 10cm dish following manufacturer protocol. RNA was precipitated with isopropanol and washed with a 75% ethanol solution and dried at room temperature. RNA was resuspended in DEPC-treated water and immediately frozen and stored at -80C. RNA integrity was verified via agarose gel electrophoresis.
Total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. For RNA quality, a RIN number of 10 was achieved. One hundred nanograms of total RNA was used. cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were then denatured, and neutralized, before loading to NovaSeq 6000 sequencer at 300pM final concentration for 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: Cells were seeded at 150,000 cells in a 10 cm culture dish and allowed to attach to the dish overnight. The following day, enzalutamide was added at 5 μM concentration diluted from 100 mM stock in DMSO. Dilutions were prepared such that DMSO content in culture plates, including DMSO control, was always 0.1%. Enzalutamide treatment was performed for 4, 7, or 14 days at 5 μM treatment. Media was refreshed and enzalutamide was re-applied to cell culture dishes every 72 h. DMSO cells were seeded at the same density and treated at same schedule as enzalutamide treatment groups but harvested at 70-80% confluency.

value: LNCaP

value: prostate

value: Enzalutamide induction, 14 days


title: LNCaP cells, DMSO treatment, 1

value: WT

value: DMSO (negative control)


title: LNCaP cells, Enzalutamide treatment, 14 days, 3


title: LNCaP cells, DMSO treatment, 3


title: B16_TriIT_34

value: Tumor tissue

value: TRI-IT combination treatment


title: LNCaP cells, Enzalutamide treatment, 14 days, 1


title: B16_Triple_60


title: LNCaP cells, DMSO treatment, 2


title: B16_TriIT_116


title: monocyte, Media, UWID082


title: B16_TLR_ACT_20

value: TLR agonist mix + ACT


title: monocyte, Mav, UWID082


title: B16_TLR_ACT_19


title: B16_TriIT_115


title: B16_TLR_ACT_18


title: monocyte, Media, UWID083


title: B16_TriIT_35


title: monocyte, Media, UWID081


title: monocyte, Mav, UWID083


title: monocyte, Media, UWID080


title: monocyte, Mav, UWID081


title: B16_TLR_ACT_118


title: B16_TLR_ACT_119


title: B16_TLR_6

value: TLR agonist mix


title: B16_TLR_5


title: monocyte, Media, UWID077


title: monocyte, Mav, UWID080


title: Eosinophils, papain, cKO 3

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: Eos ko3

data_processing:
Raw reads were mapped to the mouse (GENCODE M12.GRCm38.p5, scaffolds removed) genome with STAR (2.7.3a).
The reads were assigned to genes with featureCounts (SUBREAD v2.0.0) setting -t exon -g gene_id (Gene annotation: gencode.vM12/GRCm38) .
Assembly: GENCODE M12.GRCm38.p5
Supplementary files format and content: tsv file contains tab separated counts per gene

source_name: Lung

growth_protocol: mice were kept under SPF conditions, were treated for 7 days with papain, on day 7 mice were sacrifised and lungs were taken for cell isolation

extract_protocol:
Eosinophils were sort-purified as Sytox blue- CD45+ Lineage (CD3, CD5, CD19, Ly6G)-CD11b+ Siglec F+ from the lung of Nmur1Cre-T2A-GFP Id2flox/flox and control mice on day 7 after papain administration. Cells were sorted into RLT Plus Lysis Buffer supplemented with 40 mM DTT and RNA was isolated using the RNeasy Plus Micro kit (Qiagen) according to the protocol provided by the manufacturer.
RNA libraries for RNA-Seq were prepared using theSMARTer Stranded Total RNA-Seq Kit – Pico (Takara)

treatment_protocol: papain treatment on day 1, 2 and 3

value: Lung

value: Eosinophils

value: Nmur1Cre-T2A-GFP Id2flox/flox

value: papain


title: monocyte, Mav, UWID079

value: blood

value: monocyte

value: Mav


title: B16_PD1_TLR_72

value: aPD1 antibody + TLR agonist mix

value: subcutanous injection of B16F10 melanoma


title: B16_TLR_117


title: B16_PD1_TLR_74


title: B16_PD1_TLR_73


title: monocyte, Media, UWID076

value: Media

value: MACDZ


title: monocyte, Mav, UWID077


title: B16_PD1_TLR_70


title: B16_PD1_TLR_71


title: monocyte, Media, UWID074


title: monocyte, Mav, UWID076


title: monocyte, Mav, UWID073


title: monocyte, Media, UWID073


title: monocyte, Mav, UWID074


title: B16_PD1_TLR_69


title: B16_PD1_TLR_67


title: B16_PD1_TLR_66


title: monocyte, Media, UWID070


title: B16_PD1_TLR_65


title: monocyte, Mav, UWID071


title: B16_TLR_ACT_17


title: B16_PD1_51

value: aPD1 antibody


title: B16_PD1_50


title: monocyte, Media, UWID064


title: monocyte, Media, UWID068


title: B16_PD1_48


title: monocyte, Mav, UWID068


title: B16_PD1_47


title: monocyte, Mav, UWID064


title: B16_PD1_49


title: monocyte, Media, UWID063


title: B16_PD1_46


title: B16_Ctrl_54

value: Control group


title: monocyte, Mav, UWID063


title: B16_PD1_TLR_68

value: Tumor tissue


title: B16_Ctrl_53


title: B16_Ctrl_52


title: monocyte, Media, C350

value: healthy


title: monocyte, Mav, C350


title: B16_Ctrl_3


title: monocyte, Media, C346


title: B16_ACT_59

value: adoptive cellular therapy (ACT)


title: monocyte, Mav, UWID070


title: monocyte, Media, C343


title: monocyte, Mav, C346


title: B16_ACT_58


title: monocyte, Mav, C343


title: B16_ACT_57


title: B16_ACT_56


title: monocyte, Mav, UWID051


title: PreGTS1_DMSO_1

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
All RNA sequence reads were mapped against the mouse genome assembly mm9 using STAR v2.4.0 in a two step aproach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016. Unmapped reads were realigned using Bowtie2 v2.2 and default parameters. Duplicate reads were removed with Piccard v1.127 and default parameters. Read counts were measured with Subread 1.5.2. The transcriptome profile was quantified with Limma or edgR with default parameters.
For single cell RNA seq, the Cell Ranger v3.3.0 pipeline was used to process data generated using the 10x Chromium platform. This aligns sequencing reads to the mouse reference genome mm10 v3.0.0. Following alignment, gene expression matrices were generated. Using Seurat v3.0 package in R, We first removed cells with a low number (<200) of unique detected genes and genes (<3) with low number of cells, then we removed the cells unique detected genes less than 500 or great than 7000, finally, we removed cells in which the proportion of the UMI count attributable to mitochondrial genes was greater than 20%.
ATAC-sequence reads were mapped against the mouse genome assembly mm9 using Bowtie2 and duplicate reads were removed by Piccard. Peak calling was performed with MACS2, than quantified and normalized to cpm values with edgeR.
Genome_build: mm10 for single cell analysis, otherwice mm9
Supplementary_files_format_and_content: Conventional RNA-seq: Tab delimeted files with CPM values. scRNA-seq: Count matrix. ATAC-seq: CPM values.

