title: AC16, siMLF1, 2

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
Novagene used Illumina Novaseq 6000 platform for ATAC-seq
The clean reads were align to the reference genome sequnence using Bowtie2
Peak calling using Macs2 with default parameters
DiffBind (version 1.34.0) software was used for differential peak calculation, q value <= 0.05 was the threshold. The bigwig files were generated with Deeptools (version 3.4.3).
Assembly: NCBI, Homo_sapiens , GCF_000001405.39_GRCh38.p13
Supplementary files format and content: The bigwig files were generated with Deeptools (version 3.4.3).

growth_protocol: Cardiomyocyte AC16 cells were cultured in DMEM/F12 . DMEM/F12 supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 100 U/mL penicillin, and 100 μg/ml streptomycin.

extract_protocol:
About 50000 AC16 cells were lysed in ATAC-seq lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.5% NP-40) and centrifuged for 10 min at 4°C. Then, nuclei were spun at 1500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-01). After DNA purification with the MinElute kit, and the PCR was performed to amplify the library for 12 cycles and libraries were purified with the MinElute kit.
Amplified ATAC libraries were sequenced on the Illumina Novaseq 6000 platform.

treatment_protocol: Medium without FBS was replaced before transfection. Negative control siRNA and Mlf1 siRNA were transfected into AC16 cells at ~70% confluence using jetPRIME® (Polyplus-transfection, NY, USA). After 12 h of transfection, fresh complete medium was replaced.

value: cardiomyocyte


title: Pt11_Baseline

status: Public on Jan 29 2025

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing: Raw CEL files were imported in Transcriptome Analysis Console software version 4.0.2 and pre-processed using the gene-level signal space transformation – robust multiarray average (SST-RMA) method.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Pre-treatment HER2-positive breast cancer tumor core biopsy

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: Total RNA from FFPE tissue sections was extracted using Qiazol (Qiagen).

treatment_protocol: Neo-adjuvant chemotherapy (anthracycline-taxane) plus trastuzumab (T). All patients received chemotherapy and T administered at 3-week intervals for six cycles.

tag: patient

tag: timepoint

value: Baseline

value: decrease


title: AC16, siMLF1, 1

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: cell type

tag: treatment


title: F123 GAM library f123_0NP_GAM171108_H02_2_S112_R1_001

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
F123.GAM.nonphased.segregation.tables.zip
F123.GAM.phased.segregation.tables.zip
F123.nonphased.coseg.matrices.at100Kb.zip
F123.nonphased.npmi.matrices.at10Kb.zip
F123.nonphased.npmi.matrices.at250Kb.zip
F123.nonphased.npmi.matrices.at30Kb.zip
F123.nonphased.npmi.matrices.at50Kb.zip
F123.phased.coseg.matrices.at100Kb.zip
F123.phased.npmi.matrices.at30Kb.zip
F123.phased.npmi.matrices.at50Kb.zip

data_processing:
Sequenced reads from each GAM library were mapped to the mouse genome assembly GRCm38 (Dec. 2011, mm10) using bowtie2 with all default settings. All non-uniquely mapped reads, reads with mapping quality < 20 were filtered using the command “sed '/XS:/d' | samtools view -q 20 -F 4 -bS -”. PCR duplicates were removed with the “samtools rmdup” command. Samples were checked for contamination using fastq_screen. Number of nucleotides sequenced in each genomic bin was calculated using bedtools coverage command. Next, the optimal threshold between the sequencing noise and the signal to call positive windows was calculated as the lowest coverage per bin that gives the highest percent of clustered windows (windows that have a neighboring positive window on at-least one side) for each GAM sample in the dataset. Windows were called positive when the number of nucleotides covered by the reads is higher or equal to the optimal threshold. Each dataset was assessed for quality control by determining the percentage of orphan windows, number of uniquely mapped reads to the mouse genome, and cross-well contamination for every sample. 1NP samples that passed QC were merged into in-silico 3NPs at the level of positive windows. For good quality samples, we produced raw co-segregation, as well as normalized (NPMI) pair-wise chromatin contact matrices.
Assembly: mm10
Supplementary files format and content: Processed data files are raw GAM segregation tables, non-normalized pairwise cosegregation matrices and normalized NPMI matrices in tab-delimited format.
Library strategy: WGA

organism: Mus musculus

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from S129/Jae and Cast) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta-mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells. As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Fixation of F123 mESC was performed as described previously (Branco and Pombo, 2006). Briefly, cells were grown to 70 % confluency, media was removed, and cells were fixed in 4% and 8% paraformaldehyde in 250 mM HEPES-NaOH (pH 7.6; 10 min and 2 h, respectively), gently scrapped, and softly pelleted and embedded in saturated 2.1 M sucrose in PBS and frozen in liquid nitrogen on copper sample holders. Ultrathin cryosections were cut with a glass knife using an ultracryomicrotome (Leica Biosystems, EM UC7) at ~230 nm thickness, and transferred to PEN membrane steel frame slides 4.0 µm (Leica Microsystems, 11600289) for laser microdissection. Before laser microdissection, cryosections were washed in sterile-filtered 1x PBS (3 times, 5 min each), sterile-filtered H2O (3 times, 5 min each), and stained with sterile-filtered 1 % (w/v) cresyl violet (Sigma-Aldrich, C5042) in H2O for 10 min, followed by 2 washes with H2O (30 s each).  Individual NPs were isolated from the cryosection by laser microdissection using a laser microdissection microscope (Leica Microsystems, LMD7000). Cut NPs were collected in a PCR Cap Strip filled with opaque adhesive material (Carl Zeiss Microscopy, 415190-9161-000). For each collection day, 1 or 2 caps were left empty and taken through the whole genome amplification (WGA) and sequencing process as a negative control for quality control purposes.
Whole Genome Amplification (WGA) was performed as described previously (Winick-Ng et al, 2021) with minor modifications. Briefly, DNA was extracted from NPs at 60oC in the lysis buffer (20mM Tris-HCl pH 8.0, 1.4 mM EDTA, 560 mM guanidinium-HCl, 3.5% Tween-20, 0.35% Triton X-100) containing 0.75 units/ml Qiagen protease (Qiagen, 19155). After 24h of DNA extraction, the protease was heat inactivated at 75oC for 30 min and the extracted DNA was amplified via two rounds of PCR. At-first quasi-linear amplification was performed with random hexamer GAT-7N  primers with an adaptor sequence. The lysis buffer containing the extracted genomic DNA was mixed with 2x DeepVent mix buffer (2x Thermo polymerase buffer (10x), 400 µm dNTPs, 4 mM MgSO4 in ultrapure DNase free water), 0.5 µM GAT-7N primers (5′- GTG AGT GAT GGT TGA GGT AGT GTG GAG NNN NNN N) and 2 units/µl DeepVent® (exo-) DNA polymerase (New England Biolabs, M0259L) and incubated for 11 cycles in the BioRad thermocycler. The second exponential PCR amplification was performed in presence of 1x DeepVent mix, 10 mM dNTPs, 0.4 µM GAM-COM primers (5′-GTG AGT GAT GGT TGA GGT AGT GTG GAG) and 2 units/µl DeepVent (exo-) DNA polymerase in the programmable thermal cycler for 26 cycles.
After whole genome amplification, the DNA WGA product was purified withSPRI beads (1.7x) The DNA concentration of each sample was quantified using the Quant-iT® PicoGreen dsDNA assay kit (Invitrogen #P7589). Genomic sequencing library was prepared from 1ng of purified DNA using the Illumina Nextera XT library preparation kit (Illumina #FC-131-1096), following the manufacturer’s instructions or with reduce to 20% volume of reagents. After the library preparation, DNA was again purified with in-house SPRI beads (1.7x) and equal amounts of DNA from each sample was pooled together (up to 196 samples) for the sequencing. The final pool of libraries was additionally purified two more times with SPRI beads (1.7x) and analyzed using DNA High Sensitivity on-chip electrophoresis on an Agilent 2100 Bioanalyzer. The samples were sequenced on Illumina NextSeq500 machine as single-end 75 bp reads, according to manufacturer’s instructions.

value: mouse embryonic stem cells

tag: genotype

value: Hybrid F1 S129/Jae and Cast

tag: Sex

value: male


title: 2xdbp1 r1 mrna

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

country: USA

institute: UC Berkeley

description:
GBEP008A
mRNAseq

library_source: transcriptomic

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint or mRNA reads were assigned to one genomic position based on a-site analysis of fragment length distribution.  Alignments of raw reads to SK1 genome. mRNA seq reads were processed similarly except not assigned to one genomic position and counts were rather distribute over the entire read.
Assembly: SK1 genome (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary files format and content: RPKM values

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: treatment: cells were grown in YEPD with aeration at 30C and harvested at OD 0.6

extract_protocol:
Cells were mixermilled with frozen buffer (20mM Tris pH8, 140mM KCl, 1.5mM MgCl2, 100ug/ml cycloheximide, 1% Trition X-100), buffer was thawed, spun at 3Kg  for 5 minutes, then supernatatant was spun at 20Kg for 10 minutes.
As described in Powers and Brar, 2021, using linker ligation, circularization
size selection of 28-31 nt for ribosome footprints, 50nt for mRNA, dephosphorylation, linker ligation, RT, circularization, PCR

treatment_protocol: Cells were pretreated for 1 minute with 100uM cyclohexamide

value: four copies of DBP1 under DED1 regulatory regions


title: AC16, siNeg, 2

value: siRNA Control


title: 26591_R2_FP_37exp

description:
GBEP006L
ribosome footprints

library_source: other

molecule: other

growth_protocol: treatment: cells were grown in YEPD with aeration at either 30C or 37C and harvested at OD 0.6

value: DBP1 under DED1 regulatory regions


title: Pt12_Baseline


title: F123 GAM library f123_0NP_GAM171024_H04_1_S32_R1_001


title: AC16, siNeg, 1


title: Pt31_Post

source_name: Post-neodjuvant therapy HER2-positive breast cancer tumor surgical sample

value: Post

value: increase


title: 26662_R2_FP_37exp

description:
GBEP006K
ribosome footprints

value: DED1 under DED1 regulatory regions


title: F123 GAM library f123_0NP_GAM171024_E02_1_S13_R1_001


title: ChIP-seq for RNAPII S7p in mESC F123

data_processing:
Raw ChIP-seq reads were mapped to the N-masked genome using default parameters of bowtie2 (version 2.3.4.3) (10.1038/nmeth.1923). Genome-wide enriched regions for RNAPII-S5p, RNAPII-S7p, and H3K27me3 were identified with Bayesian Change-point Model (BCP) peak-finder (Xing et al, 2012, default settings).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes coordinates of genome-wide enriched regions for RNAPII-S5p, RNAPII-S7p, and H3K27me3.

