title: 94-09 Plate0 NKB F1

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_F1


title: KOC2

status: Public on Apr 26 2024

type: SRA

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

department: BIMSB

country: Germany

institute: Max Delbrück Center for Molecular Medicine

library_source: transcriptomic

data_processing:
fastqc to check quality of sequencing reads
bcl2fastq (v2.20.0) to demultiplex fastq files
STAR (v2.7.0a) count to align sequencing files to a reference transcriptome
featureCounts (v1.6.0) to count mapped reads for genomic features
Assembly: mm10
Supplementary files format and content: comma-separated raw read counts in matrix.csv

molecule: total RNA

organism: Mus musculus

source_name: Primary mouse cortical neuron, Cdr1as KO, DIV21

extract_protocol:
Total RNA from primary neurons was extracted using home-made TRIzol reagent in combination with Direct-zol RNA Kit (Zymo Research).
RNA libraries for RNA-seq were prepared using TruSeq (v2) library Prep Kit following manufacturer's protocols.

tag: cell type

value: Primary mouse cortical neuron

tag: genotype

value: Cdr1as KO

tag: treatment


title: MNG241

city: Seattle

first: Eric

last: Holland

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

country: USA

institute: Fred Hutch Cancer Center

data_processing:
RNA sequencing reads were aligned to the Gencode GRCh38.primary_assembly genome using STAR2 (v2.7.7a) and then using HTSeq (v0.11.0) reads were counted for each associated gene using the Gencode V39 primary assembly annotations
Gene expression values from combined datasets were batch corrected and normalized and converted to units of log2 transcripts per million (log2TPM)
Assembly: hg38
Supplementary files format and content: tab-delimited files contain log2 TPM values for each sample

organism: Homo sapiens

source_name: brain

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus mini kit. Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). Samples with RIN < 5 were removed from further analysis. RNA was normalized to 50ng/ul and 500ng was submitted for library preparation.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA kit (Illumina, Inc., San Diego, CA, USA). Sequencing was performed using an Illumina NovaSeq 6000 employing a paired-end, 50 base read length (PE50) sequencing strategy. RNA extraction was performed by the Specimen Processing & Research Cell Bank at Fred Hutch. Library preparation and sequencing was performed by the Genomics and Bioinformatics Core Services at Fred Hutch.

tag: tissue

value: brain

tag: disease state

value: Meningioma tumor


title: 94-09 Plate0 NKB F10

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_F10

library_source: transcriptomic single cell

data_processing:
The fastq files were aligned to MacaM v7 using STAR aligner v 2.5.2b. The raw counts from ReadsPerGene output of STAR was used for downstream analysis using Seurat v4.0.4.
Assembly: MacaM v7
Supplementary files format and content: The ReadsPerGene output from STAR for each cell was combined as separate columns in ReadCounts.txt.The MacaM v7.8.2 gtf was used to convert gene id to gene names.

molecule: polyA RNA

organism: Macaca mulatta

source_name: NKB

extract_protocol:
RNA was purified using RNACleanXP Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter). Beads with bound RNA were re-suspended in 5 ul of RSB buffer.
Single-cell RNA sequencing was performed by Medgenome using a modified version of the ClonTech SMART-Seq Single Cell Kit that utilized miniaturization to ¼ volumes using a MANTIS Liquid Handler (Formulatrix). Amplified cDNA was fragmented and appended with dual-indexed barcodes using Illumina Nextera kits.

value: NKB


title: R133C_pol2_rep2

city: Cambridge

first: Yi

last: Liu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: R133C (anti-GFP)

library_source: genomic

data_processing:
Sequence reads were mapped to the hg38 reference genome using Bowtie 2 with the following options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Following the CUT&Tag analysis protocol of Zheng, Ahmad and Henikoff (https://yezhengstat.github.io/CUTTag_tutorial/), bigWig files were generated after normalization the the E. coli spike-in reads.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: hES-neurons

growth_protocol: hESC- neurons were maintained in BrainPhys media supplemented with N2/B27 supplements, NT-3, GDNF, and BDNF in humidified atmosphere with 5% CO2 at 37C

extract_protocol: CUT and Tag-IT kit from Active Motif.

value: hES-neurons

value: MECP2 R133C


title: MNG239


title: R133C_GFP_rep1

description: R133C (anti-GFP)


title: MNG238


title: KOC1


title: 94-09 Plate0 NKB E9

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E9


title: R133C_GFP_clone2_rep1

description: R133C (anti-GFP)


title: MNG237


title: 94-09 Plate0 NKB E8

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E8


title: KO_GFP_ab2_rep2

description: KO (anti-MECP2)

value: MECP2 KO


title: WTm7oex3

source_name: Primary mouse cortical neuron, miR-7 overexpression, DIV21

value: WT

value: miR-7 overexpression


title: KO_GFP_ab2_rep1

description: KO (anti-MECP2)


title: 94-09 Plate0 NKB E7

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E7


title: WTm7oex2


title: 94-09 Plate0 NKB E6

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E6


title: MNG234


title: WTm7oex1


title: GD262-Hu_ATAC_S1R

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for illumina 4000 output
Reads were aligned to human genome (hg38) with bowtie2 version 2.4.2 (PMID: 22388286),Reads mapped to multiple genomic positions were removed. For reads mapped to the same genomic coordinates, only one copy was kept.
Peaks were called using MACS v3.0 with the significance cut-off q-value<=0.01
Differential accessible regions (DARs) were predicted by EdgeR (FC > 2 and FDR < 0.01)
bigwig files generated using our script.
Assembly: hg38
Supplementary files format and content: txt file; columns from left to right: chromosome, start, end, name, int(-10*log10qvalue), reserved column, fold-change at peak summit, -log10pvalue at peak summit, -log10qvalue at peak summit, relative summit position to peak start

growth_protocol: MCF10a cells grown as described in https://doi.org/10.1016/j.molimm.2018.11.006

extract_protocol: See https://doi.org/10.3390/cancers14040927 for experimental details

treatment_protocol: Poly IC in culture medium, 50 mg/ml, 3 hours

tag: cell line

value: PolyIC


title: MNG233


title: 94-09 Plate0 NKB E5

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E5


title: WTC4

source_name: Primary mouse cortical neuron, Control, DIV21


title: WTC3


title: GD256-Hu_ATAC_N2R

value: NEO


title: MNG232


title: GD255-Hu_ATAC_N1R


title: KO_GFP_ab2_rep3

description: KO (anti-MECP2)


title: MNG231


title: 94-09 Plate0 NKB E3

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E3


title: WTC2


title: 94-09 Plate0 NKB E2

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E2


title: GD139-Hu_ATAC_Sgt3PosCrct

value: NT


title: MNG230


title: WTC1


title: 94-09 Plate0 NKB E1

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E1


title: WTm7oex4


title: MNG236


title: GD138-Hu_ATAC_Sgt1PosCrct


title: BMDM csRNAinput-seq KLA 1h SPRET rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
short RNAs (20-65nt)
tss.BMDM.SpretVsC57Bl6.KLA.bed.gz

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and csRNAinput-seq reads were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”).  Reads for all genome-based assays (i.e. everything except TSS-MPRA) were aligned to the appropriate genome (GRCh38/hg38, GRCm38/mm10, ChlSab1.1) using STAR version 2.7.9a with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis.  In the case of mouse SPRET BMDM csRNA-seq, these data were analyzed in the context of C57Bl6 BMDM csRNA-seq previously published as part of GSE135498 [PMID:31649059]. To compare how TSS change between the two strains of mice, only TSS positions that were homologous between C57Bl6 and SPRET genomes and were uniquely alignable in both genomes were considered for downstream analysis (additional details available in the manuscript)
To analyze TSS positions, csRNA/csRNAinput-seq reads with spliced or soft clipped alignments were first discarded to ensure accurate TSS assignments. The alignment position of the 5’ nucleotide of each csRNA-seq read was used to create a map of putative TSS locations in the genome for each sample set. To ensure we use high quality TSS that could be reliably quantified across different conditions, only TSS locations with at least 7 reads per 10^7 total aligned reads across all compared replicates and conditions (e.g. Ctrl siRNA, NRF1 siRNA, etc.) were kept for further analysis. Furthermore, any TSS position that had higher normalized read density in the small csRNAinput-seq data was discarded as a likely false positive TSS location. These sites often include miRNAs and other high abundance RNA species which are not entirely depleted in the csRNA-seq cap enrichment protocol. To quantify the change in TSS levels between conditions, a unified map of confident TSS positions is first determined across the set of compared experiment as described above. Then, the TSS activity levels are assessed for each replicate and each experimental condition by first counting the raw read coverage and normalizing the dataset using DESeq2’s rlog variance stabilizing transform [PMID: 25516281]. Changes in transcriptional activity were then reported as the log2 fold change representing the difference between averaged rlog transformed activity levels across conditions (similar to a shrunken fold change).
ChIP-seq peaks were found using HOMER's findPeaks program using "-style factor".
TSS-MPRA anlysis: Raw sequencing reads were trimmed for the 5’ adapter sequence GGTAACCGGTCCAGCTCA on the R1 read using cutadapt version 3.4. The trimmed reads were aligned to the reporter library using STAR version 2.7.9a, specifying an option to preclude soft-clipping at the 5’ end of R1 (STAR --outSAMattributes All --genomeDir library/tfsweep.STARIndex --runThreadN 12 --readFilesIn file.fastq --outFileNamePrefix star/Sweep_1. --alignEndsType Extend5pOfRead1 --outSAMtype BAM SortedByCoordinate). For DNA plasmid control samples, the uniquely aligned read pairs were counted to later scale transcriptional output. For RNA samples, uniquely aligned read pairs were further processed to identify exact transcription start sites, yielding a matrix of start sites per sequence position. Any alignments showing mismatches at their 5’ ends were not counted and reporter sequences with fewer than 50 total DNA alignments were also ignored. A scaling factor for each sequence was determined by calculating min(10000/plasmid, 100). After multiplying the start site counts by the scaling factor, a pseudocount of 1 was added and values were log2 transformed.
Assembly: hg38, mm10, ChlSab1.1
Supplementary files format and content: bed files: Locations indicate TSS or ChIP-seq peak positions. Numerical values associated with the files represent normalized read densities or log2 ratios between two conditions as indicated by the file names.  fa files: FASTA files containing the designed insert sequences used for TSS-MPRA experiments  tsv files: tab-delimited text files containing the TSS activity levels for each TSS-MPRA insert. Each column represents the TSS position starting within the insert starting from the beginning of the variable sequence region.  fpkm.txt file: tab-delimited text file containing RNA-seq FPKM expression values for GENCODE annotated genes.

