title: 027_Hi-C

data_processing:
Library strategy: Hi-C
Paired-end reads were first trimmed by Trim_Galore! (version 0.6.0) to remove adapters and low-quality bases with parameter “--paired”
Trimmed reads were then mapped to human genome GRCh38 by BWA MEM (version 0.7.17-r1198) with parameter “-SP5M”
Mapped reads were deduplicated with “pairtools dedup” (version 0.3.0)
Reads mapped to the same MboI restriction fragment or in outward direction are removed for downstream analysis.
Final pairs files were generated using Pairtools (version 0.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: Pairs format, chromatin interaction intensity for pairs of genomic loci

extract_protocol:
One to two million cryopreserved primary samples or cell lines in cell culture were spinned down with 500g and resuspended in 1ml/million RPMI 1640 medium with 10% fetal bovine serum, immediately crosslinked with 37% formaldehyde (MilliporeSigma 252549) to a final concentration of 2%, and incubated at room temperature for 10 minutes on a tube revolver at 16 rpm to mix, quenched by 2.5M glycine solution with a final concentration of 0.2M and incubated in room temperature for 5 minutes on revolver. Cells were pelleted by centrifuge at 500g at 4°C for five minutes and washed once with 1ml cold 1X PBS by centrifuge at 500g at 4°C for five minutes and the supernatant was discarded. Cells were lysed to extract nuclei with 250ul lysis buffer (10mM Tris-HCl pH8.0, 10mM NaCl, 0.2% Igepal CA630) mixed with 50ul 50x protease inhibitor (Sigma, P8340) and incubated on ice for 15 minutes, centrifuge to pellet at 2500g, 4°C for five minutes and washed with 500ul lysis buffer. Cell pellets were resuspended in 50ul 0.5% sodium dodecyl sulfate (SDS) and incubated at 62°C for 10 minutes, quenched by 145ul water and 25ul 10% Triton X-100 (Sigma, 93443), and incubated at 37°C for 15 minutes. 25μl of 10X NEBuffer2 (NEB B7207) and 100 unit of MboI restriction enzyme (NEB, R0147) was then added to the reaction for overnight DNA digestion at 37°C on the tube revolver. The digestion was then quenched by incubation at 62°C for 20 minutes. DNA was then end repaired and Biotin labeled with 50ul fill-in master mix (37.5μl of 0.4mM biotin-14-dATP (Life Technologies, 19524-016), 1.5μl of 10mM dCTP, 1.5μl of 10mM dGTP, 1.5μl of 10mM dTTP, 8μl of 5U/μl DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210) and incubated at 37°C for 1.5 hours.Then DNA was ligated with 900ul of ligration master mix (669ul water, 120μl of 10X NEB T4 DNA ligase buffer (NEB, B0202), 100μl of 10% Triton X-100, 6μl of 20mg/ml Bovine Serum Albumin (MilliporeSigma B8667), 5μl of 400 U/ μl T4 DNA Ligase (NEB, M0202) ), incubated at room temperature for 4 hours with slow rotation. Decrosslink DNA by adding 50ul of 20mg/ml proteinase K (QIAGEN 19133) and 120ul of 10% SDS, incubated at 55°C for 30 minutes. Quench the reaction by adding 130μl of 5M sodium chloride and incubate at 68°C overnight. Precipitate DNA by adding 1.6X volume of pure ethanol and 0.1X volume of 3M sodium acetate, pH 5.2 (MilliporeSigma S7899), incubate at  -80°C for at least half hour, and centrifuge at max speed, 2°C for 15 minutes to discard supernatant. Wash DNA once with 700ul 80% ethanol. Dissolve dried DNA pellet in 130ul 10 mM Tris-HCl, pH 8. Sonicate the solution to shear DNA to average size of 300-500bp with Covaris sonicator, with parameters set as followings: PIP 140, duty factor 10, burst 200, and duration 58s-80s. Run 4ul sheared DNA in 16ul water on a 2% agarose to verify the size.
Pull down biotin-labeled DNA by washing 150μl of 10mg/ml Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) with 400μl of 1X Tween Washing Buffer (TWB: 5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20), discard the solution. Resuspend the beads in 300μl of 2X Binding Buffer (10mM Tris-HCl (pH 7.5); 1mM EDTA; 2M NaCl) and add to the sheared DNA. Incubate at room temperature for 15 minutes with rotation. Separate beads and discard the supernatant with a magnetic rack. Wash beads with 600ul TWB buffer twice. End repair of sheared DNA by resuspending beads in 100ul 1X NEB T4 DNA ligase buffer (NEB, B0202), separating the beads, and resuspending in end repair master mix (88μl of 1X NEB T4 DNA ligase buffer with 10mM ATP (NEB B0202S), 2μl of 25mM dNTP mix, 5μl of 10U/μl NEB T4 PNK (NEB, M0201), 4μl of 3U/μl NEB T4 DNA polymerase I (NEB, M0203) , 1μl of 5U/μl NEB DNA polymerase I, Large (Klenow) Fragment (NEB, M0210) ), and incubation at room temperature for half hour. Beads were washed twice with 500ul TWB buffer and resuspended in 100μl 1X Quick ligation reaction buffer (NEB, B6058), recollected, and proceeded with dATP attachment by resuspended in 100μl master mix (90μl of 1X NEBuffer 2, 5μl of 10mM dATP, 5μl of 5U/μl NEB Klenow exo minus (NEB, M0212)), incubated at 37°C for 30 minutes. Beads were washed twice with 500ul TWB buffer and resuspended in 100μl 1X Quick ligation reaction buffer (NEB, B6058), recollected, proceeded with adaptor ligation through resuspension in  50μl of 1X NEB Quick ligation reaction buffer, 2μl of NEB DNA Quick ligase (NEB, M2200), and 3ul of Illumina adaptor of choice, incubated in room temperature for 15 minutes. Beads were washed by 600ul TWB buffer and 100ul 1X Tris buffer, resuspended in 50ul 1X Tris buffer, heated on 98°C for 10 minutes to elute the DNA off the beads. Beads were discarded. Size selection was performed to remove small DNA fragments by adding 0.8X-0.9X KAPA beads to the DNA elution, incubation at room temperature for 5 minutes, and beads were collected with supernatant discarded. Wash beads twice with 500ul 80% ethanol and elute beads in 50ul 1X Tris buffer. Library amplification was performed with 4-12 cycles of PCR with KAPA 2X library mix. Size selection was performed to remove small and large fragments using KAPA beads and maintain DNA fragments of 150bp-500bp.  Libraries were sequenced as 150 bp paired-end reads with a raw sequencing depth between 300 million to 700 million read pairs per sample on Novaseq.


title: 990_Hi-C

status: Public on Jul 19 2022

type: SRA

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Chicago Ave. Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary AML

growth_protocol: HL60 (ATCC CCL-240) and Kasumi-1 (ATCC CRL-2724) cells were given to us as a gift from Dr Sinisa Dovat lab, which are new vials purchased from ATCC. Cells are cultured following the manufacturer’s culture method. Kasumi is cultured with RPMI-1640 (Gibco, 11875093) with 20% FBS. HL60 is cultured with Iscove's Modified Dulbecco's Medium (IMDM) (ATCC® 30-2005).

treatment_protocol: 5-azacytidine (MilliporeSigma A2385-100MG) was dissolved in DMSO to make 100mM stock solution, aliquoted and stored in -80°C. Working solutions (0.5uM-10uM) was made from further dilution of stock solution using complete cell culture media. Media was changed every 24 hours with freshly made 5-AZA solution. Dead cells are removed by Ficoll-Paque PLUS density gradient media at the end of cell culture before cells are further processed for any profiling experiments.

tag: cell type

value: Selected PBMC or BM cells

tag: assay

value: Hi-C


title: 168_Hi-C


title: E7.5_tet_chimera_plate3_H09_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HISAT2 (v2.1.0) using options --dta --no-softclipping --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Assembly: GRCm38
Supplementary files format and content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID

molecule: total RNA

organism: Mus musculus

source_name: Early embryo

extract_protocol: Single-cells were sorted  using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: strain

tag: tissue

value: E7.5 embryo


title: RNA_J1-ESC-1

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: mESC

data_processing:
Quality and adaptor trimming of Fastq files were performed using TrimGalore v.0.6.4
Sequence reads were aligned to mm9 (mm9/NCBIM37.67) with STAR v2.7.9a
Read number were counted by htseq v.0.11.2
Differential gene expression was analyzed using DESeq2 v.4.1.1
Assembly: mm9
Supplementary files format and content: Tab-delimited text files including normalized reads counts for each sample.

molecule: polyA RNA

source_name: mESC

growth_protocol: J1 mESCs were cultured on inactive mouse embryonic fibroblast (MEF) feeder cells (approximately 30,000 cells per cm2) or on 0.1% gelatin-coated plates in a serum-based medium with 2i (3µM CHIR99021; 1µM PD0325901) addition, which was prepared as follows: DMEM supplemented with fetal bovine serum (FBS, 15%), recombinant leukemia inhibitory factor (LIF, 1000 units/mL), β-mercaptoethanol (0.1 mM), L-glutamine (2 mM), MEM non-essential amino acids (NEAA, 0.1 mM), nucleoside mix (1%), and Penicillin/Streptomycin (50 U/mL). D-EPSCs were cultured in a base medium of N2B27 prepared as follows: DMEM/F12 and Neurobasal (1:1 ratio), N2 supplement (1X), B27 supplement (1X), Glutamax (1X), β-mercaptoethanol (0.1 mM). The base medium was supplemented with KSR (5%), NEAA (0.1 mM), LiF (1000 units/mL), CHIR99021 (3µM); dimethindene maleate (DiM, 2µM); and minocycline hydrochloride (MiH, 2µM). L-EPSCs were cultured on feeder cells or gelatin-coated plates in a base medium prepared as follows: DMEM/F12, KnockOut Serum Replacement (KSR, 20%), L-glutamine (2 mM), NEAA (0.1 mM), β-mercaptoethanol (0.1 mM). The base medium was supplemented with Lif (1000 units/mL), CHIR99021 (3µM), PD0325901 (1µM), A-419259 (0.3µM), XAV939 (5µM), JNK inhibitor VIII (4µM), SB203580 (10µM).

extract_protocol:
Total RNA from ESCs and EPSCs replicates were extracted using Trizol according to the manufacturer’s protocol.
RNA-seq libraries were prepared manually using Universal Plus mRNA-Seq with NuQuant kit, according to the manufacturer’s protocol.

treatment_protocol: Doxycycline was added to cells to deplete expression of Sox2, Oct4, or Nanog.

tag: genotype

value: WT

value: mESC

tag: treatment


title: 1360_Hi-C


title: RNA_J1-ESC-2

description: mESC


title: 936_Hi-C


title: E7.5_tet_chimera_plate3_H08_RNAseq


title: 4oht_24

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava version 1.8.2 was used for basecalling.
RNA-seq reads were aligned to human genome hg19 (GRCh37) using TopHat2 version 2.0.11 with the parameter "--library-type=fr-unstranded"
Gene annotation information from Ensembl GRCh37 were employed
Rsubread featureCounts version 1.18.0 was used to generate gene-based read counts matrix
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing gene-based read counts matrix

source_name: IMR90 ER:RAS

growth_protocol: IMR90 ER:RAS cells were grown in DMEM 10% FBS for 6 days. Media was changed at day 4.

extract_protocol:
Total RNA was extracted using Trizol and the Rneasy isolation kit (Qiagen).
Smart-Seq2 protocol using Nextera XT Dual Indexing Kit.

treatment_protocol: To induce RAS activation, cells were treated with 4OHT [100nM].