growth_protocol: Mouse F123 ESCs (a male, hybrid cell line, derived from S129/Jae and Cast) (Gribnau et al., 2003) were cultured in a layer of mitotically inactivated feeder murine embryonic fibroblasts under standard conditions (DMEM, supplemented with 15 % KSR, 1x Glutamax, 10 mM non-essential amino acids, 50 µM beta- mercaptoethanol , 1000 U / ml LIF). Before harvesting, mESCs were passaged onto feeder free 0.1% gelatin coated plates for at least 2 passages to remove feeder cells.As feeder-removal results in reduced levels of LIF in the culture, the LIF concentration in the media was doubled when the cells were in feeder-free culture conditions. Cells were harvested after ~ 48 h at 70 – 80 % confluency.

extract_protocol:
Chromatin immunoprecipitation experiments were performed as previously described (10.1038/ncb166; 10.1016/j.stem.2011.12.017; 10.15252/msb.20177754). S5p form of RNAPII was detected with mouse monoclonal antibody CTD4H8 clone (BioLegend, Cat# 904001); S7p form of RNAPII was detected with rat monoclonal antibody 4E12 clone (Chapman et al, 2007; kindly provided by Dirk Eick); Polycomb mark H3K27me3 was detected with rabbit antibodies (Millipore, Cat# 07-449).
ChIP-seq libraries were prepared from 10 ng of immunoprecipitated DNA using TruSeq ChIP Library Preparation Kit  (Illumina, IP-202-1012) according to the manufacture instructions with minor modifications. Library size was assessed before high-throughput sequencing by Bioanalyzer (Agilent) using the High Sensitivity DNA analysis kit (Agilent, Cat# 5067-4626). ChIP-seq libraries were sequenced 75bp single-end using Illumina NextSeq550/500, according to the manufacturer’s instructions.

tag: chip antibodies

value: RNAPII-S7p 4E12


title: Pt13_Post


title: Pt11_Post


title: 26591_R1_FP_37exp

description:
GBEP006H
ribosome footprints


title: Pt13_Baseline


title: ChIP-seq for RNAPII S5p in mESC F123

value: RNAPII-S5p CTD4H8


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by RA+NEN diet (Bio-replicate 1)

city: Palo Alto

first: Haowen

last: Jiang

state: CA

address: 269 Campus Dr

institute: Stanford University

description:
Library name: RN1
Pipseq

library_source: transcriptomic single cell

data_processing:
The raw single-cell RNA sequencing (scRNA-seq) FASTQ data were processed using Pipseeker(Fluent Bioscience) and Cell Ranger (10x Genomics) to generate gene expression count matrices and unspliced read counts
Assembly: hg38
Supplementary files format and content: Tap seperate values files and value files

source_name: Neuroblastoma

extract_protocol:
Tumors were dissociated using the Tumor Dissociation Kit (Miltenyi; #130-095-929) in combination with the gentleMACS™ Octo Dissociator (Miltenyi; #130-096-427). The resulting single-cell suspensions were prepared for library construction using the PIPseq™ V T10 3’ Single Cell RNA Kit.
The PIPseq™ T20 3ʹ Single Cell RNA Kit v4.0PLUS protocol begins with isolating single cells and lysing them in the provided buffer. Poly(A)+ RNA is captured using oligo(dT) primers with unique molecular identifiers (UMIs), followed by reverse transcription and template switching to generate full-length cDNA. The cDNA is amplified via PCR, purified using magnetic beads, and fragmented with a transposase for library preparation. Unique dual indices (UDIs) are added during a final limited-cycle PCR to enable multiplexing. Libraries are then purified, quality-checked using a bioanalyzer or TapeStation, and quantified by Qubit or qPCR before sequencing on an Illumina platform.

treatment_protocol: The mice were provided with one of the following diets obtained from Research Diets, Inc.: a control diet (#D11112201), a diet containing 83.37 ppm RA (#D22040408), a diet with 2,000 ppm NEN (#D20101601)45,79,80, or a combination diet of RA and NEN (#D22040411). The animals were euthanized when the tumor volume exceeded 1,000 mm^3.

tag: tissue

value: Neuroblastoma

value: All cell type in Xenograft

value: WT

value: RA+NEN

tag: batch


title: Pt16_Post


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by NEN diet (Bio-replicate 2)

description:
Library name: N2
Pipseq

value: NEN


title: 26591_R3_FP_30Cexp

description:
GBEP006F
ribosome footprints


title: Pt12_Post

value: decrease


title: ChIP-seq for H3K27me3 mark in mESC F123

value: mouse embryonic stem cells


title: 26662_R3_FP_30Cexp

description:
GBEP006E
ribosome footprints


title: Pt14_Post


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by NEN diet (Bio-replicate 1)

description:
Library name: N1
Pipseq


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by RA diet (Bio-replicate 2)

description:
Library name: R2
Pipseq

value: RA


title: eCLAP_KRBP72_mito_genome_rep3

city: Buffalo

first: Ashutosh

last: Dubey

state: New York

address: 955 Main Street

department: Microbiology & Immunology

institute: University at Buffalo

description: NextSeq 550 v2.5

data_processing:
*library strategy: iCLIP
Demultiplexed FASTQ files were sequentially processed using fastx_toolkit and CLIP Tool Kit (CTK).
The reads were first quality filtered and identical reads were collapsed to reduce redundancy and increase computational efficiency.
Then, barcode and adapter sequences were trimmed from 5’ and 3’ end of the reads.
Processed reads at least 16nt long were kept for alignment.
Processed reads were mapped to a curated T. brucei mitochondrial genome using Bowtie2 allowing up to one mismatch.
The alignment results in SAM format were converted to BAM format using Samtools, which were then used as inputs for BEDTools to generate mapped read files in BED format and mapped read coverage files in BEDGraph format.
Assembly: TriTrypDB-46 TREU927 genome that was modified to extend each gene record to the 5' end of the subsequent gene.
Supplementary files format and content: bedgraph

organism: Trypanosoma brucei brucei

growth_protocol: Cells were grown in at 27 ºC in SDM-79 medium supplemented with 10% fetal bovine serum

extract_protocol:
KRBP72-MHT tagged PCF cells were grown to ~1x107 cells/mL, and 3x109 cells were collected per experiment and three biological experiments were performed. Cells were pelleted at 5000g for 10 min, washed with ice-cold PBS containing 6 mM sucrose, and resuspended in 32 mL of the same buffer and centrifuged again. Cells were resuspended in in 50 mL SM media without FBS, distributed into two prechilled 10 cm Petri dishes, and crosslinked by irradiation at 800 mJ/cm2  twice using a Stratalinker Crosslinker. Post-crosslinking, cells were pelleted, washed with PBS, snap-frozen in liquid nitrogen, and stored at −80°C. Crosslinked cells were centrifuged at 6000g for 10 min at 4°C, resuspended in DTE buffer (1 mM Tris (pH 8), 1 mM EDTA, Complete protease inhibitor cocktail, RNaseOUT), homogenized on ice, and mixed with 60% sucrose before centrifuging at 15,800g for 10 min. The pellet was resuspended in  7.5 mL STM buffer (250 mM sucrose , 20 mM Tris (pH 8), 2 mM MgCl2, 0.2 mM CaCl2) with DNase I and incubated on ice for 1 hour, followed by the addition of 7.5 mL STE buffer (250 mM sucrose, 20 mM Tris (pH 8), 10 mM EDTA) and centrifugation at 13,000 rpm. The pellet was flash-frozen in liquid nitrogen and stored at -80°C. For lysis, the pellet was resuspended in lysis buffer (50 mM Tris (pH 8), 150 mM NaCl, 0.5% NP-40, 1% Triton X-100, Complete protease inhibitor cocktail, RNase Inhibitor), rotated at room temperature for 20 min, centrifuged at 13,000 rpm, and the supernatant was collected. For RNase treatment, reactions in 1 mL volume included DNase TURBO, 1M CaCl2, and RNase I at specified dilutions, incubated at 37°C in a thermomixer at 1500 rpm for 5 min, followed by termination with EDTA and RNase inhibitor. For immunoprecipitation, nickel-NTA agarose beads (Invitrogen) were equilibrated in binding buffer, added to the lysate, rocked at 4°C for 2 hours, washed with N150 buffer, and incubated with denaturation buffer (50 mM Tris (pH 8), 150 mM NaCl, 0.5% NP-40, 8M Urea with Complete protease inhibitor cocktail). Beads were washed, then resuspended in CIAP buffer with CIAP for 20 min at 37°C, washed with PNK buffer, and resuspended in PNK buffer with 32P-[gama-ATP] and T4 PNK for 30 min at 37°C. After adding 1 mM ATP and incubating, beads were washed, resuspended in SDS loading buffer, boiled, and the supernatant was loaded onto an SDS-PAGE gel for Western blotting, with the membrane exposed to a phosphor screen before antibody blotting against the myc tag.
eCLIP libraries were prepared according to the RBP-eCLIP kit v1.01R (Eclipse Bioinnovations) protocol with modifications. Specifically, 100 µL of His-tag isolation Dynabeads® (Thermo Fisher Scientific) were employed for immunoprecipitation, bypassing the need for magnetic beads conjugated to antibodies. The protocol was further streamlined by omitting size-matched input processing and gel purification post-AMPure PCR cleanup. Library quality was assessed using an Agilent Bioanalyzer,followed by single-end sequencing (75 cycles) on an Illumina NextSeq 550 v2.5 (High Output)at the CWRU Genomics Core.

treatment_protocol: Cells were treated with doxycycline (4µg/ml) for RNAi as well as for KRBP72 WT,RR-AA AND K-A varainats

value: procyclic


title: Pt17_Post


title: 26591_R2_FP_30Cexp

description:
GBEP006D
ribosome footprints


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by RA diet (Bio-replicate 1)

description:
Library name: R1
Pipseq


title: Pt18_Post


title: 26662_R2_FP_30Cexp

description:
GBEP006C
ribosome footprints


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by RA+NEN diet (Bio-replicate 2)

description:
Library name: RN2
Pipseq


title: Pt17_Baseline

value: Baseline


title: 26662_R1_FP_37exp

description:
GBEP006G
ribosome footprints


title: eCLAP_KRBP72_mito_genome_rep1

description: NextSeq 550 v2.5


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by CTRL diet (Bio-replicate 2)

description:
Library name: C2
Pipseq

value: CTRL


title: ASCs, chondro differentiation, 30 day, biol rep 3

city: Poznań

first: Maurycy

last: Jankowski

address: Rokietnicka 7

department: Wielkopolska Center of Digital Medicine

country: Poland

institute: Poznan University of Medical Sciences

data_processing:
Demultiplexing of the sequencing reads was performed using bcl2fastq (v. 2.20), with adapters trimmed with Skewer (v. 0.2.2)
The raw counts obtained from the initial analysis contained the numbers of reads assigned to particular geneIDs using the org.cf.db function of the Bioconductor (v3.18). These datasets were subjected to normalization using the DESeq2 package (v. 1.42.1) in R (v. 4.3.2).
Assembly: The trimmed raw reads were aligned to the CanFam3.1 canine genome using STAR
Supplementary files format and content: a .tsv file containing the raw counts used in all further analysis of the RNAseq expression data.