source_name: small RNA mapping in LPS treated BMDMs from SPRET mice (rep2)

growth_protocol: U2OS cells were grown at 37°C in DMEM (Cellgro) supplemented with 10% FBS (Gibco), 50 U Penicillin and 50 μg Streptomycin per mL (Gibco). For siRNA transfection, cells were washed once with PBS (Gibco), trypsinized for about 5 minutes and then washed twice with PBS (Gibco) by centrifugation at 400 g for 5 minutes. Subsequently, about 3 million cells were resuspended in 150 µl Gene Pulser® Electroporation Buffer (Biorad) and siRNAs in 1x siRNA buffer (60 mM KCl, 6 mM Hepes 7.5, 0.2 mM MgCl2). The following siRNAs were used: M-011796-02- 0005 siGENOME Human YY1 (7528) siRNA, M-017924-01- 0005 siGENOME Human NRF1 (4899) siRNA, and siGFP (CCACUACCUGAGCACCCAGU, (Meade et al. 2014)) as control. For transfection of the dominant-negative NRF1 mutant (AA1-304 (Gugneja, Virbasius, and Scarpulla 1996)), sequence was cloned into pGEM-T and mRNA synthesized using the mMESSAGE mMACHINE™ T7 Transcription Kit (Thermo Fisher Scientific). siRNAs and dnNRF1 were used at a final concentration of 10 μM. Mixture was transferred to a 0.2 cm cuvette and pulsed once at 250 V for a constant 20 msec. Following electroporation, 1 ml complete growth media was added and cells grown for 24h in a 6 cm dish.   Bone marrow derived macrophages (BMDMs) from SPRET mice were generated and treated with KLA as described in Link et. al (2018) [PMID:29779944].  TSS-MPRA experiments in HEK293T cells: MPRA inserts sequences were ordered as 200 bp oligos from Twist Bioscience and cloned Gibson-assembled into a BsaI-linearized pTSS-MPRA-Empty plasmid based on the background-reduced pGL4.10 reporter backbone (Promega), with a cloning site harboring the 18-bp pMPRA1-LH sequence followed by tandem BsaI sites for linearization and the TruSeq Read 2-compatible pMPRA1-RH sequence and a downstream landing site for reverse transcription primer RS2, and an EGFP ORF replacing the Luciferase 2 gene. About 800k HEK293T cells were used and 25 µg plasmid DNA was transfected using Lipofectamine® 3000 (Thermo Fisher Scientific) as described by the manufacturer. After 8 h, cells were washed 3x with PBS (Gibco) and RNA extracted using 1 ml Trizol (Thermo Fisher Scientific).

extract_protocol:
For all csRNA, RNA-seq, and TSS-MPRA experiments, to harvest RNA, plates were washed three times using ice cold PBS and 1 ml TRIzol™ Reagent added. Cells were scraped and RNA extracted as described by the manufacturer with addition of 1 μl 15 mg/ml GlycoBlue™ Coprecipitant (Thermo Fisher Scientific).  For ChIP-seq, cells were fixed for 10 minutes with 1% formaldehyde/PBS, and the extracted chromatin was sheared to an average DNA size of 300–500 bp.
csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. small RNA input (csRNAinput-seq) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.  Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina NovaSeq 6000.  For ChIP-seq, one percent of the lysate was kept as ChIP input, and dnNFR1-HA was immunoprecipiated with 2 μg anti-HA antibody (Abcam ab9110) and 20 μl of Dynabeads Protein A. Libraries were prepared directly on the antibody/chromatin-bound beads using NEBNext Ultra II reagents according to the manufacturer’s protocol. Libraries were sequenced single-end for 75 cycles (SE75) to a depth of 20-25 million reads on an Illumina NextSeq 500 instrument.  For TSS-MPRA, starting with 10-15 µg RNA (⅓ of the total), non-capped RNAs were dephosphorylated with Quick CIP (NEB) and DNA digested. Samples were mixed well and incubated at 37°C for 90 minutes. For more complete dephosphorylation of uncapped transcripts, RNA was denatured a second time at 75°C for 30 seconds in a pre-warmed water bath and then quickly chilled on ice for 2 minutes before incubating the sample at 37°C for another 30 minutes. As Quick CIP is thermolabile, the brief heat treatment leaves the enzyme active. Following Cap-enrichment, RNA was purified and then vortexed hard and subsequently spun for 10 minutes at 12k g at RT. Following phase separation, the upper layer was taken, and RNA precipitated. RNA pellets were then resuspended and 5' caps removed. Following decapping, 5’ adapters were ligated by T4RNA Ligase 1 and RNA extracted. RNA pellets were then resuspended and reverse transcribed. Samples were amplified and sequenced paired-end on a NextSeq 500 (additional details available in the manuscript)

value: Primary bone marrow derived macrophages

tag: assay

value: small RNA-seq (control for csRNA-seq)

tag: genetic perturbation

value: KLA 1h

tag: mouse strain

value: SPRET


title: MNG235


title: MNG229


title: 94-09 Plate0 NKB E11

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E11


title: 94-09 Plate0 NKB E4

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E4


title: GD134-Hu_ATAC_Noe3PosCrct


title: MNG228


title: GD133-Hu_ATAC_Noe1PosCrct


title: 94-09 Plate0 NKB E10

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_E10


title: GD506_RNA-Seq_MCF10A_GRHL2KO_PolyIC

description: RPKM.txt

data_processing:
Reads were aligned to human genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: hg38
Supplementary files format and content: Txt file, from left to right represent entrez ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

growth_protocol: MCF10a cells grown as described in PMID: 30508726

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus kit (Qiagen).  1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacture's protocols


title: BMDM csRNAinput-seq KLA 1h SPRET rep1

source_name: small RNA mapping in LPS treated BMDMs from SPRET mice (rep1)


title: BMDM csRNA-seq KLA 1h SPRET rep1

source_name: TSS mapping in LPS treated BMDMs from SPRET mice (rep1)

value: csRNA-seq (transcription initiation)


title: 94-09 Plate0 B D8

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D8

source_name: B

value: B


title: MNG227

value: brain


title: BMDM csRNAinput-seq notx SPRET rep2

description:
short RNAs (20-65nt)
tss.BMDM.SpretVsC57Bl6.notx.bed.gz

source_name: small RNA mapping in untreated BMDMs from SPRET mice (rep2)


title: GD505_RNA-Seq_MCF10A_GRHL2KO_PolyIC

description: RPKM.txt


title: GD263-Hu_ATAC_S2R


title: 94-09 Plate0 B D7

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D7


title: MNG226

value: Meningioma tumor


title: GD504_RNA-Seq_MCF10A_GRHL2KO_PolyIC

description: RPKM.txt


title: 94-09 Plate0 B D6

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D6


title: BMDM csRNA-seq notx SPRET rep2

source_name: TSS mapping in untreated BMDMs from SPRET mice (rep2)


title: GD500_RNA-Seq_MCF10A_GRHL2KO_NT

description: RPKM.txt


title: MNG224


title: BMDM csRNAinput-seq notx SPRET rep1

source_name: small RNA mapping in untreated BMDMs from SPRET mice (rep1)


title: MNG225


title: MNG223


title: 94-09 Plate0 B D5

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D5


title: BMDM csRNA-seq KLA 1h SPRET rep2

source_name: TSS mapping in LPS treated BMDMs from SPRET mice (rep2)


title: MNG222


title: GD499_RNA-Seq_MCF10A_GRHL2KO_NT

description: RPKM.txt


title: 94-09 Plate0 B D4

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D4


title: GD498_RNA-Seq_MCF10A_GRHL2KO_NT

description: RPKM.txt


title: MNG221


title: 94-09 Plate0 B D9

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D9


title: GD488_RNA-Seq_MCF10A_NEO_PolyIC

description: RPKM.txt


title: 94-09 Plate0 B D3

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D3


title: BMDM csRNA-seq notx SPRET rep1

source_name: TSS mapping in untreated BMDMs from SPRET mice (rep1)


title: ESC, RYBP-APEX

city: Guangzhou

first: Chao

last: Wei

address: No.74 Zhongshan Rd.2

country: China

institute: Sun Yat-Sen University

description: APEX labeling, pull down

data_processing:
The Fastq data underwent quality checking using trim_galore
subsequent alignment of paired-end reads to the MM9 reference genome was performed using STAR
Gene-specific read counts were generated using Htseq-count
Assembly: mm9
Supplementary files format and content: tab-delimited txt files includes raw counts for each samples

growth_protocol: ESCs were cultured in ESC medium containing DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Hyclone), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1000 U/mL recombinant LIF (Millipore) in 37 C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent
RNA library for RNA-seq was performed according the manufacture's protocol

treatment_protocol: Mouse Rybp-floxed ESCs (Rybp+/+) were cultured in ESC medium, RYBP-depleted ESCs (Rybp-/-) were generated by supplementing the medium with 5 μM 4-hydroxytamoxifen (4-OHT, Sigma) for 4 days.

value: embryonic stem cell

value: APEX labeling


title: MNG220


title: ESC, Input-APEX

description: Input


title: GD487_RNA-Seq_MCF10A_NEO_PolyIC

description: RPKM.txt


title: GD486_RNA-Seq_MCF10A_NEO_PolyIC

description: RPKM.txt


title: ESC,  Rybp-/-,Input

description: Input

value: RYBP KO


title: MNG219


title: 94-09 Plate0 B D11

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D11


title: 94-09 Plate0 B D1

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D1


title: ESC,  Rybp+/+,Input

description: Input

value: control


title: ESC,  Rybp-/-,H3K27ac, rep2

description:
H3K27ac ChIP-seq
ChIP-seq(Rybp-)_H3K27ac.narrowPeak


title: ESC,  Rybp-/-,H3K27ac, rep1


title: GD482_RNA-Seq_MCF10A_NEO_NT

description: RPKM.txt


title: 94-09 Plate0 B D10

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D10


title: GD481_RNA-Seq_MCF10A_NEO_NT

description: RPKM.txt


title: MNG217


title: 94-09 Plate0 B C8

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C8


title: MNG215


title: 94-09 Plate0 B C9

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C9


title: MNG214


title: 94-09 Plate0 B D2

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_D2


title: GD480_RNA-Seq_MCF10A_NEO_NT

description: RPKM.txt


title: Zebrafish, Riboseq, high dose, dsRNA2

city: Qingdao

first: tong

last: lu

address: 72, binghai rd

institute: ShanDong University

description:
dsR_2
high-dose-robo-density.tsv
RIBOseq-high dose-RPF count.xls

data_processing:
The library underwent quality control assessment, and was subjected to Illumina Novaseq 6000 sequencing.
Bio-informatics analysis of RIBOseq profilling was performed to analyze the library data.
Assembly: GRCz10
Supplementary files format and content: Excel file includes raw counts for each Sample
Library strategy: Ribo-seq