tag: days after 4oht

tag: passage

tag: cell line

value: IMR90 ER:RAS


title: 3DA_31

value: 3DA + 4OHT


title: E7.5_tet_chimera_plate3_H07_RNAseq


title: H3K27ac_Liu_EPS_rep1

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v1.10).
ChIP-seq peaks were determined by the MACS program (v.2.2.7) with the -broad option, using input as the control data.
Peak annotation was performed using HOMER annotatePeaks.pl script to assign nearby genes to each peak.
Assembly: mm9
Supplementary files format and content: Bed file of MACS called peaks.

source_name: mEPSC

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006).
ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina NovaSeq 6000 Sequencer. Data with 150 bp paired-end reads were obtained.

value: mEPSC

tag: antibody

value: Abcam, ab4729


title: 4oht_23


title: H3K4me1_Liu_EPS_rep2

value: Abcam, ab8895


title: E7.5_tet_chimera_plate3_H06_RNAseq


title: E8.5_plate1_A01_RNAseq

value: E8.5 embryo


title: H3K27ac_Liu_EPS_rep2


title: 4oht_22


title: 4oht_21


title: E7.5_tet_chimera_plate3_H05_RNAseq


title: DMSO_20

value: DMSO


title: 1916_Hi-C


title: H3K4me1_Liu_EPS_rep1


title: 1021_Hi-C


title: DMSO_18


title: DMSO_19


title: E7.5_tet_chimera_plate3_H04_RNAseq


title: Input_Liu_EPS


title: E7.5_tet_chimera_plate3_H03_RNAseq


title: H3K27ac_Deng_EPS_rep2


title: 260_Hi-C


title: 018_Hi-C


title: E7.5_tet_chimera_plate3_H01_RNAseq


title: H3K27ac_Deng_EPS_rep1


title: 472_Hi-C


title: E7.5_tet_chimera_plate3_H02_RNAseq


title: H3K4me1_Deng_EPS_rep1


title: E7.5_tet_chimera_plate3_G12_RNAseq


title: 566_Hi-C


title: 546_Hi-C


title: Input_Deng_EPS


title: RNASeq_Cp190-KO_rep1

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

data_processing:
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the STAR_v2.6.1a with default parameters.  Unmapped or non-unique mapped reads were discarded.
wig file is outputed by options "--outWigType bedGraph --outWigStrand Stranded"
Assembly: dm3
Supplementary files format and content: wig in dm3 outputed from STAR, example  variableStep chrom=chr2L  6969 0.01899  6970 0.01899
Supplementary files format and content: bed in dm6 transferred by UCSC liftover from above wig, example  chr2L 6969 6970 0.01899  chr2L 6970 6971 0.01899

organism: Drosophila melanogaster

source_name: Cultured cells

growth_protocol: Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate

extract_protocol:
Total RNA was isolated from cultured cells using TRI Reagent according to the manufacturer instructions (Sigma-Aldrich #T9424)
200ng of total RNA were used for indexed library preparation using Ovation RNA-Seq Systems 1–16 for Model Organisms Kit (#0350 DROSOPHILA, Nugen Technology).

tag: mutation


title: RNASeq_CTCF-KO_rep1


title: RNASeq_Cp190-KO_rep2


title: 1953_Hi-C


title: RNASeq_CTCF-KO_rep2


title: E7.5_tet_chimera_plate3_G11_RNAseq


title: 868_Hi-C


title: DMSO_17


title: E7.5_tet_chimera_plate3_G09_RNAseq


title: H3K27ac_J1_mESC_rep2


title: 773_Hi-C


title: E7.5_tet_chimera_plate3_G10_RNAseq


title: H3K27ac_J1_mESC_rep1


title: H3K4me1_J1_mESC_rep2


title: RNASeq_Ras_control_rep2


title: H3K4me1_Deng_EPS_rep2


title: 270_Hi-C


title: HiC_CTCF-KO_rep2

data_processing:
Paired-end reads were mapped to the Drosophila melanogaster genome (assembly dm3) using the bowtie program with parameters (-t -a -m 1 --best).  Unmapped or non-unique mapped reads were discarded.
We then divided read pairs into four groups: SS (reads mapping to the same restriction fragment, or to two adjacent restriction fragments); S2 (reads in which both ends mapped precisely on the DpnII site); S1 (reads in which one of the ends mapped precisely on the DpnII site); S0 (reads in which both ends did not map precisely to a DpnII site). SS, S2 and S1 pairs were discarded from subsequent analysis.
Mapped reads were then associated with the first restriction fragment end encountered when moving from the mapped position in the appropriate strand.
All subsequent analysis was done in the space of fragment end pairs. The Drosophila genome contains 464,246 restriction fragments. After discarding low mappability fragments 301,687 fragments are left (and each defines two fragment ends).
A model accounting for systematic biases in contact probability was constructed as previously (Yaffe and Tanay; Nature Genetics, 43, p.1059-65). Briefly, we used the local G+C content of up to 200 bp from the restriction site (agc, bgc), and the DpnII restriction fragment lengths (alen, blen), to correct for systematic biases in Hi-C coverage by modeling: P(Xa,b) = Pprior x Flen(alen,blen) x Fgc(agc,bgc).
We estimated maximum likelihood model parameters (the matrices Flen and Fgc) through application of an iterative algorithm as described, using 20 bins for G+C content and 20 bins for fragment length.
The matrix is normalized based on Iterative Correction  algorithm by "gcMapExplorer normIC".
Hi-C pipeline is performed based on dm3. Then, the coordinate was converted into dm6 by "liftover".
Assembly: dm3
Supplementary files format and content: The output Bin-Contact pair files are transferred into gcmap format by "gcMapExplorer bc2cmap".
Supplementary files format and content: *.gcmaps:The gcmap file is in HDF5 format to store Genome Contact Map (gcmap). As HDF5 format supports Hierarchical Data Model, therefore we implemented the contact maps in format way.

extract_protocol: [NOT PROVIDED]


title: E7.5_tet_chimera_plate3_G08_RNAseq


title: RNASeq_Ras_control_rep1


title: E7.5_tet_chimera_plate3_G06_RNAseq


title: H3K4me1_J1_mESC_rep1


title: E7.5_tet_chimera_plate3_G07_RNAseq


title: HiC_CTCF-KO_rep1


title: 629_Hi-C


title: 103_Hi-C

source_name: Primary Healthy donor


title: HiC_Cp190-KO_rep2


title: E7.5_tet_chimera_plate3_G05_RNAseq


title: 576_Hi-C

value: Selected peripheral blood mononulcear cells (PBMC) or bone marrow (BM) cells


title: 673_Hi-C


title: Input_J1_mESC


title: E7.5_tet_chimera_plate3_G04_RNAseq


title: HiC_Cp190-KO_rep1


title: 1916_CUT&TAG_IgG

data_processing:
Library strategy: CUT & Tag
Reads were first trimmed by Trim_Galore! (version 0.6.0) with “--paired” options
Trimmed reads were aligned to human genome reference GRCh38 with Bowtie2 (version 2.3.5.1)
PCR duplicates were removed by Picard MarkDuplicates tool with “VALIDATION_STRINGENCY=LENIENT” option
Peaks were called by MACS2 “-p 1e-2 --nomodel --shift 0 --keep-dup all -B --SPMR” options, and filtered agains the ENCODE hg38 blacklist regions
Bigwig files were generated using MACS2 bdgcmp tool and bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: Peak, ChIP-seq peaks called by MACS2, filter by p value < 1e-5

extract_protocol:
The CUT & TAG experiments were performed exactly following the online protocol[Kaya-Okur et al., Nat Commun, 2019]: https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6?version_warning=no. For each targeted protein we use 0.1 million cells. We use the following primary antibodies: CTCF (Active motif 2899), H3K27ac (Active motif 39133), H3K27me3 (Cell signaling C36B11), Rabbit IgG (Cell signaling 2729), and the Guinea Pig anti-Rabbit IgG (H+L) secondary antibody (NBP1-72763). The pA-Tn5 fusion protein was kindly provided as a gift from Dr Steven Henikoff Lab. Final libraries were sequenced as 150 bp paired-end reads on platform Novaseq or Hiseq Xten, with a raw sequencing depth between 10 to 20 million read pairs.
The CUT & TAG experiments were performed exactly following the online protocol[Kaya-Okur et al., Nat Commun, 2019]: https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6?version_warning=no. For each targeted protein we use 0.1 million cells. We use the following primary antibodies: CTCF (Active motif 2899), H3K27ac (Active motif 39133), H3K27me3 (Cell signaling C36B11), Rabbit IgG (Cell signaling 2729), and the Guinea Pig anti-Rabbit IgG (H+L) secondary antibody (NBP1-72763). The pA-Tn5 fusion protein was kindly provided as a gift from Dr Steven Henikoff Lab. Final libraries were sequenced as 150 bp paired-end reads on platform Novaseq or Hiseq Xten, with a raw sequencing depth between 10 to 20 million read pairs.

value: CUT&TAG

tag: antibody (if any)

value: IgG


title: ATAC_EPS_Liu_rep1

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 2000 --no-mixed
Aligned reads were filtered by samtools (v1.10) program with parameters -F 0x04 -f 0x02 -q 20.
ATAC-seq peaks were determined by the MACS program (v.2.2.7), with default settings.
Peak annotation was performed using HOMER annotatePeaks.pl script to assign nearby genes to each peak.
Assembly: mm9
Supplementary files format and content: Bed file of MACS called peaks.

extract_protocol:
The ATAC-seq libraries of ESCs and both EPSCs were prepared in technical replicates as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015)
ATAC libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina NovaSeq 6000 Sequencer. Data with 150 bp paired-end reads were obtained.


title: HiC_Ras_control_rep2


title: E7.5_tet_chimera_plate3_G03_RNAseq


title: HiC_Ras_control_rep1


title: dHPC-KO-FC-4

city: Philadelphia

first: Desi

last: Alexander

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Alignment: STAR.2.5.2a (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Bam conversion: samtools-1.1 (view -bS)
Gene quantitation: HTSeq-0.9.1 (-f sam -r pos -s reverse -t exon -i gene_id); Refseq annotations
Differential gene expression and adjustments were performed using DESeq2. For experiment 1, the design consisted of 3 conditions (Acss2 WT, het, and Acss2 KO) and was incorporated using design=~condition). For experiment 2, the design consisted of 4 conditions (baseline WT, fear conditioned WT, baseline KO, fear conditioned), and 3 batches. These were built into the model using the command design=~batch + condition. For downstream analysis (individual gene counts, heatmaps), batch effects were removed from the adjusted gene counts table using limma. The adjust counts table was first Log2 adjusted using vst (vst(dds_batch, blind=FALSE), then batch effect was removed using the command limma::removeBatchEffect.
Assembly: mm10
Supplementary files format and content: txt table containing raw gene counts (one per experiment)
Supplementary files format and content: csv table containing normalized gene counts (one per experiment)

source_name: Dorsal hippocampus

growth_protocol: Exons 3-7 of the Acss2 locus were deleted in single-cell C57Bl6/J embryos, generating mice with a constitutive loss of ACSS2.

extract_protocol:
Mice were sacrificed either 30 minutes after a single-shock fear conditioning paradigm or directly from homecages. Whole brains were dissected out and rapidly snap-frozen using liquid nitrogen, then thawed on ice. Whole hippocampi (Experiment 1) were freehand dissected. Dorsal hippocampal sections were obtained using a brain matrix. Isolated hippocampi (whole [experiment 1] or 1mm-thick dorsal hippocalal sections [experiment 2]) were homogenized in trizol and total RNA was extracted using Trizol-Chloroform extraction. Total RNA quality was assessed on the Bioanalyzer platform using the RNA 6000 Nano assay (Agilent).
mRNA was isolated from 300 ng total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L), and libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770).