organism: Canis lupus familiaris

source_name: adipose tissue

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium—high glucose (DMEM, Sigma-Aldrich, Saint Louis, MO, USA), supplemented with 10% FBS (Sigma-Aldrich, Saint Louis, MO, USA), 4 mM of L-glutamine (Sigma-Aldrich, Saint Louis, MO, USA) and 1× antibiotic-antimycotic solution (A5955, Sigma-Aldrich, Saint Louis, MO, USA).

extract_protocol:
The cells directed for RNA isolation were detached from cultures using 1× Trypsin solution and placed in 1mL of TRIzol (Thermo-Fischer Scientific, Waltham, MA, USA). The samples were then frozen at −80°C. The isolation of RNA was conducted using the TRIzol Plus Purification KIT (12183555, Thermo-Fischer Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.
The cDNA library used for the subsequent analysis was prepared from 100 ng of RNA per sample using TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA)

treatment_protocol: The cells were differentiated for 14 days (osteoblast differentiation and late control) or 30 days (chondrocyte differentiation). The differentiation media used were CN411D-250 for ostegenic differentiation and CN411D-250  for chondrocyte differentiation (both Cell Applications, Inc., San Diego, CA, USA).

value: adipose tissue

value: mesenchymal stem cells

tag: time

value: 30 day

value: chondrogenic differentiation


title: Pt15_Post

value: Post


title: Neuroblastoma xenograft derived from SK-N-BE(2) cells treated by CTRL diet (Bio-replicate 1)

description:
Library name: C1
Pipseq


title: ASCs, chondro differentiation, 30 day, biol rep 2


title: Pt30_Post

value: increase


title: 26591_R1_FP_30Cexp

description:
GBEP006B
ribosome footprints

value: DBP1 under DED1 regulatory regions


title: ASCs, chondro differentiation, 30 day, biol rep 1


title: DMSO_6h_637

city: New york

first: Yurii

last: Chinenov

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
Read quality filtering and adapter trimming were performed with fastP. Filtered reads were mapped to the mouse genome (mm10) or human genome (hg38) with the STAR aligner (2.7.0) and exonic reads were counted against GENCODE release 27 annotation with featureCount  sing a customised pipeline available at https://gitlab.com/hssgenomics/pipelines/RNAseq.
Differential gene expression analysis was performed with edgeR(3.38.4, ) using quasi-likelihood framework. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. P values were adjusted to correct for multiple testing using the Benhamini-Hochberg FDR procedure.
Assembly: mm10 or hg38
Supplementary files format and content: edgeR_DEGs_2024-08-08.xlsx excel file with the results of differential analysis and data normalization/transformation

source_name: Synovial tissues from Rheumatoid arthritis patients

growth_protocol: 3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial tissue was obtained from patients consented into the HSS FLARE study (IRB no. 2014–233). De-identified 3x3 mm synovial biopsy specimens were collected from patients undergoing synovectomy and cryopreserved in Cryostor CS10 (Sigma-Aldrich). Cryopreserved synovial tissues were digested with Liberase TL (100 μg/ml, Roche) and DNAase I (100 μg/ml, NEB) for 15 min, single cells were separated using 70-μm cell strainers and resuspended in RBC lysis buffer for 3’ before plating in RPMI 1640 - 10% FBS - 1% glutamine in 96-well plates at 2 x 105 viable cells/well.

extract_protocol:
Total RNA was isolated from cells with RNeasy Plus micro kit (Qiagen)
The integrity of total RNA samples was evaluated with BioAnalyzer 2100 system (Agilent). Sequencing compatible libraries are prepared with NEBNext Ultra II RNA Kits (NEB) and NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs (NEB) following instructions from manufacturer. In brief, total RNA was poly(A)-enriched, fragmented, and reverse transcribed to cDNA. cDNA were ligated with adaptors and indexes. Sequencing compatible libraries were then quality-controlled with BioAnalyzer 2100 system (Agilent) and sequenced

treatment_protocol: 3. YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients: Synovial cell suspensions were prepared from deidentified synovial tissue samples collected from RA patients, placed in culture and treated  YKL-5-124 (250 nm) for 6 hours

value: primary

value: Synovial single-cell suspensions

tag: age

value: unknown

value: Female


title: YKL_6h_637

description: YKL-treated synovial single-cell suspensions from Rheumatoid arthritis patients

value: Synovial tissues from Rheumatoid arthritis patients


title: eCLAP_KRBP72_mito_genome_rep2

description: NextSeq 550 v2.5


title: 26591_R2_mRNA_37exp

description:
GBEP005L
mRNAseq


title: Pt19_Baseline


title: Pt20_Baseline


title: ASCs, osteo differentiation, 14 day, biol rep 2

value: 14 day

value: osteogenic differentiation


title: ASCs, osteo differentiation, 14 day, biol rep 3


title: 26662_R2_mRNA_37exp

description:
GBEP005K
mRNAseq

value: DED1 under DED1 regulatory regions


title: 26591_R1_mRNA_37exp

description:
GBEP005H
mRNAseq


title: 26662_R1_FP_30Cexp

description:
GBEP006A
ribosome footprints


title: Pt15_Baseline

value: Baseline

value: decrease


title: ASCs, osteo differentiation, 14 day, biol rep 1

value: adipose tissue


title: DMSO_6h_635


title: 26662_R1_mRNA_37exp

description:
GBEP005G
mRNAseq


title: ASCs, late control, 14 day, biol rep 3

value: mesenchymal stem cells

value: unsupplemented control


title: 26591_R3_mRNA_30Cexp

description:
GBEP005F
mRNAseq


title: YKL_6h_614


title: DMSO_6h_614


title: Pt29_Baseline


title: 26662_R3_mRNA_30Cexp

description:
GBEP005E
mRNAseq


title: ASCs, late control, 14 day, biol rep 2


title: YKL_6h_527


title: Pt30_Baseline


title: YKL_6h_635


title: ASCs, late control, 14 day, biol rep 1


title: 26591_R2_mRNA_30Cexp

description:
GBEP005D
mRNAseq


title: DMSO_6h_527


title: Pt19_Post


title: ASCs, early control, 1 day, biol rep 3

value: 1 day


title: ASCs, early control, 1 day, biol rep 2


title: 26662_R2_mRNA_30Cexp

description:
GBEP005C
mRNAseq


title: 26591_R1_mRNA_30Cexp

description:
GBEP005B
mRNAseq


title: Pt18_Baseline


title: Pt14_Baseline


title: ASCs, early control, 1 day, biol rep 1


title: EMS EXO 03

status: Public on Jan 28 2025

city: China

first: Yuan

last: Zhu

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

data_processing:
In this project, DNBSEQ platform was used to measure 6 samples, and each sample produced 28.8M data on average. The average comparison rate of samples to genomes was 15.82%. A total of 363 miRNAs were detected.
Sequencing platform: DNBSEQ  Sequencing length: SE50  The original data of sequencing includes low quality, contaminated connectors and high content of unknown base N, which need to be removed before data analysis to ensure the reliability of the results. The quality indicators of filtered reads are shown in the filtered reads quality statistics table. The statistical diagram of filtered components of the original data, the distribution of base content and the quality distribution are shown in the distribution diagram of base content and the distribution diagram of base quality of Clean reads.
After obtaining clean reads, we use Bowtie2 to align clean reads to the reference genome sequence. The comparison results are as follows. In addition, we provide the bam format file of Reads' genome comparison results, which can be visually viewed at different scales using the IGV (Integrated Genomics Viewer) tool.
Read count extraction and normalization were performed using BGISEQ-500 platform (BGI-Shenzhen, China)
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping. The software miRDeep2 was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs. RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference.
Genome_build: GCF_000001405.39_GRCh38.p13

source_name: ovarian endometriotic stromal cell

extract_protocol:
Use the 200ng-1μg of RNA sample，then separate RNA segment of different size by PAGE gel, select 18-30nt(14-30 ssRNA Ladder Marker，TAKARA)stripe and recycle;
Adaptor ligation:Prepare connection 3’adaptor system (Reaction condition:70°C for 2min; 25°C for 2h);Secondly add RT-Primer, (Reaction condition: 65°C for 15min;ramp to 4°C at a rate of 0.3°C/sec);Thirdly add 5’adaptor mix system(Reaction condition:70°C for 2min; 25°C for 1h);  RT -PCR:Prepare First Strand Master Mix and Super Script II (Invitrogen) reverse transcription (Reaction condition:42°C for 1h;70°C for 15min);Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments (Reaction condition:95°C for 3min;15-18 cycles of(98°C for 20s，56°C for 15s，72°C for 15s);72°C for 10min;4°C hold) ;  Purify PCR products:Then the PCR products were purified with PAGE gel，dissolve the recylced products in EB solution.  2.3 Circularization  The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.  2.4 Library quality control  Library was validating on the Agilent Technologies 2100 bioanalyzer.

value: ovarian endometriotic stromal cell

value: endometrial stromal cell exosome

value: WT


title: pituitary

city: wuhan

first: xiangtong

last: zeng

address: shizishan street

institute: Huazhong Agricultural University

data_processing:
After that the raw sequencing data were processed by Fastp firstly to trim primer sequence and eliminate low-quality bases. Subsequently, SeekOneTools was used to preprocess sequencing data and align to GRCm38 in order to obtain gene expression matrix. For further analysis of scRNA-seq data, R package Seurat (version 4.3.0.1)71 and Harmony (version 0.1.1)72 were used for filtering, data normalization, dimensionality reduction, clustering and further analysis of the single-cell RNA-seq data.
Assembly: PRJNA745278
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Ctenopharyngodon idella

source_name: pituitary

extract_protocol:
Tissues were washed in ice-cold Minimum Essential Medium and dissociated using trypsin, ethylene diamine tetraacetic acid（EDTA） and DNase II. After cell counting, fresh cells were washed twice in the NeuroGro medium (BasalMedia) and then resuspended at 1 106 cells per ml in PBS. Then added to the sample well of the SeekOne® DD Chip S3 (Chip S3). Following this, Barcoded Hydrogel Beads (BHBs) and partitioning oil were then added separately to their respective wells within Chip S3. Once emulsion droplets were generated, reverse transcription was performed at a temperature of 42℃ for 90 minutes, followed by inactivation at 85℃ for 5 minutes. The cDNA was then extracted from the broken droplets and amplified by PCR reactions. The resulting amplified cDNA product underwent a series of steps including purification, fragmentation, end repair, A-tailing, and ligation to sequencing adaptors. Finally, indexed PCR was performed to amplify the DNA, which represented the 3’ polyA region of the expressing genes, including Cell Barcode and Unique Molecular Index.
The indexed sequencing libraries were purified using SPRI beads and quantified by quantitative PCR (KAPA Biosystems KK4824). The libraries were then sequenced either on either an Illumina NovaSeq 6000 platform with PE150 read length or a DNBSEQ-T7 platform with PE150 read length.