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Both control group and dsRNA-injected embryos at 5 hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4°C for 10 minutes to remove cellular components, including undigested material such as cell nuclei.Then, RNaseI was added to the supernatant and incubated at 25°C for 30 minutes to digest RNA, while the RNA fragments protected by ribosomes were preserved. Subsequently, an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation, and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction.
RNA fragments within the size range of 26-34nt was separated using polyacrylamide gel electrophoresis without RNase, and the corresponding bands were collected. The recovered bands were subjected to ligation reaction, where a preadenylylated and 3’-blocked linker (5’ rApp-CTGTAGGCACCATCAAT-NH2 3’) was attached to the 3' end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently, the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase (Epicentre, CL4111K), resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA, a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR, and barcode sequences were incorporated.

value: whole embryo

tag: developmental stage

value: 50% epi stage

value: embryonic cell

value: wild type

value: dsRNA


title: ESC,  Rybp+/+,H3K27ac, rep1

description:
H3K27ac ChIP-seq
ChIP-seq(Rybp+)_H3K27ac.narrowPeak

value: WT


title: ESC,  Rybp+/+,H3K27ac, rep2


title: 94-09 Plate0 B C7

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C7


title: MNG213


title: ESC,  Rybp-/-,WDR5, rep2

description:
WDR5 ChIP-seq
ChIP-seq(Rybp-)_WDR5.narrowPeak


title: Zebrafish, Riboseq, high dose, uninj2

description:
un_2
high-dose-robo-density.tsv
RIBOseq-high dose-RPF count.xls

value: uninjected


title: MNG212


title: MNG218


title: Zebrafish, Riboseq, high dose, dsRNA1

description:
dsR_1
high-dose-robo-density.tsv
RIBOseq-high dose-RPF count.xls


title: 94-09 Plate0 B C5

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C5


title: Zebrafish, Riboseq, high dose, uninj1

description:
un_1
high-dose-robo-density.tsv
RIBOseq-high dose-RPF count.xls


title: MNG216


title: 94-09 Plate0 B C6

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C6


title: ESC,  Rybp-/-WDR5, rep1


title: Zebrafish, Riboseq, low dose, dsRNA2

description:
dsR_2
low-dose-ribo-density.tsv
RIBOseq-low dose-RPF count.xls


title: MNG211


title: ESC,  Rybp+/+,WDR5, rep2

description:
WDR5 ChIP-seq
ChIP-seq(Rybp+)_WDR5.narrowPeak


title: MNG210


title: 94-09 Plate0 B C3

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C3


title: MNG209


title: ESC,  Rybp+/+,WDR5, rep1


title: Zebrafish, Riboseq, low dose, dsRNA1

description:
dsR_1
low-dose-ribo-density.tsv
RIBOseq-low dose-RPF count.xls


title: ESC,  Rybp-/-,H3K4me3, rep2

description:
H3K4me3 ChIP-seq
ChIP-seq(Rybp-)_H3K4me3.narrowPeak


title: 94-09 Plate0 B C2

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C2


title: Zebrafish, Riboseq, low dose, uninj2

description:
un_2
low-dose-ribo-density.tsv
RIBOseq-low dose-RPF count.xls


title: ESC,  Rybp-/-,H3K4me3, rep1


title: MNG207


title: Zebrafish, Riboseq, low dose, uninj1

description:
un_1
low-dose-ribo-density.tsv
RIBOseq-low dose-RPF count.xls


title: ESC,  Rybp+/+,H3K4me3, rep2

description:
H3K4me3 ChIP-seq
ChIP-seq(Rybp+)_H3K4me3.narrowPeak


title: MNG208


title: 94-09 Plate0 B C11

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C11


title: 94-09 Plate0 B C1

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C1


title: MNG206


title: S-209a-3

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Danio rerio-zebrafish NCBI GCA-000002035.4 (GRCz11)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: larvae

extract_protocol:
Zebrafish larvae were collected, and then flash-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: larvae

value: trim2b knockout

value: 6 days after fertilization

value: SVCV infection


title: 94-09 Plate0 B C4

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C4

value: B


title: rTRS, DOX, rep2

description: rTRS.txt

source_name: rTRS

value: rTRS

value: DOX-induced Rybp_Stat3 integration

value: DOX


title: 94-09 Plate0 NK B9

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B9

source_name: NK

value: NK


title: ESC,  Rybp+/+,H3K4me3, rep1

value: embryonic stem cell

value: control


title: S-209a-2


title: MNG203

source_name: brain

value: brain

value: Meningioma tumor


title: S-WT-3


title: rTRS, DOX, rep1

description: rTRS.txt


title: 94-09 Plate0 NK B8

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B8


title: S-209a-1


title: MNG204


title: MNG205


title: rTRS, NTC, rep2

description: rTRS.txt


title: 94-09 Plate0 B C10

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_C10


title: MNG202


title: rTRS, NTC, rep1

description: rTRS.txt


title: 94-09 Plate0 NK B6

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B6


title: S-WT-1


title: ESC,  shWdr5, rep2

value: WDR5 knock down


title: ESC,  shWdr5, rep1


title: MNG200


title: a209-3

value: untreated


title: 94-09 Plate0 NK B4

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B4


title: 94-09 Plate0 NK B5

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B5


title: MNG199


title: ESC,  shRybp, rep2

description: shRYBP.txt

value: RYBP knock down


title: 94-09 Plate0 NK B3

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B3


title: a209-1


title: ESC,  shRybp, rep1

description: shRYBP.txt


title: 94-09 Plate0 NK B7

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B7


title: 94-09 Plate0 NK B2

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B2


title: WT-3

value: WT


title: MNG198


title: ESC,  shEV, rep2

description: shRYBP.txt

value: empty vector


title: MNG197


title: ESC,  shEV, rep1

description: shRYBP.txt


title: 94-09 Plate0 NK B11

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B11


title: WT-2

value: larvae


title: S-WT-2

value: 6 days after fertilization


title: MNG201


title: ESC,  Rybp-/-, rep2

description: RYBPKO.txt

value: RYBP KO


title: MNG196


title: WT-1


title: MNG195


title: 94-09 Plate0 NK B10

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B10


title: Input for MEDIP

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Libraries were sequenced on Illumina NextSeq 2000 sequencer in a paired-end read mode of 50 base reads. Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
The reads were mapped to the reference genome rn7 using Bowtie2 v2.5.0. The numbers of mapped reads were normalized by a scale factor to adjust the total number of reads. From the aligned reads, DNA methylated peaks were identified using 6 biological replicates and the corresponding input by MACS2 (2.2.7.1) algorithm; the following parameters were applied: a shift-size window of 73 bp, no model, and q-value threshold <0.05.
To compare the control datasets of the thia-exposed and control samples, differential peaks were identified using counting reads at each peak using bedtools MultiCovBed (Version 2.30.0). Statistical significance was calculated using Limma v3.50.1 with filtering peaks with low counts.
Each normalised bam file was converted to BedGraph tracks by using the Genome Coverage 2.30.0. All analyses were performed using Galaxy platform, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351.
Assembly: rn7
Supplementary files format and content: bedgraph

organism: Rattus norvegicus

source_name: testis

growth_protocol: Specific pathogen-free male and female Sprague Dawley rats were purchased from Envigo (USA). Females were purchased at 8 weeks of age and were allowed 1 week to acclimate. At 9 weeks of age, females were randomly assigned to one of 4 treatment groups. Two groups of females were mated, and two groups of females remained virgins. Mating included placing a single female overnight with a male and examination on the following morning for the presence of sperm via vaginal swabs. If sperm was present, the dam was weighed and placed in a separate cage, and this period was marked as gestational day (GD) 0.

extract_protocol:
DNA was extracted from 6 biological replicates using DNA Easy Blood and Tissue Kit (Qiagen, 69506) according to instructions provided by manufacturer. DNA concentration was measured by fluorescent method using fluorescent reader (Promega). 10 µgs of DNA was used for MeDIP using methylated DNA Enrichment Kit (NEB, #E2600S). DNA was diluted and sonicated in Qsonica sonicator using following conditions: 20 s pulse on, 20 sec pulses off, total sonication time is 8 min. After that, sonicated DNA was incubated with MBD2-Fc -protein A Magnetic beads. The beads were washed 4 times with 1XBind/Wash Buffer. The  enriched methylated DNA was eluted from beads with miliQ water  and  and the concentration of methylated DNA was again determined by fluorescence.
6 ng of methylated DNA or input were taken for library preparation. Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645S; NEB). We performed 15 cycles for the library amplification.

treatment_protocol: Using a sterile technique, a 28-day osmotic mini-pump (2ML4-ALZET, Durect Corp., Cupertino, CA, USA) filled with either sterile saline (control; CON) or a nicotine tartrate (6 mg/kg; NIC), dissolved in sterile saline was placed subcutaneously between the scapulae, as described before (Boychuk and Hayward 2011)(Chang, Karatayev, and Leibowitz 2013). On GD19, or 13 days following pump surgery, dams were allowed to give birth.

value: testis

tag: age

value: adult 11-week-old

tag: Sex

value: male

tag: strain

value: Sprague-Dawley

value: Input

value: input


title: MNG194


title: 94-09 Plate0 NK A9

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A9

value: NK


title: ESC,  Rybp-/-, rep1

description: RYBPKO.txt

value: embryonic stem cell


title: rat testis, MEDIP nicotine 3

value: nicotine


title: MNG193

value: brain

value: Meningioma tumor


title: 94-09 Plate0 NK A8

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A8


title: ESC,  Rybp+/+, rep2

description: RYBPKO.txt

value: control


title: ESC,  Rybp+/+, rep1

description: RYBPKO.txt

value: WT


title: MNG192


title: 94-09 Plate0 NK B1

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_B1


title: rat testis, MEDIP nicotine 1


title: 94-09 Plate0 NK A7

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A7


title: MNG191


title: KO input

first: Zeyou

last: Qiu

address: Baiyun Jingxi road

institute: Southern Medical University

data_processing:
Reads were trimmed using Trimmomatic (version 0.39)
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2(Version 2.3.5)
The aligned reads with low mapping quality (MAPQ < 30) or multiple positions on the genome were removed by SAMtools(version 1.5)
Peak calling was performed using MACS2（version 2.2.6）
Aligned reads were normalized using deepTools （version 3.5.0）
Assembly: mm10

source_name: Liver

growth_protocol: Control and MeCP2-KO mice fed a standard diet were used for the liver regeneration experiment.