source_name: preGTS1 medulloblastoma tumor

extract_protocol:
Library constructed using standard ATAC-seq protocol
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.

value: DMSO

value: tumor


title: monocyte, Media, UWID051


title: B16_Ctrl_55


title: NoneGFP_2

source_name: GTML medulloblastoma tumor


title: GTS_2_1

source_name: GTS medulloblastoma tumor


title: NoneGFP_1


title: GTS_2_2


title: GTS_1_2


title: GTS_1_1


title: GTML_3_DOX_2

value: DOX


title: GTML_3_DOX_1


title: monocyte, Mav, C310


title: monocyte, Media, C289


title: monocyte, Media, C225


title: monocyte, Media, C249


title: monocyte, Mav, C242


title: monocyte, Media, C315


title: monocyte, Mav, C315


title: monocyte, Media, C248


title: monocyte, Mav, C249


title: fGTS2

extract_protocol:
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.
Single-cell library preparation on the 10x Genomics platform : Chromium Single Cell 3? Library & Gel Bead Kit v3


title: PreGTS1_DOX_1


title: monocyte, Media, C242


title: GTML_3_DMSO_1


title: monocyte, Mav, C289


title: PreGTS1_DOX_2


title: monocyte, Media, C310


title: PreGTS1_DMSO_2


title: GTML_3_DMSO_2


title: GFP_2


title: GTML_SOX9-GFP


title: monocyte, Mav, C193


title: monocyte, Media, C205


title: monocyte, Mav, C205


title: monocyte, Mav, C225


title: monocyte, Media, C193


title: monocyte, Mav, C248


title: monocyte, Media, C153


title: monocyte, Media, C130


title: Adipocytes_TD_replicate4

city: Nanjing

first: Yuxin

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Bcl2fastq software (v2.17.1.14) used for basecalling.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (v1.9.1) to be high quality clean data.
Reads were aligned to GRCm38.97 genome (ENSEMBL) using Hisat2 (v2.0.1).
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: GRCm38.97 genome (ENSEMBL)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

growth_protocol: SVFs were grown in 10% fetal bovine serum in DMEM-F12 with glutamine, Non-Essential amino acid supplement and antibiotic-antimyotics.

extract_protocol:
Total RNA was extracted from differentiated adipocytes in vitro, using the TRIzol reagent (Invitrogen).
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: Adipogenic differentiation was conducted when cells reached confluence. The differentiation culture media contained DMEM/F12, 10% FBS, 850 nM insulin, 1 nM triiodothyronine (T3), 0.5 mM 3-isobutyl-1-methylxanthine (IBMX) and 5mM dexamethasone (Dex), 125nM indomethacin. Four days after incubation, differentiation media was replaced by the maintenance medium containing DMEM/F12, 10% FBS, 850 nM insulin and 1 nM T3. All the culture media mentioned above were changed every two days. On day 8, mature adipocytes were harvested and subjected to the RNA-seq.

tag: strain background

tag: genotype/variation

value: Adipocytes


title: monocyte, Mav, C153


title: GFP_1

extract_protocol:
RNA-Seq were prepared for sequencing using standard Ion-Torrent protocols.
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.


title: Adipocytes_TD_replicate2


title: Primary human keratinocytes, NETs+NC siRNA 2

city: Xi'an

first: Tianyu

last: Cao

address: Changle Road NO.127

institute: Fourth Military Medical University

data_processing: tab-delimited text files include RPKM values for each Sample

source_name: Primary human keratinocytes

growth_protocol: Keratinocytes were cultured in a serum-free Keratinocyte-SFM Media Kit (containing 0.125μg/ml epidermalgrowth factor) (Gibco) in a humidified 5% CO2 incubator, and passage 3 to 4 cells were used for experiments.

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Keratinocytes were processed with siRNA (5 nM) and Lipofectamine 3000 (Invitrogen) following the instructions.

value: Primary human keratinocytes

value: WT

value: NETs and NCsiRNA


title: Primary human keratinocytes, NETs+AIM2 siRNA 2

value: NETs and AIM2 siRNA


title: Primary human keratinocytes, con 1

value: Negative control


title: Primary human keratinocytes, NETs+AIM2 siRNA 3


title: Primary human keratinocytes, NETs+NC siRNA 1


title: Primary human keratinocytes, con 2


title: Primary human keratinocytes, con 3


title: Primary human keratinocytes, NETs+NC siRNA 3


title: monocyte, Media, C075

value: blood

value: monocyte


title: monocyte, Mav, C075

value: Mav


title: PMS_90_S83

city: New York

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Illumina adapter sequences were trimmed from all fragmented reads using TrimGalore (options –paired –illumina) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
All high-quality trimmed reads were mapped to UCSC Homo sapiens reference genome (build hg37) using default STAR v2.4.0 parameters.
Samtools was used to convert bamfiles to samfiles and featureCounts was used to quantify gene expression levels for each individual sample using default paired-end parameters.
Assembly: hg37/hg19
Supplementary files format and content: Raw count data were generated with featureCounts and are provided as a separate matrix.

source_name: Leukocytes (PaxGene Tubes)

extract_protocol:
RNA was extracted and purified in accordance with the PAX gene RNA kit per manufacterer's instructions. Globin mRNA was depleted from samples using GLOBINclear - Human Kit (Life Technologies, USA).
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.