treatment_protocol: Mice were subjected to a single-shock contextual fear condioning paradigm (fear conditioned), or sacrficed directly from their homecages (baseline)

value: hippocampus

tag: behavior

value: Fear conditioned

value: Acss2 KO

tag: batch

tag: experiment

value: Experiment 2


title: E7.5_tet_chimera_plate3_G01_RNAseq

value: E7.5 embryo


title: ATAC_EPS_Deng_rep2


title: E7.5_tet_chimera_plate3_G02_RNAseq


title: 018_CUT&TAG_IgG

value: Selected PBMC or BM cells


title: 546_CUT&TAG_IgG


title: ATAC_EPS_Deng_rep1


title: ATAC_ESC_J1_rep2

value: mESC


title: dHPC-KO-FC-3


title: E7.5_tet_chimera_plate3_F12_RNAseq


title: 027_CUT&TAG_IgG


title: dHPC-KO-FC-2


title: ATAC_EPS_Liu_rep2


title: 168_CUT&TAG_IgG


title: ATAC_ESC_J1_rep1


title: E7.5_tet_chimera_plate3_F11_RNAseq


title: 103_CUT&TAG_IgG


title: E7.5_tet_chimera_plate3_F10_RNAseq


title: E7.5_tet_chimera_plate3_F09_RNAseq


title: MVA-TAA-Combo treated tumors biological replicate 3

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm39 whole genome using STAR v2.7.9
Read summarization were obtained using featureCounts.
Normalization were performed in R statistical environment following the limma-voom pipeline
Genome_build: mm39
Supplementary_files_format_and_content: tab-delimited text files include log2(cpm) values for each gene and every Sample
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene and every sample

source_name: tumor-bearing omentum

growth_protocol: 5x10 ID86 tumor cells were intraperitoneally injected in C57BL/6 mice. 7 days later, mice were treated intratumorally. Mice received a boost of the treatment 21 days after tumor incoculation.

extract_protocol:
Tumor-bearing omenta were excised 7 days after the last treatment. Tumor-bearing omenta were storaged in RNAlater at -80C until further processing.mRNA was isolated using Rneasy Mini Kit (Qiagen) following manufacture's instructions.
TruSeq Stranded mRNA preparation
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

treatment_protocol: Control groups received 200μL of vehiche control (PBS). Treatment groups were treated intreperitoneally with 5×107 TCID50 of the rMVA.

tag: agent

value: MVA-TAA-Combo

tag: tag


title: dHPC-KO-BL-5

value: Baseline


title: dHPC-KO-FC-1


title: 270_CUT&TAG_IgG

tag: cell type


title: 673_CUT&TAG_IgG

tag: assay


title: dHPC-KO-BL-3

tag: strain


title: E7.5_tet_chimera_plate3_F07_RNAseq

tag: tissue


title: dHPC-KO-BL-2

tag: genotype


title: 472_CUT&TAG_IgG


title: 629_CUT&TAG_IgG


title: MVA-TAA-Combo treated tumors biological replicate 2


title: MVA-TAA-Combo treated tumors biological replicate 1


title: E7.5_tet_chimera_plate3_F05_RNAseq


title: dHPC-KO-BL-1


title: 1360_CUT&TAG_IgG


title: 773_CUT&TAG_IgG


title: E7.5_tet_chimera_plate3_F04_RNAseq


title: MVA-TAA-CD137L treated tumors biological replicate 2


title: dHPC-WT-FC-3

value: WT


title: 027_CUT&TAG_CTCF

value: CTCF


title: E7.5_tet_chimera_plate3_F08_RNAseq


title: dHPC-WT-FC-2


title: E7.5_tet_chimera_plate3_F03_RNAseq


title: dHPC-WT-FC-1


title: MVA-TAA-CD40L treated tumors biological replicate 3


title: dHPC-KO-BL-4


title: MVA-TAA-CD137L treated tumors biological replicate 1


title: 168_CUT&TAG_CTCF


title: E7.5_tet_chimera_plate3_F02_RNAseq


title: E7.5_tet_chimera_plate3_F01_RNAseq


title: E7.5_tet_chimera_plate3_E12_RNAseq


title: dHPC-WT-BL-4


title: 546_CUT&TAG_CTCF


title: 472_CUT&TAG_CTCF


title: MVA-TAA-CD137L treated tumors biological replicate 3


title: MVA-TAA-CD40L treated tumors biological replicate 1


title: dHPC-WT-BL-3


title: MVA-TAA-CD40L treated tumors biological replicate 2


title: dHPC-WT-BL-2


title: 018_CUT&TAG_CTCF


title: dHPC-WT-BL-1


title: E7.5_tet_chimera_plate3_E10_RNAseq


title: E7.5_tet_chimera_plate3_F06_RNAseq


title: Vehicle (PBS) control treated tumors biological replicate 2

value: Vehicle control (PBS)


title: 773_CUT&TAG_CTCF


title: Vehicle (PBS) control treated tumors biological replicate 1


title: E7.5_tet_chimera_plate3_E09_RNAseq


title: E7.5_tet_chimera_plate3_E08_RNAseq


title: HPC-KO-1

source_name: Hippocampus (whole)

value: Experiment 1


title: 629_CUT&TAG_CTCF


title: 270_CUT&TAG_CTCF


title: 103_CUT&TAG_CTCF


title: E7.5_tet_chimera_plate3_E07_RNAseq


title: Omentum naïve replicate 1

source_name: Omentum naïve


title: 027_CUT&TAG_H3K27me3


title: HPC-Het-1

value: Acss2 heterozygote


title: Vehicle (PBS) control treated tumors biological replicate 3


title: E7.5_tet_chimera_plate3_E06_RNAseq


title: 168_CUT&TAG_H3K27me3


title: E7.5_tet_chimera_plate3_E05_RNAseq


title: HPC-KO-2


title: 1360_CUT&TAG_H3K27me3


title: ProE RNA seq Chd8 P53 DKO2

city: Cincinnati

first: Zhaowei

last: Tu

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Medical Center

description: RNA seq gene_matrix.txt

data_processing:
For CUT&RUN data processing, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).  Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85).   SEACR (https://seacr.fredhutch.org/ ) was used for peak calling. The program ngs.plot (version 2.63) was used to draw tag density plots and heatmaps for read enrichments.  The FPKM values of each gene’s promoter region (TSS±2kb) were generated using Bamscale package (version 0.0.5) for comparative expression analyses.
For RNA seq, reads were aligned to reference mouse genome mm10 and DESeq2 was used for differential gene expression analysis. EnhancedVolcano R package was used for volcano plot generation and pheatmap R package was used for heatmap generation.
Genome_build: mm10
Supplementary_files_format_and_content: CHD8N_marked.fragments.bedgraph, RNA seq gene_matrix.txt

source_name: Proerythroblasts

extract_protocol:
RNAs were extracted with Trizol following the protocol of Qiagen microRNeasy kit. Cut&Run DNA were extracted with the Phenol Chloroform.
DNA libraries were prepared with NEBNext DNA libraries Kit.

treatment_protocol: For RNA sequencing, the mice were injected with 4 times of pI:pC at a dose of 15mg/kg. The mice were sacrificed at 2 weeks post deletion and bone marrow cells were harvested.

value: Proerythroblasts


title: HPC-WT-2


title: E7.5_tet_chimera_plate3_E04_RNAseq


title: ProE RNA seq Chd8 P53 DKO1

description: RNA seq gene_matrix.txt


title: HPC-WT-1


title: 472_CUT&TAG_H3K27me3

value: CUT&TAG


title: Omentum naïve replicate 3


title: E7.5_tet_chimera_plate3_E03_RNAseq


title: ProE RNA seq P53 KO2

description: RNA seq gene_matrix.txt


title: 1916_CUT&TAG_H3K27me3


title: ProE RNA seq P53 KO1

description: RNA seq gene_matrix.txt


title: E7.5_tet_chimera_plate3_E02_RNAseq


title: Omentum naïve replicate 2


title: HPC-Het-2


title: E7.5_tet_chimera_plate3_E01_RNAseq


title: 546_CUT&TAG_H3K27me3


title: ProE RNA seq WT2

description: RNA seq gene_matrix.txt


title: 018_CUT&TAG_H3K27me3


title: ProE RNA seq WT1

description: RNA seq gene_matrix.txt


title: E7.5_tet_chimera_plate3_D12_RNAseq


title: HCT116 E5 3 (v2)

type: RNA

city: Erlangen

first: Regine

last: Schneider-Stock

address: Universitaetsstrasse 22

department: Department of Pathology

country: Germany

institute: University Hospital Erlangen

description: CRISPR/Cas9-mediated ATF2 knockout (KO), biological replicate 3

hyb_protocol: For hybridization, pre-heat a thermal cycler to 65°C, remove Reporter CodeSet, Capture ProbeSet, and RNA samples from the freezer and thaw at room temperature. Mix the tubes several time by inverting and briefly spin down reagents. Create a hybridization master mix by adding 70 µl of hybridization buffer to the tube containing the Reporter CodeSet and invert to mix. Add 8 µl of master mix to each of the tubes and then add 5 µl of sample (RNA) to each tube. Invert the Capture ProbeSet tube to mix and spin down the contents. Add 2 µl of Capture ProbeSet to each tube immediately before placing at 65 °C. Briefly spin down and immediately place the tubes in the pre-heated 65 °C thermal cycler. Incubate reactions for at least 16 h (in this study: 17 h) and ramp reactions down to 4 °C.

scan_protocol: After hybridization, labeled samples were transferred to the nCounter Prep Station (NanoString) which processed the samples for further data collection on the nCounter Digital Analyzer (NanoString). All consumables necessary for sample processing were provided in the nCounter Master Kit (NanoString) and were loaded manually on the Prep station. Sample processing was performed in an automated manner for approximately 2.5 – 3 h and involved transfer of reagents, magnetic bead separation and immobilization of molecular labels on the cartridge. Then, the cartridge was transferred to the nCounter Digital Analyzer (NanoString), a multi-channel epifluorescence scanner specifically configured for the use with NanoString nCounter cartridges, that further performed automated counting and tabulating of signals of the reporter probes.

data_processing: Data were processed using the nCounter Digital Analyzer (NanoString). The number of the counted mRNA specific reporter signals corresponded to the number of the respective mRNA molecule that was counted and present in the respective sample. For each sample, one Reported Code Count (RCC) file was generated, containing the gene expression raw data. RCC files were downloaded from the nCounter Digital Analyzer and data was analyzed using the package NanoStringDiff v. 1.14.0 (Wang et al., 2019) within the R v. 3.6.1 environment (R-Core-Team, 2019). This package included data normalization based on positive and negative controls and housekeeping genes embedded in the nCounter system. Fold changes were obtained from the three replicates of each clone, grouped together (n = 6) and set in relation to normalized counts of HCT116 WT controls (n = 3; 6 ATF2 KO vs 3 HCT116 WT). Matrix tables contain raw data (raw counts), normalized data (normalized counts), and normalized log2 fold change (FC) data.

source_name: HCT116-E5 cells

label_protocol: 100 ng (contained in 5 µl) of total RNA per sample was labeled with the Reporter CodeSet & Capture ProbeSet included in the following kit: XT_PGX_HuV1_CancerProg_CSO (Cat.no. XT-CSO-PROG1-12, NanoString Technologies).

growth_protocol: All cell lines (HCT116 WT, HCT116-F9, HCT116-E5) were cultured in a 10 cm dish and maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37 °C and 5% CO2.

