title: Adipocytes, Z000000T9 reanalysis

city: Jerusalem

first: Benjamin

last: Berman

institute: The Hebrew University

description:
Adipocytes, Z000000T9
GSM5652177

value: Abdominal Subcut.


title: 12

status: Public on Aug 02 2023

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

country: USA

institute: Indiana University Bloomington

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia and pulmonary hypertension (ICS-BPD-PH)

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Matrix normalized template shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 25 was considered as cutoff.
"Matrix non-normalized" are raw Ct values. "Matrix normalized" are normalized to the global mean. "Fold changes" are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: ICS-BPD-PH

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from premature babies with sBPD and BPD-PH. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

tag: tissue

value: tracheal aspirate

tag: ics-bpd

value: no

tag: ics-bpd-ph

value: yes


title: sample_3441

type: SRA

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-07-06, biol rep: 3

library_source: transcriptomic

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: Tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation. DMEM (Sigma D6429) RPMI (Sigma R8758) was used as purchased except in “buffer” conditions, where sterile 1M HEPES pH 7.0 was added to a final concentration of 25 mM

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

tag: cell line

tag: cell type

value: yeast cell

tag: genotype

value: WT

tag: medium

value: DMEM

tag: atmosphere

tag: temperature

tag: treatment

value: cAMP none

tag: time


title: sample_3117

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-04-23, biol rep: 2


title: sample_2717

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, time: 1440 min, librarydate: 2021-01-26, biol rep: 1


title: CTRL F1 [RA3]

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

data_processing:
After evaluating the quality of these 51bp single-ended RNAseq reads by fastqc, for each sample we left trimmed 3 bp reads with the lowest quality scores using fastx_toolkit (version 0.0.13).
The 47 bp length RNA-seq reads were alimented to the Mouse genome mm10 using tophat (version 2.0.11).
Featurecount was performed using Rsubread (version 1.14.2).
Differential expression was analyzed using DEseq2 Bioconductor package with the by default parameters.
Assembly: Mm10
Supplementary files format and content: tab-delimited text file that was the output of DEseq2 that comparing TBX5 KO samples with CTRL samples

organism: Mus musculus

source_name: right atria

growth_protocol: Mice were raised according to university protocols (protocol # 71737).

extract_protocol:
Right atria were dissected from TBX5 removed and control 6‐8 week old mice. Tissues were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Columns. Overall, 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA. Libraries were prepared from this RNA starting with 1μg per sample and using the mRNA‐seq Sample Prep Kit (Illumina) as per recommended instructions. Cluster generation and sequencing were performed as per standard Illumina HiSeq2500 Rapid Run Mode protocols to generate single-end reads of 51bp. A single pool of libraries was sequenced in two individual lanes of the HiSeq2500 2‐lane flow cell.
Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced on the HiSeq2500 in Rapid Run Mode following the manufacturer's protocols (2013).
Total RNA-seq (Ribozero purification removed only ribosomal RNA, remaining total RNA was sequenced) of 50bp

treatment_protocol: A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.

tag: strain

value: mix

value: right atria

value: Control

tag: age

value: 8-10 weeks

tag: Sex

value: F


title: CTRL F2 [RA4]


title: Spermatocytes, SP_NOA, 100, rep1

city: Shanghai

first: Wu

last: zhongqin

address: No.800 Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
Trim_galore, Adapter and PolyA cut-off
STAR, align reads to hg38 genome
umi_homopolymer.py(UMI extraction)/umi_tools (Deduplication) provided by Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.
Extract UMI and deduplication reads
FeatureCounts, Align reads preferentially to 3'end and calculate the strand-specific reads counts
RSeQC, Show reads distribution on the gene bodies
Assembly: hg38
Supplementary files format and content: csv file includes count values for each sample

source_name: FFPE testicular biopsy tissue

extract_protocol:
RNA was released directly in PCR tube during lysis from spermatocytes, which were collected from FFPE testicular biopsy tissue using laser capture microdissection systembased on Smart-3SEQ method(Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.).
each library was constructed using Smart-3SEQ protocol (Foley, J.W., et al., Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Genome research, 2019. 29(11): p. 1816-1825.)

value: FFPE testicular biopsy tissue

value: spermatocytes

tag: group

tag: patient id


title: CTRL M2 [RA2]

value: M


title: 9

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia (ICS-BPD)

source_name: ICS-BPD


title: Spermatocytes, SP_NOA, 97, rep2


title: sample_985

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-20, biol rep: 4

value: cAMP none; HEPES buffer pH 7.0 25 mM

value: 90 min


title: Spermatocytes, SP_NOA, 97, rep1


title: 8

value: tracheal aspirate


title: CTRL M1 [RA1]


title: 7

value: no


title: 16 - CD45.1 WT naïve replicate 2 - TITR 3

city: Houston

first: Bailee

last: Kain

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
5-BK

data_processing:
FASTQ files were preprocessed using HTS stream
RNA seq alignment (STAR)
Differential expression (DE) analysis of gene expression was performed using Limma-Voom
differential expresion analysis using deSeq2
Results were visualized using Tidyverse packages in R. Comparison of differentially expressed gene lists and generation of Venn diagrams were generated using the GeneVenn webto
GENEONTOLOGY of the Mus musculus database of bulk RNA-seq data
Gene set enrichment analysis (GSEA, Broad Institute and UC San Diego) was completed using normalized gene counts as previously described
Genome_build: m38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample

source_name: Hematopoietic Stem Cells

growth_protocol: HSCs were isolated via whole bone marrow from naïve or infected mice

extract_protocol:
Leg bones were isolated and HSCs were purified via FACS sorting following mechanical isolation and c-kit+ magnetic cell enrichment. DNA and RNA were isolated with the NucleoSpin ® RNA Plus XS kit (Macherey Nagel). RNA-seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were either left untransplanted or transplanted with untrained or M. avium trained HSPCs. Untransplanted or transplanted mice were then infected with M. avium intravenously for one month prior to analysis.

value: whole bone marrow (WBM)

value: murine Hematpoietic stem cells

value: no transplant, naïve


title: Spermatocytes, rST_NOA, 161, rep2


title: Spermatocytes, rST_NOA, 161, rep1


title: 6

value: yes


title: Spermatocytes, rST_NOA, 99, rep2


title: sample_905

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-06-01, biol rep: 3

value: yeast cell

value: WT

value: DMEM


title: Spermatocytes, rST_NOA, 99, rep1


title: sample_59

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-05-25, biol rep: 1


title: sample_979

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-20, biol rep: 4

value: 30 min


title: 14- CD45.1 trained infected (chimeric mice, endogenous) replicate 2 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-14

value: endogenous cells, chimeric, infected


title: 4


title: 10


title: sample_893

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-06-01, biol rep: 3


title: 13- CD45.2 untrained infected (chimeric mice, transplanted) replicate 2

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-13

value: transplanted cells, chimeric, infected


title: 3


title: Spermatocytes, rST_NOA, 96, rep1

value: FFPE testicular biopsy tissue


title: sample_282

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-02-25, biol rep: 2


title: 12-CD45.1 untrained infected (chimeric mice, endogenous) replicate 2 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-12


title: 15- CD45.2 trained infected (chimeric mice, transplanted) replicate 2 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-15

value: transplanted cells, chimeric, infected, trained


title: Spermatocytes, rST_NOA, 96, rep2

value: spermatocytes


title: 2


title: sample_47

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 30 min, librarydate: 2020-05-25, biol rep: 1

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: 11-CD45.2 trained infected (chimeric mice, transplanted) replicate 1 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-11


title: Spermatocytes, OA, 254, rep2

value: OA


title: 10-CD45.1 trained infected (chimeric mice, endogenous) replicate 1 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-10


title: 1

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia and pulmonary hypertension (ICS-BPD-PH)

value: tracheal aspirate


title: sample_288

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 90 min, librarydate: 2020-02-25, biol rep: 2

value: 90 min


title: sample_991

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-20, biol rep: 4

value: 180 min


title: 5

description: low-birth-weight infants with hemodynamically significant cardiac shunt (ICS) that develop bronchopulmonary dysplasia (ICS-BPD)

value: no


title: Spermatocytes, OA, 254, rep1


title: HK408-Stiff

city: Austin

first: Alireza

last: Sohrabi

state: TX

address: 2501 speedway, EER building, Room 5.646_Seidlits Lab, EER building_Seidlits Lab

institute: UT Austin

description:
H1
HK408-Processed data
HK408-CPM

data_processing:
Mapping done by STAR 2.27a
read counts per gene were quantified using human Ensembl GRCh38.98 GTF file. In Partek Flow
read counts were normalized by CPM +1.0E-4
Assembly: Ensembl GRCh38.98 GTF file
Supplementary files format and content: Excel File that include counts for each sample, total counts, p-value and FDR, and fold change
Supplementary files format and content: Excel File that include CMP per each cell line

growth_protocol: Patient-derived GBM cells were cultured in DMEM/F12 supplemented with FGF, EGF, Heparin, and G27. GBM Spheroids were encapsulated in 3D hydrogels and maintained for 6 days before RNA extraction.

