title: Zbtb21 mutant-2

city: Shanghai

first: ZHOU

last: FANG

address: 197, Ruijin Road II

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. We use fastp to filter.
We use HISAT(v2.0.4) to do the mapping step.
We mapped clean reads to reference using Bowtie2(v2.2.6) , and then calculate gene expression level with RSEM(v1.2.12).
Then, we calculate pearson correlation between all samples using cor, perform hierarchical clustering between all samples using hclust, perform PCA analysis with all samples using princomp, and draw the diagrams with ggplot2 with fuctions of R.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cancer

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)

extract_protocol:
RNA was extracted from sorted cells using RNeasy Micro (Qiagen, Manchester, UK)
1 μg total RNA was used for following library preparation. Paired-end libraries were prepared using the VAHTS® Universal V8 RNA-seq Library Prep Kit (vazyme Technology Co., Ltd., Nanjing, China) .The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Cancer

tag: cell line

value: Human embryonic kidney

value: MUTANT


title: WT_N_8h_2

status: Public on Apr 06 2024

type: SRA

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 8 hours after LPS treatment, replicate 2

library_source: transcriptomic

data_processing:
Possible poly-A tails and low sequence quality bases were trimmed by Cutadapt version 1.15 with `-m 20 -q 20,20 -a "A{100}"` parameters.
After the trimming, all the remaining reads were aligned to the mm9 reference genome using STAR version 2.5.3a with the primary genome annotation in GENCODE Release M1.
Cuffquant and Cuffnorm softwares, part of Cufflinks suite version 2.2.142, were used to calculate an FPKM value for each gene.
Cumulative FPKM (AUC values) were calculated by using R version 4.0.5. The AUC value for a gene was calculated as the area under the curve of LPS time-course FPKM values, i.e. AUC = (0h+2h)*2/2 + (2h+4h)*2/2 + (4h+8h)*4/2 + (8h+12h)*4/2 + (12h+24h)*12/2. Before the AUC calculation, replicates were merged as mean.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.
Supplementary_files_format_and_content: oxygen_AUC.tab: Tab-delimited text file includes AUC values for every gene and every treatment.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were obtained in the DMEM supplemented with 40 ng/ml M-CSF (PeproTech), 10% FBS and penicillin/streptomycin. The cells were cultured at 37oC under 5% CO2 and saturated humidity in 1% or 20% oxygen. After 1 week, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin without M-CSF. 20%>1%BMDM were obtained by incubation of 20%-BMDM at 1% O2 for 12h and stimulated with LPS at 1% O2.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Total RNA from the BMDMs was used to prepare cDNA sequencing libraries using the SureSelect Strand-Specific RNA library preparation kit (Agilent Technologies) after the polyA selection step.

treatment_protocol: BMDM were treated with LPS for 0, 2, 4, 8, 12, 24h and the cells were harvested for RNA purification.

tag: strain

tag: cell type

value: Bone marrow-derived macrophages

tag: treatment

tag: time point


title: conA-4h-1

description: BMDM treated with concanamycin A and harvested 4 hours after LPS treatment, replicate 1

data_processing:
Possible poly-A tails and low sequence quality bases were trimmed by Cutadapt version 1.15 with `-m 20 -q 20,20 -a "A{100}"` parameters.
After the trimming, all the remaining reads were aligned to the mm9 reference genome using STAR version 2.5.3a with the primary genome annotation in GENCODE Release M1.
Cuffquant and Cuffnorm softwares, part of Cufflinks suite version 2.2.142, were used to calculate an FPKM value for each gene.
Cumulative FPKM (AUC values) were calculated by using R version 4.0.5. The AUC value for a gene was calculated as the area under the curve of LPS time-course FPKM values, i.e. AUC = (0h+2h)*2/2 + (2h+4h)*2/2 + (4h+8h)*4/2 + (8h+12h)*4/2 + (12h+24h)*12/2. Before the AUC calculation, replicates were merged as mean.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene.
Supplementary_files_format_and_content: lysosome_AUC.tab: Tab-delimited text file includes AUC values for every gene and every treatment.

growth_protocol: Bone marrow cells were obtained in the DMEM supplemented with 40 ng/ml M-CSF (PeproTech), 10% FBS and penicillin/streptomycin. The cells were cultured at 37oC under 5% CO2 and saturated humidity in 20% oxygen. After 1 week, the culture medium was replaced with fresh DMEM supplemented with 10% FBS and penicillin/streptomycin without M-CSF and treated with DMSO, 10nM ConcanamycinA or 100nM Bafilomycin a1 for 16h.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen).
Total RNA from the BMDMs was used to prepare cDNA sequencing libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Concanamycin A


title: OlyA_PlyB_8-1 5DPT biol rep 3

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
STAR v2.7.5c, mapping to reference CPB genome using " --outFilterMultimapNmax 1" to disregard multimapped reads.
R version 4.1.1 with package edgeR_3.36.0, filtering genes with raw counts below 50 in less than 4 samples
R version 4.1.1 with package edgeR_3.36.0, TMM normalization
R version 4.1.1 with package limma_3.50.0, voom transformation, linear model fit, adj.p.val calculation (BH correction)with eBayes function, DE table export
Assembly: Ldec_2.0
Supplementary files format and content: TMM_RPMs_allsamples.txt - a tab-delimited text file with TMM-normalized CPM values for all samples
Supplementary files format and content: DGE_results.xlsx - a MS Excel file containing a data matrix that aggreates the results of differential gene expression analysis (logFC and adj.p.val) for the comparisons between treated and control larvae in both time points and corresponding normalized counts

molecule: polyA RNA

organism: Leptinotarsa decemlineata

source_name: whole larva

growth_protocol: The CPB larvae were obtained from laboratory colony established from adults collected from untreated potato fields in Central Slovenia in June 2021. The beetle colony was kept on potato foliage diet.

extract_protocol:
RNA extraction from individual larvae was performed using TRIzol reagent (Invitrogen) and Direct-zol RNA Microprep kit (Zymo Research) followed by DNase treatment and cleaning using RNeasy MinElute columns (QIAGEN).
Illumina library prep without retaining read strand specificity was performed by Novogene Ltd.

treatment_protocol: Four fresh potato leaves were soaked in PlyA2/PlyB solution and another four in the corresponding Control Buffer. One 2nd instar larva (4 days old) was placed on each leaf disk.  After 1 and 5 days of feeding , whole larvae were collected and rapidly frozen in liquid nitrogen, yielding four biological replicates per group at both time points.

tag: tissue

value: whole larva

tag: larval instar_sampled

tag: days post_treatment


title: Baf-2h-1

description: BMDM treated with Bafilomycin A1 and harvested 2 hours after LPS treatment, replicate 1

value: Bafilomycin A1


title: Zbtb21 mutant-1

country: China

organism: Homo sapiens

tag: genotype


title: conA-2h-2

description: BMDM treated with concanamycin A and harvested 2 hours after LPS treatment, replicate 2


title: WT_N_8h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 8 hours after LPS treatment, replicate 1


title: OlyA_PlyB_7-4 5DPT biol rep 2


title: OlyA_PlyB_6-6 5DPT biol rep 1


title: conA-2h-1

description: BMDM treated with concanamycin A and harvested 2 hours after LPS treatment, replicate 1


title: conA-0h-2

description: BMDM treated with concanamycin A and harvested before LPS treatment, replicate 2


title: WT_N_4h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 4 hours after LPS treatment, replicate 1


title: Zbtb21-1

value: WT


title: OlyA_PlyB_5-5 1DPT biol rep 4


title: WT_N_4h_2

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 4 hours after LPS treatment, replicate 2


title: ControlBuffer_18-1 5DPT biol rep 1

value: ControlBuffer


title: conA-0h-1

description: BMDM treated with concanamycin A and harvested before LPS treatment, replicate 1


title: WT_N_2h_2

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 2 hours after LPS treatment, replicate 2


title: WT_N_2h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously) 2 hours after LPS treatment, replicate 1


title: OlyA_PlyB_5-1 1DPT biol rep 3


title: PCS2-2

value: CONTROL


title: PCS2-1


title: OlyA_PlyB_4-5 1DPT biol rep 2


title: Zbtb21K419/845R double mutant

library_source: genomic

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.  Sequencing reads were aligned to the humangenome build hg38 using bowtie2 (v2.3.5.1) usingdefault parameters.  Regions of enrichment of HA were calculated using MACS2 (v2.1.2) using parameters -m 5 50.   For peakannotation, we adopt homer(v4.10.4) utility annotatePeaks.pl, associating peaks with their nearby genes.  The genes that were associated with super-enhancers were analyzed using clusterProfiler R package (v3.6.0).  Peakswere chosen for the motif analysis using meme (v5.1.1).
Assembly: hg38
Supplementary files format and content: narrowPeak(include wild type Zbtb21 and mutant Zbtb21)

molecule: genomic DNA

growth_protocol: Cell harvesting and cross-linked with 1% formaldehyde for 10 min, and quenched with 0.125 M glycine for 5 min.

extract_protocol:
Cells were lysed in 1 mL lysis buffer, and rotated for 30 min at 4℃. Cell lysates were centrifuged at 2,400 x g for 10 min at 4℃ to isolate the nuclei.
1.Nuclei were suspended in digestion buffer and subjected for Enzymatic shearing to shear chromatin fragments to an average size between 200 bp and 500 bp by incubate the tube at 37℃ for 10-15 min.  2.Stop the shearing reaction and the fragmented chromatin was centrifuged at 18000 x g for 10 min at 4℃.  3.Supernatant was transferred to a new Eppendorf tube and added the chip reaction mix which containing proteinA/G magnetic beads, chip IP buffer, antibody, protease inhibitor cocktail, and rotated at 4℃ overnight. 4.After overnight incubation, proteinA/G magnetic beads were washed. The chromatin was eluted in reverse cross-linking buffer followed by incubate the tube at 65℃ for 3h. Then the ChIP DNA was treated with RNase A and proteinase K at 37℃ for 30 min, and purified using Phenol chloroform. 5.ChIP DNA was processed for library generation using the QIAseq Ultralow Input Library Kit (QIAGEN) following the manufacturer’s protocol.

value: Zbtb21K419/845R double mutant


title: wild type Zbtb21


title: Zbtb21-2


title: WT_N_0h_2

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously), no LPS treatment, replicate 2


title: Differentiated cells, Day42, Bio rep 3

city: shanghai

first: yingqi

last: li

address: siping road

institute: tongji university

data_processing:
A cDNA library constructed by technology from the pooled RNA from < hESCs_1, hESCs_2, Day21_1, Day21_2, Day21_3, Day28_1, Day28_2, Day28_3, Day42_1, Day42_2, Day42_3> samples of homo sapiens was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: homo_sapiens GRCh38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Approximately 10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina（NEB，UK）following manufacturer's protocols.

value: TPH2+ mature serotonin neurons

value: TPH2-EGFP knockin

value: induced serotonin neuron differentiation


title: ControlBuffer_2-2 1DPT biol rep 3


title: WT_N_0h_1

description: BMDM normoxia (differentiated and cultured in 20% oxygen continuously), no LPS treatment, replicate 1


title: kidney, cisplatin+YSJZD, day 4, rep 2

city: Fuzhou

first: Dengyong

last: Zheng

address: 282 Wusi Road Gulou District

department: Department of Nephrology

institute: The Second Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6)
Expression level of gene was calculated by RSEM (v1.3.1)
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: grch38
Supplementary files format and content: read counts for each sample

source_name: kidney

extract_protocol:
Total ribonucleic acid (RNA) was isolated from 50 mg of kidney tissue.Only high-quality whole RNA samples were used to generate complementary deoxyribonucleic acid (cDNA) libraries.
BGI Co., Ltd. prepared a cDNA library in accordance with the manufacturer's instructions.
BGI Co., Ltd. performed RNA-Seq on a DNBSEQ platform in accordance with the manufacturer's instructions.