extract_protocol: Cells were cultured as described for 48 h. Cells were scraped off from the culture dishes and collected on ice. Cells were centrifuged at 5000 rpm for 5 min at 4 °C and supernatant was discarded. Cell pellet was washed with PBS, centrifugation was repeated, supernatants were discarded, and dry cell pellets were snap-frozen in liquid nitrogen and stored at -80 °C. Total RNA was isolated from frozen cell pellets using a QIAzole-chloroform-based extraction protocol (Qiagen), followed by RNA purification using the RNeasy Mini Kit (Qiagen), both according to the manufacturer's protocol.

treatment_protocol: No treatment was applied.

value: colorectal carcinoma

value: ATF2 knockout

tag: clone


title: HCT116 E5 2 (v2)

description: CRISPR/Cas9-mediated ATF2 knockout (KO), biological replicate 2


title: CUT&RUN CHD8N2

data_processing:
Library strategy: CUT&RUN
For CUT&RUN data processing, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) were aligned mouse (GRCm38/mm10) genome using Bowtie2 (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).  Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85).   SEACR (https://seacr.fredhutch.org/ ) was used for peak calling. The program ngs.plot (version 2.63) was used to draw tag density plots and heatmaps for read enrichments.  The FPKM values of each gene’s promoter region (TSS±2kb) were generated using Bamscale package (version 0.0.5) for comparative expression analyses.
For RNA seq, reads were aligned to reference mouse genome mm10 and DESeq2 was used for differential gene expression analysis. EnhancedVolcano R package was used for volcano plot generation and pheatmap R package was used for heatmap generation.
Genome_build: mm10
Supplementary_files_format_and_content: CHD8N_marked.fragments.bedgraph, RNA seq gene_matrix.txt

source_name: CD44+TER119+ Erythroblast

value: erythroblasts

tag: cut&run antibody

value: CHD8 (Bethyl, A301-224A)

value: wild type


title: 773_CUT&TAG_H3K27me3


title: E7.5_tet_chimera_plate3_D10_RNAseq

value: E7.5 embryo


title: HCT116 F9 3 (v2)

source_name: HCT116-F9 cells


title: E7.5_tet_chimera_plate3_D09_RNAseq


title: 2TS22C_Liu_EPSC_noDOX_1

description: Sox2 cKO EPSC no Dox

value: Sox2 Tet-off knockin

value: mEPSC

tag: treatment


title: 629_CUT&TAG_H3K27me3

value: Selected PBMC or BM cells


title: HCT116 F9 1 (v2)

description: CRISPR/Cas9-mediated ATF2 knockout (KO), biological replicate 1

tag: cell line


title: Ago2_RS_cko_3_RNA

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

data_processing:
Raw sequence files were filtered and quality was assessed using FASTX-toolkit and FASTQC as described above. Filtered paired-end reads were matched to yield a file of common reads which were then pseudoaligned to the mouse (mm10) transcriptome downloaded from Ensembl and quantified using kallisto v0.45.0 (Bray et al., 2016). Resulting transcript counts were summed to gene level and DEGs were called using DESeq2 with batch correction (Love et al. 2014). Lowly expressed genes with < 10 TPM were filtered from the analysis.
genome build: mm10
.txt file with TPM values

source_name: round spermatids

extract_protocol:
Cell pellets were homogenized in 1ml of TRIzol reagent (Invitrogen, 15596026) and incubated at room temperature for 5 mins. After incubation, 200µl of chloroform was added followed by vortexing, brief incubation at room temperature, and centrifugation at 12000xg for 15 mins at 4°C. The resultant aqueous phase was transferred to a new tube and mixed with an equal volume of 100% ethanol, then transferred to an RNeasy MinElute spin column (Qiagen, 74104). RNA was extracted on the column according to the manufacturer’s instructions. The quality of the eluted RNA was determined by measuring 28S/18S ribosomal ratios and RNA integrity number (RIN) using an Agilent Bioanalyzer.
RNA sample integrity was assessed by BioAnalyzer (Agilent Technologies), and samples with RIN >7 were used for paired-end sequence library construction using the KAPA mRNA HyperPrep Kit (Roche # 08098123702).

tag: ip antibody

tag: condition

value: Ago2 cKO


title: Ago2_RS_cko_2_RNA


title: 673_CUT&TAG_H3K27me3

tag: antibody (if any)


title: HCT116 WT ctrl 3 (v2)

description: parental HCT116 cell line (control, ctrl), biological replicate 3

source_name: HCT116 WT cells

value: WT


title: HCT116 E5 1 (v2)


title: 103_CUT&TAG_H3K27me3


title: E7.5_tet_chimera_plate3_D06_RNAseq


title: HCT116 WT ctrl 2 (v2)

description: parental HCT116 cell line (control, ctrl), biological replicate 2


title: Ago2_RS_cko_1_RNA


title: Ago2_RS_control_3_RNA


title: 027_CUT&TAG_H3K27ac

source_name: Primary AML


title: 270_CUT&TAG_H3K27me3


title: CUT&RUN CHD8N1


title: HCT116 WT ctrl 1 (v2)

description: parental HCT116 cell line (control, ctrl), biological replicate 1


title: E7.5_tet_chimera_plate3_D11_RNAseq

source_name: Early embryo


title: HCT116 F9 2 (v2)


title: E7.5_tet_chimera_plate3_D05_RNAseq


title: 1360_CUT&TAG_H3K27ac


title: 168_CUT&TAG_H3K27ac


title: Ago2_RS_control_1_RNA


title: E7.5_tet_chimera_plate3_D08_RNAseq


title: E7.5_tet_chimera_plate3_D03_RNAseq


title: 2TS22C_ESC_2

description: Sox2 cKO ESC

source_name: mESC

value: mESC


title: E7.5_tet_chimera_plate3_D04_RNAseq


title: 472_CUT&TAG_H3K27ac


title: E7.5_tet_chimera_plate3_D07_RNAseq


title: Ago2_pachytene_cko_2_RNA

source_name: pachytene spermatocytes


title: UV.amiRCtl.3

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

institute: Vall Hebron Institute Research

description: Gene expression data, UVB stimulated keratinocytes control

hyb_protocol: Total RNA was hybridized to Affymetrix Clariom S arrays as described by the manufacturers (Affymetrix/Thermo Fisher Scientific, 168 Third Avenue, Waltham, MA USA 02451.)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

label: Biotin

source_name: Skin tissue

label_protocol: Agilent 2100 bioanalyzer was used to perform quality control and samples with RNA integrity number ≥ 9 were selected (Agilent, Santa Clara, CA, USA) for further processing

growth_protocol: Normal Human epidermal adult Keratinocytes (HeKa) (Life Technologies, Carlsbad, CA, USA) were cultured in EpiLife serum-free media (Life Technologies, Carlsbad, CA, USA) supplemented with Human Keratinocyte Growth Supplement (HSGK) (Life Technologies, Carlsbad, CA, USA) in 24 well-plates at 1x10^5 cells per mL.

extract_protocol: 1ug of total RNA from about 10^5 cells was extracted with miRNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: After letting them adhere overnight, cells were transfected with 10 μM anti-miR control or 10 μM anti-miR-885-5p (mirVanaTM, Life technologies)  with Lipofectamine 2000 (Life Technologies) as a transfection agent. Next day, cells were exposed  10 ng/μL IFN alpha (Life Technologies) and 25 mJ/cm2  UVB or PBS (non-stimulated condition) for 6 hours

value: Human Epidermal Keratinocytes

value: Control

tag: stimulation

value: UVB


title: UV.amiRCtl.2


title: 1916_CUT&TAG_H3K27ac


title: UV.amiRCtl.4


title: Ago2_pachytene_cko_1_RNA


title: 546_CUT&TAG_H3K27ac


title: Ago2_RS_control_2_RNA


title: 018_CUT&TAG_H3K27ac


title: E7.5_tet_chimera_plate3_D01_RNAseq


title: 773_CUT&TAG_H3K27ac


title: Ago2_pachytene_control_1_RNA


title: E7.5_tet_chimera_plate3_C12_RNAseq


title: Ago2_RS_2_CLIPinput

data_processing:
Library strategy: eCLIP
AGO2 IP and size-matched input control (SMInput) samples were demultiplexed as previously described using the script demux_paired_end.py (Van Nostrand et al., 2016). 3’ and 5’ adapters were trimmed using Cutadapt v1.18 (Martin, 2011) with default parameters. To eliminate artifacts from rRNA and other repetitive sequences, trimmed reads were then mapped to RepBase (mouse mm10 RepeatMasker, last modified time: 05-May-2017 06:32) using STAR software v.2.6.1d (Dobin et al., 2013). Unmapped reads recovered after the RepeatMasker step were then mapped to the mouse mm10 genome assembly with options --outFilterScoreMin 0 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --alignEndsType Local. The script barcode_collapse_pe.py (Van Nostrand et al., 2016) was used to remove PCR duplicates based on unique molecular identifiers (UMIs). Peaks were called using the tag2peak.pl script from the CLIP Tool Kit (CTK) software (Shah et al., 2017) with an adjusted p-value threshold of 0.01 and normalized to the mm10 background model. Each AGO2 eCLIP replicate was also normalized to the corresponding SMInput data using the Peak_input_normalization_wrapper.pl script from (Van Nostrand et al., 2016). CTK was also used to track cross-link-induced mutation sites (CIMS) and cross-link-induced truncation sites (CITS) with a resolution of ±50nt at an empirical false discovery rate (FDR) of 0.01. Specific types of mutations, including deletions, substitutions and insertions, were detected by analysis of unique CLIP tags (trimmed mapped reads).
genome build: mm10
.bed file with peaks

molecule: nuclear RNA

extract_protocol:
Purified germ cell nuclei from adult mouse testes were crosslinked with 254nm UV light. Nuclei were lysed and sonicated in a Bioruptor sonicator (Diagenode) at 4C, 5 min, 30sec on/30sec off. The nuclear lysate was then digested with RNase I (AM2295, Thermo) and Turbo DNase (AM2239, Thermo), and immunoprecipitated using anti-AGO2 antibody (04-642, Millipore). Next, the protein-bound RNAs were ligated with 3’ end adapters. Protein-RNA complexes were subjected to gel electrophoresis and transferred to a membrane, and RNA was isolated by cutting the membrane at the expected size range.
Libraries were prepared as described in van Nostrand et al, 2016. cDNA was generated by reverse transcription, DNA adapter was ligated to the 3' end of the cDNA, and the library was amplified by PCR. Screening of subclones prior to high-throughput sequencing was performed for quality control.