extract_protocol:
ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (CST, MA, USA, #9005) according to the procedures provided by the manufacturer. Liver tissues were harvested at the indicated time and quickly cut into ~0.2 cm3 pieces, crosslinked with 1% formaldehyde for 15 min and quenched with 2.5 M glycine for 5 min at room temperature. After centrifugation, the pieces were homogenized in ice-cold PBS first with a loose pestle and then with a tight pestle, permeabilized and re-suspended in micrococcal nuclease (MNase) buffer and incubated with MNase for 20 min at 37°C. The MNase-digested chromatin was centrifuged at 14,000 rpm for 1 min. Afterwards, the cells were resuspended in ChIP buffer and the chromatin was sonicated on ice (30 s on/30 s off) to obtain soluble sheared chromatin (average DNA length of 200–500 bp). Approximately 10 µg of chromatin was diluted in ChIP buffer and pre-cleared with Dynabeads Protein G (Invitrogen, 10004D) for 2 h at 4°C. Anti-H3K27ac antibodies (5 µg, Abcam, Cambridge, UK, ab4729) and anti-MeCP2 antibodies (8 µg, Abcam, Cambridge, UK, ab2828) were added to the pre-cleared chromatin, followed by rotation overnight at 4°C. The Dynabeads were washed with low/high salt solutions and eluted twice in TE buffer containing 1% SDS at 65°C for 15 min. The combined eluates were isolated by reversal of cross-linking, incubated with RNase A (10 µg/ml) followed by proteinase K (0.1 mg/ml), and the DNA was extracted using a phenol-chloroform extraction protocol. DNA quality was assessed using an Agilent (Santa Clara, CA, USA) bioanalyzer and quantified using a Qubit fluorometer (Invitrogen).
Sequencing libraries were constructed from DNA samples (ChIP and control samples) with the Illumina TruSeq V3 library construction protocol (Illumina, San Diego, USA). Sequencing runs were performed on an Illumina HiSeq 2000 for 51 cycles in single-end mode using Illumina TruSeq V3 chemistry (flowcells C56J3ACXX and C56KBACXX), or on an Illumina NextSeq 500 for 76 cycles in single-end mode using NextSeq V4 chemistry (flowcells H0Y1PBGXX, H11P6BGXX, and H13V2BGXX).
ChIP-seq library preparation of ChIP DNA or input DNA was performed using TruSeq ChIP Sample Prep Kit (Illumina). Library DNA was quantified using KAPA Library Quantification Kit (Complete Kit (Universal) for Illumina platforms) (Kapa Biosystems) and library average size was determined by Agilent DNA 1000 Kit (Agilent Technologies) run on a 2100 Bioanalyser System (Agilent Technologies). Libraries were pooled for Single-Read 50bp sequencing on an Illumina HiSeq 2500 or 4000 platforms.

treatment_protocol: Mice were housed in the animal facility of the University of Southern Medical School in temperature-, light- and humidity-controlled rooms with a 12-h light/dark cycle. All animal procedures were approved by the institutional review board of the University of Southern Medical School. A 2/3 partial hepatectomy (PH) was performed according to a recently published standardized protocol whereby the median and left lobes of the liver were removed. Liver samples were collected from the hepatectomized (6 hours after PHx) or not mice at the end of the experiment.

value: Liver

tag: chip antibody

value: Alb+ Mecp fl/fl

value: Partial hepatectomy

tag: time point


title: MNG189


title: MNG190


title: 94-09 Plate0 NK A4

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A4


title: KO PH6h rep1 ChIP


title: rat testis, MEDIP control 1


title: rat testis, MEDIP control 3


title: KO PH0h rep1 ChIP


title: MNG188


title: rat testis, MEDIP control 2


title: 94-09 Plate0 NK A5

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A5


title: 94-09 Plate0 NK A3

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A3


title: rat testis, MEDIP nicotine 2


title: WT PH6h rep1 ChIP

value: Mecp fl/fl


title: MNG187


title: 94-09 Plate0 NK A6

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A6


title: WT input


title: MNG185


title: WT PH0h rep2 ChIP


title: WT PH0h rep1 ChIP


title: MNG184


title: MNG183


title: KO PH6h rep3

data_processing:
Total RNA quantity and purity were analyzed using a Bioanalyzer 2100 and an RNA 6000 Nano LabChip kit (Agilent), with RNA integrity values of >7.0.
The final cDNA library were created in accordance with the protocol for the TruSeq RNA Sample Preparation v.2
Before assembly, low-quality reads were removed using Trimmomatic software.
Sequencing reads were aligned to the reference genome using the HISAT2 package.
The mapped reads of each sample were assembled and counted using the featureCounts package and a matrix of read counts was generated.
Assembly: mm10
Supplementary files format and content: RNAseq-TMP.csv

extract_protocol:
Liver tissue was excised from mice and was immediately submerged in RNA later solution. For mRNA profiling, total RNA was isolated from pooled livers from the control and MeCP2-KO mice using the TRIzol® reagent as the manufacturer instructed. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
The Illumina adapters used during the library construction were removed from the reads using Trimmomatic. In order to reduce the impact of lower quality reads on the alignment, all reads were trimmed to 60 bp using the FASTX Toolkit, resulting in a Phred-Quality-Score greater than. The reads generated for each RNA sample were analyzed and compared using an Ergatis-based RNA-Seq analysis pipeline where sequencing reads were aligned and annotated to the UCSC mouse reference genome (mm10) from Ensembl using TopHat v-2.0.8,and the number of reads that aligned to the predicted coding regions were determined using HTSeq. Bedtools was used to count the reads mapping to exons according to Ensembl gene annotations. Read counts per million mapped reads values (CPM) or reads per kilobase of transcripts per million mapped reads (RPKM) were calculated and used for downstream analyses. 5′-3′ exonic coverage was calculated using CollectRnaSeqMetrics component of picard-tools, and duplication rate was calculated using Estimate Library Complexity of Picard-tools.
Total RNA was extracted using Trizol (Invitrogen, CA, USA), then incubated with RNase-free DNase I (Takara Bio, China) for 30 min at 37 °C to remove residual DNA. Quantity and quality of total RNA were assessed using NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA) and RNase free agarose gel electrophoresis. mRNA was purified using oligo-dT beads (Qiagen). Fragmentation was carried out by adding fragmentation buffer. First-strand cDNA was synthesized using random hexamer-primed reverse transcription. Second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. To select cDNA fragments at a preferential length about 150 bp to 200 bp, fragments were purified using a QIAquick PCR extraction kit. After washed with EB buffer, the gathered fragments were ligated to sequencing adapters. Then, PCR was performed to construct the final cDNA library


title: 94-09 Plate0 NK A2

description: Multi.cell_sort__44NKB__22NK__22B__Spleen_from_94.09__4_6_21_A2


title: pHSCMPP_CY195M_E121FBM

city: Japan

first: Ryo

last: Yamamoto

state: Kyoto

address: Yoshidakonoecho, Sakyo-ku

department: ASHBi

country: Japan

institute: Kyoto Univerisity

data_processing:
Raw files were processed with the “mkfastq” command in Cell Ranger (v. 7.0.0) and mapped to the cynomolgus monkey reference genome MFA1912RKSv2 with “count” command with default setting.
Assembly: MFA1912RKSv2
Supplementary files format and content: Cell ranger output

organism: Macaca fascicularis

source_name: fetal bone marrow

growth_protocol: The cynomolgus macaque breeding ,manipulation of embryo, pregnancy check, cesarean section and sample collection were performed at Research Center for Animal Life Science, Shiga University of Medical Science.

extract_protocol:
Freshly isolated or frozen-thawed MACS-enriched CD34+ samples, derived from fetal liver, fetal bone marrow, and adult bone marrow, were stained with antibodies that had been validated for binding to cynomolgus protein. The cells were FACS-enriched to collect the target population and then loaded onto each channel of a Chromium chip. This was followed by GEM generation and RT reaction according to the 10X genomics manufacturer's protocol.
Library preparation (10X Genomics, Chromium Next GEM Single Cell 5’ Reagent Kits v.2, Chromium Next GEM Single Cell 5’ HT Reagent Kits v.2) were performed following the manufacturer’s instructions, with PCR cycle for cDNA amplification were adjusted based on FACS sorted cell counts.

value: fetal bone marrow

value: pHSCMPP

value: Early 3rd trimester

value: fresh


title: MNG186


title: WT PH6h rep2 ChIP


title: pHPC_CY195M_E121FL

source_name: fetal liver

value: fetal liver

value: pHPC

value: male


title: CD34+ C4

type: RNA

city: Rio de Janeiro

first: Renata

last: Binato

address: Praça da Cruz Vermelha 23

country: Brazil

institute: INCA

description: RMA expression value derived from TAC software

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a Clariom S Array human (Thermo Scientific, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix, USA)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software (Affymetrix, USA).

label: biotin

source_name: bone marrow from healthy donors

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix, USA) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix, USA).

extract_protocol: Total RNA from all CD34+ cells used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The CD34+ cells were obtained from two conditions of co-culture assays: control condition, with hMSCs and CD34+ cells from donors; and AML condition, with hMSCs-AML and CD34+ cells from donors.

value: CD34 cells

tag: condition


title: KO PH6h rep1


title: CD34+ C3

value: AML condition, with hMSCs-AML and CD34+ cells from donors


title: 1000 Hz+Pst day3, biological rep 3

city: Cartagena

first: Antonio

middle: A

last: Calderón

state: Outside North America

address: Paseo Alfonso XIII, 48

country: Spain

institute: Universidad Politécnica de Cartagena

description: Gene expression data from leaves of 30-day-old tomato plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) and inoculated with Pst DC300 after 3 dpi.

hyb_protocol: Following Fragment and Label Single-Stranded cDNA, 0.75 ug of biotin-labeled ss-cDNA sample were hybridized for 20 h at 48ºC on GeneChip® Tomato Gene 1.1 ST Array Strip (Affymetrix,  902296). Arrays were washed and stained in GeneAtlas System.

scan_protocol: GeneChips were scanned using GeneAtlas System scanner.

data_processing: The data were analyzed with robust multi-array average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Solanum lycopersicum

source_name: Solanum lycopersicum L. cv. Micro-Tom

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChipTM WT PLUS Reagent Kit, 2017, Affymetrix).

growth_protocol: Tomato seeds were surface sterilized and germinated in Petri dishes lined with moistened filter paper. Uniformly germinated seeds were then transferred to soaked peat moss pots (Jiffy pots) and watered as required. Plants were grown in a controlled growth chamber for 30 days.

extract_protocol: Total RNA was isolated from 100 mg of leaf samples using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: One-half of the 30-day-old Micro-Tom plants were exposed to 1000 Hz (at 90 dB for 2 h for 3 consecutive days) using a wireless speaker and the Audacy software in an anechoic chamber. One-half of the untreated controls and 1000 Hz-pretreated plants were dipped upside down in 200 mL bacterial suspension (2 x 108 cfu per ml) containing 0.02% of the surfactant Silwet L-77 and 10 mM MgCl2 (mock solution); the other half of plants were dipped in 200 mL of mock solution. Then, the plants were returned to the growth chamber and leaf samples were collected after 1 day or 3 days of sound/Pst DC3000 treatments.