treatment_protocol: The mice were divided into the NC, cisplatin, and cisplatin + YSJZD groups. The NC group was treated with intraperitoneal injection of saline and intragastric injection of pure water. The cisplatin group was treated with intraperitoneal injection of cisplatin solution and intragastric injection of pure water. The cisplatin+YSJZD group was treated with intraperitoneal injection of cisplatin solution and intragastric injection of YSJZD.

value: kidney

value: cisplatin+YSJZD


title: kidney, cisplatin+YSJZD, day 4, rep 1


title: pcDNA4c Control 3

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

country: USA

institute: NIH

data_processing:
Read quantification was performed via Kallisto v0.45.0 using Ensembl release 98
One sample in the overexpression experiment (pcDNA4C-CK2) was removed because expression of the target gene was not successfully enhanced.
For all remaining samples, gene-level quantification was estimated using tximport v1.14 and then TMM-normalized using EdgeR v3.28.
We retained genes with a normalized expression of at least 5 counts per million (CPM) in all replicates of at least one treatment group.
Genome_build: mm10
Supplementary_files_format_and_content: Tables containing gene/transcript counts for each sample

source_name: Retina

extract_protocol:
Electroporated areas of the retinas were collected at postnatal day 8 and disassociated with papain solution. Intact GFP positive rod photoreceptors were manually collected with a micromanipulator. Kit v2-Pico Input Mammalian (Takara Bio USA, Inc). We prepared three independent RNA samples for each treatment and then performed paired-end sequencing with a HiSeq2500 (Illumina, San Diego, USA).
Libraries were generated from rod cells using SMARTer Stranded Total RNA-Seq

value: rod cells

value: pcDNA4c Control


title: kidney, cisplatin, day 4, rep 3

value: cisplatin+Pure water


title: ControlBuffer_2-3 1DPT biol rep 4


title: Differentiated cells, Day42, Bio rep 2


title: kidney, cisplatin, day 4, rep 2


title: Differentiated cells, Day42, Bio rep 1


title: pcDNA4c Control 2


title: pcDNA4c Control 1


title: ControlBuffer_1-4 1DPT biol rep 2


title: conA-4h-2

description: BMDM treated with concanamycin A and harvested 4 hours after LPS treatment, replicate 2


title: kidney, cisplatin+YSJZD, day 4, rep 3


title: OlyA_PlyB_4-2 1DPT biol rep 1


title: Differentiated cells, Day28, Bio rep 3

value: FEV+ immature serotonin neurons

value: FEV-EGFP knockin


title: Differentiated cells, Day28, Bio rep 2


title: ControlBuffer_1-1 1DPT biol rep 1


title: pcDNA4c mCsnk2a1 2

value: pcDNA4c mCsnk2a1


title: kidney, normal control, day 4, rep 3

value: Saline+Pure water


title: pcDNA4c mCsnk2a1 3


title: kidney, normal control, day 4, rep 2


title: Differentiated cells, Day28, Bio rep 1


title: kidney, normal control, day 4, rep 1


title: Differentiated cells, Day21, Bio rep 3

value: Neural progenitor cells


title: shRNA Control 3

value: shRNA Control


title: kidney, cisplatin, day 4, rep 1

value: WT


title: pcDNA4c mCsnk2a1 1


title: shRNA Control 2


title: mESC, Fix, rep2

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

data_processing:
Sequencing reads were trimmed by cutadapt (version 1.18) with parameter -m 20 -e 0.1 -O 3 -q 20 --quality-base=33 to remove low-quality bases and adaptor sequences.  Trimmed reads were aligned to mouse reference genome (mm10) using bowtie2 aligner (version 2.3.3.1) (Ben Langmead et al., Nature methods, 2012) with parameters –N 1 -L 25 --no-mixed --no-discordant. Reads in blacklist regions defined in the ENCODE blacklist were excluded from downstream analysis.  Duplicates were labeled by Picard MarkDuplicates (version 2.20.4) and removed by samtools (version 1.6) view –F 1024. We then merged the two replicates in each group, shifted each end of each read pair to region of length 250bp, which was taken as the open region. We generated binned bigWig of open region count, with binsize of 50bp. After that, count numbers of all windows were normalized to 95 percentile values in each sample.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: Mouse embroynic stem cell line (R1-mESC) was cultured on inactivated mouse embryonic fibroblast (MEF) feeder layers pre-coated with 0.3% gelatin (Sigma, G1890), using Serum/LIF/2i medium composed of KO DMEM (GIBCO,10829018) supplemented with 15% FBS (GIBCO,1009914), 1X L-glutaMAX (GIBCO,35050061), 1X penicillin-streptomycin (GIBCO,10378016), 1X non-essential amino acids (NEAA) (GIBCO,11140050), 1X sodium pyruvate (GIBCO,11360070), 0.1 mM 2-mercaptoethanol (ThermoFisher, 21985023), 1000 U/mL mouse leukemia inhibitory factor (mLIF) (Millipore, ESG1107), 3 μM CHIR-99021 (Selleck, S2924) and 1 μM PD0325901 (Selleck, S1036).

extract_protocol:
To permeabilize cells, the cell pellets were resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 10 min. Afterwards, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the samples mixed by inverting the containing tubes for six times.     Nuclei were then centrifuged for 10 min at 500 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed, as for Native group, nuclei were incubated with Tn5 transposome and tagmentation buffer at 37°C for 30min (Novaprotein, N248). As for Fix and 1,6-Hex+Fix conditions, nuclei were then incubated with Tn5 transposome and tagmentation buffer at 55°C for 30min. After tagmentation, stop buffer was added directly into the reaction. For the native condition, samples were incubated at 55°C for 30min to terminate the tagmentation.  The Fix and 1,6-Hex+Fix samples were incubated at 55°C overnight to terminate the tagmentation and to reverse crosslink the samples.
PCR was performed to amplify the library for 5 cycles using KAPA HiFi PCR Kit (Kapa Biosystems, kk2102)  with the following PCR conditions: 72°C for 5min; 98°C for 3mins; and thermocycling at 98°C for 20s, 63°C for 30s. The determine the optimal amplification for each sample, 5ul PCR mix was diluted with 5ul H2O (Thermo Scientific, 10977015) and combined with 2x SYBR qPCR supermix (Novoprotein, E096) to perform qPCR with following conditions: 98°C for 3mins; and thermocycling for 30 cycles at 98°C for 20s, 63°C for 30s and 72°C for 1mins. The additional number of PCR rounds (N) was determined as the qPCR cycle that reached the 1/3 maximum abundance on qPCR amplification curve. All samples were amplified for another N+3 cycles with the following PCR conditions: 98°C for 3mins; thermocycling at 98°C for 20s, 63°C for 30s and 72°C for 3min; and 72°C for 5mins for final extension. The library was sequenced on Illumina HiSeq X Ten with an average depth of 17.5 million reads per library.

treatment_protocol: First, mESCs were dissociated with 0.05% Trypsin-EDTA into single cells. Then, feeder cells were removed by replating cell suspension to the 0.3% gelatin pre-coated plate for 30min at 37°C A total of 1e5 cells were centrifuged at 500 r.c.f. for 5 min in fixed-angle centrifuge at room temperature. For the native condition, cells were resuspended and wash with ice cold PBS, permeabilized, and Tn5 tagmented as described below. For the Fix condition, cells were resuspended and wash with ice cold PBS, fixed by 1% formaldehyde at room temperature for 10 mins.  The fixation was stopped by 1.25M glycine at room temperature for 5 mins, and the cells were washed by ice cold PBS, permeabilized, and Tn5 tagmented as described below. For the 1,6-Hex+Fix condition, cells were resuspended in DMEM (Gibco, 11995065) containing 10% [w/v] 1,6-hexanediol (Sigma-Aldrich, 240117) for 30s at toom temperatures. The cells were centrifuged at 500 r.c.f. for 5 min, and the supernatant was removed by pipetting twice. The cell pellets were washed with PBS with 10% 1,6-hexanediol once and fixed in PBS containing 1% formaldehyde (Invitrogen, 28906) and 10% [w/v] 1,6-hexanediol at room temperature for 10mins.  The fixation was stopped with 0.6M glycine (final concentration) at room temperature for 5mins.  Cells were washed using ice-cold PBS once and centrifuged at 500 r.c.f. for 5 min.

value: embryonic stem cell

value: Fix


title: shRNA Control 1


title: shRNA mCsnk2a1 3

value: shRNA mCsnk2a1


title: mESC, Fresh, rep2

value: Fresh


title: Donor 5 infected with L.b. LRV1 positive

type: RNA

city: Porto Velho

first: kátia

middle: Paula

last: Felipin

state: Rondônia

address: R. da Beira, 7671.

country: Brazil

institute: Fiocruz Rondônia

description: LbLRV1+ D5

hyb_protocol: After fragmentation, 2.5 μg of ss-DNA were hybridized for 16 hours at 45°C on the Clariom S Assay human GeneChip. GeneChips were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: Microarray data were preprocessed in R employing the oligo package. CEL files were read with the read.celfiles() function and the rma() function was used to apply background correction, quantile normalization and summarization by the Robust Multichip Average (RMA) preprocessing methodology.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 25 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBMCs in supplemented culture medium were dispensed into 24-well microplates on sterile coverslips (13 mm) and maintained for 7 days in a humid atmosphere at 37ºC and 5% CO2.

extract_protocol: Total RNA was separated using Trizol (Life Technologies, California, USA) followed by extraction with the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: For the infection of macrophages derived from human monocytes with Leishmania braziliensis promastigotes, an amount of 5 x 106 PBMCs/well and a 1:10 cell/parasite ratio were used. Parasites were adjusted to 5 x107 cells/well, at a ratio of 1:10. After adding the parasites to the cell culture, the plates were incubated at 34ºC and 5% CO2 for 24 h. Cells were then washed three times with RPMI to remove non-internalized parasites and then incubated for 72 h.

tag: donor

tag: group


title: mESC, Fix, rep1


title: Donor 4 infected with L.b. LRV1 positive

description: LbLRV1+ D4


title: hESCs, Day0, Bio rep 3

value: Human embryonic stem cells

value: TPH2-EGFP knockin

value: induced serotonin neuron differentiation


title: Donor 3 infected with L.b. LRV1 positive

description: LbLRV1+ D3


title: mESC, Fresh, rep1


title: hESCs, Day0, Bio rep 2


title: Donor 4 infected with L.b. LRV1 negative

description: LbLRV1- D4


title: shRNA mCsnk2a1 2

value: rod cells


title: mESC, Fix, 1,6-Hex, rep2

value: Fix, 1,6-Hex


title: HCT116 COLORECTAL CANCER CELLS TREATED WITH 2.5 mM METFORMIN REPLICATE 4

status: Public on Apr 05 2024

city: Delhi

first: Muzaffer

middle: Ahmed

last: Bhat

state: Delhi

address: ANSARI NAGAR NEW DELHI 110029

department: Physiology

country: India

institute: AIIMS

hyb_protocol: 0.83 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: treated group

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low TOTAL RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HCT116 cells were grown in 5% CO2 at 37°C. Cells were grown in DMEM media and subcultured every third day using trypsin-EDTA.