extract_protocol:
RNA was extracted using Rneasy micorkit. 2-5µg RNA were used for library construction.
Libraries for RNA-Seq were prepared with TruSeq Stranded mRNA Library Prep Kit. The workflow consists of mRNA enrichment and fragmentation. Cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP and followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA generation is followed by A-tailing, adaptor ligation, and PCR amplification. Different adaptors were used for multiplexing samples in one lane

value: Patient-Derived Glioblastoma cells

value: Stiff


title: 9-CD45.2 untrained infected (chimeric mice, transplanted) replicate 1 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-09

value: whole bone marrow (WBM)

value: murine Hematpoietic stem cells


title: sample_917

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-06-01, biol rep: 3

value: yeast cell

value: WT

value: DMEM


title: HK408-Soft

description:
S1
HK408-Processed data
HK408-CPM

value: Soft


title: Spermatocytes, OA, 253, rep2

value: FFPE testicular biopsy tissue


title: 8- CD45.1 untrained infected (chimeric mice, endogenous) replicate 1 HSC

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-08

value: endogenous cells, chimeric, infected


title: 5 -WT naïve HSC (5 - CD45.1 naïve) replicate 1 - TITR 2

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-05

value: no transplant, naïve


title: Spermatocytes, OA, 241, rep2

value: spermatocytes


title: sample_294

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-02-25, biol rep: 2

value: cAMP none; HEPES buffer pH 7.0 25 mM


title: sample_71

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 180 min, librarydate: 2020-05-25, biol rep: 1


title: Spermatocytes, OA, 253, rep1

value: OA


title: 7- CD45.1 WT infected (no transplant) replicate 2- TITR 3

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-07V1

value: infection, no transplant


title: HK177-Soft

description:
Soft_S2
HK177-Processed data
HK177-CPM


title: sample_3635

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 4


title: 6- WT infected (no transplant) replicate 1 HSC (sample 6)

description:
gene.counts.csv
naive_vs_mavinfected.deseq.res.csv
20072FL-01-01-06V1


title: Chondrocyte secondary generation rep3

city: Hangzhou

first: shuying

last: shen

state: Zhejiang

address: 3 East Qingchun Road

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital

description: The circRNA-seq library preparation and sequencing process involves capturing circular RNA molecules, converting them into cDNA, amplifying the library, and subsequently sequencing it to obtain a comprehensive profile of circular RNAs.

data_processing:
Samples were sequenced by NovaSeq 6000 (Illumina) after quality inspection, and paired-end reads of 150nt length were obtained.
Sequence reads were trimmed for adaptor seauence/ow-gualty secuence using cutadapt(v2.7).
Trimmed sequence reads were aligned to human genome (ensembl GRCh38) with bwa (v0.7.17).
CIRI (V2.0.6) was applied to identify circRNAs and estimate the junction reads as circRNA counts.
Junction reads counts normalization were performed using DESeq2 .
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include normalization values for each sample

source_name: articular sample

extract_protocol:
The circRNA-seq data was generated using a standard RNA extraction protocol. Briefly, total RNA was isolated from the sample using TRIzol (Invitrogen) , according to the manufacturer's instructions. The extracted RNA was treated with DNase to remove any genomic DNA contamination, followed by purification steps to obtain high-quality RNA suitable for downstream applications.
The circRNA-seq library was prepared using a modified version of the standard circRNA-seq library construction protocol. The library construction process involved several steps. First, use the kit to deplete rRNA, then deplete linear RNA to enrich circRNA. Then， the circRNA was subjected to a reverse transcription reaction using random primers to convert the RNA into cDNA. The enriched circRNA was fragmented and ligated with adapters. Subsequently, PCR amplification was performed to amplify the library and generate sufficient material for sequencing.
The library strategy used for circRNA-seq was strand-specific RNA-seq. This strategy allows the identification and characterization of circular RNAs by preserving the information regarding their originating strands. It provides insights into the differential expression, alternative splicing, and other features of circular RNAs in the sample.

value: articular sample

value: chondrocyte

value: Secondary generation chondrocyte

value: wild type


title: Spermatocytes, OA, 241, rep1


title: C. elegans, set-2(ok952);crtc-1(CBD), Day 1 adult, biol rep 4

city: Boston

first: William

middle: B.

last: Mair

state: MA

address: 665 Huntington Avenue

department: Molecular Metabolism

institute: Harvard T.H. Chan School of Public Health

description:
Double mutant set-2(ok952);crtc-1(CBD)
WBM1036-4

data_processing:
Raw reads were examined for quality using TapeStation (Agilent)
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing data were suitable for further analysis.
Reads were aligned to the Ensembl94 build of the C. elegans genome using STAR
Using Salmon, expression quantification was performed to identify transcript-level abundance estimates and then collapsed down to the gene level using the R Bioconductor package tximport
Differential expression was performed at the gene level using the R Bioconductor package DESeq2
Differentially expressed genes were identified using the Wald test, and significant genes were obtained using an FDR threshold of 0.05. Significant genes were separated into clusters based on similar expression profiles across the defined sample groups
Assembly: Reads were aligned to the Ensembl94 build of the C. elegans genome
Supplementary files format and content: Excel file contains normalized counts for all genes for all samples.
Supplementary files format and content: Gene names are listed as WormBase Coding Sequence (CDS)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: lysate from ~2000 whole nematodes

growth_protocol: C. elegans were maintained on 6 cm NGM regular plates at 20 degrees celsius.

extract_protocol:
On Day 3 (1-day old animlas), animals were snap frozen in Qiazol Lysis Reagent and RNA was extracted using the Qiagen RNeasy Mini Kit.
Libraries were prepared using the Kapa mRNA HyperPrep kit (Roche Applied Science)

treatment_protocol: Animals from NGM plates were bleached, the embryos were put on EV plates at 20 degress celsius, wait 3 days until they reach the day 1 of adulthood, and then collected for the RNA extraction

value: lysate from ~2000 whole nematodes

value: Empty Vector plasmid, plates with carbenicillin

value: Day 1 of adulthood


title: sample_997

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-02-20, biol rep: 3

value: yeast cell

value: WT


title: 93T449-iMab-C&T_biorep3

city: Padua

first: Irene

last: Zanin

state: Italy

address: Via Gabelli 63

department: Molecular Medicine

country: Italy

institute: University of Padua

library_source: genomic

data_processing:
Sequencing data were uploaded to the Galaxy web platform and the public server at usegalaxy.org, together with R (version 3.4), were used to analyze all data.
Raw FASTQ reads were trimmed with TrimGalore! (v0.6.7) and aligned to GRCh38 using Bowtie2 (v2.4.2)
Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.5.1) bamCoverage with binSize 5 and the respective genome size.
Peaks were called with SEACR (v1.3) and high confidence peaks sets between biological replicates were obtained with BEDTools intersect.
Annotation of peaks was performed with the R package “ChIPseeker”.
For GVIZ visualization of genomic regions, bigwig files were merged using deeptools2 BigwigCompare function and scaled referring to the sample with the lowest sequencing depth.
BEDTools intersect function was used to identify iM/G4-unique and common peaks.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: WDLPS

growth_protocol: WDLPS cell line was cultured in RPMI-1640 supplemented with 10% FBS and1x Penicillin-Streptomycin. HEK293T cell line was cultured in DMEM supplemented with 10% FBS and 1x Penicillin-Streptomycin. Cells were grown under standard conditions (5 % CO2, 95 % humidity, 37 °C).

extract_protocol:
Cells were harvested with trypsin and subjected to CUT&Tag protocol
pA-Tn5 adaptor complex was used for library preparation

value: WDLPS

value: Tumor fibroblast-like line derived from well-differentiated liposarcoma

tag: antibody


title: sample_929

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-06-01, biol rep: 2

value: DMEM


title: C. elegans, set-2(ok952);crtc-1(CBD), Day 1 adult, biol rep 3

description:
Double mutant set-2(ok952);crtc-1(CBD)
WBM1036-3

tag: tissue


title: sample_83

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: none, HEPES buffer pH 7.0 25 mM, time: 1440 min, librarydate: 2020-05-25, biol rep: 1


title: Chondrocyte secondary generation rep2


title: Chondrocyte secondary generation rep1


title: 93T449-iMab-C&T_biorep2


title: C. elegans, set-2(ok952);crtc-1(CBD), Day 1 adult, biol rep 2

description:
Double mutant set-2(ok952);crtc-1(CBD)
WBM1036-2


title: Chondrocyte primary generation rep3

value: Primary generation chondrocyte


title: C. elegans, crtc-1(CBD), Day 1 adult, biol rep 4

description:
Single mutant crtc-1(CBD) with a point mutation in the CBD domain
WBM1041-4


title: sample_1298

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-23, biol rep: 4

value: cAMP 20 mM

value: 90 min


title: C. elegans, crtc-1(CBD), Day 1 adult, biol rep 3

description:
Single mutant crtc-1(CBD) with a point mutation in the CBD domain
WBM1041-3


title: 93T449-BG4-C&T_biorep2

value: BG4 (in-house preparation); anti-FLAG M2 (F1804)


title: C. elegans, set-2(ok952);crtc-1(CBD), Day 1 adult, biol rep 1

description:
Double mutant set-2(ok952);crtc-1(CBD)
WBM1036-1


title: 93T449-iMab-C&T_biorep1


title: HK177-Stiff

description:
Stiff_S3
HK177-Processed data
HK177-CPM

value: Patient-Derived Glioblastoma cells

value: Stiff


title: 93T449-BG4-C&T_biorep3


title: C. elegans, crtc-1(CBD), Day 1 adult, biol rep 2

description:
Single mutant crtc-1(CBD) with a point mutation in the CBD domain
WBM1041-2


title: sample_340

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-10-29, biol rep: 2


title: HEK293T-iMab-C&T_biorep3

value: Human embryonic kidney


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2080_2847-iPSC-KS1-P--pool--61-_AD010

city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

description:
Homo sapiens iPS XXY,47 KS Bulk RNAseq
Bulk RNAseq

data_processing:
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk v. by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25.
After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 101) using the STAR end-to-end alignment method
Gene expression quantification matrices were generated with featureCounts v.
Counts normalization was performed with the Trimmed Mean of M-values (TMM) method icnorporated in EdgeR v. 3.36.0
Assembly: GrCh38 release 101
Supplementary files format and content: File including FPKM values for each Sample

source_name: iPS

growth_protocol: hiPSC lines were adapted to feeder-free conditions on matrigel-coated plates in E8 medium

extract_protocol:
For bulk RNA-Seq libraries the RNA has been extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions
Bulk RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina, and profiled using a NovsSeq 6000 system with 150 bp paired-end sequencing method.