tag: cultivar

value: Micro-Tom

tag: organ

value: Leaves

value: 1000 Hz+Pst day3


title: MNG180

value: brain

value: Meningioma tumor


title: pHSCMPP_CY195M_E121FL

tag: cell type


title: KO PH0h rep3

value: Liver

value: Alb+ Mecp fl/fl

tag: treatment


title: 1000 Hz+Pst day3, biological rep 1


title: CD34+ C2


title: pHPC_CY195M_E121FBM

tag: tissue


title: 1000 Hz+Pst day3, biological rep 2


title: pHSPC_CY189M_E93FBM

value: pHSPC

value: Late 2nd trimester


title: MNG179

tag: disease state


title: pHSCMPP_CY189M_E93FBM

value: fetal bone marrow

value: pHSCMPP


title: MNG182


title: Pst DC3000, day3, biological rep 2

description: Gene expression data from leaves of 30-day-old tomato plants incubated for 2 h for 3 consecutive days in anechoic box and inoculated with Pst DC300 after 3 dpi

value: Pst DC3000


title: Pst DC3000, day3, biological rep 3


title: KO PH0h rep2

value: Partial hepatectomy


title: KO PH0h rep1


title: CD34+ C1

value: Control condition, with hMSCs and CD34+ cells from healthy donors


title: MNG177


title: WT PH6h rep3

value: Mecp fl/fl


title: KO PH6h rep2


title: MNG181


title: 1000 Hz day3, biological rep 3

description: Gene expression data from leaves of 30-day-old tomato plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) after 3 days sound treament

value: 1000 Hz day3


title: pHSPC_CY189M_E93FL

value: fetal liver

value: male

value: fresh


title: MNG178


title: pHSCMPP_CY189M_E93FL


title: WT PH6h rep1


title: MNG176


title: CD34low_CY167M_170F_E58FL

value: Early 2nd trimester

value: pooled male and female

value: thaw


title: WT PH6h rep2

value: Liver


title: MNG175

value: brain

value: Meningioma tumor


title: Pst DC3000, day3, biological rep 1

value: Micro-Tom

value: Leaves


title: MNG174


title: Control day3, biological rep 3

description: Gene expression data from leaves of 30-day-old tomato plants incubated for 2 h for 3 consecutive days in anechoic box. Samples were harvested after 3 days of treatment

value: Control day3


title: WT PH0h rep2


title: pHPC_CY167M_170F_E58FL

value: pHPC


title: 1000 Hz day3, biological rep 2


title: MNG173


title: pHSCMPP_CY167M_170F_E58FL

value: pHSCMPP


title: WT PH0h rep1

value: Partial hepatectomy


title: pHPC_CD45RAP_CE2278F_CE2064F_ABM

source_name: adult bone marrow

value: adult bone marrow

value: Adult

value: female


title: Control day3, biological rep 2


title: MNG172


title: MNG171


title: 1000 Hz day3, biological rep 1

value: 1000 Hz day3


title: pHPC_CD45RAN_CE2278F_CE2064F_ABM

value: fresh


title: Control day3, biological rep 1


title: MPRA TSR TF motif mutation DNA library

description:
(TSS-MPRA) DNA control for TF motif mutation library
TFmutation.fa.gz

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and csRNAinput-seq reads were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”). Reads for all genome-based assays (i.e. everything except TSS-MPRA) were aligned to the appropriate genome (GRCh38/hg38, GRCm38/mm10, ChlSab1.1) using STAR version 2.7.9a with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. In the case of mouse SPRET BMDM csRNA-seq, these data were analyzed in the context of C57Bl6 BMDM csRNA-seq previously published as part of GSE135498 [PMID:31649059]. To compare how TSS change between the two strains of mice, only TSS positions that were homologous between C57Bl6 and SPRET genomes and were uniquely alignable in both genomes were considered for downstream analysis (additional details available in the manuscript)
To analyze TSS positions, csRNA/csRNAinput-seq reads with spliced or soft clipped alignments were first discarded to ensure accurate TSS assignments. The alignment position of the 5’ nucleotide of each csRNA-seq read was used to create a map of putative TSS locations in the genome for each sample set. To ensure we use high quality TSS that could be reliably quantified across different conditions, only TSS locations with at least 7 reads per 10^7 total aligned reads across all compared replicates and conditions (e.g. Ctrl siRNA, NRF1 siRNA, etc.) were kept for further analysis. Furthermore, any TSS position that had higher normalized read density in the small csRNAinput-seq data was discarded as a likely false positive TSS location. These sites often include miRNAs and other high abundance RNA species which are not entirely depleted in the csRNA-seq cap enrichment protocol. To quantify the change in TSS levels between conditions, a unified map of confident TSS positions is first determined across the set of compared experiment as described above. Then, the TSS activity levels are assessed for each replicate and each experimental condition by first counting the raw read coverage and normalizing the dataset using DESeq2’s rlog variance stabilizing transform [PMID: 25516281]. Changes in transcriptional activity were then reported as the log2 fold change representing the difference between averaged rlog transformed activity levels across conditions (similar to a shrunken fold change).
ChIP-seq peaks were found using HOMER's findPeaks program using "-style factor".
TSS-MPRA anlysis: Raw sequencing reads were trimmed for the 5’ adapter sequence GGTAACCGGTCCAGCTCA on the R1 read using cutadapt version 3.4. The trimmed reads were aligned to the reporter library using STAR version 2.7.9a, specifying an option to preclude soft-clipping at the 5’ end of R1 (STAR --outSAMattributes All --genomeDir library/tfsweep.STARIndex --runThreadN 12 --readFilesIn file.fastq --outFileNamePrefix star/Sweep_1. --alignEndsType Extend5pOfRead1 --outSAMtype BAM SortedByCoordinate). For DNA plasmid control samples, the uniquely aligned read pairs were counted to later scale transcriptional output. For RNA samples, uniquely aligned read pairs were further processed to identify exact transcription start sites, yielding a matrix of start sites per sequence position. Any alignments showing mismatches at their 5’ ends were not counted and reporter sequences with fewer than 50 total DNA alignments were also ignored. A scaling factor for each sequence was determined by calculating min(10000/plasmid, 100). After multiplying the start site counts by the scaling factor, a pseudocount of 1 was added and values were log2 transformed.
Assembly: hg38, mm10, ChlSab1.1
Supplementary files format and content: bed files: Locations indicate TSS or ChIP-seq peak positions. Numerical values associated with the files represent normalized read densities or log2 ratios between two conditions as indicated by the file names. fa files: FASTA files containing the designed insert sequences used for TSS-MPRA experiments tsv files: tab-delimited text files containing the TSS activity levels for each TSS-MPRA insert. Each column represents the TSS position starting within the insert starting from the beginning of the variable sequence region. fpkm.txt file: tab-delimited text file containing RNA-seq FPKM expression values for GENCODE annotated genes.
Library strategy: TSS-MPRA

growth_protocol: U2OS, HepG2, Hek293t and Vero E6 cells were grown at 37°C in DMEM (Cellgro) supplemented with 10% FBS (Gibco), 50 U Penicillin and 50 μg Streptomycin per mL (Gibco). For siRNA transfection, cells were washed once with PBS (Gibco), trypsinized for about 5 minutes and then washed twice with PBS (Gibco) by centrifugation at 400 g for 5 minutes. Subsequently, about 3 million cells were resuspended in 150 µl Gene Pulser® Electroporation Buffer (Biorad) and siRNAs in 1x siRNA buffer (60 mM KCl, 6 mM Hepes 7.5, 0.2 mM MgCl2). The following siRNAs were used: M-011796-02- 0005 siGENOME Human YY1 (7528) siRNA, M-017924-01- 0005 siGENOME Human NRF1 (4899) siRNA, and siGFP (CCACUACCUGAGCACCCAGU, (Meade et al. 2014)) as control. For transfection of the dominant-negative NRF1 mutant (AA1-304 (Gugneja, Virbasius, and Scarpulla 1996)), sequence was cloned into pGEM-T and mRNA synthesized using the mMESSAGE mMACHINE™ T7 Transcription Kit (Thermo Fisher Scientific). siRNAs and dnNRF1 were used at a final concentration of 10 μM. Mixture was transferred to a 0.2 cm cuvette and pulsed once at 250 V for a constant 20 msec. Following electroporation, 1 ml complete growth media was added and cells grown for 24h in a 6 cm dish.  Bone marrow derived macrophages (BMDMs) from SPRET mice were generated and treated with KLA as described in Link et. al (2018) [PMID:29779944]. TSS-MPRA experiments in HEK293T cells: MPRA inserts sequences were ordered as 200 bp oligos from Twist Bioscience and cloned Gibson-assembled into a BsaI-linearized pTSS-MPRA-Empty plasmid based on the background-reduced pGL4.10 reporter backbone (Promega), with a cloning site harboring the 18-bp pMPRA1-LH sequence followed by tandem BsaI sites for linearization and the TruSeq Read 2-compatible pMPRA1-RH sequence and a downstream landing site for reverse transcription primer RS2, and an EGFP ORF replacing the Luciferase 2 gene. About 800k HEK293T cells were used and 25 µg plasmid DNA was transfected using Lipofectamine® 3000 (Thermo Fisher Scientific) as described by the manufacturer. After 8 h, cells were washed 3x with PBS (Gibco) and RNA extracted using 1 ml Trizol (Thermo Fisher Scientific).

extract_protocol:
For all csRNA, RNA-seq, and TSS-MPRA experiments, to harvest RNA, plates were washed three times using ice cold PBS and lysed using 1 ml TRIzol™ Reagent. Lysate was scraped and RNA extracted as described by the manufacturer with addition of 1 μl 15 mg/ml GlycoBlue™ Coprecipitant (Thermo Fisher Scientific) during the Isopropanol precipitation. For ChIP-seq, cells were fixed for 10 minutes with 1% formaldehyde/PBS, and the extracted chromatin was sheared to an average DNA size of 300–500 bp.
csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. small RNA input (csRNAinput-seq) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina NovaSeq 6000. For ChIP-seq, one percent of the lysate was kept as ChIP input, and dnNFR1-HA was immunoprecipiated with 2 μg anti-HA antibody (Abcam ab9110) and 20 μl of Dynabeads Protein A. Libraries were prepared directly on the antibody/chromatin-bound beads using NEBNext Ultra II reagents according to the manufacturer’s protocol. Libraries were sequenced single-end for 75 cycles (SE75) to a depth of 20-25 million reads on an Illumina NextSeq 500 instrument. For TSS-MPRA, starting with 10-15 µg RNA (⅓ of the total), non-capped RNAs were dephosphorylated with Quick CIP (NEB) and DNA digested. Samples were mixed well and incubated at 37°C for 90 minutes. For more complete dephosphorylation of uncapped transcripts, RNA was denatured a second time at 75°C for 30 seconds in a pre-warmed water bath and then quickly chilled on ice for 2 minutes before incubating the sample at 37°C for another 30 minutes. As Quick CIP is thermolabile, the brief heat treatment leaves the enzyme active. Following Cap-enrichment, RNA was purified and then vortexed hard and subsequently spun for 10 minutes at 12k g at RT. Following phase separation, the upper layer was taken, and RNA precipitated. RNA pellets were then resuspended and 5' caps removed. Following decapping, 5’ adapters were ligated by T4RNA Ligase 1 and RNA extracted. RNA pellets were then resuspended and reverse transcribed. Samples were amplified and sequenced paired-end on a NextSeq 500 (additional details available in the manuscript)

tag: cell line

tag: antibody

value: TSS-MPRA plasmid insert levels

value: TSR TF mutation library


title: 1000 Hz+Pst day1, biological rep 3

description: Gene expression data from leaves of 30-day-old tomato plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) and inoculated with Pst DC300 after 1 dpi.