extract_protocol: RNA was prepared using Trizol reagent.  The protocol includes brief pipetting and vorteing, followed by phase seperation by chloroform and precipitation using iso-propanol. This was followed by washing by 75% ethanol and elution in nuclease-free waster. Total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were treated 2.5 mM Metformin for two weeks. The DMEM media containing Metformin was changed every day.

value: colorectal cancer cell line

tag: gender

value: male

value: treated with 2.5 mM Metformin


title: Differentiated cells, Day21, Bio rep 2


title: shRNA mCsnk2a1 1


title: HCT116 COLORECTAL CANCER CELLS TREATED WITH 2.5 mM METFORMIN REPLICATE 2


title: HCT116 COLORECTAL CANCER CELLS TREATED WITH 2.5 mM METFORMIN REPLICATE 1


title: Donor 5 control

description: Control D5

source_name: Donor 5 control

value: Control


title: Differentiated cells, Day21, Bio rep 1


title: Donor 3 infected with L.b. LRV1 negative

description: LbLRV1- D3


title: UNTREATED HCT116 COLORECTAL CANCER CELLS REPLICATE 2

source_name: control group

value: untreated


title: UNTREATED HCT116 COLORECTAL CANCER CELLS REPLICATE 3


title: UNTREATED HCT116 COLORECTAL CANCER CELLS REPLICATE 1


title: UNTREATED HCT116 COLORECTAL CANCER CELLS REPLICATE 4


title: Donor 5 infected with L.b. LRV1 negative

description: LbLRV1- D5


title: Donor 4 control

description: Control D4

source_name: Donor 4 control


title: hESCs, Day0, Bio rep 1


title: siRNA_PC-3_siZFAS1_Rep2_L2

city: Houston

first: Hua-Sheng

last: Chiu

state: TX

address: 1102 Bates Avenue

institute: Baylor College of Medicine

data_processing:
CRISPRi: FASTQ files were processed using an in-house RNA-seq analysis pipeline. FastQC (v0.11.8) was first used for data quality control, after which adapter sequences, polyA readthrough, and low-quality reads were removed by BBMap v38.26. Reads were then mapped against the hg38 reference genome with STAR v2.6.0c, and gene counts were determined by HTSeq  v.0.11.0. The number of reads for each gene was adjusted to account for differences in sequencing depth and presented as counts per million (CPM).
siRNA: RNA-seq raw reads were aligned to the hg19 reference genome with GENCODE v16 gene annotation using STAR v2.3.0e. Alignment files were processed with Picard tools v1.54 (http://broadinstitute.github.io/picard/) and indexed using SAMtools v0.1.11. Transcript quantification was performed in Cufflinks v2.02 quantification mode with the GENCODE v16.gtf annotation. Transcripts Per Million (TPM) values were used for relative abundance estimation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including CPM (CRISPRi) or TPM (siRNA) values for each sample

source_name: prostate

extract_protocol:
Total RNA was isolated from each sample using the RNeasy Plus Micro Kit (Qiagen, catalog #74034) and quantified using the NanoDrop 2000c (Thermo Scientific).
CRISPRi: QuantSeq RNA-seq library preparation (Lexogen) was performed according to the manufacturer’s protocol using 5 µl of cell lysate as input. ; siRNA: 2 μg aliquots from each sample (5-6 μl) were submitted to Novogene Corporation Inc. (Sacramento, CA) for library preparation

value: prostate

value: siRNA


title: siRNA_PC-3_siZFAS1_Rep2_L1


title: siRNA_PC-3_siZFAS1_Rep1_L2


title: siRNA_PC-3_siDICER1_Rep2_L2


title: mESC, Fix, 1,6-Hex, rep1

value: WT


title: siRNA_PC-3_siZFAS1_Rep1_L1


title: siRNA_PC-3_siDICER1_Rep2_L1


title: HCT116 COLORECTAL CANCER CELLS TREATED WITH 2.5 mM METFORMIN REPLICATE 3


title: siRNA_PC-3_siDICER1_Rep1_L2


title: siRNA_PC-3_siDICER1_Rep1_L1


title: siRNA_PC-3_NT_Rep2_L2


title: siRNA_PC-3_NT_Rep2_L1


title: siRNA_PC-3_NT_Rep1_L2


title: siRNA_NCI-H460_siZFAS1_Rep1_L2

source_name: lung

value: lung


title: siRNA_NCI-H460_siZFAS1_Rep1_L1


title: siRNA_NCI-H460_siDICER1_Rep2_L2


title: siRNA_NCI-H460_siZFAS1_Rep2_L2


title: siRNA_NCI-H460_siDICER1_Rep2_L1


title: siRNA_NCI-H460_siZFAS1_Rep2_L1


title: siRNA_PC-3_NT_Rep1_L1


title: siRNA_NCI-H460_siDICER1_Rep1_L2


title: siRNA_NCI-H460_NT_Rep2_L2


title: siRNA_NCI-H460_NT_Rep1_L2


title: siRNA_NCI-H460_NT_Rep2_L1


title: siRNA_ECC-1_siZFAS1_Rep2_L2

source_name: endometrium

value: endometrium


title: siRNA_ECC-1_siZFAS1_Rep2_L1


title: siRNA_NCI-H460_NT_Rep1_L1


title: siRNA_ECC-1_siZFAS1_Rep1_L2


title: siRNA_ECC-1_siDICER1_Rep2_L2


title: Donor 3 control

description: Control D3

source_name: Donor 3 control


title: siRNA_ECC-1_siDICER1_Rep2_L1


title: siRNA_ECC-1_siZFAS1_Rep1_L1


title: siRNA_ECC-1_siDICER1_Rep1_L2


title: siRNA_NCI-H460_siDICER1_Rep1_L1


title: siRNA_ECC-1_NT_Rep1_L1


title: siRNA_ECC-1_NT_Rep1_L2


title: siRNA_ECC-1_NT_Rep2_L2


title: siRNA_ECC-1_NT_Rep2_L1


title: nill_87

city: Westmead

first: Harry

last: Robertson

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

country: Australia

institute: Westmead Institute for Medical Research

description:
processed data column: P_121
W110_3_H3LWLDMXX_TAATGCGC-TATAGCCT

data_processing:
Raw RNA-Seq reads were quality controlled and trimmed using FastQC and Trimmomatic. Alignment to the GRCh38 human reference genome was performed using STAR, followed by quantification of gene-level expression with featureCounts.
Assembly: GRCh37-hg19
Supplementary files format and content: raw counts per sample

source_name: Renal Allograft Biopsy

extract_protocol:
Kidney biopsy specimens were left in RNAlater (Sigma-Aldrich) overnight at 4°C before removal and storage at -80°C until RNA extraction. Specimens were chemically and physically lysed by using 2-Mercaptoethanol (Sigma-Aldrich) and TissueLyser II (Qiagen, Germany), follow by RNA extraction using AllPrep DNA/RNA/microRNA and MiniElute clean- up kits (Qiagen, Germany).
All RNA samples were frozen and stored at -80°C and then sent in bulk to the Australian Genome Research Facility (AGRF, Melbourne, Australia). Sample QC and library preparation were performed in-house, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina)

value: Renal Allograft Biopsy

tag: classification

value: Nill


title: nill_84

description:
processed data column: P_118
T106_3_H3MCMDMXX_TAATGCGC-TATAGCCT


title: nill_81

description:
processed data column: P_114
S123_3_H3MCMDMXX_ATTACTCG-GGCTCTGA


title: nill_88

description:
processed data column: P_122
W69_3_H3LWLDMXX_AGCGATAG-TATAGCCT


title: nill_85

description:
processed data column: P_119
T142_3_H3MCMDMXX_CGCTCATT-CAGGACGT


title: rej_34

description:
processed data column: P_117
S29_3_H3MCMDMXX_CGCTCATT-TATAGCCT

value: Rej


title: nill_80

description:
processed data column: P_112
S109_3_H3LWLDMXX_TCCGGAGA-GTACTGAC


title: nill_86

description:
processed data column: P_120
V36_3_H3MCMDMXX_CGCTCATT-GTACTGAC


title: rej_35

description:
processed data column: P_123
X96_3_H3LWLDMXX_TCCGCGAA-AGGCGAAG


title: H1975/AZDR_rep2

first: Tianxiang

last: Chen

address: Shanghai Chest hospital

institute: Shanghai Chest Hospital

description: circular RNA

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The arrays were washed, fixed, and scanned to images using the Agilent Scanner G2505C.

data_processing: Data analysis was performed using Agilent Feature Extraction software version 11.0. Expression data were quantile normalized and processed using the R software limma package.

source_name: H1975,AZD9291-resistant,replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA quality and concentration were determined from OD260/280 readings using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Montchanin, DE, USA) and assessed via 1% gel electrophoresis, respectively.