treatment_protocol: Before RNA extraction hiPSCs were adapted to Vitronectin (VTN-N) coated plates  in presence of E8 medium and passaged with Versene.

value: human induced pluripotent stem cell

tag: karyotype

value: XXY,47 KS

tag: name in the manuscript


title: Chondrocyte primary generation rep2

value: articular sample

tag: cell line

value: chondrocyte

value: wild type


title: sample_250

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-04, biol rep: 1

tag: cell type

value: yeast cell


title: 93T449-BG4-C&T_biorep1


title: sample_949

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 90 min, librarydate: 2019-11-10, biol rep: 3

tag: genotype

value: WT


title: C. elegans, crtc-1(CBD), Day 1 adult, biol rep 1

description:
Single mutant crtc-1(CBD) with a point mutation in the CBD domain
WBM1041-1

value: lysate from ~2000 whole nematodes

value: Empty Vector plasmid, plates with carbenicillin

value: Day 1 of adulthood


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2079_2846-iPSC-KS1-P--pool--61-_AD009


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2078_2845-iPSC-KS1-P--pool--61-_AD008


title: sample_943

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-10, biol rep: 3

tag: medium

value: DMEM

value: 30 min


title: C. elegans, set-2(ok952), Day 1 adult, biol rep 4

description:
Single mutant set-2(ok952)
set-2-4


title: sample_334

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-29, biol rep: 2

tag: atmosphere

value: cAMP 20 mM


title: sample_1292

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-10-23, biol rep: 4

tag: temperature


title: HEK293T_BG4-C&T_biorep3

value: BG4 (in-house preparation); anti-FLAG M2 (F1804)


title: HEK293T-iMab-C&T_biorep1


title: HEK293T-BG4-C&T_biorep2


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2076_2843-iPSC-KS1-L--pool--61-_AD001


title: HEK293T-iMab-C&T_biorep2


title: sample_1304

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-23, biol rep: 4

tag: treatment

value: 180 min


title: C. elegans, set-2(ok952), Day 1 adult, biol rep 1

description:
Single mutant set-2(ok952)
set-2-1

tag: time


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2075_2842-iPSC-KS1-L--pool--61-_AD019


title: Chondrocyte primary generation rep1

description: The circRNA-seq library preparation and sequencing process involves capturing circular RNA molecules, converting them into cDNA, amplifying the library, and subsequently sequencing it to obtain a comprehensive profile of circular RNAs.

value: Primary generation chondrocyte


title: sample_346

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-10-29, biol rep: 2


title: C. elegans, set-2(ok952), Day 1 adult, biol rep 3

description:
Single mutant set-2(ok952)
set-2-3

tag: strain


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2067_2812-iPSC-KS3-C1--pool--61-_AD006


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2077_2844-iPSC-KS1-L--pool--61-_AD003


title: P611T

city: Prague

first: Petr

last: Holý

address: Šrobárova 48/49

country: Czech Republic

institute: National Institute of Public Health

data_processing:
Quality control and trimming of raw RNA sequencing data was performed using the fastp package v0.23.2. For annotation, reference transcriptome GENCODE v35 (GRCh38.p13) was used. Quantification of protein-coding transcripts via pseudoalignment was done using kallisto v0.48 with default settings. For correlation analyses, the count data were normalized to transcripts per million (TPM) and were log2 scaled
Assembly: GRCh38.p13
Supplementary files format and content: Tab/delimited text file (.tsv) contains TPM normalized values for each sample

source_name: tumor

growth_protocol: Primary breast tumors resected from patients

extract_protocol:
Total RNA was extracted from tumor tissue using the TRIZOL reagent (Thermofisher) following the manufacturer’s protocol. The tissue was first pulverized with mortar and pestle under liquid nitrogen.
500 ng of total RNA was used for construction of RNA libraries. The cDNA libraries corresponding to mRNA were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s protocol. Samples with RIN>3.5 (n=58) were processed by the standard protocol, while samples with RIN<3.5 (n=9) were processed using the Low Quality RNA protocol. Quality of prepared libraries was checked by Bioanalyzer 2100 using High Sensitivity DNA kit (Agilent Technologies Inc., CA, USA) and quantity measured by qPCR using the KAPA Library Quantification Kit Illumina®Platforms (Roche, Switzerland) and by the Qubit instrument using the Qubit RNA HS Assay Kit (both ThermoFisher Scientific, MA, USA). The equimolar pool of prepared libraries was sequenced on the NextSeq 500 platform (Illumina Inc., CA, USA) using the High Output kit (1x75bp setting) and targeting 5-6 million reads per sample.

tag: disease

value: breast carcinoma

value: tumor


title: sample_256

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-04, biol rep: 1


title: P596T


title: C. elegans, set-2(ok952), Day 1 adult, biol rep 2

description:
Single mutant set-2(ok952)
set-2-2


title: P539T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2066_2811-iPSC-KS3-C1--pool--61-_AD005

value: human induced pluripotent stem cell

value: XXY,47 KS


title: C. elegans, wild type, Day 1 adult, biol rep 2

description:
Wild type
N2-2

value: N2 Bristol


title: sample_3627

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2021-09-08, biol rep: 4


title: sample_244

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 30 min, librarydate: 2019-11-04, biol rep: 1


title: HEK293T-BG4-C&T_biorep1

value: Human embryonic kidney


title: sample_955

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 180 min, librarydate: 2019-11-10, biol rep: 3

value: yeast cell


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2068_2813-iPSC-KS3-C1--pool--61-_AD007


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2064_2809-iPSC-KS2-B--pool--61-_AD002


title: sample_353

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 2

value: WT


title: C. elegans, wild type, Day 1 adult, biol rep 3

description:
Wild type
N2-3

value: lysate from ~2000 whole nematodes

value: wild type


title: P525T


title: Ly6C+mono_nr4a1ko_rep1

city: St. Louis

first: Kevin

middle: William

last: O'Connor

state: MO

address: 4925 Children's Place

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights7. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE8 to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term. The R/Bioconductor package heatmap39 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05. Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview10.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA11. Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data. An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix. Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler12. Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module. The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Tab-delimited text

source_name: bone marrow

growth_protocol: Ly6C+ monocytes were obtained from bone marrow of mice of the indicated genotypes

extract_protocol:
RNA was isolated using a NucleoSpin RNA XS kit (Macherey-Nagel) per manufacturer's protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: bone marrow

value: Ly6C+ classical monocyte

value: Nr4a1 KO


title: Ly6C+mono_nr4a1ko_rep2


title: C. elegans, wild type, Day 1 adult, biol rep 1

description:
Wild type
N2-1

value: Empty Vector plasmid, plates with carbenicillin

value: Day 1 of adulthood


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1917_2807-iPSC-KS2-E-pool60_AD025


title: P494T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-2065_2810-iPSC-KS2-B--pool--61-_AD004


title: Ly6C+mono_irf2ko_rep1

value: Irf2 KO


title: Ly6C+mono_bcl6cko_rep2

value: Bcl6 cKO


title: C. elegans, wild type, Day 1 adult, biol rep 4

description:
Wild type
N2-4


title: P535T

value: breast carcinoma


title: P477T

value: tumor


title: sibling, scRNAseq

city: Guangzhou

first: Wei

last: Liu

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

institute: South China University of Technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger software (version 5.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification.
Doublet GEMs was achieved by using the tool DoubletFinder (v2.0.3) by the generation of artificial doublets, using the PC distance to find each cell’s proportion of artificial k nearest neighbors (pANN) and ranking them according to the expected number of doublets.
The cell by gene matrices for each sample were individually imported to Seurat  version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs (≥40000) or mitochondrial gene percent (≥15%) were filtered out. We also excluded cells with less than 200 or more than 3500 genes detected.
After removing unwanted cells from the dataset, we employed a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the results. The formula is shown as follows:   A gene expression level=Log(1+UMIA/UMITotal ×10000)
Seurat embed cells in a shared-nearest neighbor (SNN) graph, with edges drawn between cells via similar gene expression patterns. To partition this graph into highly interconnected quasi-cliques or communities, we first constructed the SNN graph based on the euclidean distance in PCA space and refined the edge weights between any two cells based on the shared overlap in their local neighborhoods (Jaccard distance). We then cluster cells using the Louvain[6] method to maximize modularity. For visualization of clusters, t-distributed Stochastic Neighbor Embedding (t-SNE) were generated using the same PCs.
Assembly: Genome assembly: GRCz11 Ensembl release 104
Supplementary files format and content: tab-separated values files, matrix files and xls files