value: Peripheral blood

tag: Sex

value: F

tag: group/diagnosis

value: PMS

tag: batch

value: Seaver Autism Center

tag: mutational type

value: Class II


title: monocyte, Mav, C130

value: healthy


title: Adipocytes_TA_replicate4


title: Adipocytes_TD_replicate1


title: PMS_9_S7

value: M

value: RDCRN


title: Adipocytes_TA_replicate3

value: Adipocytes


title: PMS_87_S80

value: Class I


title: monocyte, Media, C057

value: Media


title: PMS_82_S75


title: PMS_81_S74


title: Primary human keratinocytes, NETs+AIM2 siRNA 1

value: Primary human keratinocytes

value: WT


title: monocyte, Mav, C057


title: Adipocytes_TD_replicate3


title: PMS_80_S73


title: PMS_68_S61


title: PMS_70_S63


title: Adipocytes_TA_replicate1


title: Adipocytes_WT_replicate4


title: PMS_55_S51


title: Adipocytes_WT_replicate3


title: PMS_50_S47


title: PMS_54_S50


title: Adipocytes_WT_replicate1


title: Adipocytes_WT_replicate2


title: PMS_40_S37


title: monocyte, Mav, C051


title: PMS_43_S40


title: PMS_44_S41


title: PMS_37_S35


title: PMS_47_S44


title: monocyte, Media, C051


title: β1 transduced+CLI 1

city: Urbana

first: Yvonne

last: Ziegler

state: IL

address: 407 S Goodwin Ave.

department: MIP

institute: University of Illinois

data_processing:
Base calling and de-multiplexing of samples within each lane were done with bcl2fastq v2.20 Conversion Software (Illumina).
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.38).
Reads were pseudo-mapped to the Homo sapiens reference transcriptome (GRCh38; Gencode v34) using Salmon (v1.2.1) with the entire GRCh38 genome as the decoy sequence. Transcript-level counts were summed to the gene level while adjusting for effective lengths using tximport's (v1.16.1) "lengthScaledTPM" method.
Gene-level counts underwent quality control and normalization in R (v4.0.2) using edgeR (Version 3.30.3). Genes were filtered out if they did not have expression levels above 0.25 CPM in at least 2 samples.
Assembly: GRCh38
Supplementary files format and content: Raw_gene_counts.xlsx
Supplementary files format and content: TMM_normalized_logCPM_data.xlsx

growth_protocol: MDA-MB-231 cells lentivirally transduced with dox-inducible expression of GFP-luciferase-estrogen receptor β isoform 1 or control GFP-luciferase  were cultured in DMEM+5%FBS + 100 ng/ml doxycycline + pen/strep

extract_protocol:
RNA was extracted using Trizol protocol, followed by DNase treatment.  RNA was then re-purified with an aqueous column-based protocol followed by gel analysis to analyze purity and quality of the RNA.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one S2 lane for 101 cycles from one end of the fragments on a NovaSeq 6000.

treatment_protocol:
Cells were treated with doxycycline for 3 days.
Cells were treated with CLI for 24 hours.

value: basal breast cancer cell line

tag: transduction

value: lentiviral-GFP-luciferase-estrogen receptor beta1 vector

value: doxycycline+CLI ligand

tag: time

value: 3 days, 24 hr ligand treatment


title: β1 transduced+CLI 2

tag: cell type


title: β1 transduced+CLI 3


title: PMS_313_S113

tag: tissue

value: Peripheral blood


title: Adipocytes_TA_replicate2


title: β1 transduced 2

tag: treatment

value: doxycycline

value: 3 days


title: b24_3

city: Haikou

first: Li

last: Wei

state: Hainan

address: No. 99 Longkun South Road, Haikou

department: Colleage of life science

institute: Hainan normal university

description:
blue light 24h replicate 3
b24_FPKM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
The filtered Illumina reads were aligned to our previously published N. oceanica IMET1 genome with TopHat (version 2.0.4, allowing no more than two segment mismatches). Reads mapped to more than one location were excluded. Thirdly, the short read mapping results from TopHat were used for the differential gene expression analysis with Cufflinks (version 2.0.4). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by Cufflinks (version 2.0.4) and normalized to FPKM values (fragments per kilobase of exon model per million mapped fragments).
For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by Cufflinks (version 2.0.4) and normalized to FPKM values (fragments per kilobase of exon model per million mapped fragments).
Genome_build: N. oceanica IMET1 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: blue light  24h

extract_protocol:
Cells were frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: type

value: microalgae (single cell)

tag: growth time

tag: genotype

value: wild type


title: b24_1

description:
blue light 24h replicate 1
b24_FPKM.txt

tag: strain


title: β1 transduced 1

tag: cell line


title: β1 transduced 3


title: PMS_300_S100

value: F

value: PMS


title: PMS_299_S99

value: RDCRN


title: b24_2

description:
blue light 24h replicate 2
b24_FPKM.txt


title: PMS_36_S34

value: M

value: Seaver Autism Center


title: control cells 3


title: PMS_297_S97

value: Class II


title: PMS_294_S94


title: PMS_285_S85

value: Class I


title: control cells 2


title: PMS_277_S77


title: b12_1

description:
blue light 12h replicate 1
b12_FPKM.txt

source_name: blue light  12h


title: b12_3

description:
blue light 12h replicate 3
b12_FPKM.txt


title: PMS_32_S30


title: control cells 1


title: PMS_273_S73


title: PMS_27_S25


title: PMS_271_S71


title: r24_2

description:
red light 24h replicate 2
r24_FPKM.txt

source_name: red light  24h


title: r24_3

description:
red light 24h replicate 3
r24_FPKM.txt


title: PMS_266_S66


title: PMS_264_S64


title: PMS_303_S103


title: PMS_26_S24


title: r12-3

description:
red light 12h replicate 3
r12_FPKM.txt

source_name: red light  12h


title: PMS_252_S52


title: monocyte, Media, UWID071

value: blood

value: monocyte

value: Media

tag: disease

value: MACDZ


title: PMS_25_S23


title: r12_2

description:
red light 12h replicate 2
r12_FPKM.txt


title: PMS_244_S44


title: r24-1

description:
red light 24h replicate 1
r24_FPKM.txt


title: b12_2

description:
blue light 12h replicate 2
b12_FPKM.txt


title: PMS_280_S80


title: r12_1

description:
red light 12h replicate 1
r12_FPKM.txt


title: w0_3

description:
white light 0h replicate 3
w0_FPKM.txt

source_name: white light  0h


title: w0_2

description:
white light 0h replicate 2
w0_FPKM.txt


title: PMS_239_S39


title: PMS_225_S25


title: PMS_209_S9


title: PMS_210_S10


title: PMS_226_S26


title: PMS_2_S1


title: PMS_192_S44


title: PMS_199_S51


title: PMS_184_S36


title: PMS_181_S33


title: PMS_18_S16


title: Pituitary, male, Nr5a1-PE homozygous deletion, rep3

city: Kurume

first: Yuichi

last: Shima

state: Fukuoka

address: Asahimachi 67

department: Department of Anatomy

country: Japan

institute: Kurume University School of Medicine

data_processing:
FASTQ files were subjected to cutadapt with default parameters to remove adapter sequence and low-quality sequences.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR with default parameters.
Read counting was performed using featureCounts with default parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts of the genes for each sample