title: 270_CUT&TAG_H3K27ac


title: E7.5_tet_chimera_plate3_C11_RNAseq


title: UV.amiR885.4

description: Gene expression data, UVB stimulated keratinocytes anti-miR-885-5p


title: E7.5_tet_chimera_plate3_C10_RNAseq


title: UV.amiRCtl.1


title: UV.amiR885.3


title: Ago2_RS_2_CLIP

value: Millipore, 04-642


title: 629_CUT&TAG_H3K27ac

value: CUT&TAG


title: E7.5_tet_chimera_plate3_C09_RNAseq


title: UV.amiR885.2


title: Ago2_RS_1_CLIPinput


title: Ago2_pachytene_control_2_RNA


title: 673_CUT&TAG_H3K27ac


title: E7.5_tet_chimera_plate3_C08_RNAseq


title: 103_CUT&TAG_H3K27ac


title: Ago2_pachytene_2_CLIPinput


title: E7.5_tet_chimera_plate3_C07_RNAseq


title: E7.5_tet_chimera_plate3_C06_RNAseq


title: IFN.amiRCtl.4

description: Gene expression data, IFNalpha stimulated keratinocytes control

value: IFN alpha


title: IFN.amiRCtl.3


title: 027_WGBS

data_processing:
Reads were first trimmed using Trim_Galore! (version 0.6.0) with “--paired --clip_R1 10 --clip_R2 10” options
Trimmed reads were then mapped with “bismark” command and deduplicated using Bismark’s “deduplicate_bismark” tool with default parameters
Per-cytosine methylation level was obtained using methylpy (version 1.4.2) “call-methylation-state” tool with “--binom-test True --paired-end True” options
CG methylation levels bigwig files were generated with methlypy (version 1.4.2) with "methylpy allc-to-bigwig --bin-size 10"
genome build: hg38
processed data files format and content: Bigwig, CG methylation levels at 10bp bins

extract_protocol:
DNA bisulfite treatment was performed using the EZ DNA Methylation-Gold Kit (catalog D5005, Zymo Research Corporation) according to the manufacturer's instructions. The recovered bisulfite-converted single-stranded DNA was processed for library construction using the Accel-NGS@Methyl-seq DNA Library kit (catalog 30024, Swift BioSciences) as per manufacturer instructions.
Briefly, using the Adaptase module, truncated adapter sequences were incorporated to the single-stranded DNA in a template-independent reaction through sequential steps. DNA was then enriched using 6 cycles of PCR with primers compatible with Illumina sequencing. The quantity and molecular size of the library was confirmed by Qubit HS DNA assay (ThermoFisher) and Tapestation 2200 system coupled with High Sensitivity D1000 ScreenTapes (Agilent). Illumina 8-nt dual-indices were used for multiplexing. Samples were pooled and sequenced on Illumina NovaSeq S4 sequencer for 150 bp read length in paired-end mode, with an output of 580 million reads per sample.

value: WGBS


title: E7.5_tet_chimera_plate3_D02_RNAseq

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HISAT2 (v2.1.0) using options --dta --no-softclipping --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Assembly: GRCm38
Supplementary files format and content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID


title: UV.amiR885.1


title: Ago2_pachytene_1_CLIPinput


title: E7.5_tet_chimera_plate3_C05_RNAseq


title: Ago2_pachytene_2_CLIP


title: 168_WGBS


title: E7.5_tet_chimera_plate3_C04_RNAseq


title: E7.5_tet_chimera_plate3_C03_RNAseq


title: IFN.amiRCtl.1


title: 472_WGBS


title: 546_WGBS


title: IFN.amiR885.4

description: Gene expression data, IFNalpha stimulated keratinocytes anti-miR-885-5p


title: IFN.amiR885.3


title: Ago2_pachy-rs_cko_ChIPinput

data_processing:
Datasets were quality filtered with the fastq_quality_filter tool from FASTX-Toolkit using parameters –q 20 –p 80 (Hannon, 2010) and quality was assessed using FastQC (Andrews, 2010). ChIP-seq data was aligned to the mouse genome build mm10 using Bowtie2 (Langmead and Salzberg, 2012). Peaks were called with MACS2 at q=0.2 for round spermatid, spermatogonia, and mESC datasets, and q= 0.05 for pachytene spermatocyte datasets (Zhang et al., 2008).
genome build: mm10
bigWig file representing ChIP minus input signal

source_name: mixed pachytene spermatocytes & round spermatids

extract_protocol:
Cells were cross-linked for ChIP-seq with 1% formaldehyde at room temperature for 10 minutes. The formaldehyde was quenched with 2.5M glycine at room temperature for 10 minutes. Fixed cells were spun down at 6000xg for 3 minutes at 4°C. Cells were washed with cold PBS twice and resuspended in 100ul ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tri-HCl at pH 8.1) before being snap frozen in liquid nitrogen. Immunoprecipitation was carried out as previously described (Lesch et al 2016)
DNA integrity and fragment size were confirmed on a BioAnalyzer.  Approximately 5-10ng of DNA was end-repaired, A-tailed, adapter-ligated, and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, #KK8504).


title: E7.5_tet_chimera_plate3_C02_RNAseq

extract_protocol: Single-cells were sorted  using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.


title: 260_WGBS


title: E7.5_tet_chimera_plate3_C01_RNAseq


title: IFN.amiRCtl.2


title: Ago2_pachytene_1_CLIP


title: IFN.amiR885.1


title: 018_WGBS


title: IFN.amiR885.2


title: E7.5_tet_chimera_plate3_B12_RNAseq


title: 773_WGBS


title: E7.5_tet_chimera_plate3_B11_RNAseq


title: 566_WGBS


title: Ago2_RS_2_ChIPinput


title: Ago2_pachy-rs_control_ChIP


title: NS.amiRCtl.4

value: None (PBS)


title: 270_WGBS


title: NS.amiRCtl.3

description: Gene expression data, non-stimulated keratinocytes control


title: E7.5_tet_chimera_plate3_B10_RNAseq


title: Ago2_RS_2_ChIP


title: Ago2_pachy-rs_cko_ChIP


title: NS.amiRCtl.2


title: NS.amiRCtl.1


title: Ago2_pachytene_2_ChIPinput


title: E7.5_tet_chimera_plate3_B09_RNAseq


title: 673_WGBS

source_name: Primary Healthy donor


title: E7.5_tet_chimera_plate3_E11_RNAseq


title: NS.amiR885.4


title: Ago2_pachytene_2_ChIP


title: E7.5_tet_chimera_plate3_B08_RNAseq


title: E7.5_tet_chimera_plate3_B07_RNAseq


title: 103_WGBS


title: dHPC-WT-BL-5

source_name: Dorsal hippocampus

value: hippocampus

tag: behavior

value: Baseline

tag: batch

value: Experiment 2


title: NS.amiR885.3

description: Gene expression data, non-stimulated keratinocytes anti-miR-885-5p


title: Ago2_pachytene_1_ChIPinput

value: wild type


title: E7.5_tet_chimera_plate3_B06_RNAseq

value: E7.5 embryo


title: Ago2_pachytene_1_ChIP


title: Ago2_spermatogonia_2_ChIPinput

source_name: spermatogonia (ckit+)


title: ChIP-seq Control Ibf1 replicate 2

data_processing:
Base calling and quality score assignment were done with HiSeq Control Software 2.2.58/RTA 1.18.64
Bcl to FastQ conversion was performed using None from the CASAVA software suite. The sequence read quality was reported in Sanger/phred33/Illumina 1.8+ scale.
Reads were aligned to the dm3 genome assembly using bowtie2 and the following parameters --phred33 -p 8.
Reads with MAPQ scores less than 30 were removed using samtools view -q 30
Genomic read count profiles were computed from the filtered bowtie2 alignments using pyicos convert software and the following parameters -f sam -F bed_wig -x 180 -O.
The resulted read count profiles were normalized to the number of corresponding MAPQ 30 filtered sequencing reads using custom R script
Assembly: dm3
Supplementary files format and content: Read count profiles in wig format
Supplementary files format and content: bed in dm6 transferred by UCSC liftover from above wig, example

source_name: Cultured cells

extract_protocol:
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C. Soluble chromatin was prepared and immunoprecipitation performed as described in Kahn et al. Nucleic Acids Res. 2016. 44:10132-10149
2ng of immunoprecipitated DNA were processed using NEBNext Ultra II DNA Library preparation Kit for Illumina (cat# E76455) and index oligonucleotides from NEBNext Multiplex Oligos for Illumina (cat# E7335).

tag: mutation

tag: antibody

value: anti-Ibf1 from Cuartero et al. 2012


title: 629_WGBS

tag: cell type

value: Selected PBMC or BM cells


title: E7.5_tet_chimera_plate3_B05_RNAseq


title: ChIP-seq Control Cp190 replicate 2

value: anti-Cp190 from Whitfield et al. 1988


title: NS.amiR885.1


title: E7.5_tet_chimera_plate3_B04_RNAseq


title: Mimic-neg

city: Montreal

first: Gabrielle

last: Perron

state: Quebec

address: 845 Sherbrooke St W

department: Human Genetics

country: Canada

institute: McGill University

description: NS.1197.002.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.MN

data_processing:
RNA-seq reads were aligned to the GRCh38 genome assembly using HISAT2
RNA-seq reads to the human genome (GRCh38 assembly, Ensembl release 85) were counted using htseq-count, with a MAPQ score cutoff of >= 30
Differentially expressed genes were identified using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files contain raw counts for each sample

source_name: 786-O cell line expressing control mimic

growth_protocol: The established renal cell lines 786-O, A-498 and ACHN cells were purchased from the American Type Culture Collection (ATCC; Rockville, MD, USA) and cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using All Prep DNA/RNA/miRNA Universal kit (Qiagen) 48 hours after mimic/inhibitor transfection.
Library preparation was performed using NEB rRNA-depleted (HMR) stranded library preparation kit according to manufacturer's instructions.

treatment_protocol: Cells (100000 cells/well in 6-well plates) were reverse-transfected in antibiotic-free medium with 10 nM of a) miR-29 mimic or miRNA mimic control, or b) miR-29 inhibitor or miRNA inhibitor control, using Lipofectamine RNAiMAX Reagent (Invitrogen) according to the manufacturer’s recommendations.

value: Clear cell renal cell carcinoma cell (ccRCC) line

tag: genotype/variation

value: expressing control mimic


title: Ago2_spermatogonia_2_ChIP


title: Ago2_mESCs_RNAse_ChIPinput

source_name: mESCs


title: ChIP-seq Control Mod(Mdg4) replicate 2

value: anti-Mod(Mdg4) from Gerasimova et al. 1998


title: NS.amiR885.2

value: Human Epidermal Keratinocytes


title: ChIP-seq Control CTCF replicate 2

value: anti-CTCF from Moon et al. 2005


title: E7.5_tet_chimera_plate3_B03_RNAseq

tag: strain


title: E7.5_tet_chimera_plate3_B02_RNAseq

tag: tissue


title: Ago2_mESCs_RNAse_ChIP

value: Millipore, 04-642


title: ChIP-seq Control Su(Hw) replicate 2

value: anti-Su(Hw) from Schwartz et al. 2012


title: Mimic-miR

description: NS.1197.002.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.M29

source_name: 786-O cell line expressing miR-29 mimic

value: expressing miR-29 mimic


title: E7.5_tet_chimera_plate3_B01_RNAseq


title: Postnatal day 35 kidney 3

city: Dallas

first: harini

last: ramalingam

state: Texas

address: 5323 Harry Hines Boulevard

department: IMN

institute: UTSW

hyb_protocol: The small RNA fraction (<300 nucleotides) was hybridized on a μParaflo Microfluidic chip containing detection probes for all mouse microRNAs (miRNAs) in the miRBase version-17 (miRBase, http://microrna.sanger.ac. uk/sequences). The hybridized microarray chips were labeled with fluorescent dyes and laser scanned to obtain fluorescent images. The signal values for each sample were derived by background subtraction and normalization. Microarray chip hybridization, fluorescent labeling, laser scanning, and background subtraction and normalization were performed by LC Sciences proprietary method.

data_processing: The signal values from each of the five age groups (P2, P7, P14, P35) were averaged, and the P values using One-way ANOVA were calculated. The differentially detected signals are defined by P < 0.05.

source_name: murine kidney

extract_protocol: Total RNA was extracted from kidneys using miRNeasy mini kits (Qiagen)


title: Postnatal day 35 kidney 1

scan_protocol: The small RNA fraction (<300 nucleotides) was hybridized on a μParaflo Microfluidic chip containing detection probes for all mouse microRNAs (miRNAs) in the miRBase version-17 (miRBase, http://microrna.sanger.ac. uk/sequences). The hybridized microarray chips were labeled with fluorescent dyes and laser scanned to obtain fluorescent images. The signal values for each sample were derived by background subtraction and normalization. Microarray chip hybridization, fluorescent labeling, laser scanning, and background subtraction and normalization were performed by LC Sciences proprietary method.