organism: Danio rerio

source_name: whole brain

extract_protocol:
Whole brains were isolated from 3 dpf sibling and rb1smu2/smu2 mutants. Brain tissues were dissociated with 300 μL papain (28 units/mL, Worthington) in papain solution (1% DNase, 12 mg/mL L-cysteine in DMEM/F12), incubated at 37°C for 15 min with proper mix methods. Dissociated cells were washed twice with washing buffer (100 mL: 650 μL 45% glucose, 500 μL 1 M HEPES and 5 mL FBS into 93.85 mL 1×DPBS, sterilized with a 0.22 μm pore size filter), and sterilized with 40 μm cell strainers (BD Falcon) into 300–400 μL washing buffer.
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Briefly, cell suspensions were loaded on a 10X Genomics GemCode Single-cell instrument to generates single-cell Gel Bead-In-EMlusion (GEMs). Upon dissolution of the Gel Bead in a GEM, primers containing an Illumina® R1 sequence, a 16 nt 10x Barcode, a 10 nt Unique Molecular Identifier (UMI), and a poly-dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. The pooled barcoded cDNA was then cleaned up with silane magnetic beads, amplified by PCR to generate sufficient mass for library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: neuron

value: whole brain

tag: development stage

value: 3 dpf

value: wt


title: Ly6C+mono_bcl6cko_rep1


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1918_2808-iPSC-KS2-B-pool60_AD027

value: human induced pluripotent stem cell

value: XXY,47 KS


title: P534T


title: sample_961

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-10, biol rep: 3

value: yeast cell

value: WT

value: DMEM

value: cAMP 20 mM


title: Ly6C+mono_irf2ko_rep2

value: bone marrow

value: Ly6C+ classical monocyte


title: sample_262

description: medium: DMEM, atmosphere: CO2 5%, temperature: 30C, cAMP: 20 mM, time: 1440 min, librarydate: 2019-11-04, biol rep: 1


title: P370T


title: rb1, scRNAseq

description: 10x Genomics

value: rb1 mutant


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1916_2806-iPSC-KS2-E-pool60_AD023

description:
Homo sapiens iPS XXY,47 KS Bulk RNAseq
Bulk RNAseq


title: NK_WTvIRF4_TimeCourse_scRNAseq

city: New York

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: 10X Genomics

data_processing:
Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. After mitochondrial and doublet cleanup, raw count matrix was normalized by median library size normalization followed by log transformation.
The Louvain algorithm with k = 30 was used to perform clustering and Euclidean distance was used as the metric to construct nearest neighbor graph. Partition-based graph abstraction (PAGA) Analysis was done as described using scanpy (https://github.com/theislab/paga). MAST was then used to perform differential expression (DE) analysis between hash-ed samples, and GSEA enrichment analysis (https://github.com/zqfang/GSEApy) was then performed on DE genes (FDR < 0.05 & |coef| > 0) using ‘MSigDB_Hallmark_2020’ gene set and significant pathways were identified based on padj <0.05. In some cases, MAGIC was used to impute transcript counts. MPEC and SLEC signatures were obtained from GSE8678.
Assembly: mm10
Supplementary files format and content: 3656_ES-1543_WTvIRF4_TimeCourse_HTO.h5ad
Supplementary files format and content: 3656_ES-1543_WTvIRF4_TimeCourse_IGO_12437_AD_4_dense.csv contains GEX data
Supplementary files format and content: tag-list.csv contains HTO sample information

source_name: Spleen

extract_protocol:
Spleens were dissociated with glass slides and filtered through 100-μm cell strainer. Flow cytometry and cell sorting were performed on the Cytek Aurora (Cytek Biosciences) and Aria II cytometers (BD Biosciences), respectively. Before cell sorting, NK cells were enriched by incubating whole splenocytes with the following antibodies at 20 μg/ml against CD3ε (17A2), CD4 (GK1.5), CD8 (2.43), Ter119 (TER-119), CD19 (1D3), Ly6G (1A8) (BioXCell) followed by magnetic depletion using goat anti-rat beads (QIAGEN). For scRNA-seq enriched splenocytes were then stained with surface markers to identify Ly49H+ NK cells (CD3/TCRb/CD19- NK1.1+ CD49b+ Ly49H+) and sorted based on congenic markers (CD45.1 and CD45.2) to identify WT and Irf4−/− cells with > 95% purity.
Ly49H+ NK cells (CD3/TCRb/CD19− NK1.1+ CD49b+ Ly49H+) from either WT or Irf4−/− NK cells were sorted from spleens of MCMV-infected WT:Irf4−/− mBMC mice as described from day 0, 2, 4 and 7 PI, and stained with barcoded antibodies (Total-Seq B, Biolegend). After hash-staining, WT and Irf4−/− Ly49H+ NK cells were mixed at 1:1 ratio for each time point. The single-cell RNA-seq from these pooled FACS-sorted cell suspensions was then performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS-sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells was above 80%, as confirmed with 0.2% (w/v) trypan blue staining (Countess II). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Samples were multiplexed together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO) following a previously published protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package.

value: Spleen

value: NK cell


title: WTc11-derived neurons, RBM12-depleted, untreated rep3

city: Durham

first: Nikoleta

middle: G

last: Tsvetanova

state: NC

address: 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

data_processing:
Quality control  using fastQC
Alignment of reads using STARaligner to the GRCh38 reference
Read count extraction using Subread/featureCounts
Read count normalization and differential expression analysis using DESeq2
Assembly: GRCh38
Supplementary files format and content: comma-separated values file showing normalized counts from DESeq2 for each sample

source_name: WTc11-derived neurons

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen, Cat. #74106) and NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. #E7490). 200 ng RNA were used as input for library generation
RNA libraries for RNA-seq were prepared using NEBNext Ultra II directional RNA Library Prep Kit for Illumina (NEB) following manufacturer's protocols.

value: WTc11-derived neurons

value: glutamatergic excitatory neurons

value: RBM12 knockdown

value: untreated


title: WTc11-derived neurons, RBM12-depleted, Isoproterenol rep1


title: P424T

value: breast carcinoma

value: tumor


title: HTO_scRNAseq

description: 10X Genomics


title: P489T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1915_2805-iPSC-KS2-E-pool60_AD022

value: human induced pluripotent stem cell


title: WTc11-derived neurons, RBM12-depleted, Isoproterenol rep3


title: P290T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1914_2804-iPSC-KS4-C1-pool60_AD021

value: XXY,47 KS


title: Ly6C+mono_wildtype_rep2

value: Wild-type


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1909_2799-iPSC-KS4-H-pool60_AD008


title: P287T


title: NK_input_10mil_CellSignalingIRF4_stim

data_processing:
Paired reads were trimmed for adaptors and subjected for removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie2 (v2.4.1). Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples using narrow peak parameters “–q 0.05 –B –SPMR”.
Assembly: mm10
Supplementary files format and content: Project_14164_atlas.bed

growth_protocol: Sorted WT NK cells were grown ex vivo for two weeks in complete IMDM media (10% FBS, 1% Pen/Strep, 1X BME, 1X MEM-NAA, 1X HEPES) in the presence of 50ng/ml of human IL-15 (Miltenyi Cat#130-095-766).

extract_protocol: Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with up to 5 ng input DNA and 8-12 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina).

treatment_protocol: 10 million IL-15 expanded NK cells were then stimulated with anti-NK1.1 + cytokines (IFNa+IL-12/18+IL-2/15) or left unstimulated in 5ng/ml of hIL-15 overnight in a 6-well plate.

value: WT

value: NK cells

tag: replicate


title: WTc11-derived neurons, RBM12-depleted, Isoproterenol rep2


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1913_2803-iPSC-KS4-C1-pool60_AD020


title: P421T


title: Ly6C+mono_wildtype_rep1


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1908_2798-iPSC-KS1-A-pool60_AD003


title: CSE S1 rep1

city: BANGALORE

first: DEEPAK

last: SAINI

state: KARNATAKA

address: GA-06,MRDG DEPARTMENT, IISC

department: MRDG

country: India

institute: INDIAN INSTITUTEOF SCIENCE

data_processing:
Illumina HiSeqX was used for basecalling
The data was checked for base call quality distribution using FastQC and MultiQC software, % bases above Q20, Q30, %GC, and sequencing adapter contamination
Raw sequence reads were processed to remove adapter sequences and low quality bases using fastp
The QC passed reads were mapped onto the indexed Human reference genome(GRCh38.p13) using STAR2 aligner
Gene level expression values were obtained as read counts using featureCounts software
Assembly: GRCh38.p13/hg38
Supplementary files format and content: Tab-delimited text file including raw gene counts for every gene and every sample

source_name: A549 CELLS

growth_protocol: Cells were cultured in 10%FBS containing DMEM in 5% CO2 at 37 degree celsius

extract_protocol:
Trizol reagent was used to harvest RNA from scr and CSE knockdown cells
RNA libraries were prepared for sequencing using NEB Next Ultra II RNA preparation kit for Illumina

treatment_protocol: for senesence induction they were subjected to 7Gy IR and harvested after 72 hours

value: Epithelial cells

tag: genotype/variation

value: CSE knockdown

tag: condition

value: senescent


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1907_2797-iPSC-KS1-A-pool60_AD001


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1910_2800-iPSC-KS4-H-pool60_AD009


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1911_2801-iPSC-KS4-H-pool60_AD010