title: H1975/AZDR_rep1

description: circular RNA

source_name: H1975,AZD9291-resistant,replicate 1


title: HCC827_rep1

description: circular RNA

source_name: HCC827,control,replicate 1


title: H1975_rep2

description: circular RNA

source_name: H1975,control,replicate 2


title: nill_79

description:
processed data column: P_111
R79_3_H3MCMDMXX_GAGATTCC-TATAGCCT


title: HCC827/AZDR_rep1

description: circular RNA

source_name: HCC827,AZD9291-resistant,replicate 1


title: H1975_rep1

description: circular RNA

source_name: H1975,control,replicate 1


title: siRNA_ECC-1_siDICER1_Rep1_L1


title: nill_78

description:
processed data column: P_110
P55_3_H3MCMDMXX_CGCTCATT-AGGCGAAG


title: nill_82

description:
processed data column: P_115
S137_3_H3MCMDMXX_GAATTCGT-TATAGCCT


title: nill_76

description:
processed data column: P_108
P133_3_H3LWLDMXX_CGGCTATG-GGCTCTGA


title: nill_75

description:
processed data column: P_107
P115_3_H3LWLDMXX_GAGATTCC-CCTATCCT


title: nill_74

description:
processed data column: P_106
N135_3_H3LWLDMXX_CGCTCATT-CCTATCCT


title: nill_77

description:
processed data column: P_109
P25_3_H3MCMDMXX_TCCGCGAA-GGCTCTGA


title: nill_83

description:
processed data column: P_116
S15_3_H3LWLDMXX_TCCGGAGA-CAGGACGT


title: nill_72

description:
processed data column: P_104
M85_3_H3MCMDMXX_TCCGGAGA-CAGGACGT


title: nill_73

description:
processed data column: P_105
M88_3_H3MCMDMXX_CGGCTATG-CCTATCCT


title: rej_33

description:
processed data column: P_113
S11_3_H3MCMDMXX_TCCGCGAA-ATAGAGGC


title: nill_71

description:
processed data column: P_102
M39_3_H3LWLDMXX_TCCGCGAA-CAGGACGT


title: rej_32

description:
processed data column: P_103
M68_3_H3LWLDMXX_GAATTCGT-TAATCTTA


title: rej_29

description:
processed data column: P_94
J145_3_H3MCMDMXX_TCCGGAGA-TATAGCCT


title: nill_65

description:
processed data column: P_93
J-H76_3_H3LWLDMXX_GAATTCGT-TATAGCCT


title: nill_69

description:
processed data column: P_99
M125_3_H3MCMDMXX_TCTCGCGC-TATAGCCT


title: nill_70

description:
processed data column: P_100
M13_3_H3LWLDMXX_TCCGCGAA-TATAGCCT


title: nill_67

description:
processed data column: P_96
J54_3_H3LWLDMXX_TAATGCGC-CAGGACGT


title: nill_68

description:
processed data column: P_97
L72_3_H3MCMDMXX_GAGATTCC-GTACTGAC


title: nill_60

description:
processed data column: P_87
F74_3_H3LWLDMXX_AGCGATAG-CAGGACGT


title: nill_61

description:
processed data column: P_88
G98_3_H3MCMDMXX_TCTCGCGC-TAATCTTA


title: rej_28

description:
processed data column: P_91
H44_3_H3MCMDMXX_CGCTCATT-GGCTCTGA


title: nill_62

description:
processed data column: P_89
H131_3_H3LWLDMXX_TCCGCGAA-ATAGAGGC


title: nill_64

description:
processed data column: P_92
H64_3_H3MCMDMXX_TAATGCGC-ATAGAGGC


title: nill_63

description:
processed data column: P_90
H33_3_H3LWLDMXX_CGGCTATG-GTACTGAC


title: rej_27

description:
processed data column: P_86
F146_3_H3LWLDMXX_CGGCTATG-TAATCTTA


title: nill_59

description:
processed data column: P_85
F102_3_H3MCMDMXX_GAATTCGT-TAATCTTA


title: nill_58

description:
processed data column: P_84
D83_3_H3MCMDMXX_TCTCGCGC-GGCTCTGA


title: rej_30

description:
processed data column: P_98
L86_3_H3MCMDMXX_AGCGATAG-AGGCGAAG


title: rej_26

description:
processed data column: P_83
C91_3_H3MCMDMXX_CTGAAGCT-CCTATCCT


title: nill_66

description:
processed data column: P_95
J40_3_H3LWLDMXX_ATTACTCG-CAGGACGT


title: nill_56

description:
processed data column: P_80
C27_3_H3LWLDMXX_CTGAAGCT-CAGGACGT


title: rej_24

description:
processed data column: P_79
C16_3_H3LWLDMXX_TCCGGAGA-CCTATCCT


title: nill_54

description:
processed data column: P_76
B71_3_H3MCMDMXX_CTGAAGCT-GGCTCTGA


title: rej_23

description:
processed data column: P_77
B82_3_H3MCMDMXX_TCCGCGAA-TAATCTTA


title: nill_55

description:
processed data column: P_78
C140_3_H3MCMDMXX_TCTCGCGC-CCTATCCT


title: nill_51

description:
processed data column: P_72
B148_3_H3MCMDMXX_GAATTCGT-GTACTGAC


title: rej_21

description:
processed data column: P_70
A84_3_H3MCMDMXX_TAATGCGC-CAGGACGT


title: nill_57

description:
processed data column: P_81
C41_3_H3MCMDMXX_CTGAAGCT-ATAGAGGC


title: nill_52

description:
processed data column: P_74
B31_3_H3MCMDMXX_ATTACTCG-CCTATCCT


title: rej_25

description:
processed data column: P_82
C75_3_H3LWLDMXX_ATTCAGAA-CAGGACGT


title: nill_53

description:
processed data column: P_75
B66_3_H3MCMDMXX_GAATTCGT-AGGCGAAG


title: nill_49

description:
processed data column: P_69
561_HVLK3DRXX_ATATCTCG-ACTAAGAT


title: rej_22

description:
processed data column: P_73
B24_3_H3LWLDMXX_TCCGCGAA-GGCTCTGA


title: rej_20

description:
processed data column: P_68
559_HVLK3DRXX_ACCTTGGC-ATGAGGCC


title: rej_19

description:
processed data column: P_67
557_HVLK3DRXX_GTTCCAAT-GCAGAATT


title: nill_48

description:
processed data column: P_66
556_HVLK3DRXX_GCAATGCA-AACGTTCC


title: nill_50

description:
processed data column: P_71
B127_3_H3LWLDMXX_CTGAAGCT-CCTATCCT


title: rej_18

description:
processed data column: P_63
551_HVLK3DRXX_ATATGGAT-TAATACAG


title: nill_47

description:
processed data column: P_65
553_HVLK3DRXX_AAGATACT-ATGTAAGT


title: nill_44

description:
processed data column: P_61
549_HVLK3DRXX_TAAGTGGT-GGCTTAAG


title: nill_45

description:
processed data column: P_62
550_HVLK3DRXX_CGGACAAC-AATCCGGA


title: nill_43

description:
processed data column: P_60
545_HVLK3DRXX_TCGTAGTG-CCAAGTCT


title: rej_17

description:
processed data column: P_59
539_HVLK3DRXX_GATTCTGC-CTCTCGTC


title: nill_46

description:
processed data column: P_64
552_HVLK3DRXX_GCGCAAGC-CGGCGTGA


title: nill_41

description:
processed data column: P_56
535_HVLK3DRXX_TACCGAGG-AGTTCAGG


title: rej_16

description:
processed data column: P_57
536_HVLK3DRXX_CGTTAGAA-GACCTGAA


title: nill_38

description:
processed data column: P_53
530_HVNL5DRXX_TCCAACGC-TTGGACTT


title: nill_42

description:
processed data column: P_58
538_HVLK3DRXX_AGCCTCAT-TCTCTACT


title: nill_40

description:
processed data column: P_55
532_HVLK3DRXX_TTACAGGA-GCTTGTCA


title: rej_15

description:
processed data column: P_52
529_HVNL5DRXX_CTTGGTAT-CCAAGTCC


title: rej_14

description:
processed data column: P_50
527_HVNL5DRXX_ACTAAGAT-AACCGCGG


title: nill_37

description:
processed data column: P_51
528_HVNL5DRXX_GTCGGAGC-GGTTATAA


title: nill_36

description:
processed data column: P_49
526_HVNL5DRXX_ATGAGGCC-GTTAATTG


title: nill_33

description:
processed data column: P_44
517_HVNL5DRXX_CGGCGTGA-GCGCCTGT


title: nill_35

description:
processed data column: P_47
523_HVNL5DRXX_AACGTTCC-GGAGTACT


title: nill_32

description:
processed data column: P_43
516_HVNL5DRXX_TAATACAG-ATATTCAC


title: nill_34

description:
processed data column: P_45
520_HVNL5DRXX_ATGTAAGT-ACTCTATG


title: rej_13

description:
processed data column: P_48
525_HVNL5DRXX_GCAGAATT-ACCGGCCA


title: rej_31

description:
processed data column: P_101
M134_3_H3LWLDMXX_ATTACTCG-GTACTGAC


title: sgZNF397DHT-3

city: Dallas

first: Ping

last: Mu

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Cente

data_processing:
Data were analyzed as the following: FastQC Tool (v0.11.8) was used for quality control and pre-processing (https://github.com/s-andrews/FastQC).
Alignment to human genome GRCh38 was performed using Bowtie 2 (v2.4.2).
Accessible chromatin peaks were called using MACS3 (v3.0.0, https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137) with ‘BAMPE’ mode and q-value cutoff at 0.01.
Assembly: hg38
Supplementary files format and content: narrowPeak (information on called peaks)

source_name: LnCaP/AR

growth_protocol: LNCaP/AR cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 3 days.

extract_protocol:
80,000 LnCaP/AR cells were used in ATACseq assay, the libraries were prepared by Active Motif ATAC-seq kit (#53150).
Follow the instructions of Active Motif ATAC-seq kit (#53150).
Illuminal NextSeq 2000 P2 100cycles

treatment_protocol: LNCaP/AR cells were starved in RPMI medium supplemented with 10% charcoal-stripped serum (CSS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate for 3 days and treated with Vehicle (0.1% Ethanol) or dihydrotestosterone (DHT) for 4 hours.

value: LnCaP/AR

value: prostate cancer cell line

value: CSS 10nM DHT


title: rej_12

description:
processed data column: P_46
522_HVNL5DRXX_GGTACCTT-AAGACGTC


title: sgZNF397DHT-2


title: sgZNF397-3

value: CSS


title: nill_31

description:
processed data column: P_42
514_HVNL5DRXX_AATCCGGA-CTACAGTT


title: sgZNF397DHT-1


title: nill_29

description:
processed data column: P_40
512_HVNL5DRXX_TTGGACTC-GGAAGCAG


title: nill_30

description:
processed data column: P_41
513_HVNL5DRXX_GGCTTAAG-TCGTGACC


title: nill_28

description:
processed data column: P_39
511_HVNL5DRXX_CCAAGTCT-AAGGATGA


title: sgZNF397-1


title: nill_39

description:
processed data column: P_54
531_HVLK3DRXX_CCGTGAAG-ATCCACTG


title: sgZNF397-2


title: sgNTDHT-3

value: sgNTDHT


title: nill_27

description:
processed data column: P_37
508_HVNL5DRXX_TCTCTACT-CGCGGTTC


title: sgNTDHT-2


title: rej_11

description:
processed data column: P_38
509_HVNL5DRXX_CTCTCGTC-TATAACCT


title: sgNTDHT-1


title: nill_25

description:
processed data column: P_35
505_HVNL5DRXX_AGTTCAGG-CCAACAGA


title: nill_26

description:
processed data column: P_36
507_HVNL5DRXX_GACCTGAA-TTGGTGAG


title: nill_24

description:
processed data column: P_34
504_HVNL5DRXX_TGGATCGA-GTGCGATA


title: sgNT-2

value: sgNT


title: sgNT-3


title: nill_23

description:
processed data column: P_33
503_HVNL5DRXX_CAAGCTAG-ACATAGCG


title: sgZNF397_sgTET2_5hmC_ChIPed_2

data_processing:
Raw sequencing reads were quality controlled using FastQC Tool (v0.11.9).
Reads were aligned to human reference genome assembly (GRCh38/hg38) using Bowtie 2 (v2.4.4, RRID: SCR_016368)90 with default parameters.
5hmC-Seq peaks were called using MACS2 (v2.1.2). Input DNA was used as the control for peak calling.
Counts for called peaks were done using FeatureCounts (v1.5.3) .
Assembly: hg38
Supplementary files format and content: csv (counts for called peaks)
Library strategy: 5hmC

extract_protocol:
Genomic DNA were extracted and sheared into fragments with an average size of 200 bp. 60 μg sonicated genomic DNA used in glucose transfer reaction and then proceeded biotinylation reaction. DNA were captured by Dynabeads Myone Streptavidin C1 (Invitrogen™ 65001) and libraries were prepared.
Libraries were prepared by using NEBNext1100 ® Ultra™ II DNA Library Prep kit (NEB, E7103)
Illuminal NextSeq 2000 P2 100cycles

tag: fraction

value: IP


title: nill_22

description:
processed data column: P_32
502_HVNL5DRXX_GCTTGTCA-GAACATAC


title: sgNT-1


title: nill_21

description:
processed data column: P_31
501_HVNL5DRXX_ATCCACTG-AGGTGCGT


title: nill_20

description:
processed data column: P_30
500_HVNL5DRXX_AAGTCCAA-TATGAGTA


title: sgZNF397_5hmC_ChIPed_2


title: nill_19

description:
processed data column: P_29
499_HVNL5DRXX_GGACTTGG-CGCAGACG


title: sgZNF397_sgTET2_5hmC_ChIPed_1


title: rej_9

description:
processed data column: P_26
493_HVWM5DMXX_CGTCTGCG-ATTGTGAA


title: nill_17

description:
processed data column: P_25
492_HVWM5DMXX_TACTCATA-GCCACAGG


title: rej_10

description:
processed data column: P_27
494_HVWM5DMXX_TCGATATC-ACTCGTGT


title: sgZNF397_5hmC_input

value: input


title: sgNT_5hmC_ChIPed_1


title: sgNT_5hmC_ChIPed_2


title: nill_16

description:
processed data column: P_24
491_HVWM5DMXX_ACGCACCT-CCTTCACC


title: rej_8

description:
processed data column: P_22
488_HVWM5DMXX_CGCTATGT-GTGTCGGA


title: nill_15

description:
processed data column: P_23
490_HVWM5DMXX_GTATGTTC-TTCCTGTT


title: sgZNF397_H3K4me3_1

data_processing:
Raw sequencing reads were quality controlled using FastQC Tool (v0.11.9).
Reads were aligned to human reference genome assembly (GRCh38/hg38) using Bowtie 2 (v2.4.4, RRID: SCR_016368)90 with default parameters.
5hmC-Seq peaks were called using MACS2 (v2.1.2). Input DNA was used as the control for peak calling.
Assembly: hg38
Supplementary files format and content: FeatureCounts.csv (counts for called peaks); .narrowpeak file (information on called peaks)