source_name: pituitary

extract_protocol:
RNeasy micro kit (Qiagen)
NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina

value: pituitary

value: Nr5a1-PE homozygous deletion

value: male


title: PMS_174_S26

value: Peripheral blood


title: PMS_262_S62


title: PMS_205_S5


title: Pituitary, male, Nr5a1-PE homozygous deletion, rep2


title: PMS_17_S15


title: PMS_23_S21


title: Pituitary, male, Nr5a1-PE homozygous deletion, rep1


title: PMS_15_S13


title: Teratoma_H1_12, scRNAseq, Microwell-seq

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The teratoma data were aligned to a merged hg19-mm10 reference genome, the ESCs data were aligned to GRCh38, and the mouse data were mapped to mm10. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. The TagReadWithGeneExon function was employed to recognize the reads that were mapped to the exonic regions of genes. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat. For teratoma data that mix human cells with mouse cells, the aligned BAM files should be divided into human.bam and mouse.bam before generating the digital expression matrices.
Assembly: Teratoma: A merged hg19-mm10 reference genome; ESCs: GRCh38; Mouse: mm10
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.

organism:
Homo sapiens
Mus musculus

extract_protocol:
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: NOD/SCID

tag: age

value: female


title: Pituitary, male, Nr5a1-PE heterozygous deletion, rep3

value: Nr5a1-PE heterozygous deletion


title: PMS_148_S136

value: F

value: PMS


title: Pituitary, male, Nr5a1-PE heterozygous deletion, rep4


title: w0_1

description:
white light 0h replicate 1
w0_FPKM.txt

value: microalgae (single cell)

value: wild type


title: Teratoma_H1_11, scRNAseq, Microwell-seq


title: Pituitary, male, Nr5a1-PE heterozygous deletion, rep2


title: Teratoma_H1_10, scRNAseq, Microwell-seq


title: PMS_145_S133

value: M

value: Seaver Autism Center

value: Class II


title: PMS_140_S128

value: Class I


title: Pituitary, male, Nr5a1-PE homozygous deletion, rep4


title: PMS_19_S17

value: RDCRN


title: Teratoma_H1_8, scRNAseq, Microwell-seq


title: Teratoma_H1_9, scRNAseq, Microwell-seq


title: Pituitary, female, Nr5a1-PE homozygous deletion, rep3


title: PMS_138_S126


title: Pituitary, female, Nr5a1-PE homozygous deletion, rep2


title: PMS_16_S14


title: Teratoma_H1_6, scRNAseq, Microwell-seq

value: 13-15 weeks


title: Pituitary, female, Nr5a1-PE heterozygous deletion, rep4

value: pituitary


title: PMS_131_S120


title: Pituitary, female, Nr5a1-PE heterozygous deletion, rep3


title: Pituitary, female, Nr5a1-PE heterozygous deletion, rep2


title: PMS_117_S108


title: PMS_128_S118


title: Pituitary, male, Nr5a1-PE heterozygous deletion, rep1


title: Teratoma_H1_7, scRNAseq, Microwell-seq


title: Pituitary, female, Nr5a1-PE homozygous deletion, rep1

value: Nr5a1-PE homozygous deletion


title: Teratoma_H1_4, scRNAseq, Microwell-seq


title: PMS_11_S9


title: Teratoma_H1_3, scRNAseq, Microwell-seq


title: Teratoma_H1_2, scRNAseq, Microwell-seq

value: 12-14 weeks


title: PMS_139_S127

value: Peripheral blood


title: Pituitary, female, Nr5a1-PE heterozygous deletion, rep1


title: Teratoma_H1_1, scRNAseq, Microwell-seq

value: NOD/SCID


title: PMS_107_S99


title: scRNA data for Teratoma_H9_9, with corresponding scATAC data

value: 15-17 weeks

value: female


title: Pituitary gonadotrope, male, rep2

description:
sorted cells
gonadotrope_m2

source_name: pituitary gonadotrope

value: pituitary gonadotrope

tag: cell marker

value: EGFP-expressing cells

value: Ad4BP-BAC-EGFP mouse

value: male


title: Pituitary gonadotrope, male, rep4

description:
sorted cells
gonadotrope_m4


title: PMS_104_S96

tag: Sex

value: M

value: PMS


title: Control_94_S86

value: F

tag: group/diagnosis

value: Sibling

value: Seaver Autism Center

value: Control


title: scRNA data for Teratoma_H9_8, with corresponding scATAC data


title: PMS_100_S92

tag: batch

value: Class II


title: Teratoma_H1_5, scRNAseq, Microwell-seq

value: 13-15 weeks


title: Pituitary gonadotrope, male, rep1

description:
sorted cells
gonadotrope_m1


title: Pituitary gonadotrope, male, rep3

description:
sorted cells
gonadotrope_m3


title: Control_61_S56

tag: mutational type


title: Control_76_S69


title: Pituitary gonadotrope, female, rep2

description:
sorted cells
gonadotrope_f2


title: Pituitary gonadotrope, female, rep4

description:
sorted cells
gonadotrope_f4


title: Control_85_S78


title: Control_56_S52


title: N14_SMT2_2C_KO_sc8

description:
scRNA-sequencing data
N14_SMT2_MII_2C_counts.txt
N14_SMT2_MII_2C_counts_maternal.txt
N14_SMT2_MII_2C_counts_paternal.txt