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1906_2796-iPSC-KS1-A-pool60_AD019


title: WTc11-derived neurons, RBM12-depleted, untreated rep2


title: P368T


title: CSE NS2 rep1

value: non-senescent


title: Conditional Knockout, replicate 3

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
The NGS-Data-Charmer pipeline was used for preprocessing, QC, and alignment of the FASTQ files (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adaptor trimming was achieved by using the Trim-Galore tool, followed by alignment of trimmed reads to the mouse mm10 genome assembly using HISAT2.
Duplicated read pairs were removed using the ‘rmdup’ module of SAMtools3 (v1.10).
featureCounts was used to obtain a gene expression matrix, using the parameters “--fraction -t gene” on the GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: The file "counts_genic_matrix" is a tab-delimited text file containing the read counts in each mouse gene. The file "fpkm_genic_matrix" is a tab-delimited text file containing the normalized gene expression values in FPKM (Fragments Per Kilobase per Million).

source_name: Dorsal root ganglia neuron

growth_protocol: Thoracic and lumbar DRG were dissociated at ZT2-4 and enriched neuronal cultures were seeded on PLO/Laminin coated plates at ZT8

extract_protocol:
QIAGEN RNeasy plus mini kit
TruSeq Stranded mRNA

treatment_protocol: DRG neuron cultures from Bmal1 cKO (Bmal1f/f Thy1-CRE-ERT2/EYFP) or control (Bmal1f/f or Bmal1 f/+) were used with no further treatment. RNA was isolated using Qiagen RNeasy Plus mini kit.

value: Dorsal root ganglia neuron

value: Bmal1 f/f Thy1-CRE(ERT2/EYFP)

value: conditional KO


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1902_2792-iPSC-KS3-G-pool60_AD014


title: NK_input_10mil_CellSignalingIRF4_unstim

tag: tissue

value: Spleen


title: Conditional Knockout, replicate 2


title: CSE S3 rep2


title: P272T


title: P215T


title: NK_IP_10mil_CellSignalingIRF4_unstim


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1912_2802-iPSC-KS4-C1-pool60_AD011

tag: karyotype


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1901_2791-iPSC-KS3-G-pool60_AD013

tag: name in the manuscript


title: NK_IP_10mil_CellSignalingIRF4_stim


title: P227T


title: P220T


title: WTc11-derived neurons, RBM12-depleted, untreated rep1

tag: cell line

value: WTc11-derived neurons

value: glutamatergic excitatory neurons

value: RBM12 knockdown


title: CSE NS3 rep2

tag: cell type


title: scr NS1 rep1

value: scr knockdown


title: Control, replicate 2

tag: genotype

value: Bmal1 f/+


title: scr S3 rep2


title: P189T

value: breast carcinoma

value: tumor


title: Conditional Knockout, replicate 1


title: Control, replicate 1

value: Bmal1 f/f

value: WT


title: scr S2 rep1

value: Epithelial cells


title: P188T


title: P061T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1899_2789-iPSC-KS2-N-pool60_AD007

value: human induced pluripotent stem cell

value: XXY,47 KS


title: P179T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1898_2788-iPSC-KS2-N-pool60_AD006


title: scr NS3 rep2

value: non-senescent


title: M420T


title: LA_8

description: non-oligodT

data_processing:
Concatenate FastQ files for each sample. After evaluated the quality of these 50bp signle-ended, stranded RNAseq data by fastqc, we excluded the sample #11 due to higher GC contant and other contamination.
The 50 bp length RNA-seq reads were alimented to the Mouse genome mm10 uisng tophat (version 2.0.13).
Cufflinks de novo assembly (v2.2.1 using the -g  for the gtf guide) and the parameters --frag-bias-correct, --multi-read-correct, --upper-quartile-norm)
Featurecount was performed using Rsubread
Analysis of differential expression was performed using a count-based differential expression analysis strategy for RNA sequencing and normalized using the R package DESeq.
Assembly: Mm10, gencode.vM4
Supplementary files format and content: Merged alignment per sample using PICARD:MergeSamFiles.jar. Transcript alignment was performed using TopHat (version 2.0.10, using the parameters --segment-length 24 --segment-mismatches 2 --no-coverage-search).
Supplementary files format and content: Excel tables conatin the idefined 1577 ncRNAs downregulated in the absence of TBX5 (“TBX5-activiated”) and 1490 ncRNAs upregulated in the absence of TBX5 (“TBX5-repressed”), respectively. The mm10 genomic coordinates of identified noncoding transcripts were lifted over to the mouse mm9 genome when overlay with identifeid or published enhancer regions (see PMC5745077).

source_name: left atrium

extract_protocol:
Total RNA was extracted by TRIzol Reagent (Invitrogen), followed by ribosomal and polyA depletion. RNA was processed by RiboZero purification and oligo-dT depletion.
RNA Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeQ RNA Sample prep kit v2 (Part# RS‐122‐2001). Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. Electrophoresis System (Bio-Rad).

treatment_protocol: Mouse, mixed genetic background, ~8wks old, male

value: mix

tag: Sex

value: male

tag: age

value: left atrium


title: LA_10

description: non-oligodT


title: M415T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1897_2787-iPSC-KS2-N-pool60_AD005


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1896_2786-iPSC-KS4-C2--pool59_AD004


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1900_2790-iPSC-KS3-G-pool60_AD012


title: LA_9

description: non-oligodT


title: KO_E_rep3

city: Pullman

first: Kimberly

middle: M

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

description: processed data files are output from feature counts

data_processing:
Quality of raw data before and after trimming was assessed using FastQC v0.11.7. Adapters and low-quality bases (Phred score < 20) were trimmed from reads using Trim Galore! V0.6.6.The reads were then mapped to the mouse reference genome (GRCm39) using STAR v2.7.10b with transcript annotation index. Raw read counts per gene were quantified with featureCounts v2.0.3.
Assembly: GRCm39
Supplementary files format and content: Tab-separated raw gene counts (output from feature counts)

source_name: Esr1 knockout endometrial epithelial organoids, estrogen treatment, bulk RNA-seq

growth_protocol: Uteri were removed from mice and digested in 1% trypsin (Sigma, T4799) in calcium and magnesium-free HBSS (Gibco, 14175-095) for 45 minutes at 4°C followed by 45 minutes at 37°C using an orbital shaker. The digestion was stopped with 1% soybean trypsin inhibitor (Gibco, 17075-029) in HBSS with 5 mM MgCl2 and 0.1 mg/mL DNAse-1 (Roche, 10104159001). For PND 15, Pasteur pipettes were carefully forged to create a slightly smaller diameter than the uterus, and sheets of epithelium retrieved by gentle suction using a mouth pipette. For PNDs 30 and 60, the digested uterine horns were gently squeezed with forceps. The epithelial tube sheets from each uterus were rinsed gently with HBSS and placed into 1.5 mL Eppendorf tubes. After centrifugation (300 x g for 3 minutes), the supernatant was removed, and epithelium pellet resuspended in base organoid media. Following another round of centrifugation, the epithelium pellet was resuspended in 80% Cultrex (R&D Systems, 3445-005-01) and 20% organoid expansion media. EEO were passaged (1:3 ratio) every 7-10 days. To passage the EEO, Cultrex/EEO drops were detached from the cell culture plate by gentle pipetting and transferred into 1.7 mL Eppendorf tubes. After centrifugation (300 x g for 3 minutes), the supernatant was removed, replaced by 1.5 mL of HBSS, and pipetted up and down to dissociate the pellet. Following an additional centrifugation step, the cell pellet was resuspended in Cultrex and plated in 12-well plates (25 μL drops; 4 drops per well). Cultrex drops were incubated at 37 °C for 15 min prior to adding 800 μL of organoid expansion media per well. Organoid cryopreservation was performed with freezing medium consisting of 10% DMSO in fetal bovine serum (FBS, Sigma, F0926) as described previously. All experiments were performed using passage 3 EEO. Brightfield images were captured on a Leica DMi8 inverted microscope and Leica K8 camera using Leica Application Suite X (LAS X).

extract_protocol:
RNA was isolated using a Direct-zol kit (Zymo Research, R2070) according to the manufacturer’s instructions
Libraries were prepared by the University of Missouri DNA core using an Illumina TruSeq mRNA kit (Illumina Inc., San Diego, CA, USA)
Libraries were sequenced (paired end 150; 30 million read pairs) using an Illumina NovaSeq 6000

treatment_protocol: WT and KO organoids did not respond to estrogen treatment

value: Endometrial epithelial organoids

value: Esr1 KO

value: estrogen


title: KO_E_rep2


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1894_2784-iPSC-KS4-C2--pool59_AD027


title: Control, replicate 3

value: Dorsal root ganglia neuron


title: LA_2b

description: non-oligodT

value: control


title: KO_E_rep1


title: M408T


title: P176T


title: KO-RZ

description: non oligodT


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1893_2783-iPSC-KS3-A--pool59_AD025


title: M406T


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1892_2782-iPSC-KS3-A--pool59_AD023


title: KO_noE_rep2

source_name: Esr1 knockout endometrial epithelial organoids, no estrogen treatment, bulk RNA-seq

value: no estrogen


title: M396T

value: breast carcinoma


title: KO_noE_rep1


title: C-RZ

description: non oligodT


title: M394T

value: tumor


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1891_2781-iPSC-KS3-A--pool59_AD022


title: Homo sapiens iPS XXY,47 KS Bulk RNAseq M-21-1895_2785-iPSC-KS4-C2--pool59_AD002