title: Postnatal day 21 kidney 3

label_protocol: The small RNA fraction (<300 nucleotides) was hybridized on a μParaflo Microfluidic chip containing detection probes for all mouse microRNAs (miRNAs) in the miRBase version-17 (miRBase, http://microrna.sanger.ac. uk/sequences). The hybridized microarray chips were labeled with fluorescent dyes and laser scanned to obtain fluorescent images. The signal values for each sample were derived by background subtraction and normalization. Microarray chip hybridization, fluorescent labeling, laser scanning, and background subtraction and normalization were performed by LC Sciences proprietary method.


title: ChIP-seq Control Cp190 replicate 1


title: ChIP-seq Control Input replicate 2


title: E7.5_tet_chimera_plate3_A12_RNAseq


title: Ago2_mESCs_nuclei_ChIP


title: E7.5_tet_chimera_plate3_A11_RNAseq


title: Postnatal day 21 kidney 1


title: ChIP-seq Control Ibf1 replicate 1


title: BMMs, Infection1

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: GRCm38

source_name: Bone marrow derived macrophage (BMM)

growth_protocol: BMMs were grown in Minimum Essential Media (alpha-MEM, Thermo) supplemented with 10% fetal bovine serum (FBS, Thermo) and 1% penicillin-streptomycin (Thermo) and maintained at 37 ℃ in a fully humidified incubator containing 5% CO2, and in the presence of M-CSF (30 ng/ml)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
The SMART-seq protocol was performed on single or pooled sorted cells following the manufacturer’s instructions with some modifications. Briefly, the whole transcriptome was amplified with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech).

treatment_protocol: BMMs were seeded on to plates, and infected with SARS-CoV-2

value: Bone marrow derived macrophage (BMM)

tag: age

tag: infection


title: ChIP-seq Control Mod(Mdg4) replicate 1


title: BMMs, Infection2


title: E7.5_tet_chimera_plate3_A09_RNAseq


title: Postnatal day 14 kidney 3


title: BMMs, Infection3


title: BMMs, Mock3

value: Mock


title: Postnatal day 14 kidney 2


title: Ago2_mESCs_nuclei_ChIPinput


title: ChIP-seq Control CTCF replicate 1


title: E7.5_tet_chimera_plate3_A07_RNAseq


title: E7.5_tet_chimera_plate3_A08_RNAseq


title: ChIP-seq Control Su(Hw) replicate 1


title: Postnatal day 35 kidney 2


title: E7.5_tet_chimera_plate3_A06_RNAseq


title: Postnatal day 14 kidney 1


title: BMMs, Mock2


title: Postnatal day 21 kidney 2


title: E7.5_tet_chimera_plate3_A10_RNAseq


title: BMMs, Mock1


title: ChIP-seq CTCF-KO Cp190 replicate 2


title: E7.5_tet_chimera_plate3_A05_RNAseq


title: Postnatal day 7 kidney 2


title: ChIP-seq CTCF-KO Ibf1 replicate 2


title: Postnatal day 7 kidney 1


title: E7.5_tet_chimera_plate3_A03_RNAseq


title: E7.5_tet_chimera_plate3_A04_RNAseq


title: ChIP-seq CTCF-KO Su(Hw) replicate 2


title: P0 Npas3+/- rep3

city: Beijing

first: liqiu

last: Liu

address: Yard 1, Beichen West Road, Chaoyang District, Beijing, China

institute: Beijing Institutes of Life Science, Chinese Academy of Sciences

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 using trimmomatic version 0.3.8, then mapped to mm10 whole genome using hisat2 v2.1.0 with default parameters.
Raw gene counts for every gene and every sample were quantitated with featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Cortex

extract_protocol:
Cortices were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Then, total RNA was quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system. And 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Cortex

value: Post natal day 0

tag: genotype


title: Postnatal day 0 kidney 3


title: P0 WT rep2

value: wild type


title: Postnatal day 0 kidney 4


title: ChIP-seq CTCF-KO Mod(Mdg4) replicate 2


title: ChIP-seq CTCF-KO Input replicate 2


title: P0 WT rep1


title: Postnatal day 0 kidney 2


title: E7.5_tet_chimera_plate3_A01_RNAseq

value: E7.5 embryo


title: ChIP-seq CTCF-KO Cp190 replicate 1


title: P0 Npas3+/- rep2


title: P0 WT rep3


title: ChIP-seq Control Input replicate 1


title: Ldi_Sb_EV_3

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

data_processing:
Quality control analysis of the raw sequence reads was performed using the FastQC tool (Babraham Bioinformatics).
Adapters and low-quality bases were trimmed by Trimmomatic (Bolger et al., 2014).
Trimmed EV DNA sequences were mapped onto the Leishmania infantum reference genome assembly (LINF GCA_900500625.2) using the short-read aligner Bowtie2 (Langdon, 2015) using default parameters.
Quality of mapping was analyzed using Qualimap (Garcia-Alcalde et al., 2012) and reads with low mapping quality score (MAPQ <=2) were removed using Samtools (Li et al., 2009).
PCR duplicates in EV DNA libraries were flagged and removed using Picard.
Coverage tracks for the visualization in Integrated Genome Viewer (IGV) were created using deepTools (Ramirez et al., 2016), where the scaling factors were calculated using the following formula: genome size / (mapped read pairs * read length).
For the analysis of copy number variation (CNV), read depth coverage was calculated for 5-kb non-overlapping genomic windows tilling the 36 chromosomes using featureCounts (Liao et al., 2014). Read depth coverage was normalized based on the library size.
The EVs DNA differential abundance analysis was performed using edgeR with exactTest method and Benjamini-Hochberg multiple testing correction (adjusted p-value threshold 0.05). Five-kb windows with a minimal coverage of 50 counts per million in at least three samples were included in the CNV analysis.
To visualize the results of the CNV analyses, the circular and linear Miami plots were created using the CMplot package in R 3.5.3.
Assembly: LINF GCA_900500625.2
Supplementary files format and content: Matrix table with CPM values
Supplementary files format and content: Bigwig files scaled per million reads mapping onto 5-kb genomic windows
Library strategy: DNA-Seq

organism: Leishmania infantum

source_name: small EVs

growth_protocol: All strains were grown at 25°C in M199 medium supplemented with 10% fetal bovine serum and 5 μg/mL of haemin at pH 7.0. Sb-resistant strains were grown in the presence of  2 mM Sb (Potassium antimonyl tartrate, Sigma-Aldrich).

extract_protocol:
Leishmania small EVs were isolated and purified as we previously described (Atayde et al., 2019; Douanne et al., 2020a). Briefly, 1 L of Leishmania parasites (2.5–5.0 x 107 parasites/mL) was grown in drug-free M199 at 25°C (supplemented with 10% FBS and 5 μg/mL of haemin at pH 7.0) and left to divide in 10 non-ventilated 75 cm2 culture flasks (Corning, USA) until they reached late-log phase. Next, parasites were washed twice in PBS and resuspended in 5 mL RPMI-1640 medium (no FBS, no phenol red) (Life Technologies) at a final concentration of 2.5–5.0 x 10^8 parasites/mL, in non-ventilated 25 cm2 culture flasks (Corning, USA) at 37°C. Parasites were stimulated for 4 h at 37°C to maximize the release of EVs in the medium (Atayde et al., 2019; Douanne et al., 2020a). The viability of parasites was evaluated by propidium-iodide (PI) staining before and after incubation at 37°C. Only cultures with a viability > 95.0% were submitted to subsequent EV-purification steps. After the 4-h incubation, samples were centrifuged 10 min at 3,000 g to eliminate parasites and 10 min at 8,500 g to clear out debris, followed by two subsequent filtrations using 0.45 and 0.22 μm syringe filters. EVs were then recovered by a 1 h ultracentrifugation at 100,000 g and resuspended in EVs buffer (137 mM NaCl, 20 mM Hepes, pH 7.5). EV proteins were dosed using the Micro BCA Protein Assay Kit (Pierce Biotechnology, USA) and size and concentration measurements of the purified EV samples were performed with a ZetaView Nanoparticle tracking analyzer (Particle Metrix, USA).
DNA was extracted using the DNeasy Blood and Tissue Kit (QIAGEN, USA) from purified EVs, following the manufacturer’s instructions, to eliminate external DNA. Dried DNA pellets were resuspended in ddH2O and further concentrated using a Savant DNA SpeedVac Concentrator (Thermo Electron Corporation, USA). Purified DNAs were fluorometrically quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific, USA) in a Take 3 platform (BioTek, USA). DNA was stored at -20°C until use in subsequent next generation sequencing or PCR experiments.
Extracellular vesicle DNA libraries were constructed using the KAPA HyperPrep kit following the manufacturer’s protocol without fragmentation; the final library fragment size was 250-400 bp. Sequencing was performed using an Illumina NovaSeq 6000 sequencer in a 50 bp pair-end configuration. An average 29-fold and 32-fold genome coverage was achieved for the EV DNA samples from the WT and the Sb-resistant mutant, respectively.

value: Sb-Resistant


title: Postnatal day 0 kidney 1


title: ChIP-seq CTCF-KO Ibf1 replicate 1

value: anti-Ibf1 from Cuartero et al. 2012


title: 933_RNA-seq

data_processing:
Raw sequencing reads were first adapter-trimmed by Trimm_Galore! (version 0.6.0) with “--paired” option
Trimmed raeds were aligned to human genome reference GRCh38 with STAR (version 2.5.3a_modified) with “--outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1” options
mRNA expression was quantified using RSEM (version 1.2.31) with GENCODE v24 annotation and “--paired-end --estimate-rspd --calc-ci” options
Genome_build: hg38
Supplementary_files_format_and_content: Text format, gene-level mRNA quantification in read counts, FPKM, and TPM

source_name: Primary AML

growth_protocol: Kasumi-1 (ATCC CRL-2724) cells were given to us as a gift from Dr Sinisa Dovat lab, which are new vials purchased from ATCC. Cells are cultured following the manufacturer’s culture method. Kasumi is cultured with RPMI-1640 (Gibco, 11875093) with 20% FBS.