extract_protocol:
The DNA were sheared into 200-300 bp by Bioruptor® Pico, 1% sample was saved as input and the rest samples were incubated overnight with antibody for each reaction in 4 °C. Dynabeads Protein G was added to each reaction the next day and incubated for 4 hours in 4 °C. The samples were washed sequentially with low salt wash buffer, high salt wash buffer, LiCl wash buffer and TE buffer. DNA was eluted from the beads and reverse-crosslinked in 0.2M NaCl at 65°C for 4 hours. The input DNA and ChIPed DNA were prepared for ChIPseq.
ChIP-Seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep kit (NEB, E7103).
Illuminal NextSeq 2000 P2 100cycles

treatment_protocol: For AR, H3K4me3 and H3K27ac ChIP, cells then were crosslinked with 1% PFA for 10 min and 0.125 M glycine for 5 min. For GFP-tagged ZNF397 ChIP, cells were two-step cross-linked with 2 mM DSG (Disuccinimidyl glutarate) for 45 min and 1% PFA for 10 min, cross-link were stopped by 0.125 M glycine for 5 min.

tag: chip antibody

value: Anti-Histone H3 (tri methyl K4) antibody - ChIP Grade (ab8580)


title: sgZNF397_H3K4me3_2


title: sgNT_5hmC_input


title: nill_14

description:
processed data column: P_21
485_HVWM5DMXX_TATCGCAC-ACACTAAG


title: nill_13

description:
processed data column: P_20
480_HVWM5DMXX_CTCACCAA-TTGCCTAG


title: sgNT_H3K4me3_1


title: rej_7

description:
processed data column: P_17
477_HVWM5DMXX_TCATCCTT-AGCTCGCT


title: sgZNF397Input


title: sgZNF397_sgTET2_5hmC_input


title: sgNTInput


title: nill_18

description:
processed data column: P_28
498_HVNL5DRXX_TTATAACC-GATATCGA


title: sgZNF397_H3K27ac_2

value: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (ab4729)


title: nill_10

description:
processed data column: P_16
476_HVWM5DMXX_CTGCTTCC-GATCTATC


title: sgZNF397_H3K27ac_1


title: rej_6

description:
processed data column: P_15
472_HVWM5DMXX_AACTGTAG-TGCGGCGT


title: sgNT_H3K27ac_2


title: nill_9

description:
processed data column: P_14
470_HVWM5DMXX_GTGAATAT-GAATGAGA


title: GFP_ZNF397_ChIPed_2

value: Anti-GFP antibody (ab290)


title: GFP_ZNF397_ChIPed_1


title: nill_8

description:
processed data column: P_13
469_HVWM5DMXX_ACAGGCGC-AGGCAGAG


title: rej_5

description:
processed data column: P_12
465_HVWM5DMXX_CATAGAGT-TGGTGGCA


title: GFP_ZNF397_input_1


title: GFP_ZNF397_input_2


title: rej_4

description:
processed data column: P_11
464_HVWM5DMXX_TGCGAGAC-CAACAATG


title: sgNT_H3K4me3_2


title: rej_3

description:
processed data column: P_10
463_HVWM5DMXX_GACGTCTT-GGTGAACC


title: diseased nucleus pulposus (Thompson grade III-IV) single cell RNAseq, donor4

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced raw reads were processed using the Cell Ranger (v6.0.0, 10X Genomics) pipeline. Reads were aligned to the GRChg38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated feature and barcode files and matrix files

source_name: nucleus pulposus

extract_protocol:
Spine samples from postmortem donors with no recorded history of spine trauma or disc degeneration were obtained from Lifesharing under IRB approval. Lumbar spines were resected with surrounding muscles intact, wrapped in sterile gauze and transported on ice. The specimens were washed with 70% EtOH and the discs were isolated intact using an Orthopedic bone saw OTS-1 (Orthopedic Drills & Medical Devices, Covina, USA). IVDs were cut to expose the center and macroscopic grading was performed by applying the Thompson grading system. Using a sterile scalpel, the AF and NP tissues were isolated. The inner transition zone between the NP and AF was removed to prevent mixing of the cells from the two compartments. AF and NP were separately stored on ice in sterile DPBS (Gibco #14190144) containing 10% calf-serum. Under sterile conditions the isolated NP and AF tissues were washed in 70% EtOH, weighed, and homogenized into very fine pieces for enzymatic digestion and single cell isolation.
Single cell RNA-seq was performed using the 10X Genomics Chromium technology. Briefly, cells were partitioned into droplets using the Chromium Controller with the Next GEM Single Cell 3’ Reagent Kit v3.1 using dual indexing. Next, cells were lysed and the polyadenylated transcripts reverse transcribed to generate barcoded cDNA following the recommended 10X Genomics protocol. The quality of both the cDNA and the final libraries were assessed using the Agilent Bioanalyzer 2100 following the guidance provided by the 10X Genomics user guide. Libraries were loaded onto 100-cycle flowcells for sequencing using the NextSeq2000 (Ilumina) and sequenced as follows: read1 = 28 cycles, i7 index = 10 cycles, i5 index = 10 cycles, read 2 = 90 cycles. 10,000 cells were targeted per sample with a target of 20,000-25,000 reads per cell.

value: nucleus pulposus

tag: disease state

value: diseased

tag: patient id

tag: age

tag: Sex

value: M

tag: disc


title: nill_7

description:
processed data column: P_9
462_HVWM5DMXX_AGTACTCC-AACAGGTT

value: Renal Allograft Biopsy


title: nill_6

description:
processed data column: P_8
460_HVWM5DMXX_TGGCCGGT-GCGCTCTA

value: Nill


title: sgZNF397_5hmC_ChIPed_1

tag: cell line

tag: cell type


title: nill_11

description:
processed data column: P_18
478_HVWM5DMXX_AGGTTATA-CGGAACTG

tag: tissue


title: diseased nucleus pulposus (Thompson grade III-IV) single cell RNAseq, donor3

description: 10X Genomics


title: diseased nucleus pulposus (Thompson grade III-IV) single cell RNAseq, donor2

description: 10X Genomics


title: nill_12

description:
processed data column: P_19
479_HVWM5DMXX_GAACCGCG-TAAGGTCA


title: nill_2

description:
processed data column: P_4
456_HVWM5DMXX_ATTGTGAA-GCAATGCA


title: nill_4

description:
processed data column: P_6
458_HVWM5DMXX_GTCTACAC-ACCTTGGC


title: diseased nucleus pulposus (Thompson grade III-IV) single cell RNAseq, donor1

description: 10X Genomics


title: nill_3

description:
processed data column: P_5
457_HVWM5DMXX_ACTCGTGT-GTTCCAAT


title: Y6 endothelial cells

city: Atlanta

first: Katherine

last: Owsiany

state: GA

address: 1365 Clifton Rd NE

institute: Emory University

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: tab-separated values files and matrix files

source_name: iPSC-derived endothelial cells

extract_protocol:
Y6-Ecs were washed with PBS and lifted with 0.05% trypsin for 3 minutes at 37 degrees. Digestion was stopped with media containing 5% FBS. Cells were centrifuged for 10 minutes at 300 xg and resuspended in growth media, and strained using a 30 um filter before submission to the Emory Genomics Core for 10x sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence and paired-end constructs with P5 and P7 sequences were added.

value: iPSC-derived endothelial cells

value: iPSC- derived endothelial cells


title: diseased nucleus pulposus (Thompson grade III) single cell RNAseq, donor2

description: 10X Genomics


title: diseased nucleus pulposus (Thompson grade II-III) single cell RNAseq, donor2

description: 10X Genomics


title: sgNT_H3K27ac_1

value: LnCaP/AR

value: prostate cancer cell line


title: rej_2

description:
processed data column: P_3
454_HVWM5DMXX_GCCACAGG-ATGGCATG

value: Rej


title: nill_1

description:
processed data column: P_2
453_HVWM5DMXX_CCTTCACC-GGAGCGTC


title: diseased nucleus pulposus (Thompson grade II-III) single cell RNAseq, donor1

description: 10X Genomics


title: diseased nucleus pulposus (Thompson grade III) single cell RNAseq, donor1

description: 10X Genomics


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor3

description: 10X Genomics

source_name: annulus fibrosus

value: annulus fibrosus


title: rej_1

description:
processed data column: P_1
452_HVWM5DMXX_TTCCTGTT-AAGATACT


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor4

description: 10X Genomics


title: nill_5

description:
processed data column: P_7
459_HVWM5DMXX_CAATTAAC-ATATCTCG


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor2

description: 10X Genomics


title: diseased annulus fibrosus (Thompson grade II-III) single cell RNAseq, donor2

description: 10X Genomics


title: Renal Allograft Biopsy_P_135

data_processing:
Raw RNA-Seq reads were quality controlled and trimmed using FastQC and Trimmomatic. Alignment to the GRCh38 human reference genome was performed using STAR, followed by quantification of gene-level expression with featureCounts.
Assembly: GRCh37-hg19
Supplementary files format and content: A comma-seperated text file includes raw counts per sample

source_name: Kidney

value: Kidney

tag: protocol

tag: disease

value: Australian Chronic Allograft Dysfunction

tag: treatment

value: Delayed


title: Renal Allograft Biopsy_P_134

value: Immediate


title: Renal Allograft Biopsy_P_132


title: Renal Allograft Biopsy_P_133


title: Renal Allograft Biopsy_P_136


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor1

description: 10X Genomics


title: Renal Allograft Biopsy_P_131


title: diseased annulus fibrosus (Thompson grade III) single cell RNAseq, donor2

description: 10X Genomics


title: diseased annulus fibrosus (Thompson grade III) single cell RNAseq, donor1

description: 10X Genomics


title: diseased annulus fibrosus (Thompson grade II-III) single cell RNAseq, donor1

description: 10X Genomics


title: Renal Allograft Biopsy_P_129


title: Renal Allograft Biopsy_P_127


title: Renal Allograft Biopsy_P_128


title: Renal Allograft Biopsy_P_126


title: Renal Allograft Biopsy_P_130


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor5

description: 10X Genomics


title: Renal Allograft Biopsy_P_125


title: healthy nucleus pulposus (Thompson grade II) single cell RNAseq, donor2

description: 10X Genomics

extract_protocol:
Spine samples from tissue bank donors (3 males; aged 21-27) with no recorded history of spine trauma or disc degeneration were obtained from Lifesharing under IRB approval (#15-6648).Lumbar spines were resected with surrounding muscles intact, wrapped in sterile gauze and transported on ice.The specimens were washed with 70% EtOH and the discs were isolated intact from T12-L1, L3–L4 and T12-L1 using an Orthopedic bone saw OTS-1 (Orthopedic Drills & Medical Devices, Covina, USA). IVDs were cut to expose the center and macroscopic scoring was performed by applying the Thompson grading system.All IVDs used for this study were scored as Thompson grade II. Using a sterile scalpel, the AF and NP tissues were isolated. The inner transition zone between the NP and AF was removed to prevent mixing of the cells from the two compartments and separately stored on ice in sterile DPBS (Gibco #14190144) containing 10% calf-serum. Under sterile conditions the isolated NP and AF tissues were washed in 70% EtOH, weighed, and homogenized into very fine pieces for enzymatic digestion and single cell isolation.
Single cell RNA-seq was performed using the 10X Genomics Chromium technology. Briefly, cells were partitioned into droplets using the Chromium Controller with the Next GEM Single Cell 3’ Reagent Kit v3.1 using dual indexing. Next, cells were lysed and the polyadenylated transcripts reverse transcribed to generate barcoded cDNA following the recommended 10X Genomics protocol. The quality of both the cDNA and the final libraries were assessed using the Agilent Bioanalyzer 2100 following the guidance provided by the 10X Genomics user guide. Libraries were loaded onto 100-cycle flowcells for sequencing using the NextSeq2000 (Ilumina) and sequenced as follows: read1 = 28 cycles, i7 index = 10 cycles, i5 index = 10 cycles, read 2 = 90 cycles. 10,000 cells were targeted per sample with a target of 20,000-25,000 reads per cell.