value: 1000 Hz+Pst day1


title: MPRA TSR TF motif mutation HEK293T 5'RNA rep2

description:
(TSS-MPRA) TSS mapping from TF motif mutation library in HEK293T cells (rep2)
TFmutation.fa.gz

tag: assay

value: TSS-MPRA (transcription iniation from plasmid library)

tag: genetic perturbation


title: pHSCMPP_CE2278F_CE2064F_ABM

tag: developmental stage


title: MNG170

value: brain


title: 1000 Hz+Pst day1, biological rep 2


title: MPRA TSR TF motif mutation HEK293T 5'RNA rep1

description:
(TSS-MPRA) TSS mapping from TF motif mutation library in HEK293T cells (rep1)
TFmutation.fa.gz

tag: mouse strain


title: pHPC_CY145F_E96FBM

value: fetal bone marrow

value: Late 2nd trimester

tag: Sex

value: thaw


title: Lactotroph PitNET 5

city: Bunkyo-ku

first: Yujiro

last: Hattori

state: Tokyo

address: 1-1-5 Sendagi

institute: Nippon Medical School

data_processing:
Quality check for sequence reads were performed using FastQC version 0.11.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic version 0.38 with LEADING:20TRAILING:20SLIDINGWINDOW:4:15MINLEN:36 as command option
Trimmed sequence reads were mapped to hg38 using HISAT2 version 2.1.0
Raw read counts were determined using featureCounts version 1.6.3
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Lactotroph PitNET

extract_protocol:
Total RNAs were extracted from the tissues immediately after extirpation, using NucleoSpin® RNA Plus kits (Macherey-Nagel GmbH & Co.KG, Düren, Germany)
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module for PolyA selection and NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina for strand specific library follwing manufacturer's protocols.

value: Lactotroph PitNET


title: 1000 Hz+Pst day1, biological rep 1

value: Micro-Tom

value: Leaves


title: U2OS ChIP-seq input for NRF1 and YY1

description: Input for NRF1/YY1 ChIP-seq

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and csRNAinput-seq reads were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”). Reads for all genome-based assays (i.e. everything except TSS-MPRA) were aligned to the appropriate genome (GRCh38/hg38, GRCm38/mm10, ChlSab1.1) using STAR version 2.7.9a with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. In the case of mouse SPRET BMDM csRNA-seq, these data were analyzed in the context of C57Bl6 BMDM csRNA-seq previously published as part of GSE135498 [PMID:31649059]. To compare how TSS change between the two strains of mice, only TSS positions that were homologous between C57Bl6 and SPRET genomes and were uniquely alignable in both genomes were considered for downstream analysis (additional details available in the manuscript)
To analyze TSS positions, csRNA/csRNAinput-seq reads with spliced or soft clipped alignments were first discarded to ensure accurate TSS assignments. The alignment position of the 5’ nucleotide of each csRNA-seq read was used to create a map of putative TSS locations in the genome for each sample set. To ensure we use high quality TSS that could be reliably quantified across different conditions, only TSS locations with at least 7 reads per 10^7 total aligned reads across all compared replicates and conditions (e.g. Ctrl siRNA, NRF1 siRNA, etc.) were kept for further analysis. Furthermore, any TSS position that had higher normalized read density in the small csRNAinput-seq data was discarded as a likely false positive TSS location. These sites often include miRNAs and other high abundance RNA species which are not entirely depleted in the csRNA-seq cap enrichment protocol. To quantify the change in TSS levels between conditions, a unified map of confident TSS positions is first determined across the set of compared experiment as described above. Then, the TSS activity levels are assessed for each replicate and each experimental condition by first counting the raw read coverage and normalizing the dataset using DESeq2’s rlog variance stabilizing transform [PMID: 25516281]. Changes in transcriptional activity were then reported as the log2 fold change representing the difference between averaged rlog transformed activity levels across conditions (similar to a shrunken fold change).
ChIP-seq peaks were found using HOMER's findPeaks program using "-style factor".
TSS-MPRA anlysis: Raw sequencing reads were trimmed for the 5’ adapter sequence GGTAACCGGTCCAGCTCA on the R1 read using cutadapt version 3.4. The trimmed reads were aligned to the reporter library using STAR version 2.7.9a, specifying an option to preclude soft-clipping at the 5’ end of R1 (STAR --outSAMattributes All --genomeDir library/tfsweep.STARIndex --runThreadN 12 --readFilesIn file.fastq --outFileNamePrefix star/Sweep_1. --alignEndsType Extend5pOfRead1 --outSAMtype BAM SortedByCoordinate). For DNA plasmid control samples, the uniquely aligned read pairs were counted to later scale transcriptional output. For RNA samples, uniquely aligned read pairs were further processed to identify exact transcription start sites, yielding a matrix of start sites per sequence position. Any alignments showing mismatches at their 5’ ends were not counted and reporter sequences with fewer than 50 total DNA alignments were also ignored. A scaling factor for each sequence was determined by calculating min(10000/plasmid, 100). After multiplying the start site counts by the scaling factor, a pseudocount of 1 was added and values were log2 transformed.
Assembly: hg38, mm10, ChlSab1.1
Supplementary files format and content: bed files: Locations indicate TSS or ChIP-seq peak positions. Numerical values associated with the files represent normalized read densities or log2 ratios between two conditions as indicated by the file names. fa files: FASTA files containing the designed insert sequences used for TSS-MPRA experiments tsv files: tab-delimited text files containing the TSS activity levels for each TSS-MPRA insert. Each column represents the TSS position starting within the insert starting from the beginning of the variable sequence region. fpkm.txt file: tab-delimited text file containing RNA-seq FPKM expression values for GENCODE annotated genes.

value: ChIP-seq input


title: pHSCMPP_CY145F_E96FBM

value: pHSCMPP


title: U2OS ChIP-seq YY1

description: ChIP-seq for YY1

value: anti YY1 (ActiveMotif AB_2793763)

value: ChIP-seq (TF genomic localization)


title: pHPC_CY145F_E96FL

value: fetal liver

value: pHPC

value: female


title: U2OS ChIP-seq NRF1

description: ChIP-seq for NRF1

value: anti NRF1 (Abcam , ab55744)


title: Lactotroph PitNET 3


title: Lactotroph PitNET 4


title: pHSCMPP_CY145F_E96FL


title: Lactotroph PitNET 1


title: pHPC_CE1959F_ABM

value: adult bone marrow

value: Adult

value: fresh


title: NCP2 derived CD66b+ cells replicate 2

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using salmon
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM
Assembly: hg38
Supplementary files format and content: FPKM

source_name: blood

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation
Libraries for transcriptome analysis were prepared using Smart-seq protocol (PMID: 24056875)

treatment_protocol: To assess the differentiation potential,  sorted NCP2s (PMID: 35484408) were cultured on the MS-5 stromal cell line (ACC 441,  Leibniz-Institut DSMZ,  Braunschweig,  Germany),  according to established protocols (PMID:26292072)

value: blood

value: NCP2s-derived CD66b+ neutrophilic

value: SFGc


title: NCP2 derived CD66b+ cells replicate 1


title: Pst DC3000, day1, biological rep 3

description: Gene expression data from leaves of 30-day-old tomato plants incubated for 2 h for 3 consecutive days in anechoic box and inoculated with Pst DC300 after 1 dpi

value: Pst DC3000


title: Lactotroph PitNET 2

value: Lactotroph PitNET


title: Pst DC3000, day1, biological rep 2

value: Micro-Tom

value: Leaves


title: MPRA TF motif sweep DNA library

description:
plasmid DNA
TFposSweep.fa.gz

source_name: (TSS-MPRA) DNA control for TF motif sweep library

value: HEK293T cell line

value: TSS-MPRA plasmid insert levels

value: TF sweep insertion library


title: 1000 Hz day1, biological rep 3

description: Gene expression data from leaves of 30-day-old tomato plants subjected to 1000 Hz sound vibration (at 90 dB for 2 h for 3 consecutive days) after 1 day sound treament

value: 1000 Hz day1


title: pHSCMPP_CE1959F_ABM

value: pHSCMPP


title: Normal pituitary gland 3

source_name: Normal pituitary gland

value: Normal pituitary gland


title: pHPC_CE2032F_ABM

value: pHPC

value: female


title: MPRA TF motif sweep HEK293T 5'RNA rep2

description:
RNA
TFposSweep.fa.gz
TFposSweep-r2.tssLevels.tsv.gz

source_name: (TSS-MPRA) TSS mapping from TF motif sweep library in HEK293T cells (rep2)

value: TSS-MPRA (transcription iniation from plasmid library)


title: Pst DC3000, day1, biological rep 1


title: a209-2

value: larvae

tag: genotype

value: trim2b knockout

value: 6 days after fertilization

value: untreated


title: Normal pituitary gland 1


title: pHSCMPP_CE2032F_ABM

value: adult bone marrow

value: Adult

value: fresh


title: MPRA TF motif sweep HEK293T 5'RNA rep1

description:
RNA
TFposSweep.fa.gz
TFposSweep-r1.tssLevels.tsv.gz

source_name: (TSS-MPRA) TSS mapping from TF motif sweep library in HEK293T cells (rep1)


title: pHPC_CY168M_E58FL

value: fetal liver

value: Early 2nd trimester

value: male


title: MECP2.WT.rep3

data_processing:
Paired-end reads (51 x 51) were mapped withSTAR(v 2.7.1a, PMID 23104886) to a genome index created from the human (hg38) genome and the ERR spike-in sequences, using Ensembl Release 106 annotations (withsjdbOverhang=50).
Genecountswere obtained for all human genes and ERCC spike-ins usingfeatureCounts(PMID 24227677) and the same GTF file as forSTARand options "-p -s 1".
Only protein-coding and lncRNAs with gene symbols were used for further analysis.
Differential expression analysis was performed in R (v 4.2.1) using DESeq2 (v 1.36.0).
Countsfrom ERCC spike-inswere used for normalization (applying estimateSizeFactors(dds, controlGenes = ERCC)), independentFiltering was set to false, and logFC shrinkage was performed with the ashr method.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text; gene symbol and normalized counts

extract_protocol:
Total RNA was collected using the RNeasy Mini Plus kit (QIAGEN).
A fixed amount of ERCC RNA Spike-In (Invitrogen; 4456740) was added to each sample in proportion to the number of cells for RNA-seq normalization.  Samples were treated with NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB; E7490S) before library preparation using the YourSeq (FT & 3’DGE) Strand-Specific mRNA Library Prep (Active Motif; 23001) for full-transcript (FT) sequencing.