value: pituitary

value: pituitary cells


title: EMS EXO 02


title: CTL EXO 03

source_name: endometrial stromal cell

value: endometrial stromal cell


title: EMS EXO 01


title: Pt6_Post

value: Post

value: increase


title: F123 GAM library f123_0NP_GAM180117_H06_2_S144_R1_001

value: mouse embryonic stem cells

value: Hybrid F1 S129/Jae and Cast

value: male


title: Hy

city: Wuhan

first: Hangyu

last: Li

state: 湖北省

address: No.1,Shizishan Street

source_name: hypothalamus

value: hypothalamus

value: hypothalamu cells


title: Pt16_Baseline

value: Baseline


title: 26662_R1_mRNA_30Cexp

description:
GBEP005A
mRNAseq

value: DED1 under DED1 regulatory regions


title: Pt29_Post


title: Pt20_Post


title: CTL EXO 01


title: VprBP1KD3

city: Los Angeles

first: Yonghwan

last: Shin

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to mm38 - GENCODE Genes - release 40 using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: mm10
Supplementary files format and content: txt file type

source_name: BMDM

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: BMDM

value: Bone-marrow-derived macrophage

value: VprBP1 Knockdown


title: VprBP1KD2


title: VprBP1KD1


title: Control2


title: Control3


title: Jurkat_mock_rep1

city: Nanjing

first: Benquan

last: Liu

address: 639 Longmian Avenue, Jiangning District

institute: China Pharmaceutical University

description: Jurkat cells with vector control that do not express HBZ

hyb_protocol: Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).

scan_protocol: Scanning procedures were carried out as described by Affymetrix, Santa Clara.

data_processing: RMA normalization and probe summarization was carried out on the human specific and control probe sets only.

label: biotin

source_name: Vector control Jurkat cells without HBZ expression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Two stable cell lines are grown in RPMI-1640 supplemented with 10% FBS, penicillin (100 U/mL), and streptomycin (100 μg/mL).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 800 μg/ml of G418 was added to the culture medium to screen for successfully constructed stable cells.

value: T lymphoblast

tag: tumor

value: acute T cell leukemia

tag: gender


title: Jurkat_HBZ_rep1

description: Jurkat cells that can stably express HBZ

source_name: Jurkat cells stably expressing HBZ


title: Control1

value: WT


title: moto_homozygote_5

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

description: small RNA-Seq of moto-/- testis, replicate 5

data_processing:
Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2.
The raw NGS reads in FastQ format were cleaned from partial 3’ adapter sequences using Flexbar v.2.4 using parameters: -m 18 -ao 10 -as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Read mapping to the Danio rerio reference genome (Zv9/danRer7 build from Illumina iGenomes) was carried out using Bowtie v.0.12.8 with parameters: -n 0 -e 80 -l 18 -y --best --nomaqround.
All mapped reads in the piRNA range 24-32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter -minlen 24 -maxlen 32.
Transposon annotation for zebrafish DNA, LTR, LINE and SINE elements was derived from the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables - Zv9/danRer7 RepeatMasker track). The 24-32nt reads mapping in sense or antisense orientation to DNA, LTR, LINE and SINE transposon elements (2446490 genomic loci with 967 unique names) were summarised per meta-feature (transposon type) using Subread featureCounts v.1.5.0 and options: -M -F SAF -s 1 (for sense-mapping reads) and -M -F SAF -s 2 (for antisense-mapping reads).

Genome_build: Zv9 (danRer7)
Supplementary_files_format_and_content: Tab-delimited table with sense- and antisense-mapping read counts summarised per transposon type.

organism: Danio rerio

source_name: testis

extract_protocol:
Testes from moto+/- and moto-/- zebrafish were removed and total RNA was isolated using Trizol reagent (Thermo Fisher Scientific).
RNAs smaller than 40nt were isolated using a 15% TBE-Urea polyacrylamide gel (BioRad), and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) as recommended by the manufacturer (protocol version 2.0 8/13), with 14 PCR cycles for library amplification. The PCR-amplified DNA was purified using AMPure XP beads (Beckman Coulter). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using a DNA 300 assay kit. The library fractions in the range 120-161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike-in DNA and sequenced (single read, 51 cycles, high output mode) on 2 lanes of HiSeq 2000 system (Illumina).

tag: strain

value: Tuebingen/WIK

value: 10 months

value: homozygote mutant (moto-/-)


title: CTL EXO 02

value: endometrial stromal cell

value: endometrial stromal cell exosome


title: IM-9_2Gy_1

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: gene expression sense and cis-NATs in irradiated IM-9 cells

hyb_protocol: The sense and antisense sequences of 60 nt custom-designed were arranged in an Agilent 44K x 4 system (Agilent eArray Design ID = 19052). Agilent 44K x 4 human sense/antisense custom-microarray slides were hybridized with the Cy3-labeled cDNA (2 μg) in a hybridization solution prepared with a GE Hybridization kit (Agilent Technologies).

scan_protocol: The Cy3 fluorescence signal images on the slides were obtained by the Agilent Technologies Scanner (G2505B).

data_processing: The scanned images were analyzed with Feature Extraction Software 8.1 (Agilent Technologies) using default parameters (Protocol name: GE1-v5_95_Feb07 and Grid name: 019052_D_F_20080116) to obtain Processed Signal intensities. Probe names with “s” at the end indicate the expression of sense transcripts, and those with “a” indicate the expression of cis-NATs.

source_name: Culture cells

label_protocol: Cyanine 3 (Cy3)-labeled cDNA was synthesized from 10 μg total RNA of irradiated or non-irradiated samples using a LabelStar Array kit (Qiagen, Valencia, CA, USA), Cy3-dUTP (GE Healthcare, Buckinghamshire, UK) and random nonamer primer.

growth_protocol: The human B lymphoblastic cell line IM-9 (JCRB0024) was purchased from the Health Science Research Resources Bank (Osaka, Japan). The IM-9 cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin, at 37˚C in an atmosphere of 5% CO2. The IM-9 cells were seeded onto 6-well plates at a concentration of 2x105 cells/well for X-ray irradiation experiments.

extract_protocol: For microarray analysis, total RNAs were extracted from the cells using ISOGEN II (Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions. The qualities and concentrations of the RNAs extracted were examined using the NanoDrop Spectrophotometer (ThermoFisher Scientific) according to the manufacturer’s instructions. In addition, the integrities of the RNAs were examined using Agilent Bioanalyzer (Agilent Technologies), according to the manufacturer’s instructions.

treatment_protocol: The IM-9 cells plated on the wells were cultured as described above for 24 h prior to X-ray irradiation. Irradiation (150 kVp, 20 mA, 0.5-mm aluminium and 0.3-mm copper filters) was performed using an X-ray generator (MBR-1520R-3; Hitachi Medical Corporation, Tokyo, Japan) at a distance of 45 cm between the focus and the target. The dose rate was 80 cGy/min. The dose was monitored with a thimble ionization chamber that was placed next to the sample during the irradiation. The irradiated cells were further cultured for 24 h under the same conditions, and then collected by centrifugation.

value: 2 Gy


title: moto_homozygote_4

description: small RNA-Seq of moto-/- testis, replicate 4


title: IM-9_4Gy_1

value: 4 Gy


title: IM-9_1Gy_1

value: 1 Gy


title: moto_heterozygote_5

description: small RNA-Seq of moto+/- testis, replicate 5

value: heterozygote mutant (moto+/-)


title: moto_homozygote_1

description: small RNA-Seq of moto-/- testis, replicate 1


title: moto_homozygote_2

description: small RNA-Seq of moto-/- testis, replicate 2


title: moto_heterozygote_2

description: small RNA-Seq of moto+/- testis, replicate 2


title: moto_heterozygote_3

description: small RNA-Seq of moto+/- testis, replicate 3


title: moto_heterozygote_4

description: small RNA-Seq of moto+/- testis, replicate 4


title: moto_heterozygote_6

description: small RNA-Seq of moto+/- testis, replicate 6


title: attf-6 depletion smRNA sequencing rep. 1

city: Columbus

first: Yi-Hui

state: OH

address: 1060 Carmack Road

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Adapter trimming and quality assessment using TrimGalore and FASTQC.
Processed raw fastqs were aligned to genome with STAR and mapped to transposons with Salmon.
Reads were assigned to genomic features using FeatureCounts. Bam files were converted to BigWig files using DeepTools BamCoverage.
Downstream analysis was preformed using R/Python/IGV. Notably DESEQ2 was used for normalization and differential gene expression analysis.
Assembly: Wormbase WS279
Supplementary files format and content: Tab Delimmited Counts Matrix (Unnormalized)
Supplementary files format and content: BigWig Coverage File

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached adulthood.

extract_protocol:
Synchronized adult worms were collected, washed three times with the M9 buffer and once in ddH2O, and resuspended suspended in TRI Reagent (Sigma). Worms were lysed using the Bead Mill 24 homogenizer (Thermo Fisher Scientific) and the lysate was transferred to a clean tube. 0.1 volumes of bromochloropropane (Sigma) were added to the lysis to perform RNA extraction. Isopropanol (Sigma) was then used to precipitate RNA from the aqueous phase.
Ribosomal RNAs were depleted using the RNase H-based method(Price, et al. 2023a). 3 μg total RNA was incubated with antisense DNA oligonucleotides targeting C. elegans and E. coli ribosomal RNAs, followed by treatment with Hybridase Thermostable RNase H (Biosearch Technologies) at 45 °C for 30 min. The ribosomal RNA-depleted samples were treated with Turbo DNase (Thermo Fisher Scientific) at 37 °C for 30 min. RNAs longer than 200 nts were enriched using RNA Clean & Concentrator-5 (Zymo Research). mRNA sequencing libraries were constructed using Ultra II Directional RNA Library Prep Kit (NEB), following the manufacturer’s instructions. The library samples, each containing unique barcodes, were pooled and sequenced on the HiSeq 4000 platform (2x150 bp, Illumina).

treatment_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . After reaching L4s stage, all worms were transferred to NGM containing 4 mM Auxin plate with OP50 E. coli . Animals were then harvested when the population reached adulthood.

