title: SPT16 Anchor-away strain, 1hr rapamycin, 3'READS, Rep B

description:
3' READS
YFR1478_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: YFR1321 parent with SPT16-FRB-KanMX6


title: HCC1806 TAZ+IPATA (COMBO) rep3, ATAC

status: Public on Jul 08 2024

type: SRA

city: Los Angeles

first: Simon

last: Knott

state: CA

address: 8687 Melrose Ave.

country: USA

institute: Cedars Sinai

library_source: genomic

data_processing:
ATAC-seqs were read and aligned to the UCSC hg38 genome reference using ENCODE pipeline.
Peaks were called using MACS2. The consensus peak's read counts were obtained using featureCounts function in Rsubread package in R.
Assembly: hg38
Supplementary files format and content: tab separated values files include ATAC raw counts for each sample.
Supplementary files format and content: tab separated values file includes peak annotation for each peakID

molecule: genomic DNA

organism: Homo sapiens

source_name: breast

extract_protocol:
Suspensions of 50,000 cells with viability > 90% were subjected to nuclei isolation, followed by Tn5-mediated transposition.
ATAC-Seq libraries were prepared using the Omni-ATAC-Seq protocol. The Zymo DNA Clean and Concentrator 5 kit was used to clean up the transposed reactions, after which Illumina adapter sequences and barcodes were added to the transposed DNA fragments in a pre-amplification step.  Quantitative PCR was performed to determine the appropriate number of additional PCR amplification cycles, as to not overamplify the reaction.  Amplified libraries were purified using the Zymo DNA Clean and Concentrator 5 kit, followed by a double-sided SPRIselect Bead cleanup (Beckman Coulter, Brea, CA).   Final libraries were analyzed on a 4200 TapeStation (Agilent Technologies, Santa Clara, California) and quantified via quantitative PCR using the Collibri Library Quantification Kit (Thermo Fisher Scientific, Waltham, MA).

tag: tissue

value: breast

tag: cell line

tag: treatment

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: SPT16 Anchor-away strain, 1hr rapamycin, 3'READS, Rep A

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Prep fastq files for mapping (discard reads with ambiguous base calls, remove of library adapters, count/remove of initial Ts in each read) python
Map to Sac cer 3 genome, using first 17 nt after adapter and initial T removal; no mismatches allowed, keeping only uniquely mapped reads, Bowtie
Discard reads for which the number of initial Ts could be explained by A residues in the genome adjacent to the mapped position, python
Tally remaining read starts by strand and genomic position, scaling each replicate to 25M total reads (or combined reps scaled to 50M), python
Assembly: Sac cer 3
Supplementary files format and content: Tab-delimited text files giving relative 3' isoform end frequencies by coordinate in the 400nt downstream of each CDS
Supplementary files format and content: Tab-delimited text files of merged A and B replicates giving relative isoform frequencies by genomic coordinate  in the 400nt downstream of each CDS
Library strategy: 3'READS

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Exponential growth at 30°C in YPD or YPGal

extract_protocol:
Total RNA extracted with hot acid phenol and subjected to Qiagen RNEasy purification with DNase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

treatment_protocol: As described under "treatment,"  some samples  were treated with 1µM rapamycin for 1 hr for the anchor-away method,  other cells were filtered and switched from YPGal to YPD for 3 hours for shutoff

tag: genotype

value: YPD, 1uM rapamycin for 1 hr


title: EpiLC 6h, WT mESCs, Rep3

city: Beijing

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

country: China

institute: Peking University

description:
EpiLC_6h_WT.Rep3
EpiLC_FLII_KO_JUN_KO.txt

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA.,mouse Cdna database(UCSC, NCBI37)  was used for alignment. Reads per Million was calculated for the normalization
Assembly: mm10,hg38
Supplementary files format and content: the txt file provide the CPM of each gene in every sample

molecule: polyA RNA

organism: Mus musculus

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while  those stated as EB D0/SL were cultured in Serum/Lif medium.The human naïve hESCs (WIBR3) were cultured on MEF feeder layer in 5i/L/A medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
The RNA was reverse transcribed with superscript IV, followed by 3’ DNA adaptor ligation using T4 RNA ligase (NEB). Libraries were amplified with Q5 2× Master Mix. Finally, the DNA above 175 bp in libraries was isolated by gel-purification.