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2074_2819-iPSC-KS5-F1--pool--61-_AD018

description:
Homo sapiens iPS XY,46 Bulk RNAseq
Bulk RNAseq

value: HC #B or XY#B


title: LR UM Case20

first: Nestor

last: Zhang

address: Dongchuan Road

data_processing:
Short reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d). All annotated and unannotated isoforms were merged to generate a combined isoform annotation file in “GTF” format.
With the cufflinks program and corresponding short reads data we estimated the expression level for each isoform based on the combined annotation file.
We used two different pipelines, including FLAIR and pinfish, to identify isoforms from long reads. For the FLAIR pipeline, “flair align” first aligns long reads to the reference human genome GRCh38 genome using minimap2, then “flair correct” corrects misaligned splice sites using GENCODE v24 annotations and corresponding short-read splice junctions, and finally “flair collapse” defines high-confidence isoforms from corrected long reads. For pinfish pipeline, we also use minimap2 to mapping the long reads to the reference genome, then “cluster_gff” clusters together the long reads having similar exon/intron. We used “polish_clusters” to creates error corrected long reads based on the cluster definitions generated by “cluster_gff”. Finally, we used “collapse_partials” to collapse identical isoforms to obtain final set of unique, full-length, high-quality isoforms.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: eye

extract_protocol:
For short reads sequencing, total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies), then the concentration, quality and integrity of RNA were determined by NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
For long reads sequencing, total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), and the concentration, quality and integrity were determined by NanoDrop spectrophotometer (Thermo Scientific).
For short reads sequencing, sequencing libraries were generated according to the following steps. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. 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 and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).
For long reads sequencing, A total of 1ug RNA was prepared for cDNA libraries using cDNA-PCR Sequencing Kit (SQK-PCS109) according to the instructions of Nanopore Technologies (ONT). Defined PCR adaptors were directly added to both ends of the first-strand cDNA by reverse transcriptase. After 14-cycle of PCR by LongAmp Tag (Martin,  #21), the PCR products were subjected to ONT adaptor ligation using T4 DNA ligase (Martin,  #21). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flow-cells and were sequenced on PromethION platform.

value: eye

value: uveal melanoma cell


title: WT_E_rep2

source_name: Wild-type endometrial epithelial organoids, estrogen treatment, bulk RNA-seq

value: wild type


title: M384T


title: LR UM Case19


title: LR UM Case18


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2072_2817-iPSC-KS5-F1--pool--61-_AD015

value: human induced pluripotent stem cell


title: M367T


title: WT_E_rep1


title: L3B-RZ

first: Xinan

last: Yang

address: 900 East 57th Street, KCBD Room 5121

description: non oligodT


title: WT_noE_rep3

source_name: Wild-type endometrial epithelial organoids, no estrogen treatment, bulk RNA-seq


title: KO_noE_rep3


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2071_2816-iPSC-KS5-A2--pool--61-_AD014

value: HC #A or XY#A


title: M366T


title: WT_noE_rep2


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2070_2815-iPSC-KS5-A2--pool--61-_AD013


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2069_2814-iPSC-KS5-A2--pool--61-_AD012


title: WT_E_rep3


title: LR UM Case15


title: LR UM Case16


title: M389T


title: Dorsomedial hypothalamus 2

city: Dallas

first: Allan-Hermann

last: Pool

address: 6124 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequencing data were aligned to optimized pre-mRNA reference transcriptome (https://www.nature.com/articles/s41586-020-2821-8) and digital gene-cell matrices were generated with the 10x Genomics Cell Ranger v.6.0.0 count pipeline. The resulting scRNAseq data were analyzed in R (4.1.2) using Seurat (v.4.1.0.9007) as previously described (https://www.nature.com/articles/s41586-020-2821-8). Briefly, expression data were filtered to exclude cells with fewer than 1,000 unique transcripts as well as cells exhibiting more than 15% of mitochondrial transcripts. Female-specific marker Xist was used to determine sex origin of cells and validated by additional query of male-specific genes Ddx3y, Eif2s3y, Gm29650, Kdm5d, and Uty. We followed the standard Seurat workflow to identify transcriptomic celltypes and assigned cell class identities based on canonical cell-type markers: Ndrg4, Snap25, Eno2 and Tubb3 for neurons, Ntsr2, Gfap, Fabp7 for astrocytes, Slco1c1, Fn1, Slco1a4 and Cldn5 for endothelial cells, Fcer1g, Aif1 and C1gc for microglia and Mag, Mbp, Ugt8 and Mog for oligodendrocytes. We digitally extracted neuronal clusters from our dataset resulting in expression data for 10028 neurons that we used to establish an unbiased neuronal nomenclature for DMH.
Supplementary files format and content: Gene-cell matrix of extracted neurons from the DMH dataset. First column is gene names, first row is cell indexes.

source_name: Dorsomedial hypothalamus

extract_protocol: Single-cell RNA-seq data from mouse Dorsomedial Hypothalamus was generated as previously described (https://www.nature.com/articles/s41586-020-2821-8). Briefly, six 7.5-week-old C57BL6/J mice (3 male, 3 female per sample) were anaesthetized with isoflurane. Brains were rapidly extracted and dropped into ice-cold carbogenated NMDG-HEPES-ACSF. Brain sections (2 mm) containing DMH were cut with a razor blade on a stainless-steel brain matrix (51392, Stoelting) and transferred to a dissection dish on ice containing NMDG-HEPES-ACSF. DMH was bilaterally microdissected in ~700x700x350 µm tissue block. The tissue was aggregated in a collection tube on ice containing NMDG-HEPES-ACSF and 30 µM actinomycin D. For enzymatic tissue digestion, NMDG-HEPES-ACSF was replaced by trehalose-HEPES-ACSF containing papain (50 U/ml; P3125, Sigma Aldrich, pre-activated with 2.5 mM cysteine and a 30-min incubation at 34 °C and supplemented with 0.5 mM EDTA) and 15 µM actinomycin D. Extracted DMH tissue was incubated at room temperature with gentle carbogenation for 55 min. During enzymatic digestion the tissue was pipetted periodically every 10 min. At the end of enzymatic digestion, the medium was replaced with 200µl of room temperature trehalose-HEPES-ACSF containing 3 mg/ml ovomucoid inhibitor (OI-BSA,Worthington) 25 U/ml DNase I (90083, Thermo Scientific) and 15 µM actinomycin D and tissue was gently triturated into a uniform single-cell suspension with fire-polished glass Pasteur pipettes. The resulting cell suspension volume was brought up to 1 ml with trehaloseHEPES-ACSF with 3 mg/ml ovomucoid inhibitor and pipetted through a 40µm cell strainer. Single-cell suspension was centrifuged down at 300g for 5 min at 4 °C and the supernatant was replaced with 1 ml fresh ice-cold trehalose-HEPES-ACSF and the cell pellet was resuspended. Cells were pelleted again and resuspended in 100 µl of ice-cold resuspension-ACSF. Cell suspensions were kept on ice while cell densities were quantified with a hemocytometer and the final cell densities were verified to be in the range of 300–1,000 cells/µl. Cell suspension volumes estimated to retrieve ~10,000 single-cell transcriptomes were added to the 10x Genomics RT reaction mix and loaded to the 10X Next GEM Chip G (2000177, 10x Genomics) per the manufacturer’s protocol. We used the Chromium Next GEM Single Cell 3’ Reagents Kit v3.1 (1000128, 10x Genomics) and the Single Index Kit Set A (100213) to prepare Illumina sequencing libraries downstream of reverse transcription following the manufacturer’s protocol. Resulting scRNA-seq sequencing library was sequenced on an Illumina NovaSeq 6000 sequencers (paired-end 150).

value: Dorsomedial hypothalamus


title: M330T


title: Dorsomedial hypothalamus 1


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-1905_2795-iPSC-KS5-P-pool60_AD018

value: HC #C or XY#C


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-2073_2818-iPSC-KS5-F1--pool--61-_AD016


title: LR UM Case13


title: LR UM Case14


title: M326T


title: LR UM Case12


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-1904_2794-iPSC-KS5-P-pool60_AD016


title: LR UM Case17


title: M358T


title: Female, KO, rep2, GEX library [A4_399_GEX]