value: healthy


title: healthy nucleus pulposus (Thompson grade II) single cell RNAseq, donor3

description: 10X Genomics


title: Renal Allograft Biopsy_P_124


title: Renal Allograft Biopsy_P_122


title: healthy annulus fibrosus (Thompson grade II) single cell RNAseq, donor2

description: 10X Genomics


title: healthy annulus fibrosus (Thompson grade II) single cell RNAseq, donor3

description: 10X Genomics


title: healthy annulus fibrosus (Thompson grade II) single cell RNAseq, donor1

description: 10X Genomics


title: Renal Allograft Biopsy_P_121


title: Renal Allograft Biopsy_P_118


title: Renal Allograft Biopsy_P_119


title: Renal Allograft Biopsy_P_117


title: Control 3

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

data_processing:
Sequencing reads were trimmed and filtered to remove adaptor contamination and poor-quality bases using trimmomatic.
The resulting read files were mapped to the GRCm38 genome assembly using Hisat2 with default parameters.
The number of reads mapping to the genomic features annotated in Ensembl with a MAPQ score higher than or equal to 10 was calculated using htseq-count with default parameters.
Assembly: GRCm38
Supplementary files format and content: Text files in comma-separated value format with the raw counts of read pairs uniquely and concordantly mapped to each gene

source_name: colon

extract_protocol:
2cm distal colon segments were taken from mice after confirmation of death, and placed into 1 ml of RNA later. RNA was extracted with Qiazol reagent (Invitrogen). Distilled solutions of RNA were purified using chloroform and isopropanol and eluted with ethanol before being resuspended in RNAse free water. RNA was cleaned up using the Qiagen RNeasy Microkit according to the manufacturer’s guidelines.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: colon

tag: genotype


title: Control 1


title: Renal Allograft Biopsy_P_123


title: DKO 2

value: Rag1-/- x Ctla4-/-


title: diseased annulus fibrosus (Thompson grade III-IV) single cell RNAseq, donor6

description: 10X Genomics

value: diseased


title: Renal Allograft Biopsy_P_116


title: Renal Allograft Biopsy_P_115


title: DKO 1


title: healthy nucleus pulposus (Thompson grade II) single cell RNAseq, donor1

description: 10X Genomics

value: nucleus pulposus

value: M


title: Renal Allograft Biopsy_P_114

value: Renal Allograft Biopsy


title: Control 2


title: Sample 4b [WT High Rep 1]

city: San Francisco

first: Yang

last: Sun

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

data_processing:
Bulk RNA Seq: The raw fastq files were clipped and filtered using fastq-mcf v.1.04.636 to remove low quality reads and bases, homopolymers, and adapter sequences. The filtered reads were aligned using the STAR v.2.4 with the default settings to the mm10 transcriptome to produce count matrices for each sample.
Single cell RNA seq: The raw fastq files were aligned using CellRanger v3.0.1 and 3.0.2 software with the default settings to the mm10 transcriptome with the addition of the sequence for the eGFP transcript and the vdj GRCm38 v 3.1.0 reference for the GEX and TCR fastqs, respectively.
We filtered out 721 cells with less than 100 or more than 3000 genes detected and filtered out 14,388 genes detected in less than 3 cells. We also filtered out 1,066 cells with more than 10% of total counts (UMIs) mapping to mitochondrial genes and 1008 cells determined to be contaminating B cells based on CD19 expression.
The raw counts were normalized to 10,000 counts, log1p-normalized and scaled.
For technical and batch correction, we regressed out total UMI counts and % counts mapping to mitochondrial genes and used combat for batch correction with each sample as a batch.
We identified 1119 highly variable genes (excluding all Trav and Trbv genes to avoid clustering cells based on expression of those genes) which were used with the default settings in scanpy v.1.4.3 for PCA analysis followed by leiden clustering after nearest neighbor detection and UMAP projection. This analysis identified 13 clusters which we collapsed into 9 cell sub-types based on differential gene analysis.
For each 10x well alignment output from cellranger, we used velocyto v.0.17.17 to create a loom file with the spliced, unspliced, and ambiguous counts with the Dec. 2011 GRCm38/mm10 repeat masking gtf file from the UCSC genome browser 70, 71. The loom files across all wells were merged and then subsetted to all cells in the T.4NNr4a1 cluster.
The resulting object was used to run the dynamical model from scvelo v.0.2.1 with the default settings to uncover the RNA velocity to predict the latent time for each cell.
We used we used a Gaussian mixture model with the GaussianMixture tool from sklearn v.0.23.1  to deconvolute four underlying individual Gaussian distributions from the latent time distribution for cells from the T.4NNr4a1 cluster.
For trajectory inference between the four distributions (“Stage 1” – “Stage 4”), we used the graph-based tool PAGA within scvelo to predict velocity-inferred transitions among the clusters.
Genome_build: mm10
Genome_build: vdj GRCm38 v 3.1.0
Supplementary_files_format_and_content: comma separated text file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: h5ad file with filtered, processed, and cluster annotated data from all eight combined single cell RNA seq libraries
Supplementary_files_format_and_content: h5ad file with cells from T.4 Nr4a1 cluster from single cell RNA seq data post trajectory analysis with scvelo
Supplementary_files_format_and_content: comma separated text file with clonotype and TCR chain assignment for each cell barcode in the indicated library

source_name: naive CD4 T cells

extract_protocol:
Negatively selected CD4 T cells from the lymph node were sorted for CD62LhiCD44loCD25- and the 10% highest (GFPhi) expressing T cells. Cells were washed, pelleted and immediately flash frozen using dry ice in ethyl alcohol. Sample was processed with Illumina TruSeq Stranded mRNA kit (Cat#: RS-122-2103) for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Balb/c

value: lymph node

value: wild type

tag: subgroup

value: naive CD4 T cells


title: Sample 6b [WT High Rep 3]


title: Renal Allograft Biopsy_P_111


title: Renal Allograft Biopsy_P_120


title: Sample 6a [WT Low Rep 3]

extract_protocol:
Negatively selected CD4 T cells from the lymph node were sorted for CD62LhiCD44loCD25- and the 10% lowest (GFPlo) expressing T cells. Cells were washed, pelleted and immediately flash frozen using dry ice in ethyl alcohol. Sample was processed with Illumina TruSeq Stranded mRNA kit (Cat#: RS-122-2103) for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Renal Allograft Biopsy_P_112


title: Renal Allograft Biopsy_P_110


title: Renal Allograft Biopsy_P_109


title: Sample 4a [WT Low Rep 1]


title: Sample 3b [SKG High Rep 3]

value: SKG


title: Renal Allograft Biopsy_P_108


title: DKO 3


title: Sample 2b [SKG High Rep 2]


title: Renal Allograft Biopsy_P_106


title: Sample 3a [SKG Low Rep 3]


title: Renal Allograft Biopsy_P_107


title: Renal Allograft Biopsy_P_103


title: Sample 1a [SKG Low Rep 1]


title: Renal Allograft Biopsy_P_104


title: Renal Allograft Biopsy_P_105


title: Sample 5b [WT High Rep 2]


title: Renal Allograft Biopsy_P_113


title: Renal Allograft Biopsy_P_100


title: CRISPRi_HEK293T_TERC_RepB_LysisPlate6

source_name: embryonic kidney

value: embryonic kidney

value: CRISPRi


title: CRISPRi_HEK293T_TERC_RepD_LysisPlate6


title: Sample 5a [WT Low Rep 2]


title: CRISPRi_HEK293T_PVT1_RepD_LysisPlate4


title: Renal Allograft Biopsy_P_99

value: Kidney

value: Australian Chronic Allograft Dysfunction


title: CRISPRi_HEK293T_TERC_RepC_LysisPlate6


title: CRISPRi_HEK293T_TERC_RepA_LysisPlate6


title: Renal Allograft Biopsy_P_102

value: Immediate


title: CRISPRi_HEK293T_PVT1_RepC_LysisPlate4


title: CRISPRi_HEK293T_PVT1_RepB_LysisPlate4


title: Sample 1b [SKG High Rep 1]


title: Sample 2a [SKG Low Rep 2]


title: Bacterial culture treatment MBOA5

city: Bern

first: Marco

last: Kreuzer

state: Bern

address: Baltzerstrasse 6

country: Switzerland

institute: University of Bern

data_processing:
The fastq files were mapped to the reference of LMB2 using HiSat2. The count table was created using FeatureCounts
Assembly: SAMN37150065
Supplementary files format and content: tab delimited file containing the raw counts of each RNA library mapped to the reference of Biosample SAMN37150065

organism: Microbacterium sp. LMB2-1.2

source_name: bacterial culture

growth_protocol: The Microbacterium LMB2 was grown for 16 h in 96-well plates containing 200 µL of liquid 50% TSB (tryptic soy broth) under continuous shaking on a laboratory shaker (28°C, 180 rpm shaking). For details, see Thoenen et al. (2024).