tag: cell type

value: mESCs

value: WT

value: EpiLC 6h


title: EpiLC 48h, WT mESCs, Rep3

description:
EpiLC_48h_WT.Rep3
EpiLC_FLII_KO_JUN_KO.txt

value: EpiLC 48h


title: SPT6 and SPT16 double Anchor-away strain, 1hr rapamycin, Rep A

description:
3' READS
JZY139_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: YFR1321 parent with SPT6-FRB-KanMX6 SPT16-FRB-KanMX6


title: HCC1937 TAZ+IPATA (COMBO) rep3, ATAC


title: SPT6 Anchor-away strain, 1hr rapamycin, 3'READS, Rep B

description:
3' READS
YFR1480_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: YFR1321 parent with SPT6-FRB-KanMX6


title: EpiLC 48h, JUN-/- mESCs, Rep2

description:
EpiLC_48h_JUN_KO.Rep2
EpiLC_FLII_KO_JUN_KO.txt

value: JUN knockout


title: YFR1321 Anchor-away parental strain, 3' READS, Rep B

description:
3' READS
YFR1321_YPD_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: tor1-1 fpr1::NAT RPL13A-2xFKBP12

value: YPD


title: YFR1321 Anchor-away parental strain, 3' READS, Rep A


title: HCC1806 TAZ+IPATA (COMBO) rep1, ATAC


title: EpiLC 6h,JUN-/- mESCs, Rep2

description:
EpiLC_6h_JUN_KO.Rep2
EpiLC_FLII_KO_JUN_KO.txt


title: Histone shutoff control, 0hr glucose, Rep A

description:
3' READS
DCB220-1_YPGal_0h_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: hhf1::TRP1 Kan-pGal1-HHF2

value: YP + 2% galactose, before shift to glucose


title: PCF11 Anchor-away strain, 1hr rapamycin, 3 READS, Rep B

description:
3' READS
YJ012_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: HHY168 parent with PCF11-FRB


title: SPT6 Anchor-away strain, 1hr rapamycin, 3'READS, Rep A


title: EpiLC 48h, Flii-/- mESCs, Rep2

description:
EpiLC_48h_FLII_KO.Rep2
EpiLC_FLII_KO_JUN_KO.txt

value: FLII knockout


title: HCC1395 DMSO rep2, ATAC

value: DMSO


title: HHY168 Anchor-away parental strain, 1hr rapamycin, 3' READS, Rep B

description:
3' READS
HHY168_YPD_1hRap_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt


title: HHY168 Anchor-away parental strain, 1hr rapamycin, 3' READS, Rep A


title: HCC1395 DMSO rep1, ATAC

value: breast


title: EpiLC 6h,Flii-/- mESCs, Rep2

description:
EpiLC_6h_FLII_KO.Rep2
EpiLC_FLII_KO_JUN_KO.txt


title: npl3∆ 3' READS, Rep B

description:
3' READS
JZY63_YPD_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: JGY2000 parent with npl3[delta]


title: HCC1395 DMSO rep3, ATAC


title: EpiLC 48h, WT mESCs, Rep2

description:
EpiLC_48h_WT.Rep2
EpiLC_FLII_KO_JUN_KO.txt


title: npl3∆ 3' READS, Rep A


title: PCF11 Anchor-away strain, 1hr rapamycin, 3' READS, Rep A

value: YPD, 1uM rapamycin for 1 hr


title: HCC1806 TAZ+IPATA (COMBO) rep2, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: ref2∆ 3' READS, Rep B

description:
3' READS
JZY24_YPD_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: JGY2000 parent with ref2[delta]