data_processing:
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
RNA-seq: For Smart-seq2 data, raw sequencing data were processed as our previously reported (Gu et al., 2019). Briefly, the raw reads were trimmed by using Cutadapt (v1.15). The sequences for adapters, oligo-dT, TSO sequences were trimmed from raw reads. The trimmed reads were further aligned to the mm9 mouse transcriptome by using STAR (v2.6.0a). Raw counts for genes expression were quantified by using HTSeq (v0.10.0). For bulk RNA-seq, raw sequencing data was processed by Trim Galore (v0.6.6) and was further aligned to the mouse transcriptome by using STAR (v2.6.0a). The 33  featureCounts (v2.0.1) was used for raw counts of genes expression. In this study, for comparing among different datasets, gene expression levels were defined as log2(TPM+1).
scBS-seq: Adaptor sequences, random primers and low-quality bases were removed by Trim Galore (v0.6.6). Reads shorter than 50 bp after trimming were excluded. The retained reads were then mapped to the mouse reference genome mm9 by Bismark (v0.23.0) in paired-end mode, and unmapped reads were re-mapped to the reference genome in single-end mode. SAMtools (v0.1.18) were adopted to remove PCR duplicates. The methylation level of CpG and CH sites were quantified by MethylDackel (v0.5.0).
scCOOL-seq: The pipeline of data processing of single-cell COOL-seq data was basically the same as the pipeline of processing single-cell bisulfite sequencing data which has been described (Gu et al., 2019; Yan et al., 2021). After determination of CpG and CH methylation level by MethylDackel, the WCG (W=A or T) and GCH (H= A,T or C) sites were summed from each single cell.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files; Count matrix files in tab-separated format

source_name: Mouse 2-Cell

value: Mouse 2-Cell

value: N14 maternal KO


title: Control_75_S68

value: Peripheral blood


title: N14_SMT2_2C_KO_sc7


title: Pituitary gonadotrope, female, rep3

description:
sorted cells
gonadotrope_f3


title: N14_SMT2_2C_KO_sc9


title: B-Exosome Non-fasting

city: Honolulu

first: Masaki

last: Nasu

state: HI

address: 651 Ilalo st. University of Hawaii, JABSOM BSB 222 Masaki Nasu

institute: University of Hawaii

description: Circulating small RNA

data_processing:
Single-end 76 bp reads were explored using FASTQC. GeneGlobe Data Analysis Center (https://geneglobe.qiagen.com/us/products/analysis-type/), an online platform from Qiagen was used for the small RNA-seq data analysis. piRNA and tRNA were used for differential expression analysis using DESeq2 Bioconductor in R. The small RNA species with logFC > |1| and adj.P-value <0.05 were called differentially expressed.
The mapped read counts for miRNA,  piRNA and tRNA were used for differential expression analysis using DESeq2 Bioconductor in R.
The small RNA species with logFC > |1| and adj.P-value <0.05 were called differentially expressed.
Supplementary files format and content: xlsx; contains raw read counts and DESeq2 results

source_name: Exosome

extract_protocol:
Total RNA including smal non-coding RNAs were extracted using miRNeasy Serum/Plasma Kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using QIASeq miRNA Library kit protocols

value: Exosome

value: cell-free

value: Non-fasting


title: D-Exosome Fasting

description: Circulating small RNA

value: Fasting


title: C-Exosome Non-fasting

description: Circulating small RNA


title: C-Exosome Fasting

description: Circulating small RNA


title: Control_49_S46

first: Michael


title: A-Exosome Non-fasting

description: Circulating small RNA


title: D-Exosome Non-fasting

description: Circulating small RNA


title: Control_289_S89


title: N14_SMT2_2C_KO_sc5

extract_protocol:
To collect preimplantation embryos, 6-8week old females (C57BL/6) were super-ovulated by injection of PMSG and hCG. MII oocytes were collected at 14-15 hours after hCG injection. As to preimplantation embryos, superovulated female mice were mated with either C57BL/6 or PWK males. Embryos were collected at 25-26 h (zygotes), 42-43 h (2-cell), 56-57 h (4-cell), 70-71 h (8-cell), and 94-96 h (blastocysts) after hCG injection. To isolate pronuclei, mouse zygotes at PN3- PN4 stages were collected and pronucleus were isolated as previously described (Guo et al., 2014). Zygotes which were maternally deficient in Tet3 were obtained through Zp3-Cre mediated conditional knockout in oocytes as previously described (Guo et al., 2014). To inhibit DNA replication, zygotes were treated with aphidicolin until the collection of pronuclei (Guo et al., 2014). The inhibition of DNA replication in mouse zygotes was validated by EdU incorporation assay.
ACE-seq: The construction of ACE-seq libraries followed the published protocol (Schutsky et al., 2018), with minor modifications. Fragmented gDNA was first modified using UDP- glucose and T4 Phage β-glucosyltransferase at 37 °C for 1 h. Then 0.1 N NaOH was added to the modified gDNA for denaturation at 55 °C for 10 min. APOBEC enzyme was used to deaminate gDNA at 37°C for 3 hrs. After deamination, gDNA was purified using Ampure XP beads before library construction according to the TAILS procedure (Gu et al., 2019; Yan et al., 2021). Finally, the ACE-seq libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. scBS-seq: The zona pellucida of MII oocytes and 2-cell embryos were firstly removed by Tyrode's Solution. Construction of the scBS-seq or scCOOL-seq libraries were performed as previously described (Guo et al., 2017a; Smallwood et al., 2014). DNA libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. Single-cell RNA-seq: Single-cell RNA-seq of 2-cell embryos were conducted by using smart-seq2 protocol (Picelli et al., 2014). In brief, single cell was picked into lysis buffer and Poly(A)+ RNA was captured by Oligo(dT) primer. The first strand of cDNA was synthesized by reverse transcription, then amplified, purified and fragmented. Fragmented cDNA was processed to construct RNA-seq library by NEBNext UltraII DNA Library Prep Kit for Illumina.
ACE-seq, scBS-seq and scRNA-seq