value: whole animal

value: GFP::tev::aid::attf-6 (I)/ wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] II

value: 4mM Auxin


title: attf-6 depletion smRNA sequencing rep. 2


title: ATTF-6_Flag-IP ChIP sequencing using 21ur4606 promoter both-AT mut strain

data_processing:
Adapter trimming and quality assessment using TrimGalore and FASTQC.
Processed raw fastqs were aligned to genome with BWA and mapped to transposons with Salmon.
Bam files were converted to BigWig files using DeepTools BamCoverage.
MACS2 was used for peak calling.
Analysis was conducted with custom R and python scripts. Data were visualized at the genome scale with IGV.
Assembly: Wormbase WS279
Supplementary files format and content: BigWig Coverage File

extract_protocol:
ChIP experiments were conducted as previously described (Guang, et al. 2010; Weng, et al. 2019) with minor modifications. Briefly, 60,000 worms were crosslinked in 2% formaldehyde in M9 buffer for 30 minutes at room temperature with constant agitation. Crosslinking was quenched by adding 125 mM glycine in M9 for 5 minutes at room temperature. After washing with M9 and water, the worm pellets were resuspended in FA buffer (50 mM Tris/HCl, pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl) supplemented with a protease inhibitor (Thermo). The worm pellets were then homogenized using a mixture grinder at 6 m/s for 45 seconds, repeated three times. Next, crosslinked chromatin was sonicated for 30 cycles of 30 seconds ON and 30 seconds OFF at HIGH output. After sonication, worm lysates were centrifuged, and the supernatants were immunoprecipitated with 6 μg of anti-Flag antibody. The antibody-protein-DNA complex was pulled down using Dynabeads Protein G (Invitrogen). After washing sequentially with FA buffer, FA buffer containing 500 mM NaCl, and TE buffer (pH 8.0), reverse crosslinking was carried out by adding 1x TE/1% SDS/250 mM NaCl and incubating at 65°C for 4 hours. RNA and proteins were digested by treating the samples with 20 μg of DNase-free RNase A (Invitrogen) at 37°C, followed by incubation with 200 μg of proteinase K at 60°C for 1 hour. DNA was extracted using phenol-chloroform and dissolved in Tris buffer.
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, ctalog: E7103), following manufacturer’s instructions.

value: attf-6::3xflag (I)/ 21u-4606 endogenous promoter both-AT edited  (IV)


title: ATTF-6_Flag-IP ChIP sequencing rep. 1

value: attf-6::3xflag (I)


title: control-IP ChIP sequencing rep. 1

value: wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II)


title: control smRNA sequencing rep. 1


title: control-IP ChIP sequencing rep. 2


title: Rpa190HTP_air1d-air2d_37C-2h_3

city: Warsaw

first: Tomasz

middle: Wojciech

last: Turowski

address: Pawinskiego 5a

department: Laboratory of Transcription Mechanisms

institute: Insitute of Biochemistry and Biophysics PAS

description:
Library name: Rpa190HTP_air1d-air2d_37C-2h_3
nascent RNA covalently attached to RNAPI

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were kept. Barcode is always first segment of each name.
Collapsing reads: To remove PCR duplicates, reads were collapsed usinf fastx_collapser, part of FASTX Toolkit 0.0.14
Debrarcoding: The 5' barcodes were removed using FASTX-trimmer from FASTX toolkit v0.0.14
Filtering reads: Reads were trimmed using flexbar v3.5.0 to remove the 3’-linker sequence and were additionaly filtered and only 3'linker-containing reads were included to further analyses.
Reads alignment: Reads were aligned to the Saccharomyces cerevisiae genome sequence (Ensembl release EF4.74) by STAR v2.7.10a
Additional processing: novoalign SAM reads were modified using custom made script to keep only the 5' or 3' ends of reads. SAM files were converted to BAM format using samtools v1.15.1 and BigWig files were generated using using bamCoverage script from deepTools package v3.5.1 (reads) or trxtools v0.2.2 (5' ends, 3' ends and non-coded RNA on the 3' ends)
Assembly: sacCer3, EF4.74
Supplementary files format and content: Genomic coordinates of the 3' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of the non-coded polyA on the 3' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of the 5' ends of mapped reads in BigWig format
Supplementary files format and content: Genomic coordinates of mapped reads in BigWig format

source_name: Rpa190-HTP air1d-air2d

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified using three step purification. Last purification was performed under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking at 254 nm for 100s usnig Megatron.

value: Rpa190-HTP air1d-air2d

tag: in line_barcode

value: NNNGTGAGC


title: Rpa190HTP_air1d-air2d_25C_2

description:
Library name: Rpa190HTP_air1d-air2d_25C_2
nascent RNA covalently attached to RNAPI

value: NNNTGTCAC


title: Rpa190HTP_air1d-air2d_25C_1

description:
Library name: Rpa190HTP_air1d-air2d_25C_1
nascent RNA covalently attached to RNAPI

value: NNNCACTGT


title: moto_homozygote_3

description: small RNA-Seq of moto-/- testis, replicate 3

value: Tuebingen/WIK

value: 10 months

value: homozygote mutant (moto-/-)


title: IM-9_0Gy_1

value: 0 Gy


title: Rpa190HTP_trf4ts-trf5∆_37C-4h_3

description:
Library name: Rpa190HTP_trf4ts-trf5∆_37C-4h_3
nascent RNA covalently attached to RNAPI

source_name: Rpa190-HTTP trf4ts-trf5d

value: Rpa190-HTTP trf4ts-trf5d

value: NNNCGCTTAGC


title: moto_heterozygote_1

description: small RNA-Seq of moto+/- testis, replicate 1

value: heterozygote mutant (moto+/-)


title: Rpa190HTP_trf4ts-trf5∆_37C-4h_2

description:
Library name: Rpa190HTP_trf4ts-trf5∆_37C-4h_2
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_trf4ts-trf5∆_25C_2

description:
Library name: Rpa190HTP_trf4ts-trf5∆_25C_2
nascent RNA covalently attached to RNAPI

value: NNNAGAGC


title: Rpa190HTP_trf4ts-trf5∆_25C_3

description:
Library name: Rpa190HTP_trf4ts-trf5∆_25C_3
nascent RNA covalently attached to RNAPI

value: NNNGCGCAGC


title: control smRNA sequencing rep. 2

value: whole animal

value: 4mM Auxin


title: Rpa135HTP_Rpa12dC-rrp44D551N_none_2

description:
Library name: Rpa135HTP_Rpa12dC-rrp44D551N_none_2
nascent RNA covalently attached to RNAPI

source_name: Rpa135-HTP rrp44D551N Rpa12dC

value: Rpa135-HTP rrp44D551N Rpa12dC

value: NNNACTCAGC


title: Rpa190HTP_trf4ts-trf5∆_25C_1

description:
Library name: Rpa190HTP_trf4ts-trf5∆_25C_1
nascent RNA covalently attached to RNAPI


title: Rpa135HTP_Rpa12dC-rrp44D551N_none_3

description:
Library name: Rpa135HTP_Rpa12dC-rrp44D551N_none_3
nascent RNA covalently attached to RNAPI


title: Rpa135HTP_Rpa12dC-rrp44D551N_none_1

description:
Library name: Rpa135HTP_Rpa12dC-rrp44D551N_none_1
nascent RNA covalently attached to RNAPI


title: ATTF-6_Flag-IP ChIP sequencing rep. 2

value: attf-6::3xflag (I)


title: Rpa135HTP_rrp44D551N_none_3

description:
Library name: Rpa135HTP_rrp44D551N_none_3
nascent RNA covalently attached to RNAPI

source_name: Rpa135-HTP rrp44D551N

value: Rpa135-HTP rrp44D551N

value: NNNGACTTAGC


title: Rpa135HTP_rrp44D551N_none_2

description:
Library name: Rpa135HTP_rrp44D551N_none_2
nascent RNA covalently attached to RNAPI

value: NNNACAGTG


title: Rpa190HTP_rrp44D551N_none_1

description:
Library name: Rpa190HTP_rrp44D551N_none_1
nascent RNA covalently attached to RNAPI

source_name: Rpa190-HTP rrp44D551N

value: Rpa190-HTP rrp44D551N

value: NNNGTGACA


title: Rpa190HTP_rrp44D551N_none_3

description:
Library name: Rpa190HTP_rrp44D551N_none_3
nascent RNA covalently attached to RNAPI

value: NNNTGGAGC


title: Rpa190HTP_rrp44D551N_none_2

description:
Library name: Rpa190HTP_rrp44D551N_none_2
nascent RNA covalently attached to RNAPI


title: Rpa135HTP_rrp44D551N_none_1

description:
Library name: Rpa135HTP_rrp44D551N_none_1
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_air1d-air2d_37C-2h_2

description:
Library name: Rpa190HTP_air1d-air2d_37C-2h_2
nascent RNA covalently attached to RNAPI

value: Rpa190-HTP air1d-air2d


title: Rpa190HTP_rat1-1_37C-2h_1

description:
Library name: Rpa190HTP_rat1-1_37C-2h_1
nascent RNA covalently attached to RNAPI

source_name: Rpa190-HTP rat1-1

value: Rpa190-HTP rat1-1

value: NNNGCACTA


title: Rpa190HTP_air1d-air2d_37C-2h_1

description:
Library name: Rpa190HTP_air1d-air2d_37C-2h_1
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_rat1-1_37C-2h_3

description:
Library name: Rpa190HTP_rat1-1_37C-2h_3
nascent RNA covalently attached to RNAPI

value: NNNATCACG


title: Rpa190HTP_rat1-1_25C_2

description:
Library name: Rpa190HTP_rat1-1_25C_2
nascent RNA covalently attached to RNAPI

value: NNNTAGTGC


title: Rpa190HTP_air1d-air2d_25C_3

description:
Library name: Rpa190HTP_air1d-air2d_25C_3
nascent RNA covalently attached to RNAPI

value: NNNAGAGC


title: Rpa190HTP_rat1-1_37C-2h_2

description:
Library name: Rpa190HTP_rat1-1_37C-2h_2
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_rat1-1_25C_1

description:
Library name: Rpa190HTP_rat1-1_25C_1
nascent RNA covalently attached to RNAPI

value: NNNCGTGAT


title: Rpa190HTP_rat1-1_25C_3

description:
Library name: Rpa190HTP_rat1-1_25C_3
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_trf4ts-trf5∆_37C-4h_1

description:
Library name: Rpa190HTP_trf4ts-trf5∆_37C-4h_1
nascent RNA covalently attached to RNAPI

value: Rpa190-HTTP trf4ts-trf5d

value: NNNCGCTTAGC


title: Rpa190HTP_Rnt1-AID_4h_3

description:
Library name: Rpa190HTP_Rnt1-AID_4h_3
nascent RNA covalently attached to RNAPI

source_name: Rpa190-HTP Rnt1-AID

value: Rpa190-HTP Rnt1-AID

value: NNNCACTGT


title: Rpa190HTP_Rnt1-AID_4h_1

description:
Library name: Rpa190HTP_Rnt1-AID_4h_1
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_Rnt1-AID_0h_3

description:
Library name: Rpa190HTP_Rnt1-AID_0h_3
nascent RNA covalently attached to RNAPI


title: Rpa190HTP_Rnt1-AID_0h_2

description:
Library name: Rpa190HTP_Rnt1-AID_0h_2
nascent RNA covalently attached to RNAPI

value: NNNGTGAGC


title: Rpa190HTP_Rnt1-AID_4h_2

description:
Library name: Rpa190HTP_Rnt1-AID_4h_2
nascent RNA covalently attached to RNAPI

value: NNNCTAGC


title: WT vs Mutant D389V

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: 11000-plex RNA Panel for Cell Typing and Cell-Cell Interaction Studies

hyb_protocol: Hybridization was performed at 37°C with this ISH probe mix followed by blocking with 100 mM NHS-acetate for 15 min.