title: EpiLC 6h, WT mESCs, Rep2

description:
EpiLC_6h_WT.Rep2
EpiLC_FLII_KO_JUN_KO.txt

value: mESCs

value: WT

value: EpiLC 6h


title: HCC1395 TAZ+IPATA (COMBO) rep3, ATAC


title: HCC1395 TAZ+IPATA (COMBO) rep2, ATAC


title: EpiLC 48h, JUN-/- mESCs, Rep1

description:
EpiLC_48h_Jun_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: EpiLC 48h


title: paf1∆ 3' READS, Rep B

description:
3' READS
JZY23_YPD_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: JGY2000 parent with paf1[delta]


title: paf1∆ 3' READS, Rep A


title: dst1∆ 3' READS, Rep B

description:
3' READS
JZY21_YPD_READS_RepsABmerged_RelCountsByPosition_1_to_400.txt

value: JGY2000 parent with dst1[delta]


title: dst1∆ 3' READS, Rep A

value: YPD


title: HCC1395 TAZ+IPATA (COMBO) rep1, ATAC


title: HCC1143 DMSO rep3, ATAC


title: EpiLC 24h, JUN-/- mESCs, Rep1

description:
EpiLC_24h_Jun_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: JUN knockout

value: EpiLC 24h


title: EpiLC 12h, JUN-/- mESCs, Rep1

description:
EpiLC_12h_Jun_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: EpiLC 12h


title: HCC1143 DMSO rep2, ATAC


title: CD4_mem_IFNalpha_IgG_CnR_Rep1

city: Chicago

first: Calvin

last: Law

state: IL

address: 303 E Superior St Lurie 5-220

department: Dermatology

institute: Northwestern University

description: L32 IFN-alpha

data_processing:
All libraries were proccessed with using a pipeline with script adapted and modified from the following repository: https://github.com/wherrylab/jogiles_ATAC. The pipeline assess FASTQ files using FASTQC, reads were aligned to GRCh38 using Bowtie 2. Samtools was used to remove unmapped, unpaired and mitochondrial reads and ENCODE blacklist regions.  PCR duplicates were removed uisng Picard.
We used SEACR with 'relaxed' peak selection mode to call target peaks over IgG control therefore no peaks files for IgG. Number of reads in each peak was determined using BedTools coverage. Peak annotation was done using ChIPseeker package in R.
Differentially bound peaks were identified using Diffbind package in R, following DESeq2 normalization using FDR cut-off of 0.05 unless otherwise indicated.
Motif enrichment analysis was performed using HOMER.
Tracks were visualized using Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigwig, for graph viewing on integrative genomics viewer.
Supplementary files format and content: bed, called peaks.

source_name: primary CD4+ memory T cells

extract_protocol:
CUT&RUN was performed using the CUTANA ChIC / CUT&RUN Kit (EpiCypher #14-1048) and following manufacture protocol with minor modifications.
CUT&RUN library prep was performed using KAPA HyperPrep Kit (Roche)

value: primary CD4+ memory T cells

value: IFN-alpha


title: CD4_mem_IFNalpha_IgG_CnR_Rep3

description: L37 IFN-alpha


title: HCC1143 DMSO rep1, ATAC

value: breast

value: DMSO


title: CD4_mem_PBS_IgG_CnR_Rep2

description: L36 PBS

value: PBS


title: ref2∆ 3' READS, Rep A


title: EpiLC 6h,JUN-/- mESCs, Rep1

description:
EpiLC_6h_Jun_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: HCC1143 TAZ+IPATA (COMBO) rep2, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: EpiLC 48h, Flii-/- mESCs, Rep1

description:
EpiLC_48h_FLII_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: FLII knockout


title: CD4_mem_IFNalpha_JUN_CnR_Rep2

description: L36 IFN-alpha


title: CD4_mem_PBS_IgG_CnR_Rep3

description: L37 PBS


title: CD4_mem_PBS_IgG_CnR_Rep1

description: L32 PBS


title: HCC1143 TAZ+IPATA (COMBO) rep3, ATAC


title: EpiLC 0h, JUN-/- mESCs, Rep1

description:
EpiLC_0h_Jun_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: mESCs