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus kit (74034). RNA quality was assessed by Agilent RNA ScreenTape on Agilent 2200 Tapestation and quantified by Qubit. The mRNA was enriched by poly-A selection and the second strand synthesis was performed with NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module following manufacturer’s instructions (E6111S).
Average final library size is between 380-400 bp. Illumina 8-nt dual-indices were used for multiplexing. Samples were pooled and sequenced on Illumina HiSeq X sequencer as 150 bp paired-end reads, with an output of 40 million reads per sample.

value: Selected PBMC or BM cells

tag: assay

value: RNA-seq


title: P0 Npas3+/- rep1


title: ChIP-seq CTCF-KO Mod(Mdg4) replicate 1

tag: cell line


title: Astrocyte Npas3-/- rep2

description: HM

source_name: Astrocyte

growth_protocol: Every postnatal day 0 (P0) mouse cortical tissue was dissociated with papain prior to plating onto flasks coated with poly-D-lysine (PDL). Isolated astrocytes were cultured in astrocyte growth medium containing DMEM plus 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured for 7 days with flasks rigorously shaken daily to remove neurons and non-astrocytic cells. After reaching confluence, astrocytes were disassociated using 0.25% trypsin-ethylenediaminetetraacetic acid followed by centrifugation for 5 min at 216 g, re-suspended, and then cultured in astrocyte growth medium on PDL-coated flasks.

extract_protocol:
RNA was extracted from astrocytes (DIV 14) by TRIzol method. Then, total RNA was quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system . And 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: DIV 14

value: Astrocyte


title: Ldi_Sb_EV_2


title: 838_RNA-seq


title: E7.5_tet_chimera_plate3_A02_RNAseq

source_name: Early embryo


title: Astrocyte Npas3-/- rep1

description: HM


title: Ldi_Sb_EV_1


title: ChIP-seq CTCF-KO Su(Hw) replicate 1


title: Astrocyte WT rep2

description: WT


title: 504_RNA-seq


title: 798_RNA-seq


title: ChIP-seq CTCF-KO Input replicate 1


title: Ldi_WT_EV_3

value: Wild Type


title: Astrocyte WT rep1

description: WT


title: Astrocytes-WT rep2 NPAS3

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence using trimmomatic version 0.3.8, then mapped to mm10 genome assembly using bowtie2 version 2.1.0 with default parameters.
bigwig files were generated by bedtools v2.27.1, genomeCoverageBed v2.27.1 and bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files, contained coordinates for an interval and an associated score.

source_name: Astrocytes

growth_protocol: Every postnatal day 0 (P0) mouse cortical tissue was dissociated with papain prior to plating onto flasks coated with poly-D-lysine (PDL). Isolated astrocytes were cultured in astrocyte growth medium containing DMEM plus 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured for 7 days with flasks rigorously shaken daily to remove neurons and non-astrocytic cells. After reaching confluence, astrocytes were disassociated using 0.25% trypsin-ethylenediaminetetraacetic acid followed by centrifugation for 5 min at 216 g, re-suspended, and then cultured in astrocyte growth medium on PDL-coated flasks. The cultured primary astrocytes were collected at days in vitro (DIV14) for ChIP-seq.

extract_protocol:
Lysates were clarified from sonicated cells and histone-DNA complexes were enriched using NPAS3 antibody.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired end reads were generated.

value: Primary astrocytes are derived from mixed glial cultures obtained from mouse pups at postnatal day 0(P0)

tag: chip antibody

value: NPAS3(Invitrogen, Cat# PA5-20365)

tag: treatment

value: untreated


title: 496_RNA-seq


title: ChIP-seq Cp190-KO Ibf1 replicate 2


title: Ldi_WT_EV_2


title: Ago2_RS_1_CLIP

source_name: round spermatids

tag: ip antibody

value: Millipore, 04-642

tag: condition


title: 1324_RNA-seq


title: ChIP-seq Cp190-KO Mog(Mdg4) replicate 2

value: anti-Mod(Mdg4) from Gerasimova et al. 1998


title: Ventral ribosome-depleted 3

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

data_processing:
Sequenced reads were mapped to the Rnor6.0 version of rat genome using STAR (v. 2.7.9a) with default parameters.
For each dataset, raw read counts were obtained using FeatureCounts (v 2.0.1) with GTF file for Rnor 6.0, taken from ENSEMBL ftp. Used parameters: -T 8 -p -a Rattus_norvegicus.Rnor_6.0.101.gtf -s 0 (for polyA dataset, unstranded) -s 2 (for ribosome-depleted dataset, reverse-stranded).
Counts from both datasets were combined in single matrix and normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).

organism: Rattus norvegicus

source_name: Ventral Hippocampus

extract_protocol:
Poly-A enriched data: total RNA was extracted using Qiazol reagent according to manufacturer’s protocol. Ribosomal RNA depleted data: total RNA was extracted using ExtractRNA reagent (Evrogen, Russia) following manufacturer’s protocol. Depletion of ribosomal RNA was performed using MGIEasy rRNA Depletion kit.
1) mRNA isolation from total RNA with oligo(dT)-coated magnetic beads; 2) RNA fragmentation; 3) cDNA generation by reverse transcription using random primers followed by double-stranded cDNA synthesis; 4) reparation of ends, 3'-adenylation, ligation of adapters; 5) polymerase chain reaction using adapters. PCR products were purified with Ampure XP Beads and dissolved in EB solution; 6) the library has been validated with an Agilent Technologies 2100 bioanalyzer; 7) the double-stranded PCR product was denatured and cyclic molecules were synthesized from it using the splint oligo sequence. The result was a library of single-stranded cyclic molecules; 8) the library was amplified with phi29 DNA polymerase to form nanodroplets containing more than 300 copies of a single DNA molecule

treatment_protocol: Control handled rats not subjected to any treatments

tag: rna fraction

value: ribosome-depleted

value: Ventral Hippocampus

value: Wistar

tag: animal id

tag: Sex

value: male


title: Dorsal ribosome-depleted 3

source_name: Dorsal Hippocampus

value: Dorsal Hippocampus


title: Ldi_WT_EV_1


title: Astrocytes-WT rep2 Input


title: 027_RNA-seq

city: Chicago

first: Feng

last: Yue

growth_protocol: Kasumi-1 (ATCC CRL-2724) cells were given to us as a gift from Dr Sinisa Dovat lab, which are new vials purchased from ATCC. Cells are cultured following the manufacturer’s culture method. Kasumi is cultured with RPMI-1640 (Gibco, 11875093) with 20% FBS. HL60 is cultured with Iscove's Modified Dulbecco's Medium (IMDM) (ATCC® 30-2005).


title: Astrocytes-WT rep1 Input

value: Primary astrocytes are derived from mixed glial cultures obtained from mouse pups at postnatal day 0 (P0)


title: ChIP-seq Cp190-KO Su(Hw) replicate 2

tag: mutation

tag: antibody

value: anti-Su(Hw) from Schwartz et al. 2012


title: Dorsal ribosome-depleted 2


title: 1071_RNA-seq

source_name: Primary Healthy donor

tag: cell type

value: Selected PBMC or BM cells


title: ChIP-seq Cp190-KO Ibf1 replicate 1

value: anti-Ibf1 from Cuartero et al. 2012


title: ChIP-seq Cp190-KO Input replicate 2


title: Astrocytes-WT rep1 NPAS3

tag: strain


title: 472_RNA-seq

value: RNA-seq


title: ChIP-seq Cp190-KO Mod(Mdg4) replicate 1


title: ChIP-seq Cp190-KO CTCF replicate 2

value: anti-CTCF from Moon et al. 2005


title: ccT4 sgMSRA

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming
We perform a pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data
Genome_build: GRCm38
Supplementary_files_format_and_content: estimated counts and tpm values for each gene (computed from tximport R package)

source_name: Pancreatic cancer cells

growth_protocol: All cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Monolayer KPC (KrasG12D;p53R172H;PdxCre) primary pancreatic cancer cells were generated from tumors derived from KPC mice.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: Cancer cells derived from murine pancreatic tumors from KrasG12D;p53R172H;PdxCre model


title: 424_RNA-seq

address: 303 E Chicago Ave. Simpson Querrey 7-518

institute: Northwestern University


title: Ventral polyA-enriched 7

value: polyA-enriched

tag: tissue


title: Ventral ribosome-depleted 2


title: 168_RNA-seq


title: 546_RNA-seq


title: Dorsal polyA-enriched 7


title: ChIP-seq Cp190-KO Su(Hw) replicate 1

source_name: Cultured cells


title: ccT7 sgROSA


title: ccT7 sgMSRA


title: 018_RNA-seq


title: Dorsal ribosome-depleted 1


title: Ventral ribosome-depleted 1


title: ChIP-seq Cp190-KO CTCF replicate 1


title: 566_RNA-seq


title: ccT1 sgMSRA


title: Ago2_pachy-rs_control_ChIPinput

source_name: mixed pachytene spermatocytes & round spermatids

value: wild type


title: 773_RNA-seq


title: Ventral polyA-enriched 6


title: E11 AGM cells - PDGFRB -/- (KO)

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

institute: The University of Edinburgh

data_processing:
Alignment of scRNA-seq data and barcode counting using 10X Genomics Cell Ranger (v3.1.0) with reference dataset mm10/GRCm38-3.0.0.
Filtering of empty and/or low quality cells using EmptyDrops and Scater (v1.14.6) Bioconductor packages
Differential expression computed using the Scran (v1.14.6) Bioconductor package
Enrichment analysis of differential expression results and additional data mining of Gene Ontology terms with the Panther classification system and AmiGO (v2.5.13)
Genome_build: mm10
Supplementary_files_format_and_content: tsv.gz files contain tab separated feature and barcode sequences corresponding to matrix row and column indices respectively, as output by 10X Cell Ranger
Supplementary_files_format_and_content: mtx.gz files contain market exchange formatted matrices of UMI counts associated with a feature (row) and barcode (column), as output by 10X Cell Ranger

source_name: aorta-gonads-mesonephros region

extract_protocol:
Hematopoietic organs were dissected and dissociated into single cells with collagenase type I (Sigma, C0130, 0.12% v/v)
AGMs from PDGRFβ+/+ and PDGRFβ-/- embryos were dissociated, washed, counted and assessed for viability using a Bio-Rad TC20. Cells were then loaded at a concentration for the recovery of 7,000 cells and processed through the 10x Chromium Controller. Single cell libraries were obtained according to manufacturer protocol. RNA concentration was obtained using Quibit RNA HS (Thermo-Fisher) and the quality of the libraries was verified using the LabChip GX24 (Perkin Elmer).

value: aorta-gonads-mesonephros

tag: developmental stage

value: PDGFRB -/- (KO)


title: CC23_responder

city: Guangzhou

first: jiang

last: li

address: 651 Dongfeng East Road, Yuexiu District, Guangzhou

institute: Sun yat-sen university

description: instrument model: DNBSEQ-T1&T5

data_processing:
Raw single-cell RNA-seq data were processed using the program PISA (https://github.com/shiquan/PISA), including the gene expression data was mapped to human genome reference sequence (GRCh38). A number of steps were performed to filter out poor quality data. Firstly, cells for which with < 200 expressed genes or > 15% of detected genes linked to mitochondrial genes were removed. Secondly, Genes detected in fewer than three cells and cells with more than 7,000 detected genes were filtered out. Thirdly, The R package DoubletFinder was applied to remove doublets, with an expected doublet rate of 0.04.
For downstream analyses, the R package Seurat (4.0.0) was applied to normalize the raw count matrix to identify highly variable genes, scale genes, and integrate samples. Next, we clustered and visualized the cells using a graph-based clustering approach.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files containing gene/barcode matrices for each Sample

source_name: TIL infusion product

growth_protocol: In brief, the fresh tumor samples were collected in Roswell Park Memorial Institute (RPMI) 1640 medium with antibiotics and resected into small fragments, and enzymatic dissociated into single-cell suspension by collagenase type IV (0.1 mg/mL, Sigma-Aldrich), and then planted into 24-well cell culture plates in X-vivo (Lonza) culture medium containing recombinant human interleukin-2 (IL-2, 1000 IU/mL) for 1 to 2 weeks to get the purified T cells. Once a sufficient number of T cells (>10 *10^6) was generated, they were cryopreserved for further expansion. Clinical infusion products were generated by a rapid expansion protocol (REP) for “young TILs”:  Cryopreserved TILs were thawed and further expanded to treatment levels using an anti-CD3 antibody (OKT-3, 30 ng/mL, R&D Systems) and 3500IU/ml IL-2 (Beijing sihuan pharmaceutical company) and irradiated feeder cells for 14 days under conditions in accordance with current good manufacturing practices (GMP) in the Biotherapy Center at Sun Yat-sen University Cancer Center.