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: CA

address: 1975 Zonal Ave

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description: 10X Chromium multiome ATAC + gene expression kit

data_processing:
Sequencing reads were aligned to the mouse genome (mm10) with the Cell Ranger ARC software (version 2.0.0) on the University of Southern California High Performance Computiong Cluster.
Assembly: mm10
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Supplementary files format and content: Tab-separated file containing fragment information
Supplementary files format and content: Index of the tab-separated file

source_name: Kidney

extract_protocol:
Flash frozen kidney pieces were thawed on ice and minced into small pieces (<1mm) with a sterile razor blade and then dounced in Nuclei EZ Lysis Buffer (Sigma). The tissue was dounced 15X loose, filtered with a 200uM filter, and then 5X tight, incubated for 5 mins on ice, filtered through 40uM filter and spun down at 500G x 5min at 4°C in a swinging bucket centrifuge. Supernatant was removed and nuclei pellet resuspended in Nuclei EZ lysis buffer, incubated an additional 5 mins on ice and spin down again. The final pellet was resuspended in Nuclei Buffer provided in 10X Chromium Single Cell ATAC Library Kit v1.1 and passed through a pre-wetted 5uM filter. The targeted number of nuclei were ascertained by Trypan Blue hemocytometer count then transposed and loaded onto a GEM H Chip as per the manufacturer’s specifications. v1.1 (10x – PN:1000175) reagents and index plate were used to generate the snATACSeq libraries. Libraries were processed using 10X Genomics Manual CG000209 using 9 cycles for Sample Index PCR. Libraries were checked using Tapestation D5000 tapes before sending to BGI for PE 150 sequencing (DNBSEQ-G400).
snRNA-seq + snATAC-seq; 10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)

value: Kidney

value: Mus musculus

value: Kidney cells

value: Female

value: 10 weeks

tag: molecule type

value: nuclear polyA RNA


title: Female, KO, rep2, ATAC library [A4_399_ATAC]


title: M325T


title: iNeuron, RBM12 knockdown, Isoproterenol, rep3

description:
neuron.csv
KD_ISO_3

data_processing:
Quality control  using fastQC
Alignment of reads using STARaligner to the GRCh38 reference
Read count extraction using Subread/featureCounts (-T 16 -t exon)
Read count normalization and differential expression analysis using DESeq2
Assembly: GRCh38
Supplementary files format and content: comma-separated values file showing normalized counts from DESeq2 for each sample

source_name: human iPSC-derived neurons

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen, Cat. #74106) and NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs, Cat. #E7490). 1 ug RNA and 500 ng RNA were used as input for library generation for HEK293 and neurons, respectively.
NEBNext Ultra RNA Library prep Kit for Illumina or NEBNext Ulta II Directional RNA Library Prep Kit for Illumina were used according to the manufacturer's instructions.

treatment_protocol: 1 uM Isoproterenol for 1 hour for drug-treated cells, otherwise left untreated

value: human iPSC-derived neurons

value: human glutamatergic excitatory neurons

value: RBM12 CRISPR interference knockdown

tag: treatment

value: beta-2-adrenergic receptor induced (1 uM Isoproterenol)


title: M318T

value: breast carcinoma

value: tumor


title: LR UM Case10

institute: Shanghai Jiao Tong University

value: eye

value: uveal melanoma cell


title: WT_noE_rep1

value: Endometrial epithelial organoids

value: wild type

value: no estrogen


title: iNeuron, RBM12 knockdown, Isoproterenol, rep2

description:
neuron.csv
KD_ISO_2


title: Female, KO, rep1, ATAC library [A3_395_ATAC]

value: Kidney


title: M315T


title: Female, KO, rep1, GEX library [A3_395_GEX]

value: Mus musculus


title: LR UM Case9


title: LR UM Case11


title: M338T


title: iNeuron, RBM12 knockdown, Isoproterenol, rep1

description:
neuron.csv
KD_ISO_1


title: Female, WT, rep2, ATAC library [A2_397_ATAC]

value: Kidney cells

value: WT


title: iNeuron, RBM12 knockdown, no drug, rep3

description:
neuron.csv
KD_ND_3

value: no drug


title: M294T


title: iNeuron, RBM12 knockdown, no drug, rep2

description:
neuron.csv
KD_ND_2


title: LR UM Case6


title: Female, WT, rep2, GEX library [A2_397_GEX]

value: Female

value: 10 weeks

value: nuclear polyA RNA


title: Homo sapiens iPS XY,46 Bulk RNAseq M-21-1903_2793-iPSC-KS5-P-pool60_AD015

source_name: iPS

value: human induced pluripotent stem cell

value: HC #C or XY#C


title: M291T

source_name: tumor

value: breast carcinoma


title: Female, WT, rep1, ATAC library [A1_396_ATAC]


title: M290T

value: tumor


title: iNeuron, RBM12 knockdown, no drug, rep1

description:
neuron.csv
KD_ND_1

value: human iPSC-derived neurons

value: human glutamatergic excitatory neurons

value: RBM12 CRISPR interference knockdown


title: Male, KO, rep3, ATAC library [B6_199_ATAC]

value: Male


title: M284T


title: Female, WT, rep1, GEX library [A1_396_GEX]


title: LR UM Case4

value: eye

value: uveal melanoma cell


title: Male, KO, rep3, GEX library [B6_199_GEX]

value: Kidney

value: Mus musculus


title: M277T


title: iNeuron, WT, Isoproterenol, rep2

description:
neuron.csv
CTRL_ISO_2

value: WT

value: beta-2-adrenergic receptor induced (1 uM Isoproterenol)


title: LR UM Case3


title: M305T


title: iNeuron, WT, Isoproterenol, rep1

description:
neuron.csv
CTRL_ISO_1


title: PH-1: ΔFgSwc6 H3K27 me3 IP rep 2

first: SUN

last: Kewei

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Further, ChIP-enriched DNA with a monoclonal anti-H3K27 me3 were sequenced on an Illumina NovaSeq 6000,For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20. Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters. The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools. BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9). RPKM (Reads Per Kilobase per Million mapped reads) were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.
Assembly: ASM24013v3 (reference genome of F. graminearum strain PH-1)
Supplementary files format and content: BW

organism: Fusarium graminearum PH-1

source_name: Mycelium

extract_protocol: Fresh mycelia were cross-linked with 1% formaldehyde for 15 min and then stopped with 125 mM glycine. The cultures were ground with liquid nitrogen and resuspended in lysis buffer (250 mM, HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% deoxycholate, 10 mM DTT) and 1% protease inhibitor. The DNA was sheared into ~300 bp fragments with 20 pulses of 10 s with 20 s of resting at 35% amplitude (Qsonica*sonicator, Q125, Branson, USA). After centrifugation, the supernatant was diluted with 10 × ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl, pH 8.0, and 167 mM NaCl). Samples were pre-washed with 20 μl of protein A agarose (sc-2001, Santa Cruz, CA, USA) for 1 h at 4°C. Then immunoprecipitation was performed using a monoclonal anti-H3K27 me3 (39155, Active Motif, Shanghai, China), polyclonal anti-H2A.Z (ABclonal® Technology, Wuhan, China) or monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody together with protein A agarose (Santa Cruz, CA, USA). A mock sample was incubated with anti-IgG antibody (MA1-10406, Invitrogen-Thermo Fisher Scientific, Waltham, MA, USA). DNA was immunoprecipitated with ethanol after washing, eluting, reversing the cross-linking, and digesting with proteinase K.

value: Mycelium

value: FgSwc6 knockout

value: Day 2 of fresh mycelium

tag: antibody

value: H3K27 me3


title: Male, WT, rep3, ATAC library [B5_197_ATAC]

value: Kidney cells

value: 10 weeks


title: iNeuron, WT, no drug, rep3

description:
neuron.csv
CTRL_ND_3

value: no drug


title: LR UM Case7


title: M259T

value: breast carcinoma

value: tumor


title: Male, WT, rep3, GEX library [B5_197_GEX]

value: nuclear polyA RNA


title: M266T


title: PH-1: ΔFgSwc6 H3K27 me3 IP rep 1


title: M255T


title: iNeuron, WT, no drug, rep1

description:
neuron.csv
CTRL_ND_1

value: human iPSC-derived neurons

value: human glutamatergic excitatory neurons


title: LR UM Case5

value: eye

value: uveal melanoma cell


title: PH-1: ΔFgSwc6 H3K27 me3 Input rep 2


title: iNeuron, WT, no drug, rep2

description:
neuron.csv
CTRL_ND_2


title: M251T


title: iNeuron, WT, Isoproterenol, rep3

description:
neuron.csv
CTRL_ISO_3


title: Male, KO, rep2, ATAC library [B4_198_ATAC]

value: Kidney

value: Mus musculus

value: Male


title: Male, KO, rep2, GEX library [B4_198_GEX]


title: HEK293, RBM12 KO 2, no drug, rep3

description:
hek293.csv
KO2_ND_3

value: human embryonic kidney

value: RBM12 CRISPR knockout, guide 2


title: M250T


title: PH-1: ΔFgSwc2 H3K27 me3 IP rep 2

value: Mycelium

value: FgSwc2 knockout

value: Day 2 of fresh mycelium


title: Male, WT, rep2, ATAC library [B3_180_ATAC]

value: Kidney cells

value: WT

value: 10 weeks


title: PH-1: ΔFgSwc6 H3K27 me3 Input rep 1

value: FgSwc6 knockout


title: LR UM Case2


title: HEK293, RBM12 KO 2, no drug, rep2

description:
hek293.csv
KO2_ND_2

value: no drug


title: PH-1: ΔFgSwc2 H3K27 me3 IP rep 1

value: H3K27 me3


title: Male, WT, rep2, GEX library [B3_180_GEX]

value: nuclear polyA RNA


title: M234T

value: breast carcinoma

value: tumor


title: M235T


title: HEK293, RBM12 KO 2, no drug, rep1

description:
hek293.csv
KO2_ND_1


title: Male, KO, rep1, GEX library [B2_179_GEX]

value: Kidney


title: HEK293, RBM12 KO 1, no drug, rep2

description:
hek293.csv
KO1_ND_2

value: RBM12 CRISPR knockout, guide 1


title: M226T


title: PH-1: ΔFgSwc2 H3K27 me3 Input rep 2


title: Male, KO, rep1, ATAC library [B2_179_ATAC]

value: Mus musculus

value: Male


title: M233T


title: Male, WT, rep1, ATAC library [B1_100_ATAC]