value: EpiLC 0h


title: CD4_mem_IFNalpha_JUN_CnR_Rep3

description: L37 IFN-alpha


title: CD4_mem_IFNalpha_JUN_CnR_Rep1

description: L32 IFN-alpha


title: CD4_mem_IFNalpha_IgG_CnR_Rep2

description: L36 IFN-alpha


title: HCC1143 TAZ+IPATA (COMBO) rep1, ATAC


title: EpiLC 12h, Flii-/- mESCs, Rep1

description:
EpiLC_12h_FLII_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: CD4_mem_sgAHR_IgG_CnR_Rep3

data_processing:
All libraries were proccessed with using a pipeline with script adapted and modified from the following repository: https://github.com/wherrylab/jogiles_ATAC. The pipeline assess FASTQ files using FASTQC, reads were aligned to GRCh38 using Bowtie 2. Samtools was used to remove unmapped, unpaired and mitochondrial reads and ENCODE blacklist regions.  PCR duplicates were removed uisng Picard.
We used SEACR with 'relaxed' peak selection mode to call target peaks over IgG control therefore no peaks files for IgG. Number of reads in each peak was determined using BedTools coverage. Peak annotation was done using ChIPseeker package in R.
Differentially bound peaks were identified using Diffbind package in R, following DESeq2 normalization using FDR cut-off of 0.05 unless otherwise indicated.
Motif enrichment analysis was performed using HOMER.
Tracks were visualized using Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigwig, for graph viewing on integrative genomics viewer.
Supplementary files format and content: bed, called peaks.
Library strategy: CUT&RUN

source_name: human blood

value: human blood

value: sgAHR, AHR agonist (TCDD)


title: CD4_mem_sgNT_IgG_CnR_Rep3

value: Non-targeting guide, AHR agonist (TCDD)


title: BT-549 DMSO rep3, ATAC


title: EpiLC 6h,Flii-/- mESCs, Rep1

description:
EpiLC_6h_FLII_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: EpiLC 6h


title: CD4_mem_PBS_JUN_CnR_Rep2

description: L36 PBS


title: CD4_mem_sgNT_AHR_CnR_Rep3


title: CD4_mem_PBS_JUN_CnR_Rep3

description: L37 PBS


title: BT-549 DMSO rep2, ATAC


title: EpiLC 0h, Flii-/- mESCs, Rep1

description:
EpiLC_0h_FLII_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: CD4_mem_sgAHR_AHR_CnR_Rep3


title: CD4_mem_JUN_OE_IgG_CnR_Rep3

data_processing:
All libraries were proccessed with using a pipeline with script adapted and modified from the following repository: https://github.com/wherrylab/jogiles_ATAC. The pipeline assess FASTQ files using FASTQC, reads were aligned to GRCh38 using Bowtie 2. Samtools was used to remove unmapped, unpaired and mitochondrial reads and ENCODE blacklist regions.  PCR duplicates were removed uisng Picard.
We used SEACR with 'relaxed' peak selection mode to call target peaks over IgG control therefore no peaks files for IgG. Number of reads in each peak was determined using BedTools coverage. Peak annotation was done using ChIPseeker package in R.
Differentially bound peaks were identified using Diffbind package in R, following DESeq2 normalization using FDR cut-off of 0.05 unless otherwise indicated.
Motif enrichment analysis was performed using HOMER.
Tracks were visualized using Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigwig, for graph viewing on integrative genomics viewer.
Supplementary files format and content: bed, called peaks.
Supplementary files format and content: csv, Diffbind normalized counts.
Library strategy: CUT&RUN

value: JUN overexpression, AHR inhibitor (CH-223191)


title: EpiLC 24h, Flii-/- mESCs, Rep1

description:
EpiLC_24h_FLII_KO.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: EpiLC 48h, WT mESCs, Rep1

description:
EpiLC_48h_WT.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: WT