title: scRNA data for Teratoma_H9_7, with corresponding scATAC data

value: NOD/SCID

value: 15-17 weeks

value: female


title: Control_308_S108

value: M


title: N14_SMT2_2C_KO_sc6


title: A-Exosome Fasting

description: Circulating small RNA


title: D-Plasma Non-fasting

description: Circulating small RNA

source_name: Plasma

value: Plasma


title: Control_279_S79

value: F

value: Sibling


title: Pituitary gonadotrope, female, rep1

description:
sorted cells
gonadotrope_f1

value: pituitary gonadotrope

value: EGFP-expressing cells

value: Ad4BP-BAC-EGFP mouse


title: C-Plasma Non-fasting

description: Circulating small RNA


title: Control_241_S41

value: Seaver Autism Center

value: Control


title: Control_237_S37

value: Peripheral blood


title: N14_SMT2_2C_KO_sc3

value: Mouse 2-Cell

value: N14 maternal KO


title: A-Plasma Non-fasting

description: Circulating small RNA

value: cell-free

value: Non-fasting


title: B-Exosome Fasting

description: Circulating small RNA

value: Exosome

value: Fasting


title: B-Plasma Non-fasting

description: Circulating small RNA


title: Control_187_S39


title: Control_216_S16


title: Control_235_S35


title: N14_SMT2_2C_WT_sc8

value: WT


title: B-Plasma Fasting

description: Circulating small RNA


title: N14_SMT2_2C_KO_sc1


title: A-Plasma Fasting

description: Circulating small RNA


title: N14_SMT2_2C_WT_sc7


title: Control_14_S12

value: M


title: Control_206_S6


title: N14_SMT2_2C_KO_sc4


title: C-Plasma Fasting

description: Circulating small RNA

value: Plasma


title: N14_SMT2_2C_WT_sc5


title: N14_SMT2_2C_WT_sc6


title: N14_SMT2_2C_WT_sc4


title: Control_133_S122

value: F


title: Control_179_S31

value: Sibling


title: N14_SMT2_2C_WT_sc3


title: H3K27ac LNCaP cells, Enzalutamide treatment, 14 days

data_processing:
Base calling and quality scoring were performed in Illumina NextSeq
Bowtie2 was used for Cut & Run reads alignment on the human genome (hg38). Duplicated reads were removed using Picard.
Peak calling of mapped reads were performed by SICER2 compared with IgG with a bonferroni adjusted cutoff of p value less than 0.01. Differential peak calling between two conditions was performed using SICER2 sicer_df.
The signal at each base was normalized by per 10 million reads
Assembly: hg38
Supplementary files format and content: Bigwig file showing the normalized read signal
Library strategy: CUT&RUN

source_name: prostate

extract_protocol:
The 15 cm cell culture dishes were removed from the 37 °C incubator, medium was removed via aspiration, and cells were immediately washed once with 10 mL of 37 °C phosphate buffered saline (PBS), pH 7.4. PBS was removed via aspiration.  Samples were fixed for 1 minute with 0.1% formaldehyde and quenched with 125 mM glycine for 5 minutes. Media was removed and cells were again washed with PBS. Subsequently, 3 mL 0.25% trypsin (Corning) was added to the dishes. Dishes were rotated for complete coverage of the trypsin and incubated on the benchtop for 30 seconds. Roughly 2 mL of the trypsin was removed via aspiration, and dishes were transferred to a 37 °C incubator for exactly 4 minutes. 10 mL of 4 °C RPMI supplemented with 10% FBS was used for resuspension of the trypsinized cell suspension. Nuclei were then isolated following incubation with 20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% triton X-100, and 20% glycerol. Nuclei were checked for quantitation on Countess II prior to freezing down to -80C and shipment to EpiCyppher.
For each CUT&RUN reaction, 500K nuclei [5 million cells/mL prepared in 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete Protease Inhibitor Cocktail] were dispensed to individual wells of a 96-well plate, immobilized onto Concanavalin-A beads (Con-A; EpiCypher #21-1401), and incubated overnight (4°C) with 0.5 µg of antibody (IgG, H3K4me3, H3K27me3, H3K27ac and 3 PRMT5 antibodies). pAG-MNase (EpiCypher #15-1016) was added / activated (2 hours @ 4°C) and CUT&RUN enriched DNA (crosslink reversal not necessary for lightly fixed samples) purified using Serapure beads after mixing at 2:1 (Bead:DNA) ratio. Recovered DNA was quantified using PicoGreen and reactions were normalized to 5ng DNA (or entirety of the reaction if <5ng DNA was recovered) before preparing sequencing libraries (CUTANA CUT&RUN Library Prep kit; EpiCypher #14-1001)

treatment_protocol: Cells were seeded at 450,000 cells per 15 cm culture dish and allowed to attach to the dish overnight. The following day, enzalutamide was added at 5 μM concentration diluted from 100 mM stock in DMSO. Dilutions were prepared such that DMSO content in culture plates, including DMSO control, was always 0.1%. Enzalutamide treatment was performed for 14 days at 5 μM treatment. Media was refreshed and enzalutamide was re-applied to cell culture dishes every 72 h. DMSO cells were seeded at the same density and treated at same schedule as enzalutamide treatment groups but harvested at 70-80% confluency.

value: prostate

value: LNCaP

value: prostate adenocarcinoma cell

value: Enzalutamide induction, 14 days

tag: antibody


title: H3K27me3 LNCaP cells, Enzalutamide treatment, 14 days


title: N14_SMT2_2C_KO_sc2


title: Control_118_S109

value: Seaver Autism Center

value: Control


title: D-Plasma Fasting

description: Circulating small RNA


title: H3K4me3 LNCaP cells, Enzalutamide treatment, 14 days


title: N14_SMT2_2C_WT_sc2

value: Mouse 2-Cell


title: N14_SMT2_2C_WT_sc1


title: Control_102_S94

value: Peripheral blood


title: IgG LNCaP cells, Enzalutamide treatment, 14 days

value: IgG


title: Control_103_S95


title: PMS_136_S125

value: PMS

value: Class I


title: H3K27ac LNCaP cells, DMSO treatment

value: DMSO (negative control)