title: PH-1: PH-1 H3K27 me3 IP rep 2


title: HEK293, RBM12 KO 1, no drug, rep3

description:
hek293.csv
KO1_ND_3

value: human embryonic kidney


title: HEK293, WT, no drug, rep7

description:
hek293.csv
CTRL_ND_7


title: HEK293, RBM12 KO 1, no drug, rep1

description:
hek293.csv
KO1_ND_1


title: M218T


title: M205T


title: Male, WT, rep1, GEX library [B1_100_GEX]


title: PH-1: PH-1 H3K27 me3 Input rep 2

value: Mycelium


title: PH-1: PH-1 H3K27 me3 IP rep 1


title: CMV, replicate1, scRNAseq

city: Hefei

first: Tingyue

last: Zhou

address: Huangshan road

institute: USTC

description: 10x Genomics

data_processing:
cell-ranger
Seurat
Single R
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: liver

extract_protocol:
Liver tissue was dissociated for single cell RNA sequencing. Viability enrichment was performed using the Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) as manufacturer's protocol. The cells were resuscitated to a concentration of 700-1200 cells/ul (viability≥85%) in a final solution of 1 x PBS + 0.04 % BSA prior to loading on the 10×Genomics Chromium platform.
10,000 cells were used to prepare scRNA-seq libraries. Chromium Single cell 3’ Library and Gel Bead Kit V3.1 (10× Genomics, PN1000268) was used to generate single cell gel beads in emulsion (GEM). After quality control, the libraries were sequenced on Illumina Novaseq 6000 platform in 150 bp pair-ended manner (Berry Genomics Corporation, Beijing, China).

value: liver

tag: strain

value: Infant

value: MCMV infection


title: HEK293, WT, no drug, rep5

description:
hek293.csv
CTRL_ND_5

value: WT


title: ctrl, replicate1, scRNAseq

description: 10x Genomics

value: Untreated


title: PH-1: PH-1 H3K27 me3 Input rep 1

value: Day 2 of fresh mycelium


title: M172T

tag: disease


title: M202T


title: HEK293, WT, no drug, rep4

description:
hek293.csv
CTRL_ND_4

value: no drug


title: HLE Fiber-seq

city: Seattle

middle: Ben

last: Stergachis

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

description: assembly: de novo genome assembly

data_processing:
CCS reads generated using CCS --hifi-kinetics (v6.4.0).
CCS reads aligned to the reference genome with pbmm2 -N1 (v1.9.0)
Subreads aligned to CCS reads using actc (v0.2.0).
ipdRatios generated for reach molecule using ipdSummary(v3.0).
primrose (v1.3.0) udentified per-molecule 5mCpG sites using CCS reads.
Custom scripts then used ipdRatio output to identify m6A sites using a Gaussian Mixture model.
Custom scripts then utilized per-molecule m6A calls to identify nucleosome footprints.
Supplementary files format and content: single-molecule Nucleosome calls, Methyltransferase Accesible Patch calls, m6A calls, and 5mC calls (CpG) in a bed12 format.
Supplementary files format and content: bam files containing alignment information for single molecules to appropriate reference genome.
Library strategy: Fiber-seq

organism: Hoolock leuconedys

source_name: HLE

extract_protocol:
DNA extracted using the Promega Wizard HMW DNA Extraction Kit A2920
PacBio SMRTbell library construction

value: HLE

value: Lymphoblastoid cell line

value: Eastern hoolock gibbon, female, Betty, Hoolock leuconedys (HLE) lymphoblastoid cell linenuclei treated with 200U Hia5 for 10min at 25C, 15kb shearing and pippin size selection


title: HEK293, WT, no drug, rep6

description:
hek293.csv
CTRL_ND_6


title: ctr_MEF

city: Houston

first: Lanlan

last: Shen

address: 1100 Bates Ave

institute: Baylor College of Medicine

data_processing:
The WGBS reads were mapped to mouse genome (mm10) using BSMAP 2.90 with default parameters.
The average methylation ratio of each CpG was calculated using “CAMDA” toolkit(https://github.com/JiejunShi/CAMDA).
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Mouse embryonic fibroblast

extract_protocol:
Genomic DNA from MEF cells was extracted using AllPrep DNA/RNA Mini Kit (QIAGEN).  500 ng genomic DNA  was used for bisulfite treatment and the construction of sequencing libraries.
Sonicated, adaptor-ligated DNA was treated with sodium bisulfite by the EZ DNA Methylation-Direct kit (Zymo Research). The bisulfite modified DNA was amplified (18 cycles) using adaptor-specific primers and fragments of 200-500 bp were isolated. The quantity and size distribution of libraries were determined using the Pico Green fluorescence assay and the Agilent 2100 Bioanalyzer, respectively.

value: Mouse embryonic fibroblast


title: PH-1: ΔFgSwc2 H3K27 me3 Input rep 1

value: FgSwc2 knockout


title: cis_MEF


title: HEK293, WT, no drug, rep3

description:
hek293.csv
CTRL_ND_3


title: M164T

data_processing:
Quality control and trimming of raw RNA sequencing data was performed using the fastp package v0.23.2. For annotation, reference transcriptome GENCODE v35 (GRCh38.p13) was used. Quantification of protein-coding transcripts via pseudoalignment was done using kallisto v0.48 with default settings. For correlation analyses, the count data were normalized to transcripts per million (TPM) and were log2 scaled
Assembly: GRCh38.p13
Supplementary files format and content: Tab/delimited text file (.tsv) contains TPM normalized values for each sample

extract_protocol:
Total RNA was extracted from tumor tissue using the TRIZOL reagent (Thermofisher) following the manufacturer’s protocol. The tissue was first pulverized with mortar and pestle under liquid nitrogen.
500 ng of total RNA was used for construction of RNA libraries. The cDNA libraries corresponding to mRNA were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s protocol. Samples with RIN>3.5 (n=58) were processed by the standard protocol, while samples with RIN<3.5 (n=9) were processed using the Low Quality RNA protocol. Quality of prepared libraries was checked by Bioanalyzer 2100 using High Sensitivity DNA kit (Agilent Technologies Inc., CA, USA) and quantity measured by qPCR using the KAPA Library Quantification Kit Illumina®Platforms (Roche, Switzerland) and by the Qubit instrument using the Qubit RNA HS Assay Kit (both ThermoFisher Scientific, MA, USA). The equimolar pool of prepared libraries was sequenced on the NextSeq 500 platform (Illumina Inc., CA, USA) using the High Output kit (1x75bp setting) and targeting 5-6 million reads per sample.

value: breast carcinoma

value: tumor


title: MP_KO_3

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

institute: Mayo Clinic Arizona

data_processing:
DNBSEQ-G50
Sequence reads were trimmed for adaptor sequence/low-quality sequence by the BGI Americas bioinformatics team.
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT. Clean reads were aligned to the reference genes using Bowtie2.
Read count extraction and normalization were performed by the BGI Americas bioinformatics team.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM, FPKM, Read Counts values for each Sample; it also shows log2 fold differences, P-values and Q-Values (FDR) between: TE KO/TE WT, MP KO/MP WT, TE KO/MP KO and TE WT/MP WT.

source_name: Spleen CD8 T cells, Panx1-KO MP, 7d post LCMV-Arm

extract_protocol:
RNA was extracted using the QIAgen RNeasy kit following manufacturer instructions.
RNA samples were submitted to BGI Americas, where libraries were constructed and sequence was done using the DNBSEQ-G50 platform.

treatment_protocol: gp33-tetramer+ CD8+ T cells were sorted from pooled spleens (n=5 mice per group per replicate) of WT or T cell-specific Panx1-KO mice (CD4-Cre and CD4-Cre Panx1fl/fl, respectively) at day 7 post-LCMV-Armstrong infection. From each mouse cohort, TE cells (KLRG1+CD127-) or MP cells (CD127+KLRG1-) cells were sorted.

value: Spleen

value: CD8 T cell

value: 7d post-LCMV Armstrong infection


title: MP_KO_2


title: M154T

last: Holý

address: Šrobárova 48/49


title: M130T


title: HEK293, WT, no drug, rep2

description:
hek293.csv
CTRL_ND_2

value: human embryonic kidney


title: MP_KO_1


title: HEK293, WT, no drug, rep1

description:
hek293.csv
CTRL_ND_1


title: M122T


title: replicate_6_AP1159_coT1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

source_name: Colon tumor

extract_protocol:
Adjacent mucosa were dissociated by 9mM EDTA for 1h, and then followed by TrypLE™ Express Enzyme (1X) (ThermoFisher Scientific) incubation (37°C, 5min) to dissociate into single cells. Colon tumor cells were dissociated using the Miltenyi Biotec MACS Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer instructions. Colon tumors and adjacent mucosa tissues were collected and processed on the same day for scRNA-seq.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Colon tumor

value: ApcMin/+; p16cis/cis

value: Male

value: 22 wks

tag: tumor size

value: Large tumor


title: replicate_5_AP1152_coT4

description: 10x Genomics

value: Female


title: SR UM Case20

city: Shanghai

value: eye

value: uveal melanoma cell


title: MP_WT_3

source_name: Spleen CD8 T cells, WT MP, 7d post LCMV-Arm


title: M111T


title: M098T


title: replicate_4_AP1152_coT3

description: 10x Genomics


title: MP_WT_2


title: SR UM Case19


title: M068T


title: MP_WT_1


title: replicate_2_AP11701_coT

description: 10x Genomics

value: 18 wks


title: SR UM Case18


title: TE_KO_3

source_name: Spleen CD8 T cells, Panx1-KO TE, 7d post LCMV-Arm