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) with subsequent DNAse treatment using the RapidOut DNA removal kit. After quantification the RNA was depleted of ribosomal RNA using the Ribo-Zero plus rRNA depletion Kit (illumina).
RNA libraries were prepared using Illumina TruSeq Stranded total RNA Sample Prep kit following the manufacturers protocol

treatment_protocol: Half of the cultures were grown in TSB containing 500 µM MBOA (dissolved in DMSO) and the other half in TSB containing the equivalent amount of the solvent DMSO. For details, see Thoenen et al. (2024).

value: bacterial culture

value: MBOA


title: CRISPRi_HEK293T_NORAD_RepD_LysisPlate3


title: Renal Allograft Biopsy_P_98


title: Renal Allograft Biopsy_P_95


title: CRISPRi_HEK293T_NORAD_RepB_LysisPlate3


title: CRISPRi_HEK293T_NORAD_RepA_LysisPlate3


title: CRISPRi_HEK293T_NORAD_RepC_LysisPlate3


title: Bacterial culture treatment MBOA3


title: Renal Allograft Biopsy_P_101

value: Delayed


title: Bacterial culture treatment MOBA2


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate6


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate5


title: Renal Allograft Biopsy_P_94


title: Renal Allograft Biopsy_P_97


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate3


title: CRISPRi_HEK293T_PVT1_RepA_LysisPlate4


title: Renal Allograft Biopsy_P_96


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate4


title: Bacterial culture treatment MBOA7


title: Renal Allograft Biopsy_P_92


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate1


title: Renal Allograft Biopsy_P_93


title: Renal Allograft Biopsy_P_91


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate5


title: Bacterial culture control DMSO5

value: DMSO


title: CRISPRi_HEK293T_NEAT1_RepB_LysisPlate2


title: Renal Allograft Biopsy_P_90


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate4


title: Bacterial culture control DMSO6


title: Bacterial culture control DMSO4


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate3


title: Renal Allograft Biopsy_P_89


title: Bacterial culture treatment MBOA1


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate2


title: Bacterial culture control DMSO2


title: Renal Allograft Biopsy_P_88


title: CRISPRi_HEK293T_JPX_RepD_LysisPlate2


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate1


title: Renal Allograft Biopsy_P_87


title: Bacterial culture control DMSO1


title: CRISPRi_HEK293T_NEAT1_RepA_LysisPlate6


title: CRISPRi_HEK293T_JPX_RepA_LysisPlate2


title: CRISPRi_HEK293T_JPX_RepC_LysisPlate2


title: CRISPRi_HEK293T_FTX_RepD_LysisPlate2


title: CRISPRi_HEK293T_FTX_RepB_LysisPlate2


title: Renal Allograft Biopsy_P_85


title: Renal Allograft Biopsy_P_84


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate6


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate5


title: Renal Allograft Biopsy_P_86


title: Renal Allograft Biopsy_P_83


title: CRISPRi_HEK293T_FTX_RepA_LysisPlate2


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate4


title: Sham_Wk18F

first: Josh

last: Stone

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
Raw reads were filtered by the BGI pipeline SOAPnuke. Cleaned reads were mapped to the mouse genome mm10 using Bowtie2.
FPKM values were calculated from raw counts within DESeq2 using the fpkm() function.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

source_name: Lung adenocarcinoma

growth_protocol: KrasLSL-G12D/+; Trp53LSL-R172H/+ (KP) mice were purchased from Jackson Laboratory (Bar Harbor, ME) and housed under SPF conditions in accordance with the approved NIH-NCI/CCR animal use protocol (# ASP-19-334) and biosafety protocol (#19-51)

extract_protocol:
RNA was extracted by Quick-DNA/RNA Miniprep kit (Zymo Research) and quality determined by TapeStation (Agilent).
1 µg of RNA was polyA-enriched and cDNA synthesis was performed with first strand random hexamer reverse transcription. Adapters were ligated to cDNA then closed to form single-stranded circular DNA and subjected to rolling circle relication for sequencing, according to the manufacturer's instructions (BGI).

treatment_protocol: Tumors were activated by intranasal instillation of Adeno-Cre-CMV virus in mice aged 5-9 weeks. Bacterial or PBS instillations began two weeks following adenovirus, then biweekly for a total of six bacterial instillations. Mice were sacrificed at two timepoints, 10 weeks (5 instillations) or 14 weeks (6 instillations).

value: Lung adenocarcinoma

tag: timepoint

value: KrasLSL-G12D/+; Trp53LSL-R172H/+

value: Sham


title: Sham_Wk18G


title: Sham_Wk18H


title: CRISPRi_HEK293T_FTX_RepC_LysisPlate2


title: Sham_Wk18J


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate3


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate2


title: CRISPRi_HEK293T_JPX_RepB_LysisPlate2


title: Renal Allograft Biopsy_P_81

value: Renal Allograft Biopsy


title: CRISPRi_HEK293T_PoolCTL_RepB_LysisPlate1


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate6


title: Sham_Wk18D


title: Renal Allograft Biopsy_P_80


title: Sham_Wk18I


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate5


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate4


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate3


title: Renal Allograft Biopsy_P_79


title: Sham_Wk18C


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate2


title: CRISPRi_HEK293T_PoolCTL_RepA_LysisPlate1


title: Sham_Wk18A


title: Sham_Wk18E


title: KD, Input

data_processing:
Raw sequencing reads from ChIP-Seq experiments were quality controlled using FastQC Tool (v0.11.9) and aligned to human reference genome assembly (GRCh38/hg38) using Bowtie2 (v2.4.4) with default parameters.
Duplicated reads were removed using Picard MarkDuplicates (v2.26.11).
ChIP-Seq peaks were called using MACS2 (v2.1.2).
Genome browser tracks were generated using bamCoverage (v2.4.1) with parameter “—normalizeUsingRPKM” and visualized using Integrative Genomics Viewer.
Motif analysis was performed using homer (v4.11).
Assembly: hg38
Supplementary files format and content: bw, txt(peak files)

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 3 days.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonication device.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep kit (NEB, Cat E7103). 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit by Agilent 2100 Bioanalyzer.

treatment_protocol: LNCaP/AR cells were starved in RPMI medium supplemented with 10% charcoal-stripped serum (CSS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate for 3 days and treated with dihydrotestosterone (DHT) for 4 hours.

value: LnCaP/AR

value: prostate cancer cell line

value: DHT


title: Renal Allograft Biopsy_P_78


title: KD, Androgen Receptor, Abcam

value: Andogen Receptor, Abcam


title: Renal Allograft Biopsy_P_82


title: Ctrl, Input


title: Sham_Wk14D


title: Ctrl, Androgen Receptor, Abcam


title: rs10_Sleep_Deprivation

city: NY

first: Riddhi

last: Shah

state: NY

address: 630W 168th Street

department: Medicine

institute: CUIMC

data_processing:
RNA-seq samples were sequenced (paired-end with 75bp read length) with Illumina NEXTSEQ 500 Mid Output System, and analyzed using Illumina’s BaseSpace software (www.illumina.com).
Reads were aligned to the Human Genome Consortium's reference human genome hg19 using TopHat (app v1.0.0).
Differential gene expression was calculated using Cufflinks assembly and Differential expression (DE) (app v1.1.0).
PCA was plotted using R-package ggfortify (v0.4.11)
Gene Ontology (GO) was performed using Metascape (https://metascape.org)
Genome_build: human genome hg19

source_name: Human Forearm Vein

growth_protocol: A 20-gauge angiocatheter was inserted into a superficial forearm vein. Under sterile conditions, 3 J-shaped vascular guide wires (Arrow, Reading, PA) were sequentially advanced into the vein up to 10 cm. ECs were retrieved from wire tips by washing with EC dissociation buffer. Harvesting yielded ~2000-5000 ECs.

extract_protocol:
For mRNA extraction, the harvested endotheial cell pellet was re-suspended with isolation buffer, incubated with biotinylated mouse anti-human monoclonal antibody directed against CD146 (Millipore, Temecula, CA,1:200) at 4°C for 15 min, then incubated at 4°C with Streptavidin FlowComp Dynabeads (Invitrogen, Solo, Norway; 1:100) for 45 min, followed by EC isolation by magnet. mRNA was extracted using RNAqueous Micro Kit (Invitrogen by Thermo Fisher Scientific) and used for constructing sequencing libraries.
Total RNA harvested from endothelial cells at the end of adequate sleep and sleep restriction was converted and amplified to cDNA using Ovation Pico WTA System V2. Amplified cDNA was then used to prepare sequencing libraries using the Ultra II DNA Library Preparation Kit (NEBNext). Briefly, mRNA was prepared from the total RNA by generation of first strand cDNA using primers containing oligo dT, which selects for the 3’ poly A tails of mRNA. The samples are fragmented and reverse transcribed into cDNA. The ends are repaired by addition of an “A” base and ligated to adapters which enable multiplexing of samples, and all fragments are enriched with PCR to get a final cDNA library. Samples were then sequenced on the Illumina NEXTSEQ 500 Mid Output System, and analyzed using Illumina’s BaseSpace software (www.illumina.com).

treatment_protocol: No Treatment

value: Endothelial cells


title: Sham_Wk14C


title: rs09_Adequate_Sleep


title: rs08_Sleep_Deprivation


title: rs07_Adequate_Sleep


title: Renal Allograft Biopsy_P_77


title: rs06_Sleep_Deprivation


title: Renal Allograft Biopsy_P_74


title: Sham_Wk14A


title: Renal Allograft Biopsy_P_73


title: rs05_Adequate_Sleep


title: rs04_Sleep_Deprivation


title: Sham_Wk18B


title: Renal Allograft Biopsy_P_72


title: rs03_Adequate_Sleep


title: rs02_Sleep_Deprivation


title: Sham_Wk10C


title: Renal Allograft Biopsy_P_76


title: gZNF397_Enz [KOCE3]

description: countTable.fpkm.txt

data_processing:
Bulk RNAseq:
Adapter trimming and quality trimming was performed with trimgalore (v0.5.0), and ribosomal RNA was removed using SortMeRNA (v4.1.0), using the original FASTQ files.
Trimmed and filtered reads were aligned to reference (GRCh38) with STAR (vSTAR2.6.1d). FeatureCounts (v1.6.4) was used for gene counts, biotype counts, and rRNA estimation.
Reads counts.csv files for genes and transcripts were generated by StringTie (v1.3.5), and RSeQC (v3.0.0) was used for generating RNA quality control metrics.
Reads counts from all samples were normalized using the R package DESeq2 1.26. The vst command in DESeq2 were also used to perform the variance stabilizing transformation.
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

extract_protocol:
LNCaP/AR cells transduced with Caspase 9 and different sgRNA constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol.
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA.

treatment_protocol: When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum.

value: LNCaP/AR cells

value: enzalutamide 10µM

tag: time

value: 6 days


title: Sham_Wk10B


title: rs01_Adequate_Sleep


title: Renal Allograft Biopsy_P_70

value: Kidney

value: Australian Chronic Allograft Dysfunction

value: Immediate


title: Renal Allograft Biopsy_P_71

value: Delayed


title: gZNF397_Enz [KOCE2]

description: countTable.fpkm.txt


title: Renal Allograft Biopsy_P_75


title: Sham_Wk10A


title: Renal Allograft Biopsy_P_69


title: gNT_Enz [CtrlCE3]

description: countTable.fpkm.txt

value: gNT


title: gZNF397_Enz [KOCE1]

description: countTable.fpkm.txt


title: gNT_Enz [CtrlCE2]

description: countTable.fpkm.txt


title: Renal Allograft Biopsy_P_68


title: Sham_Wk14B

value: Lung adenocarcinoma


title: gNT_Enz [CtrlCE1]

description: countTable.fpkm.txt


title: NAC_Wk18D

source_name: Lung tissue

value: Lung tissue

value: KrasLSL-G12D/+; Trp53LSL-R172H/+


title: gZNF397_Veh [KOFS3]

description: countTable.fpkm.txt

value: Vehicle DMSO


title: NAC_Wk18C


title: Sham_Wk10D

value: Sham


title: gZNF397_Veh [KOFS2]

description: countTable.fpkm.txt

value: prostate cancer cell line


title: NAC_Wk18B


title: gZNF397_Veh [KOFS1]

description: countTable.fpkm.txt


title: Renal Allograft Biopsy_P_67

value: Renal Allograft Biopsy


title: gNT_Veh [CtrlFS3]

description: countTable.fpkm.txt


title: Renal Allograft Biopsy_P_66


title: gNT_Veh [CtrlFS2]

description: countTable.fpkm.txt


title: gNT_Veh [CtrlFS1]

description: countTable.fpkm.txt


title: NAC_Wk18A


title: Renal Allograft Biopsy_P_65


title: NAC_Wk14D


title: NAC_Wk14C


title: Renal Allograft Biopsy_P_64


title: Renal Allograft Biopsy_P_63


title: Renal Allograft Biopsy_P_62


title: NAC_Wk14B


title: Renal Allograft Biopsy_P_61


title: NAC_Wk10D


title: NAC_Wk14A


title: Renal Allograft Biopsy_P_60


title: NAC_Wk10C


title: Renal Allograft Biopsy_P_59


title: NAC_Wk10B


title: S98-30414

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: ON

address: 60 Murray Street

department: Cancer Biology

country: Canada

institute: Sinai Health System (LTRI)

hyb_protocol: The miRtagged miRNA was then hybridized to a probe pair where the Reporter Probe carried the signal and the Capture Probe allowed the complex to be immobilized for data collection.