scan_protocol: The flow cell was loaded onto the SMI instrument and scanned for 45 fields of view (FOVs) of one slide for RNA readout. After RNA readout, organoid samples were incubated with a fluorophore-conjugated antibody cocktail against CD298 (Abcam, EP1845Y), B2M (Abcam, EP2978Y), PanCK (Novus, AE-1/AE-3), CD45 (Novus, 2B11 + PD7/26), and DAPI in the same instrument for 1 hr. Eight to nine Z-stack images for 5 channels (5 antibodies and DAPI) were captured.

data_processing:
The Z-stack images of nuclear (DAPI) and CD298/B2M (surface) staining were used to draw cell boundaries. A cell segmentation pipeline using a machine learning algorithm was used to accurately assign transcripts to cell locations and subcellular compartments. The transcript profile of individual cells was generated by combining target transcript location and cell segmentation boundaries. Cells with fewer than 60 total transcripts were omitted from downstream analysis
Expression profiles were normalized for each cell by dividing its raw count vector by total counts and multiplied by the scale factor 10,000 before log transformation. To obtain reference profiles for each cell type, we calculated the average gene expression of cells classified as a given type in the snRNA-seq dataset. Clustered cells were displayed using the runUMAP function in Giotto

source_name: Cardiac organoids

label_protocol: CosMx Human RNA TAP Panel (1000-plex) plus SMI-0119 custom panel probe mix were placed in the hybridization chamber overnight at 37°C. After hybridization, samples were washed twice with 50% formamide (VWR) in 2X SSC at 37°C for 25 min, rinsed twice with 2X SSC for 2 min at room temperature, then blocked with 100 mM NHS-acetate for 15 min. After blocking, the samples were washed twice using 2X SSC for 2 min at room temperature.

growth_protocol: Cardiac organoids were generated from hiPSC using Wnt modulation pathway by first activating it using CHIR99021 and then inhibting it using IWP2 in RPMI b27 minus insulin media. Freshly isolated organoids were fixed in formalin and embedded in paraffin, sectioned at 4-6m, and mounted on slides

extract_protocol: The samples were fixed with 10% neutral buffered formalin (NBF) for 5 minutes at room temperature. Prepared samples were rinsed with 2X saline sodium citrate (SSC) for 5 min and then an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs, Cat. # SKU: 621101) was placed to cover the samples.

treatment_protocol: Samples underwent deparaffinization, 3 µg/ml proteinase K digestion for 30 min at 40°C, and ER2 (Leica, AR9640) heat-induced epitope retrieval (HEIR) procedures to expose target RNAs and epitopes using the Leica Bond RX system.

value: Male


title: Rpa190HTP_Rnt1-AID_0h_1

description:
Library name: Rpa190HTP_Rnt1-AID_0h_1
nascent RNA covalently attached to RNAPI


title: SF3A2 IPseq wt rep2

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description: SF3B1-wt, SF3A2 IPseq rep2

data_processing:
3’ adapter were trimmed using Cutadapt (cutadapt -a TGAGATCGGAAGAGCGGTTCAG -m 19 -e 0.1 -u 4 --max n 5)
Trimmed sequencing were splitted by sample barcodes using FASTX. PCR diplicated were removed using in-house pipeline.
Sequencing R1 reads were then maped to hg19 using STAR-2.7.6a --outWigStrand Stranded --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --quantMode GeneCounts
bigwig files were generated using the RSeQc bam2wig.py function.
Assembly: hg19
Supplementary files format and content: xlsx,predicted BP

growth_protocol: IMDM+10% FBS

extract_protocol:
HMW extracts with TDNase+RNasaA+RNaseT1+NucA.
IP-seq, 11-14 PCR cycles.
The reads from these libraries should look as follows:  NNNNabcNNNNxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxTGAGATCGGAAGAGCGGTTCAG  Where  - NNNN is a four nucleotide degenerate sequence region. The first to these is to ensure high complexity sequence at the beginning, and the second - to serve as a reference for removing PCR duplications.  - abc is a three letter barcode: - xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx denotes the insert in the read. The insert starts at position 12 (1-based) of the read, and originate from human (HEK293) RNA fragments 28-70 nt in length.  - The TGAGATCGGAAGAGCGGTTCAG sequence is common for all reads and should be immediately downstream of the insert.

value: WT

tag: insert length

tag: barcode

value: GTT


title: SF3A2 IPseq K700E rep2

description: SF3B1-K700E, SF3A2 IPseq rep2

value: ATC


title: SF3A2 IPseq K700E rep3

description: SF3B1-K700E, SF3A2 IPseq rep3

value: GAA


title: SF3B1-Flag IPseq wt

description: SF3B1-wt, SF3B1-Flag IPseq

value: SF3B1-3xFlag WT

value: CTG


title: SF3A2 IPseq wt rep1

description: SF3B1-wt, SF3A2 IPseq rep1

value: AAG


title: SF3B1-Flag IPseq K700E

description: SF3B1-K700E, SF3B1-Flag IPseq

value: SF3B1-3xFlag K700E

value: GGG


title: SF3A2 IPseq K700E rep1

description: SF3B1-K700E, SF3A2 IPseq rep1

value: AGA


title: Wnt3a+ATRA sample 4

city: New York

first: Ioanna

last: Mosialou

institute: Columbia University

data_processing:
Kallisto
Assembly: hg38/GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes TPMs for each sample

source_name: primary osteoblasts

extract_protocol:
RNA was extracted using Trizol.
Total RNA libraries were prepared using Illumina TruSeq Stranded Total RNA kit  with a modified protocol  replacing the Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step

value: primary osteoblasts


title: Wnt3a sample 4


title: Wnt3a sample 3


title: Wnt3a+ATRA sample 1


title: High beta catenin patient 3

first: Anqi

last: Wang

state: NY

address: 530 West 166th Street

department: Systems Biology

source_name: Bone marrow

extract_protocol:
RNA was extracted using AllPrep kit (Qiagen).
Total RNA libraries were prepared using Illumina TruSeq Stranded Total RNA kit with a modified protocol replacing the Illumina TruSeq PCR reaction with KAPA HiFi HotStart Ready Mix for the final PCR step

value: Bone marrow

value: CD34+ cells


title: Wnt3a sample 2


title: Wnt3a+ATRA sample 2


title: Low beta catenin patient 3


title: Wnt3a sample 1


title: Wnt3a+ATRA sample 3


title: High beta catenin patient 1


title: Low beta catenin patient 2


title: High beta catenin patient 2


title: 14d_iPNs, HEV, 5d

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

institute: Ruhr University Bochum

data_processing:
CLC Genomics Workbench 22.0 (Qiagen)
Paired reads were mapped to the Hg38 genome scaffold.
For each sample, read counts for each human gene were normalised (RPKM, TPM)
Assembly: Hg38
Supplementary files format and content: Comma separated table, includes read counts per gene

source_name: Primary cells

extract_protocol:
Total RNA was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer’s instructions. RNA quality and quantity were analyzed using the NanoDrop One (Thermo Scientific).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit.

value: Primary cells

value: Neuronal cells

tag: differentiation stage

value: HEV

tag: incubation time


title: 14d_iPNs, Mock, 5d

tag: cell line

tag: cell type

value: Mock


title: SF3A2 IPseq wt rep3

description: SF3B1-wt, SF3A2 IPseq rep3

tag: genotype

value: WT

value: CAT


title: 21d_iPNs, HEV, 5d

tag: treatment


title: 7d_iPNs, Mock, 5d


title: 7d_iPNs, HEV, 5d


title: 2d_iPNs, Mock, 5d


title: 2d_iPNs, HEV, 48h


title: 2d_iPNs, Mock, 48h


title: WIDR-SH3-2

city: Guangzhou

first: Yingguo

last: Gan

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw reads obtained from the sequencing machines were filtered using fastp (version 0.23.4) with the following parameters: 1) Removing reads containing adapters. 2) Removing reads containing more than 10% of unknown nucleotides (N). 3) Removing low-quality reads containing more than 50% of low-quality (Q-value≤20) bases.
Paired-end clean reads were mapped to the reference genome using HISAT2 (version 2.2.1) with default parameters. The index of the reference genome was built prior to alignment.
Mapped reads of each sample were assembled using StringTie (version 2.2.1) in a reference-based approach. The expression abundance for each transcription region was quantified using FPKM (fragments per kilobase of transcript per million mapped reads).
Correlation analysis of replicas was performed using R to evaluate the reliability and operational stability of the experimental results. Principal component analysis (PCA) was conducted using the R package gmodels to convert correlated variables (gene expression) into principal components and to reveal the structure/relationship of the samples.
Differential expression analysis was performed using DESeq2 between two different groups, and edgeR between two samples. Genes/transcripts with an FDR below 0.05 and absolute fold change≥2 were considered differentially expressed. GO and pathway enrichment analyses were conducted using the calculated p-values with FDR correction, taking FDR ≤ 0.05 as the threshold for significance. Gene set enrichment analysis (GSEA) was performed using GSEA software and MSigDB with default parameters.
Assembly: hg38 (GRCh38)
Supplementary files format and content: transcript counts

source_name: WIDR

extract_protocol:
Total RNA was extracted using the TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase-free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched using Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse-transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. The ligation reaction was purified with AMPure XP Beads (1.0X) and PCR amplified. The resulting cDNA library was sequenced using the Illumina Novaseq 6000 (Repugene Technology, Hangzhou, China).