value: hESCs

value: NGN2-derived neurons


title: MPRA TSR TF motif insertion DNA library

description:
plasmid DNA
TFposScreen.fa.gz

source_name: (TSS-MPRA) DNA control for TF motif insertion library

value: HEK293T cell line

value: TSS-MPRA plasmid insert levels

value: TSR TF insertion library


title: SedSeq~tg_1~L13~EW_TSPP~BY4741~46C~10min~none~BR2~Sup

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

data_processing:
Sequencing reads were trimmed using TrimGalore (v0.6.10, https://github.com/FelixKrueger/TrimGalore) using default settings (e.g. trim_galore --gzip --fastqc_args '--outdir fastqc/' -j 4 -o trimmed --basename FW32 EW_FW32_R1.fastq.gz). They were mapped using STAR v2.7.10b(Dobin et al. 2013) (e.g. STAR --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --sjdbGTFfile saccharomyces_cerevisiae_R64-3-1_20210421_nofasta_geneid.gff --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS --sjdbGTFtagExonParentGene gene_id --runThreadN 4 --alignMatesGapMax 20000 --limitBAMsortRAM 1445804817 --genomeDir STAR_saccharomyces_cerevisiae_R64-3-1_20210421_allchrom --outFileNamePrefix mapped_reads/FW32/FW32_ --readFilesIn trimmed/FW32_trimmed.fq.gz). To generate estimated counts and transcript per million (TPM) values, sequencing reads were mapped to the yeast transcriptome using kallisto v0.48.0(Bray et al. 2016) (e.g. kallisto quant -i Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta.idx -o kallisto_quant/FW32 --single -l 200 -s 1 --rf-stranded --bootstrap-samples=50 -t 1  trimmed/FW32_trimmed.fq.gz).
No spike-in RNA was added, and reads were mapped to saccharomyces_cerevisiae_R64-3-1_20210421_allchrom.fasta (STAR) using the annotation file saccharomyces_cerevisiae_R64-3-1_20210421_nofasta_geneid.gff, and Scerevisiae_orf_coding_all_Scerevisiae_rna_coding.fasta (kallisto).
In general, sequencing reads were mapped to the transcriptome using kallisto to extract estimated counts and TPMs.
Assembly: S288C R64.3.1
Supplementary files format and content: estimated counts and TPMs per RNA sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown overnight at 30¬∞C with shaking for at least 12 hours to OD600 = 0.4 in synthetic complete dextrose media (SCD) before being exposed to stress.

extract_protocol:
Biochemical fractionation was completed similarly to Wallace et al. [2015], with the major exception that 20,000 g for 10 min was used rather than the original 100,000 g for 20 min. In short, 50 mL cultures of treated yeast were harvested by centrifugation at 3000 g for 5 minutes, then resuspended in 100 ¬µL of soluble protein buffer (SPB: 20 mM HEPES, pH 7.4, 140 mM KCl, 2 mM EDTA, 0.1 mM TCEP, 1:200 protease inhibitor (Millipore #539136), 1:1000 SUPERase‚Ä¢In RNase Inhibitor (Invitrogen #AM2696)), and flash frozen in liquid nitrogen as a pellet in a 2 mL Eppendorf Safe-Lock tube (Eppendorf #0030123620) with a 7 mm steel ball (Retsch #05.368.0035). The cells were then lysed using a Retsch MM400 for 5x90s at 30 Hz, chilling in liquid nitrogen between each shaking repeat. The lysed cells were resuspended in 600 ¬µL of SPB, and 100 ¬µL of total sample was transferred to 300 ¬µL of Trizol LS (Invitrogen #10296010). The remainder was centrifuged for 30 seconds at 3000 g, and 300 ¬µL of clarified lysate was transferred to a new 1.5 mL tube. This was then centrifuged for 10 minutes at 20,000 g. A 100 ¬µL supernatant sample was transferred to 300 ¬µL of Trizol LS, and 400 ¬µL of SPB was added to the pellet as a wash. After another spin at 20,000 g for 10 minutes, the supernatant was removed and the pellet was resuspended by vortexing for 15 minutes in 300 ¬µL of Trizol LS and 100 ¬µL of water. If required, 1 ng of spike-in nanoluc transcript was added to each sample at this step before RNA was isolated using Zymo Direct-Zol RNA extraction columns (Zymo #R2052), and RNA integrity was assessed by the appearance of two sharp rRNA bands on a 1% agarose gel and quantified using the absorbance at 260 nm.
Sequencing libraries were prepared by the University of Chicago Genomics Facility from DNase I treated RNA using Illumina RiboZero (Illumina #MRZY1306) and Illumina TruSeq library prep kits. Single end 50 bp sequencing was performed on an Illumina HiSeq 4000 sequencer.
In general, cells were first lysed by cryo-grinding with a steel ball. When appropriate, fractionation by sedimentation or sucrose gradients was performed and RNA was dissolved in Trizol. The RNA was then purified using Zymo Direct-Zol columns. For more details, please see the protocol associated with each sample.
In general, RNA sequencing libraries were prepared using either Illumina RNA sequencing kits or NEBNext Ultra II RNA sequencing kits.

treatment_protocol: Temperature stresses for sedimentation experiments were completed by centrifuging the culture and exposing the yeast pellet to either 42¬∞C or 46¬∞C water baths for 10 minutes. Control cells were placed inside a 30¬∞C incubator. If cycloheximide treatment was used, cells were pre-treated for 10 minutes with 100 Œºg/mL cycloheximide before heat shock.

value: yeast cells


title: pHSCMPP_CY168M_E58FL

value: pHSCMPP


title: Control day1, biological rep 2

description: Gene expression data from leaves of 30-day-old tomato plants incubated for 2 h for 3 consecutive days in anechoic box. Samples were harvested after 1 day of treatment

value: Micro-Tom

value: Leaves

value: Control day1


title: 1000 Hz day1, biological rep 1

value: 1000 Hz day1


title: Control day1, biological rep 3


title: Control day1, biological rep 1


title: MECP2.WT.rep2


title: SedSeq~tg_1~L13~EW_TSPP~BY4741~46C~10min~none~BR2~Total


title: MPRA TSR TF motif insertion HEK293T 5'RNA rep2

description:
RNA
TFposScreen.fa.gz
TFposScreen-r2.tssLevels.tsv.gz

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and csRNAinput-seq reads were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”).  Reads for all genome-based assays (i.e. everything except TSS-MPRA) were aligned to the appropriate genome (GRCh38/hg38, GRCm38/mm10, ChlSab1.1) using STAR version 2.7.9a with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis.  In the case of mouse SPRET BMDM csRNA-seq, these data were analyzed in the context of C57Bl6 BMDM csRNA-seq previously published as part of GSE135498 [PMID:31649059]. To compare how TSS change between the two strains of mice, only TSS positions that were homologous between C57Bl6 and SPRET genomes and were uniquely alignable in both genomes were considered for downstream analysis (additional details available in the manuscript)
To analyze TSS positions, csRNA/csRNAinput-seq reads with spliced or soft clipped alignments were first discarded to ensure accurate TSS assignments. The alignment position of the 5’ nucleotide of each csRNA-seq read was used to create a map of putative TSS locations in the genome for each sample set. To ensure we use high quality TSS that could be reliably quantified across different conditions, only TSS locations with at least 7 reads per 10^7 total aligned reads across all compared replicates and conditions (e.g. Ctrl siRNA, NRF1 siRNA, etc.) were kept for further analysis. Furthermore, any TSS position that had higher normalized read density in the small csRNAinput-seq data was discarded as a likely false positive TSS location. These sites often include miRNAs and other high abundance RNA species which are not entirely depleted in the csRNA-seq cap enrichment protocol. To quantify the change in TSS levels between conditions, a unified map of confident TSS positions is first determined across the set of compared experiment as described above. Then, the TSS activity levels are assessed for each replicate and each experimental condition by first counting the raw read coverage and normalizing the dataset using DESeq2’s rlog variance stabilizing transform [PMID: 25516281]. Changes in transcriptional activity were then reported as the log2 fold change representing the difference between averaged rlog transformed activity levels across conditions (similar to a shrunken fold change).
ChIP-seq peaks were found using HOMER's findPeaks program using "-style factor".
TSS-MPRA anlysis: Raw sequencing reads were trimmed for the 5’ adapter sequence GGTAACCGGTCCAGCTCA on the R1 read using cutadapt version 3.4. The trimmed reads were aligned to the reporter library using STAR version 2.7.9a, specifying an option to preclude soft-clipping at the 5’ end of R1 (STAR --outSAMattributes All --genomeDir library/tfsweep.STARIndex --runThreadN 12 --readFilesIn file.fastq --outFileNamePrefix star/Sweep_1. --alignEndsType Extend5pOfRead1 --outSAMtype BAM SortedByCoordinate). For DNA plasmid control samples, the uniquely aligned read pairs were counted to later scale transcriptional output. For RNA samples, uniquely aligned read pairs were further processed to identify exact transcription start sites, yielding a matrix of start sites per sequence position. Any alignments showing mismatches at their 5’ ends were not counted and reporter sequences with fewer than 50 total DNA alignments were also ignored. A scaling factor for each sequence was determined by calculating min(10000/plasmid, 100). After multiplying the start site counts by the scaling factor, a pseudocount of 1 was added and values were log2 transformed.
Assembly: hg38, mm10, ChlSab1.1
Supplementary files format and content: bed files: Locations indicate TSS or ChIP-seq peak positions. Numerical values associated with the files represent normalized read densities or log2 ratios between two conditions as indicated by the file names.  fa files: FASTA files containing the designed insert sequences used for TSS-MPRA experiments  tsv files: tab-delimited text files containing the TSS activity levels for each TSS-MPRA insert. Each column represents the TSS position starting within the insert starting from the beginning of the variable sequence region.  fpkm.txt file: tab-delimited text file containing RNA-seq FPKM expression values for GENCODE annotated genes.