data_processing: miRNA abundance was normalized using the R package NanoStringNorm (v1.1.21). It examined the signal intensities of housekeeping genes, positive genes and negative genes by changing optimization options (such as SampleContent, CodeCount, and Background) and normalizes abundance values to show high abundance of housekeeping genes and positive genes but low abundance for negative controls. We used seven metrics for SampleContent, three metrics for CodeCount, four metrics for Background and three other optimization options to correct scale of abundance values. In total, 252 parameter combinations were tested. To find the best parameter combinations, we adopted a new strategy to use control sample. Control sample is composed of miRNAs that are extracted from the mix of four prostate cancer cell lines (DU-145, PC-3, C42, and LNCaP). They were equally mixed together and loaded to each batch. We measured the similarity of abundance profiles between control samples in batches and the similarity of entire miRNA profiles across batches. Also, we counted the fraction of misinterpreted samples that are erroneously normalized in the parameter settings. Additionally, we examined whether miRNAs showing significant abundance changes in TCGA data set also show differential abundances in our miRNA profiles. Finally, we identified the best parameter combination that minimizes batch effect, the variability of control samples across the two batches and misinterpreted samples, and maximize concordance of abundance changes between TCGA data set and our miRNA profiles. Similarity between control samples is measured using Spearman’s correlation coefficient (ρ). Batch effect is measured using standard deviation between batches that is estimated from linear mixed effect-model. Misinterpreted samples occur when positive controls (ratio of average abundance of positive controls and abundance of each positive control was either < 0.3 or > 3), negative controls (Z-score > 5), and housekeeping genes (Z-score > 5) are not expressed or show high abundance variation as well as the fraction of detected miRNAs (normalized transcript count > 0) in a sample is less than 10% of total endogenous miRNAs. To combine all criteria, rank product was calculated and the best optimal parameter combination was selected. In results, the data was normalized using geometric means of genes showing low coefficient of variation (low.cv.geo.mean). Quantile normalization was performed based on pegging each sample to an empirically derived distribution. The distribution is simply the mean abundance across all samples for each gene rank. Normalized miRNA abundances were log2 transformed.

label: miRtag

source_name: Macrodissected tissue

label_protocol: DNA sequences called miRtags were ligated to the mature miRNAs through base complementarity. Excess tags were removed via enzymatic digestion.

extract_protocol: Areas with ≥80% neoplastic cellularity were marked on the matched H&E slides for tumour macrodissection as described previously. RNA was extracted using mirVana miRNA Isolation Kit (Thermo-Fisher). The quality (260/230, 260/280 ratios), and concentrations of each sample were assessed using NanoDrop 1000 spectrophotometer (Thermo Scientific). Samples were stored at -80°C. RNA was eluted to a final concentration of 35 ng/uL and a total of 100 ng of RNA was analyzed on NanoString's nCounter® platform.

value: prostate cancer

tag: biochemical recurrence

value: TRUE

tag: time to last event

tag: pt

tag: preoperative psa

tag: pathological gleason score

tag: metastasis

value: FALSE


title: S01-20605

tag: age


title: Renal Allograft Biopsy_P_58

extract_protocol:
Kidney biopsy specimens were left in RNAlater (Sigma-Aldrich) overnight at 4°C before removal and storage at -80°C until RNA extraction. Specimens were chemically and physically lysed by using 2-Mercaptoethanol (Sigma-Aldrich) and TissueLyser II (Qiagen, Germany), follow by RNA extraction using AllPrep DNA/RNA/microRNA and MiniElute clean- up kits (Qiagen, Germany).
All RNA samples were frozen and stored at -80°C and then sent in bulk to the Australian Genome Research Facility (AGRF, Melbourne, Australia). Sample QC and library preparation were performed in-house, and the resultant libraries sequenced using the NovaSeq 6000 platform (Illumina)


title: S99-2902

tag: cell type


title: S99-5617


title: S99-29112


title: S99-22153


title: S99-12205


title: S99-25081


title: S01-24902


title: S99-4562


title: S01-29357


title: NAC_Wk10A

tag: tissue


title: Renal Allograft Biopsy_P_57

tag: protocol


title: S01-7166


title: S99-14582


title: S01-14083


title: S00-7363


title: S01-14768


title: S99-24747


title: Lacto_Wk18F

value: Lactobacillus gasseri


title: Renal Allograft Biopsy_P_56

tag: disease


title: S01-25468


title: Renal Allograft Biopsy_P_55

tag: treatment


title: Lacto_Wk18E

tag: genotype


title: Lacto_Wk18D


title: S98-29520


title: S99-14633


title: S01-24820


title: S01-26318


title: Lacto_Wk18C


title: Renal Allograft Biopsy_P_53


title: Lacto_Wk18A


title: Renal Allograft Biopsy_P_52


title: Renal Allograft Biopsy_P_54


title: Lacto_Wk18B


title: Renal Allograft Biopsy_P_51


title: S99-5302


title: Lacto_Wk14C


title: Renal Allograft Biopsy_P_50


title: Renal Allograft Biopsy_P_48


title: Lacto_Wk10D


title: Lacto_Wk14B


title: S99-7879


title: S01-28567


title: Lacto_Wk10B


title: S99-1438


title: S01-12197


title: S98-29388


title: S99-26891


title: S01-19813


title: S00-9309


title: S99-25773


title: Renal Allograft Biopsy_P_49


title: Renal Allograft Biopsy_P_47


title: S99-27302


title: S99-8316


title: S99-17438


title: S99-27461


title: S99-21029


title: Acido_Wk18C

value: Acidovorax temperans


title: S01-22160


title: S99-5152


title: Renal Allograft Biopsy_P_45

value: Kidney


title: Renal Allograft Biopsy_P_43

value: Australian Chronic Allograft Dysfunction


title: Renal Allograft Biopsy_P_42

value: Immediate


title: Acido_Wk10F


title: Renal Allograft Biopsy_P_41


title: S01-27204


title: S99-21332


title: S99-7898


title: S99-1222


title: Renal Allograft Biopsy_P_40

value: Delayed


title: Renal Allograft Biopsy_P_46


title: Acido_Wk10B


title: S01-10988


title: Peripheral blood cells, EPO, 4.0 hour, biol rep 1

city: Shinjuku

first: Kazuki

last: Omata

state: Tokyo

address: Wakamatsucho, 2-2

department: Graduate school of advanced science and engineering

institute: Waseda University

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) 1 using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to the reference transcriptome sequences of X. tropicalis was prepared from the Xenbase v10.0 (https://www.xenbase.org/xenbase/), using BWA mem (version 0.7.17-r1188) 2 with the default parameters.
The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0) 3.
Then, using R (version 4.3.2) 4, the sums of read counts per gene were calculated.
Assembly: UCB_Xtro_10.0
Supplementary files format and content: csv data file includes raw counts for each sample.

organism: Xenopus tropicalis

source_name: Blood

growth_protocol: Blood cells were corrected from the heart and mixed with anti-coagulator EDTA-2Na. Cells were washed three times with 7/9 x phosphate buffered serine containing 2 mM EDTA-2Na and 2% fetal calf serum.

extract_protocol:
Total RNA was extracted by the acid guanidine phenol-chloroform method. 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared by Lasy-Seq v1.1 (https://sites.google.com/view/lasy-seq/)

treatment_protocol: 5,000,000 cells were suspended in 7/9 x IMDM-10% FCS and reacted with 1 ng/mL Xenopus tropicalis EPO expressed in E.coli for 1.5 or 4.0 hours.

value: Blood

tag: cell line

value: Total peripheral blood cells

value: Blood cells

value: Wild type

value: Culture with EPO


title: Peripheral blood cells, EPO, 4.0 hour, biol rep 3


title: S99-14350


title: S99-23231


title: Peripheral blood cells, EPO, 4.0 hour, biol rep 2


title: S01-29631


title: Acido_Wk18D

value: Lung adenocarcinoma

value: KrasLSL-G12D/+; Trp53LSL-R172H/+


title: S99-21951


title: S01-16521


title: Acido_Wk14B


title: S99-14059


title: S99-12521


title: Renal Allograft Biopsy_P_44

value: Renal Allograft Biopsy


title: Renal Allograft Biopsy_P_39


title: Peripheral blood cells, EPO, 1.5 hour, biol rep 3


title: Renal Allograft Biopsy_P_38


title: S99-15987

value: prostate cancer


title: S99-7275


title: Renal Allograft Biopsy_P_37


title: S00-8369

value: TRUE


title: Renal Allograft Biopsy_P_36


title: Peripheral blood cells, control, 4.0 hour, biol rep 3

value: Control culture


title: Renal Allograft Biopsy_P_35


title: Peripheral blood cells, EPO, 1.5 hour, biol rep 2


title: S00-28952

value: FALSE


title: S01-6353


title: S98-31223


title: Peripheral blood cells, control, 4.0 hour, biol rep 1


title: Renal Allograft Biopsy_P_34


title: S99-22739


title: Peripheral blood cells, control, 1.5 hour, biol rep 3


title: Renal Allograft Biopsy_P_33


title: Renal Allograft Biopsy_P_32


title: S99-11876


title: S01-13153


title: S99-5210


title: Peripheral blood cells, control, 4.0 hour, biol rep 2


title: S99-3971


title: S98-29072


title: S99-17086


title: Peripheral blood cells, control, 1.5 hour, biol rep 2


title: Peripheral blood cells, EPO, 1.5 hour, biol rep 1


title: Renal Allograft Biopsy_P_31


title: S01-12884


title: S00-24905


title: Renal Allograft Biopsy_P_29


title: Peripheral blood cells before culture, biol rep 2


title: Peripheral blood cells before culture, biol rep 3


title: S01-21517


title: Renal Allograft Biopsy_P_28


title: S00-13386


title: Peripheral blood cells before culture, biol rep 1


title: S00-3542


title: S01-15896


title: S99-6147


title: S99-26740


title: egr3 wild-type siblings 2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) and batch corrected using CountClust (each biological replicate = one batch) (Dey K et al., Visualizing the structure of RNA-seq expression data using grade of membership models).
Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
Assembly: danRer11
Supplementary files format and content: libryr size notmalize amd batch corrected counts

organism: Danio rerio

source_name: Heart

extract_protocol:
Total RNA was isolated using the miRNeasy micro Kit (Qiagen 217084), followed by on-column DNase digestion (DNase-Free DNase Set, Qiagen 79254), and final elution was performed in 12μl of RNase-free water
10ng total RNA was used for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio).

value: Heart


title: S01-22967


title: egr3 wild-type siblings 1


title: S99-22822


title: S00-23910


title: S00-150


title: Peripheral blood cells, control, 1.5 hour, biol rep 1


title: Renal Allograft Biopsy_P_26

value: Kidney