extract_protocol:
All steps from single-cell encapsulation to library preparation were done at BGI-Shenzhen, completing as per manufacturer’s instructions. Single cell capture, cDNA synthesis and preamplification was constructed using DNBelab C4-V1 system. And libraries were sequenced at the MGISEQ2000 platforms.
RNA libraries were prepared for sequencing using standard MGISEQ2000 protocols

treatment_protocol: Patients were treated with external-beam radiotherapy (EBRT) to a dose 45Gy for the primary tumor and regional lymphatics at risk. The primary cervical tumor was then boosted, using brachytherapy, with an additional 30 to 40Gy for a total point a dose of ≥ 85Gy. During EBRT, cisplatin was given weekly 30 to 40 mg/m2 for a maximum of 6 doses. Ex vivo expanded auto-TIL was infused 1 day after the completion of CCRT and brachytherapy. After cell infusion, Interleukin-2 (IL-2) was administered as an IM bolus at 400,000 IU/dose every 24 hours to 7 doses

tag: individual

value: patient id CC23

tag: disease state

value: cervical cancer

tag: Stage

value: III to IV

value: TIL plus CCRT

tag: response

value: responder


title: ChIP-seq Cp190-KO Input replicate 1

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

tag: cell line


title: 868_RNA-seq

tag: assay


title: CC22_responder

description: instrument model: DNBSEQ-T1&T5

value: patient id CC22

tag: treatment


title: E11 AGM cells - PDGFRB +/+ (WT)

tag: genotype

value: PDGFRB +/+ (WT)


title: ccT4 sgROSA

city: New York


title: CC17_non-responder

description: instrument model: DNBSEQ-T1&T5

value: patient id CC17

value: non-responder


title: Ventral polyA-enriched 5

tag: rna fraction

value: Ventral Hippocampus

value: Wistar

tag: animal id

value: male


title: CC13_non-responder

description: instrument model: DNBSEQ-T1&T5

value: patient id CC13


title: utricle_EJ05_bulkATAC-seq

city: Bethesda

first: Erin

last: Jimenez

state: MD

address: 50 South Drive

department: NHGRI

institute: NIH

data_processing:
Binary Base Call (BCL) files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 (10x Genomics).  Cell Ranger Version 3.0.2 (10x Genomics) was used to demultiplex, for barcode processing, for single cell gene counts, for single-cell accessibility counts, and aggregating files. For bulk ATAC-seq, libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC-seq reads were aligned to reference zebrafish genome (danRer11) using bowtie2. Peaks were called by MACS2 from individual replicate.
Genome_build: danRer11
Supplementary_files_format_and_content: scRNA-seq and scATAC-seq outputs were generated using the 10x Cell Ranger pipeline. scRNA-seq H5 (filtered feature bc matrix) files contain the UMI counts for each cell. scATAC-seq processed data files include three file formats per sample: CSV, TBI, and H5. CSV (singlecell.csv) files contain per barcode QC information associated with the fragments per barcode, ATAC signal per barcode, and cell calling information. TBI (Fragments.tsv.gz.tbi) files are tabix index of the fragment intervals. H5 (filtered peak bc matrix.h5) files contain only detected cellular barcodes. For bulk ATAC-seq, narrowPeak files contain MACS2 called peaks in BED format.

organism: Danio rerio

source_name: Untreated wild-type utricle

extract_protocol:
For single-cell experiments, non-regenerating (untreated) and regenerating inner ears (saccule and utricle) were dissected at consecutive time-points and dissociated into single-cells using trypsin and collagenase. For bulk ATAC-seq experiments, untreated inner ears (saccule and utricle) were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers.
For scRNA-seq, cDNA libraries were generatated with Chromium Controller and Chromium Single Cell 3' GEM, Library and Gel Bead Kit V3 (10x Genomics). For scATAC-seq, libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit (1000111, 10X Genomics). For bulk ATAC-seq, libraries were generated using Nextera DNA Library Preparation Kit (Catalog # FC-121-1030). Transposed DNA were amplified by PCR with indexed primers and libraries were purified.

tag: embryo age

value: 6-10 month old adult zebrafish


title: Ventral polyA-enriched 4

value: polyA-enriched

tag: Sex


title: 629_RNA-seq

tag: cell type

value: Selected PBMC or BM cells

value: RNA-seq


title: ccT1 sgROSA

value: Cancer cells derived from murine pancreatic tumors from KrasG12D;p53R172H;PdxCre model

tag: strain


title: Dorsal polyA-enriched 6

value: Dorsal Hippocampus


title: CC11_responder

value: patient id CC11

value: cervical cancer

value: III to IV


title: Dorsal polyA-enriched 4


title: 673_RNA-seq


title: Postnatal day 7 kidney 3

source_name: murine kidney


title: CC10_responder

value: patient id CC10

value: TIL plus CCRT

value: responder


title: Ventral polyA-enriched 3


title: 103_RNA-seq


title: utricle_EJ03_bulkATAC-seq


title: Dorsal polyA-enriched 5


title: 270_RNA-seq


title: 576_RNA-seq


title: saccule_EJ02_bulkATAC-seq

source_name: Untreated wild-type saccule


title: Ventral polyA-enriched 2


title: CC01_non-responder

value: patient id CC01

value: non-responder


title: 260_RNA-seq


title: suppressor mutant of delta fixC (Sample 4)

city: St. Paul

first: Kathryn

last: Fixen

state: MN

address: 1445 Gortner Ave

institute: University of Minnesota

data_processing:
Quality base calling in sequencing data was analyzed using the FastQC application (v 0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and TrimGalore (v 0.6.2) was used to remove adapter sequences, process, and validate all reads using the default parameters.
Further analysis was performed on the Avadis software package (v 3.1.1, Strand Life Sciences, Bengaluru, India).
Reads were aligned to the published genome of R. palustris CGA009 (BX571963.1) and differentially expressed genes were identified using the DESeq2 package (34) in R version 3.6 using the default parameters.
Assembly: BX571963.1
Supplementary files format and content: Excel file includes RPKM values for each gene in each sample

organism: Rhodopseudomonas palustris

source_name: bacterial cell

growth_protocol: R. palustris cells were harvested from 10 mL of liquid minimal medium lacking ammonium sulfate (nitrogen-fixing) with 20 mM acetate after cultures had grown to an optical density (660 nm) of 0.45-0.47.

extract_protocol:
Total RNA was isolated using the miRNAeasy Mini Kit (QIAGEN, Hilden, Germany), and DNA was removed by incubating each sample with TURBO DNase (Invitrogen, Carlsbad, CA). Following DNA digestion, RNA was purified and concentrated using the RNeasy MiniElute Cleanup Kit (QIAGEN, Hilden, Germany).
cDNA library construction and library sequencing were performed at GENEWIZ, LLC (South Plainfield, NJ). During cDNA library construction, ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA). cDNA was prepared using the NEBNext Ultra RNA Library Prep Kit

treatment_protocol: Cells were incubated on ice for 10 minutes then harvested by centrifugation. The cell pellet was flash frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed and resuspended in 1 mL QIAzol Lysis Reagent (QIAGEN, Hilden, Germany) and homogenized using a BioSpec Products BeadBeater-24 (Bartlesville, OK) at maximum rpm for one minute at 4°C, then allowed to cool for one minute on ice. This cycle was repeated four times to fully homogenize the sample.

value: bacterial cell

value: suppressor mutant of delta fixC

tag: growth protocol

value: minimal medium without ammonium sulfate (nitrogen-fixing) and 20 mM acetate


title: utricle_EJ01_bulkATAC-seq

value: 6-10 month old adult zebrafish


title: Dorsal polyA-enriched 2

value: polyA-enriched

tag: tissue

value: Wistar

value: male


title: suppressor mutant of delta fixC (Sample 3)


title: CC04_responder

value: patient id CC04


title: Ventral polyA-enriched 1

value: Ventral Hippocampus


title: wild-type control (Sample 2)

value: wild-type control


title: WT-25mo_S2_L004

city: Daejeon

first: Eunbeol

last: Lee

address: Daehak-ro 291

country: South Korea

institute: KAIST

data_processing:
Raw BCL files obtained from Illumina HiSeq sequencing were demultiplexed to generate FASTQ files using the ‘cellranger mkfastq’ pipeline
The raw FASTQ files were analyzed using ‘cellranger count’
The ‘cellranger count’ step includes mapping to the mouse reference genome (mm10-3.0.0)
Measuring gene expression with a unique molecular identifier (UMI) and cell barcode,
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hippocampal cells

extract_protocol:
The hippocampus was dissected from each mouse brain, minced into small pieces, enzymatically dissociated (using papain ~20 units/ml) and mechanically dissociated to generate a single-cell suspension. Myelin was removed using myelin removal beads (Miltenyi Biotec)
Libraries were prepared using a Chromium controller according to the 10x Chromium Next GEM Single Cell 3’ v3.1 protocol (CG000204). Briefly, cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. The cell suspension was mixed with Master Mix and loaded with Single Cell 3’V3.1 Gel Beads and partitioning oil into Chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled, and the cDNA pool was subjected to an end-repair process, the addition of a single ‘A’ base, and ligation of adapters. The products were then purified and enriched by PCR to create the final cDNA library.

tag: age

value: hippocampus


title: WT_S1_L005


title: WT_S2_L002


title: Dorsal polyA-enriched 1

value: Dorsal Hippocampus


title: wild-type control (Sample 1)


title: lps2_hisp

status: Public on Jul 18 2022

city: Vienna

first: Sylvia

last: Knapp

address: Währinger Gürtel 18-20

country: Austria

institute: Medical University of Vienna

description: 200310_K00288_0194_BHH3T3BBXY_4_L2_HK_S62850_1

data_processing:
umi2index processto add  UMI sequence to identifier of each read and trim the UMI.: Lexogen, QuantSeq specific, technical parameters not provided
Trim adapter sequences and polyA tails: bbduk v35.92: bbduk.sh in=$fq out=${fq_clean} ref=$resource_dir/polyA.  fa.gz,$resource_dir/truseq-rna.fa.gz k=13 ktrim=r useshortkmers=t  mink=5 qtrim=r trimq=10 minlength=20
Read QC: FastQC v0.11.5: fastqc -o ${out_dir} -t 8 --nogroup $fq $fq_clean
Alignment: STAR v2.5.2a: STAR --runThreadN 8 --genomeDir $resource_dir/index  --readFilesIn ${fq_clean} --outFilterType BySJout  --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20  --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate  --outFileNamePrefix $out_prefix
UMI read collapsing tool: Lexogen, QuantSeq specific, technical parameters not provided
Read Indexing: samtools index v1.3: samtools index $bam
Gene Read Counting: HTSeq-count v0.6.0: htseq-count -m intersection-nonempty -s yes -f bam -r pos $bam  $resource_dir/annotation.gtf > $bam_dir/read_counts.txt
Mapping QC: RSeQC v2.6.4: read_distribution.py -i $bam -r $resource_dir/annotation.bed >  $bam_dir/read_distribution.txt
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts.txt:  raw counts per sample and gene, tabstop-delimited .txt file

source_name: alveolar macrophages

extract_protocol:
After stimulation, cells were washed twice with cold PBS and lysed in RLT buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma). Total RNA was isolated using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.
QuantSeq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina in combination with the PCR Add-on Kit for Illumina and the UMI Second Strand Synthesis Module for QuantSeq FWD (all from Lexogen), following the manufacturers’ instructions. Libraries were prepared with 150 ng total RNA input and 15 amplification cycles. Sample quality was assessed on a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: AMs were obtained by BAL, seeded at equal numbers (2 wells per biological replicate) and left to adhere in RPMI medium (10% FCS, 1%PS). After 2 h, non-adherent cells were washed off with PBS. Subsequently, each biological replicate was incubated with HISP (ATCC6303, MOI 100) in RPMI medium (3% FCS, 1% PS) or with medium only for 3 h.

value: broncho-alveolar lavage (BAL) fluid

value: LPS

tag: restimulation

value: Heat-inactivated S. pneumoniae


title: lps4_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_L4_HK_S62848_1


title: ctrl3_hisp

description: 200310_K00288_0194_BHH3T3BBXY_4_N3_HK_S62854_1

value: Control