title: Control_101_S93


title: H3K27me3 LNCaP cells, DMSO treatment

value: WT


title: N14_SMT2_MII_KO_sc19

source_name: Mouse MII oocyte

value: Mouse MII oocyte

value: N14 maternal KO


title: Control_10_S8

value: F


title: N14_SMT2_MII_KO_sc18


title: IgG LNCaP cells, DMSO treatment


title: hnRNPU-03

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

description:
Replicate si-hnRNPU-03
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines:    @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT     NAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT  +  #55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHH    Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).Line 2 is the raw sequence letters.Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.    The details of Sequencing identifier of Illumina are as follows:    (1) HWI-ST1276:71 HWI-ST1276,Instrument – unique identifier of the sequencer; 71,run number – Run number on instrument  (2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX(Flowcell ID)flowcell,line 1, 1101 tile is(x=1208,y=2458)  (3) 1:N:0:CGATGT the first number is 1 or 2, 1 means single reads or the first read of paired ends, 2 means the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence.
Data filtering    The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. It was necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows:    (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.    RNA-seq Adapter information:    NEBNext® UltraTM RNA Library Prep Kit  RNA 5' Adapter(5'Adaptor)    5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT    RNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index)    5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. For the spieces(Human and mice) whose gene annotation information are more completed, if only need the differential expression significant genes, can map reads to the transcriptome directly. If research the study of alternative splicing, variation, the fusion gene, the alignment should be carried out at the genome level. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely.
Reads distribution on genome    Reads were mapped to exon, intron and intergenic.  According to the mapping result, summary the percentage of statistics for reads in the genome exon, intron and intergenic region seperately. In general, the gene annotation of the species is more complete (such as mouse and human), the ratio of reads mapped to exon is supposed to be the highest.  Reads mapped to intron may result from the remaining pre-mRNA or alternative splicing event.  Reads mapped to intergenic may due to some ncRNA or DNA fragment contamination or the incomplete gene annotation.
Distribution of mapped reads on chromosome    After getting the information about distribution of mapped reads on genome area, we  focused the distribution of mapped reads on chromosome. On one hand we can get insight into how many regions on chromosome is covered, on the other hand we can get the information about transcription activity on chromosome.    We calculated mapped reads density on every chromosome , then plot based on the mapped reads density. In general, the longer the chromosome is, the more reads were mapped to the chromosome. The statistics of reads mapped to chromosome indicates the relationship between chromosome length and reads number. The plot method are as follows:    (1) 1 Kbp as an unit when window size is set, counting number of reads that mapped to the every base in window;  (2) Mid-value is chosen to represent the number of reads that mapped to the every base in window; the longer chromosome is, the more reads will be calculated(Marquez et al.);  (3) log2 (mid-value) is used to plot.
Gene expression level analysis    The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Genome_build: Homo sapiens - GRCh38
Supplementary_files_format_and_content: DU_fpkm_genename.xlsx: FPMK + Gene annotations (Excel format)
Supplementary_files_format_and_content: DU_readcount_genenames.xlsx: Readcounts + Gene annotations (Excel format)

growth_protocol: DMEM+FBS10%+Pen/Strep 1%

extract_protocol:
RNA was obtained using Eurogold Trifast (Euroclone, Milan, Italy), following the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/).  RNA libraries were prepared for sequencing using standard Illumina protocols.  Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies).  Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: Human neuroblastoma SH-SY-5Y cells were cultured in DMEM–Glutamax-I (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) supplemented with 10% fetal bovine serum (Gibco-BRL, Life Technologies Inc., Frederick, MD, USA) and Antibiotic-Antimycotic-stabilized suspension (SigmaAldrich, St. Louis, MO, USA) at 37°C incubator with humidified atmosphere of 5% CO2. The siRNA sense sequences used for silencing the different target proteins were the following: luciferase (control): uaaggcuaugaagagauac, TDP-43: gcaaagccaagaugagccu, DAZAP1: gagacucugcgcagcuacu. After twice gene silencing by Hyperfectamine (Qiagen Inc, Gaithersburg, Maryland), cells were collected and divided into two aliquots; one half for western blot and the other half for RT–PCR analysis.

tag: disease state

value: neuroblastoma

value: si-hnRNPU


title: N14_SMT2_MII_KO_sc16

tag: cell type


title: hnRNPU-02

description:
Replicate si-hnRNPU-02
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx


title: hnRNPD-03

description:
Replicate si-hnRNPD-03
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx

value: si-hnRNPD


title: BMDM-7-3

city: WuHan

first: Yugang

last: Li

address: shizishan street

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus musculus (house mouse) whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mus musculus (house mouse)
Supplementary_files_format_and_content: gene_expression.xls file includes FPKM values for each Sample ...

source_name: BMDM cell

extract_protocol:
RNA was harvested using Trizol reagent. RNeasy Mini Kit （250） Qiagen#74106 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: h37ra strain


title: BMDM-7-2


title: N14_SMT2_MII_KO_sc14

city: Beijing


title: BMDM-7-1


title: N14_SMT2_MII_KO_sc15


title: BMDM-3-3

value: mpbR-deleted


title: N14_SMT2_MII_KO_sc12


title: N14_SMT2_MII_KO_sc13


title: hnRNPD-01

description:
Replicate si-hnRNPD-01
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx

tag: treatment


title: BMDM-3-2


title: N14_SMT2_MII_KO_sc17


title: CTR-03

description:
Replicate siLUC-03
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx

value: control


title: H3K4me3 LNCaP cells, DMSO treatment

tag: tissue

value: prostate

value: LNCaP

value: prostate adenocarcinoma cell


title: N14_SMT2_MII_KO_sc11


title: N14_SMT2_MII_KO_sc10


title: hnRNPD-02

description:
Replicate si-hnRNPD-02
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx


title: BMDM-3-1


title: BMDM-1-3

value: wild type


title: CTR-02

description:
Replicate siLUC-02
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx


title: N14_SMT2_MII_KO_sc8


title: BMDM-1-1


title: CTR-01

description:
Replicate siLUC-01
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx


title: hnRNPU-01

description:
Replicate si-hnRNPU-01
DU_fpkm_genename.xlsx
DU_readcount_genename.xlsx


title: N14_SMT2_MII_KO_sc9


title: BMDM-1-2


title: Macrophages infected with Mtb MKR at 4 hour rep3

city: Bangkok

first: Marisa

last: Ponpuak

address: 272 Rama 6 Road

country: Thailand

institute: Department of Microbiology, Faculty of Science, Mahidol University

data_processing:
Basecalling was performed using Illumina Casava1.7 software
Samples were demultiplexed using Illumina bcl2fasq software
To trim the adapters and to remove low-quality reads, the total RNA sequences from each experiment were pre-processed by Trimmomatic V0.32 with the following parameters, ILLUMINACLIP: TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36
The remaining high-quality reads were mapped to the prebuilt index of the human reference genome GRCh38 by using HISAT2 v2.1.0 . To quantify the number of reads per transcript, the read alignments were processed using featureCounts (version 1.4.6) Subsequently, DESeq2 V1.24.0 was used to identify differentially expressed genes between two experimental conditions.
DESeq2 V1.24.0 was used to identify differentially expressed genes between 0 hour and 4 hour of the M. tuberculosis strains.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Macrophages

extract_protocol:
Total RNAs were isolated from 1.5 x 106 Macrophage infected cells by using the RNeasy kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using QIAseq FastSelect RNA removal and QIAseq stranded total RNA library preparation kits (QIAGEN).