value: WIDR

value: CRC cancer cells

value: DKC1 knockdown

value: KD (SH3)


title: WIDR-SH1-2

value: KD (SH1)


title: WIDR-SH3-1


title: WIDR-SH1-1


title: A431, 60min EGF, Rep 1

city: Stanford

first: Luca

last: Ducoli

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: EGF timecourse analysis

data_processing:
FASTQs were quantified at the transcript level using Salmon and GENCODE Human Release 39
Assembly: GENCODE Human Release 39
Supplementary files format and content: Salmon quantification output

growth_protocol: A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
Total RNA was extracted using the RNeasy Plus mini kit (QIAGEN).
Libraries for mRNA splicing and stability analyses were prepared at Novogene. Libraries of EGF timecourse analysis were prepared using QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: Cells were treated with 50ng/mL recombinant human EGF and, where specified, also with 5µg/mL actinomycin D. Samples were collected in RLT plus buffer at the specified time points.

value: human epidermoid carcinoma cell line


title: A431, 60min EGF, Rep 2

description: EGF timecourse analysis


title: WIDR-NC-2

value: shRNA control

value: NC


title: A431, 30min EGF, Rep 1

description: EGF timecourse analysis


title: A431, 15min EGF, Rep 2

description: EGF timecourse analysis


title: WIDR-NC-1


title: A431, 30min EGF, Rep 2

description: EGF timecourse analysis


title: A431, 0min EGF, Rep 2

description: EGF timecourse analysis


title: siUPF1, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: A431, 15min EGF, Rep 1

description: EGF timecourse analysis


title: Low beta catenin patient 1


title: siUPF1, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: A431, 0min EGF, Rep 1

description: EGF timecourse analysis


title: siHNRNPC, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: 21d_iPNs, Mock, 5d


title: 2d_iPNs, HEV, 5d


title: Control siRNA, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA splicing analysis


title: siUPF1, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: Control siRNA 1h EGF, Rep 2

description: mRNA splicing analysis


title: Control siRNA, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA splicing analysis


title: Control siRNA, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: siCSDE1, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: UPF1, siHNRNPC, irCLIPv2, A431, 60min EGF, Rep 2

description: Re-CLIP protocol

data_processing:
Custom processing scripts available at https://github.com/lducoli/irCLIP-RNP/.
Assembly: Human GRCh38 Gencode release 39 and a custom chromosome made of repetitive elements
Supplementary files format and content: Tab separated text file of RT stops counts at genomic windows as determined by htseq-clip. Scaled bigwig files using scale factors estimated from window counts using DEWSeq.
Library strategy: CLIP-seq

growth_protocol: HEK293T and A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
For irCLIPv2, immunoprecipitation (IP) followed by 3'ligation. For Re-CLIP, 1st IP, 3' ligation, IP destruction and reconstitution, 2nd IP. Then, ligated RNPs were resolved on SDS-page, transferred to nitrocellulose, and RNA was recovered after protein K digestion using streptavidin beads.
On-beads 1st strand cDNA synthesis, 3’ cDNA-tailing, 2nd strand synthesis, and amplification.

treatment_protocol: UV cross-linked at 253nm on plates. Where specified, cells were treated with 50ng/mL recombinant human EGF for the given time.


title: UPF1, siHNRNPC, irCLIPv2, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: UPF1, siHNRNPC,  irCLIPv2, A431, 0min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, siRNA control, irCLIPv2, A431, 60min EGF, Rep 2

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 60min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, siRNA control, irCLIPv2, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: siCSDE1, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: UPF1, siRNA control, irCLIPv2, A431, 0min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, siRNA control, irCLIPv2, A431, 0min EGF, Rep 1

description: Re-CLIP protocol


title: Control siRNA, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA stability analysis


title: HNRNPC, UPF1, Re-CLIP, A431, 30min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: UPF1, siHNRNPC,  irCLIPv2, A431, 0min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 0min EGF, Rep 2

description: Re-CLIP protocol

value: Human embryonic kidney cell line


title: siUPF1, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: HNRNPC, UPF1, Re-CLIP, A431, 0min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 30min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 30min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 30min EGF, Rep 1

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 60min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 15min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HNRNPC, KHSRP, Re-CLIP, HEK293T, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, KHSRP, Re-CLIP, HEK293T, Rep 1

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 30min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 30min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 15min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, HuR, Re-CLIP, HEK293T, Rep 2

description: irCLIPv2 protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, HuR, Re-CLIP, HEK293T, Rep 1

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: UP015,HC,Uninfected,ScRNAseq

city: Atlanta

first: Jyothi

last: Rengarajan

state: GA

address: 954 Gatewood Road NE

department: Emory Primate Center

institute: Emory University

description:
10x Genomics
UP015_0hrs

data_processing:
Raw data was processed with Cell Ranger v6.1.0 (10x Genomics) using standard pipeline
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: bronchoalveolar lavage

extract_protocol:
Fresh BAL fluid was filtered through a 70-um strainer into a 50 ml falcon conical tube to remove any clumped cells and mucus. Pelleted BAL cells were isolated by centrifugation at 1500 rpm for 5 min at 40∘C and supernatant removed and stored. BAL cells were washed twice in 1x DPBS (Gibco) and re-suspended in complete RPMI 1640 media with L-glutamine, 10%  fetal bovine serum (Gibco), and penicillin-streptomycin (Gibco). BAL cells were infected with Mtb H37Rv at an MOI of 2:1 (bacteria: cells) and only media was added to control wells. For optimal contact, the cells in the plate were further centrifuged at 1500 rpm for 5 min at 23∘C and placed at 37∘C in a 5% CO2 incubator for 4 hours, after which they were centrifuged at 1500 rpm for 5 min at 23∘C. Then cells were washed with once with 1X DPBS and resuspended in complete media.
Single cell suspensions were prepared and loaded onto the 10X Genomics Chromium Controller in the BSL3 facility using the Chromium NextGEM Single Cell 5’ Library & Gel Bead Kit v2 to capture individual cells and barcoded gel beads within droplets for reverse transcription. The libraries were prepared according to manufacturer instructions and sequenced on an Illumina NovaSeq 6000 with a paired-end 26x91 configuration targeting a depth of 50,000 reads per cell.

value: bronchoalveolar lavage

value: BAL Cells

tag: Sex

value: male

tag: disease state

value: HC

value: Uninfected


title: UP015,HC,Post-infection,ScRNAseq

description:
10x Genomics
UP015_4hrs

tag: tissue

value: Post-infection


title: UP014,HC,Uninfected,ScRNAseq

description:
10x Genomics
UP014_0hrs


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: UP014,HC,Post-infection,ScRNAseq

description:
10x Genomics
UP014_4hrs


title: UP013,PLWH,Post-infection,ScRNAseq

description:
10x Genomics
UP013_4hrs

value: PLWH


title: UP012,PLWH,Post-infection,ScRNAseq

description:
10x Genomics
UP012_4hrs


title: UP013,PLWH,Uninfected,ScRNAseq

description:
10x Genomics
UP013_0hrs


title: UP012,PLWH,Uninfected,ScRNAseq

description:
10x Genomics
UP012_0hrs


title: UP011,HC,Post-infection,ScRNAseq

description:
10x Genomics
UP011_4hrs


title: UP009,HC,Post-infection,ScRNAseq

description:
10x Genomics
UP009_4hrs


title: UP011,HC,Uninfected,ScRNAseq

description:
10x Genomics
UP011_0hrs


title: KHSRP, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: UP010,HC,Uninfected,ScRNAseq

description:
10x Genomics
UP010_0hrs


title: UP007,PLWH,Post-infection,ScRNAseq

description:
10x Genomics
UP007_4hrs


title: UP008,PLWH,Post-infection,ScRNAseq

description:
10x Genomics
UP008_4hrs


title: UP010,HC,Post-infection,ScRNAseq

description:
10x Genomics
UP010_4hrs


title: p2-pre ATRA

city: shanghai

first: Cui

last: Liang

address: changhai road 168

institute: changhai hospital

description:
671
p2 RNA-seq.xlsx

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.5 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
The read length was 2×150 bp.Clean reads were aligned to the Human genome hg38 using Hisat2.
The expression of the transcript was calculated by normalized count using FeatureCounts .Differentially expression genes (DEGs) were determined using the Random Sampling (MARS) model in the DESeq2 package. The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.
Assembly: hg38/GRCh38
Supplementary files format and content: normalized count

source_name: bone marrow

extract_protocol:
In this RNA-seq workflow, bone marrow cells are first collected, then bone marrow mononuclear cells are isolated using lymphocyte separation solution (ficol) and RNA is extracted using tizol (Thermo).
The library was constructed using Roche's total RNA-Riboerase v2.17 reagent. For experimental procedures, see Roche's official website. The protocol version: KAPA-total RNA-Riboerase-TDS_KR1351_v2.17

value: bone marrow

value: AML

tag: individual

value: pre ATRA


title: UP007,PLWH,Uninfected,ScRNAseq

description:
10x Genomics
UP007_0hrs


title: p2-post ATRA

description:
1416
p2 RNA-seq.xlsx

value: post ATRA


title: p1-post ATRA

description:
691
p1 RNA-seq.xlsx


title: Jurkat_plerixafor_pstat3_1

first: Canhui

last: Cao

state: China

address: Jiefang Road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Tec

data_processing:
Basecalls were performed using bcl2fastaV217 for Novaseg output.
ChlP-seq reads were trimmed from 3' end until the final base had a quality score>30, using Trimmomatic v0.33, discarding reads left with <20bp
ChlP-seq reads were aligned to the hg38/GRCm38.p6  genome usina Bowtie version 1.1.2.
To create ChlP-seq coverage plots, the locations of the mapped ChlP-seg reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.0
Assembly: hg38/GRCm38.p6
Supplementary files format and content: none

source_name: cell line

growth_protocol: Jurkat cells were cultured in Roswell Park Memorial Institute (RPMI)-1640 medium (Gibco, Cat. No. 11875093). U14, TC-1 and ID8 were grown in Dulbecco’s Modification of Eagle’s Medium (DMEM) medium (Gibco, Cat. No. 11966025).  All mediums contain 10% fetal bovine serum (FBS, Thermo Fisher Scientific, Cat. No. A4766801) and 1% Penicillin/streptomycin (Servicebio, Cat. No. G4003). Cells were kept at 5% CO2 and at 37 ℃. T cells were cultured in RPMI 1640 Medium (Gibco, Cat. No. 11875093) supplementing with 10% FBS (Thermo Fisher Scientific, Cat. No. A4766801), 1% penicillin/streptomycin (Servicebio, Cat. No. G4003), interleukin-2 (IL-2) at a concentration of 150 U/mL (Thermo Fisher Scientific, Cat. No. PMC0025), 50 mmol/L of β-mercaptoethanol (Gibco, Cat. No.21985023), and 2 mmol/L of GlutaMAXTM (Gibco, Cat. No. 35050061). T cells were maintained in a controlled environment with 20% O2, 5% CO2, and a temperature of 37 °C.