source_name: (TSS-MPRA) TSS mapping from TF motif insertion library in HEK293T cells (rep2)

value: TSS-MPRA (transcription iniation from plasmid library)


title: pHPC_CY167M_E58FL

value: pHPC


title: MPRA TSR TF motif insertion HEK293T 5'RNA rep1

description:
RNA
TFposScreen.fa.gz
TFposScreen-r1.tssLevels.tsv.gz

source_name: (TSS-MPRA) TSS mapping from TF motif insertion library in HEK293T cells (rep1)


title: 1000 Hz day1, biological rep 2


title: SedSeq~tg_1~L12~EW_TSPP~BY4741~42C~10min~none~BR2~Pellet


title: MECP2.WT.rep1


title: SedSeq~tg_1~L12~EW_TSPP~BY4741~42C~10min~none~BR2~Sup


title: U2OS ChIP-seq input for HA-tagged dnNRF1

description:
genomic DNA
peaks.U2OS.dnNRF1.HA.bed.gz

source_name: input for ChIP-seq

value: U2OS cell line

value: ChIP-seq input

value: dnNRF1 mRNA


title: MECP2.R168X.rep3


title: pHSCMPP_CY167M_E58FL

value: fetal liver

value: Early 2nd trimester

value: male

value: fresh


title: MECP2.R168X.rep2

value: hESCs

value: NGN2-derived neurons


title: SedSeq~tg_1~L13~EW_TSPP~BY4741~46C~10min~none~BR2~Pellet

value: yeast cells


title: CD34low_CY165M_E58FL_HTkit


title: SedSeq~tg_1~L12~EW_TSPP~BY4741~42C~10min~none~BR2~Total


title: MECP2.R168X.rep1


title: U2OS ChIP-seq HA-tagged dnNRF1

description:
genomic DNA
peaks.U2OS.dnNRF1.HA.bed.gz

source_name: ChIP-seq for dnNRF1

value: ChIP-seq (TF genomic localization)


title: Normal pituitary gland 2

value: Normal pituitary gland


title: pHSCMPP_CY165M_E58FL_HTkit

value: pHSCMPP


title: HEK293T csRNAinput-seq rep2

description:
short RNAs (20-65nt)
tss.HEK293T.bed.gz

source_name: small RNA mapping in HEK293T cells (rep2)

value: HEK293T cell line

value: small RNA-seq (control for csRNA-seq)


title: HEK293T csRNA-seq rep2

description:
short RNAs (20-65nt)
tss.HEK293T.bed.gz

source_name: TSS mapping in HEK293T cells (rep2)

value: csRNA-seq (transcription initiation)


title: pHPC_CY165M_E58FL_HTkit

source_name: fetal liver

value: pHPC


title: MECP2.R133C.rep3


title: MECP2.R133C.rep2


title: CD34low_CY165M_E58FL_STkit


title: SedSeq~tg_1~L11~EW_TSPP~BY4741~30C~10min~none~BR2~Total


title: MECP2.R133C.rep1


title: pHPC_CY165M_E58FL_STkit


title: HEK293T csRNA-seq rep1

description:
short RNAs (20-65nt)
tss.HEK293T.bed.gz

source_name: TSS mapping in HEK293T cells (rep1)


title: SedSeq~tg_1~L9~EW_TSPP~BY4741~46C~10min~none~BR1~Pellet


title: HepG2 csRNAinput-seq rep2

description:
short RNAs (20-65nt)
tss.HepG2.bed.gz

source_name: small RNA mapping in HepG2 cells (rep2)

value: HepG2 cell line


title: pHSCMPP_CY165M_E58FL_STkit


title: MECP2.KO.rep3


title: SedSeq~tg_1~L9~EW_TSPP~BY4741~46C~10min~none~BR1~Sup


title: HepG2 csRNA-seq rep2

description:
short RNAs (20-65nt)
tss.HepG2.bed.gz

source_name: TSS mapping in HepG2 cells (rep2)


title: SedSeq~tg_1~L9~EW_TSPP~BY4741~46C~10min~none~BR1~Total


title: pHPC_CY158F_E58FL

value: female


title: MECP2.KO.rep2


title: SedSeq~tg_1~L11~EW_TSPP~BY4741~30C~10min~none~BR2~Pellet


title: MECP2.KO.rep1


title: pHSCMPP_CY158F_E58FL


title: SedSeq~tg_1~L8~EW_TSPP~BY4741~42C~10min~none~BR1~Pellet


title: In vitro cell line on day 25

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics

data_processing:
Alignment and gene quantification using CellRanger
Assembly: hg38
Supplementary files format and content: Sparse matrix of gene quantifications

extract_protocol:
No extraction
Library construction protocol was followed per MSKCC's IGO core facility.
10x Single cell RNA-seq

value: Human PSC derived neurons

value: WT


title: HepG2 csRNAinput-seq rep1

description:
short RNAs (20-65nt)
tss.HepG2.bed.gz

source_name: small RNA mapping in HepG2 cells (rep1)

extract_protocol:
For all csRNA, RNA-seq, and TSS-MPRA experiments, to harvest RNA, plates were washed three times using ice cold PBS and 1 ml TRIzol™ Reagent added. Cells were scraped and RNA extracted as described by the manufacturer with addition of 1 μl 15 mg/ml GlycoBlue™ Coprecipitant (Thermo Fisher Scientific).  For ChIP-seq, cells were fixed for 10 minutes with 1% formaldehyde/PBS, and the extracted chromatin was sheared to an average DNA size of 300–500 bp.
csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. small RNA input (csRNAinput-seq) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.  Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina NovaSeq 6000.  For ChIP-seq, one percent of the lysate was kept as ChIP input, and dnNFR1-HA was immunoprecipiated with 2 μg anti-HA antibody (Abcam ab9110) and 20 μl of Dynabeads Protein A. Libraries were prepared directly on the antibody/chromatin-bound beads using NEBNext Ultra II reagents according to the manufacturer’s protocol. Libraries were sequenced single-end for 75 cycles (SE75) to a depth of 20-25 million reads on an Illumina NextSeq 500 instrument.  For TSS-MPRA, starting with 10-15 µg RNA (⅓ of the total), non-capped RNAs were dephosphorylated with Quick CIP (NEB) and DNA digested. Samples were mixed well and incubated at 37°C for 90 minutes. For more complete dephosphorylation of uncapped transcripts, RNA was denatured a second time at 75°C for 30 seconds in a pre-warmed water bath and then quickly chilled on ice for 2 minutes before incubating the sample at 37°C for another 30 minutes. As Quick CIP is thermolabile, the brief heat treatment leaves the enzyme active. Following Cap-enrichment, RNA was purified and then vortexed hard and subsequently spun for 10 minutes at 12k g at RT. Following phase separation, the upper layer was taken, and RNA precipitated. RNA pellets were then resuspended and 5' caps removed. Following decapping, 5’ adapters were ligated by T4RNA Ligase 1 and RNA extracted. RNA pellets were then resuspended and reverse transcribed. Samples were amplified and sequenced paired-end on a NextSeq 500 (additional details available in the manuscript)


title: HepG2 csRNA-seq rep1

description:
short RNAs (20-65nt)
tss.HepG2.bed.gz

source_name: TSS mapping in HepG2 cells (rep1)


title: SedSeq~tg_1~L8~EW_TSPP~BY4741~42C~10min~none~BR1~Sup


title: HEK293T csRNAinput-seq rep1

description:
short RNAs (20-65nt)
tss.HEK293T.bed.gz

source_name: small RNA mapping in HEK293T cells (rep1)


title: pHSCMPP_CY153F_E58FL

value: fetal liver

value: Early 2nd trimester


title: SedSeq~tg_1~L11~EW_TSPP~BY4741~30C~10min~none~BR2~Sup


title: Graft TP53 KO replicate 2 additional resequencing

description: 10x Genomics

value: TP53 KO


title: U2OS csRNAinput-seq dnNRF1 mRNA rep2

description:
short RNAs (20-65nt)
tss.U2OS.dnNRF1vsEGFP.bed.gz

source_name: small RNA mapping in U2OS cells expressing dominant negative NRF1 (rep2)

value: U2OS cell line

value: dnNRF1 mRNA


title: SedSeq~tg_1~L8~EW_TSPP~BY4741~42C~10min~none~BR1~Total

value: yeast cells


title: Pituitary gland control 3

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Reads were mapped onto rn7 assembly of rat genome using Hisat2 (v2.1.0).
For each biological replicate, a transcriptome was generated using featureCounts and Gene annotation file ncbiRefSeq.gtf.gz from UCSC
Differentially expressed genes were determined by DESeq2 (Version 2.11.40.7). All analyses were performed using Galaxy platform, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351
Assembly: rn7
Supplementary files format and content: featureCount.txt

source_name: Pituitary gland

growth_protocol: Specific pathogen-free male and female Sprague Dawley rats were purchased from Envigo (USA). Females were purchased at 8 weeks of age and were allowed 1 week to acclimate. At 9 weeks of age, females were randomly assigned to one of 4 treatment groups. Two groups of females were mated, and two groups of females remained virgins. Mating included placing a single female overnight with a male and examination on the following morning for the presence of sperm via vaginal swabs. If sperm was present, the dam was weighed and placed in a separate cage, and this period was marked as gestational day (GD) 0

extract_protocol:
Testes were stored at –80 ºC before the RNA extraction. The extraction was performed using RNeasy Plus Mini Kit 250 (QIAGEN™). Approximately 30 mg of each testis was used . Testis samples were lysed and homogenized using TissueLyser (QIAGEN™). Once homogenized, the RNA extraction protocol was followed. We added additional DNA extraction step using RNase-Free DNase Set (Qiagen, 79254).
The libraries were prepared using the NEBNEXT® Ultra II Directional RNA Library kit for Illumina® (NEB E7760S) using 1µg of total RNA according to the manufacturer’s instructions.

treatment_protocol: Using a sterile technique, a 28-day osmotic mini-pump (2ML4-ALZET, Durect Corp., Cupertino, CA, USA) filled with either sterile saline (control; CON) or a nicotine tartrate (6 mg/kg; NIC), dissolved in sterile saline was placed subcutaneously between the scapulae, as described before (Boychuk and Hayward 2011)(Chang, Karatayev, and Leibowitz 2013). On GD19, or 13 days following pump surgery, dams were allowed to give birth.  Male progeny from both control and nicotine dams was sacrificed at 11 weeks of age.

value: Pituitary gland

value: adult 11-week-old

value: male

tag: strain

value: Sprague-Dawley

value: control


title: U2OS csRNA-seq dnNRF1 mRNA rep2

source_name: TSS mapping in U2OS cells expressing dominant negative NRF1 (rep2)

value: csRNA-seq (transcription initiation)


title: SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Pellet

source_name: yeast cells


title: Pituitary gland control 2


title: Graft TP53 KO replicate 1 additional resequencing

description: 10x Genomics


title: U2OS csRNAinput-seq dnNRF1 mRNA rep1

source_name: small RNA mapping in U2OS cells expressing dominant negative NRF1 (rep1)

value: small RNA-seq (control for csRNA-seq)


title: U2OS csRNA-seq dnNRF1 mRNA rep1

source_name: TSS mapping in U2OS cells expressing dominant negative NRF1 (rep1)


title: SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Sup


title: Pituitary gland control 1


title: Graft TP53 KO replicate 1

description: 10x Genomics


title: SedSeq~tg_1~L7~EW_TSPP~BY4741~30C~10min~none~BR1~Total


title: pHPC_CY153F_E58FL

value: pHPC

value: fresh


title: Graft TP53 wild-type replicate 2 additional resequencing

description: 10x Genomics

value: Human PSC derived neurons


title: Pituitary gland nicotine 3

value: nicotine 6mg/kg/day