value: THP-1 cells

value: infected with Mtb MKR at 4 hour


title: Macrophages infected with Mtb MKR at 4 hour rep2


title: Macrophages infected with Mtb MKR at 4 hour rep1


title: N14_SMT2_MII_KO_sc5

first: Fan

last: Guo

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences


title: Macrophages infected with Mtb H37Rv at 4 hour rep3

value: infected with Mtb H37Rv at 4 hour


title: N14_SMT2_MII_KO_sc6


title: Macrophages infected with Mtb H37Rv at 4 hour rep2


title: N14_SMT2_MII_KO_sc4


title: N14_SMT2_MII_KO_sc3


title: Macrophages infected with Mtb H37Rv at 4 hour rep1


title: N14_SMT2_MII_KO_sc2


title: Macrophages infected with Mtb MKR at 0 hour rep3

value: infected with Mtb MKR at 0 hour


title: Macrophages infected with Mtb MKR at 0 hour rep2


title: N14_SMT2_MII_KO_sc7


title: S662034

first: Yanfei

last: Jia

address: South Fourth Ring West Road

department: Department of Neurosurgery

institute: Beijing Tiantan Hospital

description:
Normal
S662034

data_processing:
A total of 16 tissue samples (11 PCP tumor tissues and 5 normal tissues) were subjected  to whole transcriptome analysis using high-throughput sequencing. Ribosomal RNA  (rRNA) was removed from total RNA (1 μg) using the Ribo-Zero Gold rRNA kit  (Illumina, San Diego, CA, USA)
Strand-specific cDNA libraries were prepared using  the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the  manufacturer’s instructions without purification and enrichment of mRNAs.
RNA was ligated with T4 RNA Ligase 1 at the 3’ ends and T4 RNA Ligase 2 at the 5’  adapters, followed by reverse transcription into cDNA
After PCR amplification, the  products were purified using polyacrylamide gel electrophoresis.
The resulting libraries were validated using the Agilent Bioanalyzer 2100 system  (Agilent Technologies, CA, USA), followed by sequencing using the HiSeq™ 2000  platform (Illumina, San Diego, CA, USA). Subsequently, we applied Cutadapt adapters  (version 1.16) to trim the raw reads and used the FastQC software (v0.11.7) to obtain  quality control reports of the sequence reads.
Assembly: hg38
Supplementary files format and content: the sequencing data were aligned  to the human reference genome (hg38) using the STAR software (V2.3.0), and the count  data were normalized as the fragments per kilobase of transcript per million data after  filtering read count files with low expression.
Supplementary files format and content: The original sequence count data was  normalized by transcript per million (TPM) and then calculated by log(x+1)

source_name: Normal Brain Tissue

extract_protocol:
Total RNA was extracted from PCP tissues using Trizol reagent (Thermo Fisher  Scientific, Waltham, MA, USA). The concentration and quality of total RNA were  evaluated using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies,  Wilmington, DE, USA), and the integrity of total RNA was determined using the  Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality  RNA samples (RNA integrity number≥7) were used for further analysis.

value: Normal Brain Tissue


title: S671123

description:
Normal
S671123


title: S610942

description:
PCP
S610942

source_name: Papillary Craniopharyngioma

value: Papillary Craniopharyngioma


title: S657709

description:
Normal
S657709


title: S665888

description:
Normal
S665888


title: S657634

description:
Normal
S657634


title: S639433

description:
PCP
S639433


title: Macrophages infected with Mtb MKR at 0 hour rep1


title: N14_SMT2_MII_WT_sc14

value: Mouse MII oocyte

value: WT


title: S631932

description:
PCP
S631932


title: N14_SMT2_MII_KO_sc1

value: N14 maternal KO


title: N14_SMT2_MII_WT_sc13


title: Macrophages infected with Mtb H37Rv at 0 hour rep2

value: infected with Mtb H37Rv at 0 hour


title: S625441

description:
PCP
S625441


title: N14_SMT2_MII_WT_sc12


title: N14_SMT2_MII_WT_sc11


title: Macrophages infected with Mtb H37Rv at 0 hour rep1

value: infected with Mtb H37Rv at 0 hour


title: N14_SMT2_MII_WT_sc10


title: S600996

description:
PCP
S600996


title: S636377

description:
PCP
S636377


title: S629208

description:
PCP
S629208


title: frpe_d10_5f_x9

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (hg38) using Hisat2
the number of reads uniquely mapped to each gene was determined using featurecount
Genome_build: hg38
Supplementary_files_format_and_content: reads count per gene

source_name: frpe derived CiPCs

extract_protocol:
Total RNA was purified using RNeasy per manufacturer’s instructions (Qiagen)
PolyA-tailed RNA was purified from total RNA and libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

tag: tag

value: 5 Factors

tag: passage


title: N14_SMT2_MII_WT_sc9

tag: genotype


title: frpe_d10_only_aso_x8

value: ASO


title: N14_SMT2_MII_WT_sc8


title: N14_SMT2_MII_WT_sc7


title: frpe_d10_5fa_x7

value: 5 Factors + ASO


title: Macrophages infected with Mtb H37Rv at 0 hour rep3

tag: cell line


title: S652529

description:
PCP
S652529


title: S608752

description:
PCP
S608752


title: frpe_d10_5f_x3


title: S667090

description:
PCP
S667090


title: N14_SMT2_MII_WT_sc6


title: HDF_d10_5fa_x4

source_name: HDF derived CiPCs


title: frpe_d10_5fa_x10


title: N14_SMT2_MII_WT_sc2


title: HDF_d10_5f_x5


title: frpe_d10_only_aso_x2

source_name: frpe with ASO treatment