extract_protocol:
The Chromatin immunoprecipitation (ChIP) assay was performed according to manufacturer instructions with SimpleChip Plus sonication chromatin IP kit (Cell Signaling Technology (CST), Cat. No. 56383) in Jurkat T cells or mouse T cells after treatment with DMSO or plerixafor for 48h, and T cells isolated from the spleens of tumor-bearing mice as described above. For each ChIP, 5106 cells were used. Briefly, cells were cross-linked with 1% methanol-free formaldehyde and quenched by 125mM glycine, and then the chromatin was sonicated to generate 500-800bp DNA fragments. The DNA-protein supernatant was used for immunoprecipitation by incubating with TOX (CST, Cat. No. 5638336778) or p-STAT3 (CST, Cat. No. 9145). Subsequently, the chromatin was eluted and the cross-link was reversed
The DNA libraries were prepared using TruSeq ChIP library preparation kit (Illumina) and sequenced on NovaSeq 6000

value: cell line

value: Jurkat

value: Leukaemic T-cell line

value: Plerixafor


title: Jurkat_control_pstat3_2

value: Control


title: p1-pre ATRA

description:
505
p1 RNA-seq.xlsx


title: Jurkat_control_pstat3_1


title: Jurkat_plerixafor_tox_2


title: Jurkat_plerixafor_tox_1


title: TEC4D6 cells, GFP, Rep4

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to mm10 using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (GRCh38.p14; gencode.v45.chr_patch_hapl_scaff.annotation.gtf.gz) obtained from https://www.gencodegenes.org/human/
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file contain raw RPKM values for each Sample

source_name: thymic epithelial cells derived from TEC4D6 lines

growth_protocol: TEC4D6 cells were placed in 6 well plates (5 x 105, combined with 3 mL of RPMI + 10% FBS without antibiotics).

extract_protocol:
RNA was harvested from Total epithelial cells using RNAqueous Micro Kit (AM1931, Invitrogen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Poly(A) mRNA capture and Library prep Kits (E7770 and E7490, source: neb) following manufacturer's protocols.

treatment_protocol: A transfection solution containing 1 µg of WT or mutant (Mu) AIRE ORF clone with 157 µL of medium and 2.5 µL of FuGene was prepared at room temperature, vortexed, and incubated for 5 minutes. Subsequently, 150 µL was gently added dropwise to the cells, with gentle swirling to mix. After 48h, cells were harvested for downstream analysis.

value: thymic epithelial cells

value: GFP-control


title: Jurkat_control_tox_1


title: Jurkat_control_input


title: TEC4D6 cells, GFP, Rep3

value: thymic epithelial cells derived from TEC4D6 lines


title: Jurkat_control_tox_2


title: Jurkat_plerixafor_input


title: TEC4D6 cells, GFP, Rep1


title: UP008,PLWH,Uninfected,ScRNAseq

description:
10x Genomics
UP008_0hrs

value: bronchoalveolar lavage

value: BAL Cells

value: male


title: TEC4D6 cells, Mu_AIRE Rep 4


title: TEC4D6 cells, Mu_AIRE Rep 2


title: TEC4D6 cells, Mu_AIRE Rep 3


title: TEC4D6 cells, WT_AIRE, Rep 3


title: UP009,HC,Uninfected,ScRNAseq

description:
10x Genomics
UP009_0hrs

value: HC

value: Uninfected


title: TEC4D6 cells, WT_AIRE, Rep 4


title: TEC4D6 cells, Mu_AIRE Rep 1


title: TEC4D6 cells, WT_AIRE, Rep 2


title: Jurkat_plerixafor_pstat3_2


title: B15

city: Beijing

first: Yanhua

last: Li

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner
down-sample reads as required to generate normalized aggregate data across samples
producing a matrix of gene counts versus cells
Single-cell data were integrated and clustered using the Seurat R package (version 4). A total of 124,541 cells were obtained from single-cell sequencing of the nine samples, and 108,306 cells remained after quality control. The cell quality control was conducted as follows: cells with a mitochondrial gene ratio exceeding 10% were removed, and only cells with gene numbers ranging from 300 to 4,000 and UMI numbers ranging from 600 to 10,000 were retained. DoubletFinder R package was used to remove potential doubles. The filtered data were then standardized and normalized, and principal component analysis was performed on the top 2,000 genes with the highest coefficients of variation. The Harmony R package was used to remove inter-batch effects between the samples and groups for cell clustering. Based on the turning point and significance of the different principal components, the first 30 PCs were selected for subsequent cell clustering, and different resolutions were set to determine the cell clusters. Dimensionality reduction and visualization of single cells were performed using the Uniform Manifold Approximation and Projection (UMAP). The specific execution process of Seurat can be found on the website tutorial (https://satijalab.org/seurat/v4.0/pbmc3k_tutorial.html). Detailed information of methods and data analysis are with the supplementary methods.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell, features table and barcode for every cell
Supplementary files format and content: filtered_contig_annotations of TCR and BCR for every T or B cell

source_name: PBMC

extract_protocol:
Frozen peripheral blood mononuclear cells (PBMCs) were resuscitated and converted into single-cell suspensions when cell viability exceeded 85%. We utilized Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (Cat. CG000331, 10x Genomics, USA) for single-cell library preparation. The prepared cell suspension, 10X barcode gel beads, and reaction reagents were distributed to different channels of the Chromium Next GEM Chip G, forming water-in-oil GEMs (gel bead in emulsion) through microfluidics. These GEMs facilitated gel bead dissolution, cell lysis to release mRNA, reverse transcription for cDNA generation, and barcode incorporation for sequencing. Following the disruption of the liquid oil layer, a cDNA amplification reaction ensued, culminating in quality inspection after purification.
The single-cell suspension was prepared in water for cDNA library amplification using the 10× Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits (version 2.0; Cat. No. 1000165). The Chromium™ Single Cell 5ʹ Library Construction Kit (Cat. No. 1000020) was used to construct the DNA library. The constructed library was then sequenced using PE150 sequencing on an Illumina Nova 6000 platform. T cell V(D)J and B cell V(D)J enrichment analyses were performed using the 10× Genomics Chromium™ Single Cell V(D)J Enrichment Kit, Human T Cell (Cat. No. 1000005) and Human B Cell (Cat. No. 1000016) according to the manufacturer’s instructions. The libraries were amplified using a Chromium TCR amplification kit (Cat. No. 1000252) and BCR amplification kit (Cat. No. 1000253), and the experiment was performed according to the manufacturer’s instructions.

value: PBMC

tag: time

value: 1 month post BA.5.2 or BF.7 breakthrough infection


title: B17


title: B12


title: B24


title: B4


title: B5


title: B2


title: A17

value: 2 weeks post BA.5.2 or BF.7 breakthrough infection


title: A20


title: A15


title: TEC4D6 cells, GFP, Rep2


title: A12


title: A4


title: A8


title: A2


title: A5


title: P587

first: Wenjie

last: Zhang

state: Not applicable

address: No. 5, Summer Palace Road, Haidian District, Beijing

department: BIOPIC

institute: Peking University

description:
10X Genomics
NSCLC_immune_scRNA_counts.mtx.gz
barcodes.csv
genes.csv
NSCLC_immune_scRNA_metadata.csv

data_processing:
The generated scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell toolkit (version 6.1.2) against the GRCh38 human reference genome. The preliminary filtered data generated from Cell Ranger were used for downstream analysis. The TCR sequence data from 10X Genomics was processed using Cell Ranger software (version 6.1.2) with the manufacturer-supplied human VDJ reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: UMAP_info.tar includes files with UMAP coordinates.
Supplementary files format and content: T_with_TCR_annotation.csv includes TCR annotation of T cells, only including T cells with matched TCR sequence data and RNA sequence data.

source_name: lung

extract_protocol:
Fresh tumor tissues were cut into pieces of approximately 1mm3 in the RPMI-1640 medium (Gibco, 11875093) with 10% fetal bovine serum (FBS; Gibco, 10099141), and enzymatically digested with Tumor Dissociation Kit (Miltenyi, 130-095-929) for 60 minutes on a rotor at 37 °C. Dissociated cells were subsequently passed through a 100μm MACS SmartStrainers (Miltenyi, 130-110-917) and centrifuged at 300g for 8 minutes. After removing supernatant, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ, 90309-100) and incubated on ice for 5 minutes to lyse red blood cells. After washing with PBS (Gibco, 10010023), cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% FBS). Single-cell suspensions were then stained with 7-AAD Viability Staining Solution (Invitrogen, 00-6993-50) and an antibody against CD235a (BioLegend, 349114) for FACS sorting on a BD Aria III instrument. Non-erythrocytic living cells were enriched by gating 7AAD−CD235a− cells. The concentration of single-cell suspensions was then adjusted to 700~1,200 cells μl–1 and single-cell suspensions with viable cell rate greater than 80% were used for single cell sequencing.
In total, ~18,000 cells for each sample were used for 10X Chromium Single cell 5′ and human TCR library construction (10X Genomics), according to the manufacturer’s instructions. All subsequent steps were performed following the standard manufacturer protocols. Purified libraries were subsequently sequenced using an Illumina NovaSeq 6000 sequencer with 150-base pair (bp) paired-end reads.

value: lung

value: non-small cell lung cancer


title: P579


title: TEC4D6 cells, WT_AIRE, Rep 1


title: P595


title: P592


title: P550


title: P540


title: P574


title: P528


title: B8


title: P527


title: P520


title: P523


title: P524


title: P525


title: P533


title: P510


title: P511


title: P498


title: P496


title: P509


title: P491


title: P495


title: P485


title: P486


title: P494


title: P488


title: P567


title: P490


title: P482


title: P481


title: P483


title: P470


title: P473


title: P467


title: P469


title: P464


title: P472


title: P471


title: P477


title: P502


title: P454


title: P462


title: P453


title: P457


title: P463


title: P433


title: P459


title: P435


title: P445


title: P428


title: P427


title: P418


title: P420


title: P414


title: P416


title: P412


title: P407


title: P405


title: P402


title: P403


title: P399


title: P404


title: P395


title: P394


title: P391


title: P390


title: P387


title: P389


title: SC-islets unsorted

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 Euclid

institute: Washington University in St. Louis

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Sequencing files were processed with cell ranger 7.1.0
Assembly: GRCh38-2020-A
Supplementary files format and content: Processed files are in barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz

source_name: Stem cell-derived islet

growth_protocol: Stem cells were cultured, grown, and differentiated into SC-islets as described (Hogrebe et al., Nature Protocols 2021)

extract_protocol:
Cells were single cell dispersed with TrypLE, counted, and resuspended in DMEM at 1000 cells/uL
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: Cells were sorted using magnetic sorting with an anti-CD49a antibody

value: Stem cell-derived islet

value: Islets of Langerhans

tag: sorting for_cd49a

value: unsorted


title: SC-islet, magnetic sorting for CD49a, negative sample

value: negative sample


title: P382


title: P432


title: P377