value: EpiLC 48h


title: CD4_mem_JUN_OE_IgG_CnR_Rep1


title: BT-549 TAZ+IPATA (COMBO) rep2, ATAC


title: BT-549 TAZ+IPATA (COMBO) rep3, ATAC


title: CD4_mem_control_IgG_CnR_Rep3

value: control vector, AHR inhibitor (CH-223191)


title: EpiLC 24h, WT mESCs, Rep1

description:
EpiLC_24h_WT.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: EpiLC 24h


title: CD4_mem_control_IgG_CnR_Rep2

value: primary CD4+ memory T cells


title: CD4_mem_PBS_JUN_CnR_Rep1

description: L32 PBS


title: BT-549 TAZ+IPATA (COMBO) rep1, ATAC

value: breast


title: CD4_mem_JUN_OE_JUN_CnR_Rep3


title: EpiLC 6h, WT mESCs, Rep1

description:
EpiLC_6h_WT.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: CD4_mem_JUN_OE_JUN_CnR_Rep1


title: EpiLC 0h, WT mESCs, Rep1

description:
EpiLC_0h_WT.Rep1
EpiLC_FLII_KO_JUN_KO.txt


title: BT-20 DMSO rep3, ATAC

value: DMSO


title: CD4_mem_control_JUN_CnR_Rep3


title: CD4_mem_control_JUN_CnR_Rep2


title: BT-20 DMSO rep2, ATAC


title: CD4_mem_control_JUN_CnR_Rep1


title: BT-549 DMSO rep1, ATAC


title: CD4_mem_JUN_OE_IgG_CnR_Rep2


title: CD4_mem_TCDD_IgG_CnR_Rep4

value: AHR agonist (TCDD)


title: EB differentiation D1,  KH2-DGCR8, no Dox, PD0325901 25μm, Rep1

description:
EBD1_KH2-DGCR8_noDox_MEK_inhibitor_25μm.Rep1
EB_MEK_inhibitor.txt

value: EB differentiation D1,  PD0325901 25μm


title: CD4_mem_TCDD_IgG_CnR_Rep2


title: EB differentiation D1,  KH2-DGCR8, no Dox, PD0325901 1μm, Rep1

description:
EBD1_KH2-DGCR8_noDox_MEK_inhibitor_1μm.Rep1
EB_MEK_inhibitor.txt

value: EB differentiation D1,  PD0325901 1μm


title: CD4_mem_control_IgG_CnR_Rep1


title: CD4_mem_TCDD_IgG_CnR_Rep1


title: EpiLC 12h, WT mESCs, Rep1

description:
EpiLC_12h_WT.Rep1
EpiLC_FLII_KO_JUN_KO.txt

value: mESCs

value: EpiLC 12h


title: EB differentiation D1,  KH2-DGCR8, no Dox, PD0325901 5μm, Rep1

description:
EBD1_KH2-DGCR8_noDox_MEK_inhibitor_5μm.Rep1
EB_MEK_inhibitor.txt

value: EB differentiation D1,  PD0325901 5μm


title: BT-20 TAZ+IPATA (COMBO) rep3, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: CD4_mem_JUN_OE_JUN_CnR_Rep2


title: CD4_mem_AHRinh_IgG_CnR_Rep3

value: AHR inhibitor (CH-223191)


title: CD4_mem_AHRinh_IgG_CnR_Rep4


title: BT-20 TAZ+IPATA (COMBO) rep2, ATAC


title: BT-20 TAZ+IPATA (COMBO) rep1, ATAC


title: CD4_mem_AHRinh_IgG_CnR_Rep1


title: CD4_mem_AHRinh_IgG_CnR_Rep2


title: EB differentiation D1, KH2-DGCR8, + Dox, Rep3

description:
EB_D1_KH2-DGCR8_Dox.Rep3
EB_DGCR8_overexpression.txt

value: EB differentiation D1,+Dox


title: EB differentiation D4, KH2-DGCR8, + Dox, Rep3

description:
EB_D4_KH2-DGCR8_Dox.Rep3
EB_DGCR8_overexpression.txt

value: EB differentiation D4,+Dox


title: MDA-MB-468 TAZ rep3, ATAC

value: EZH2i (tazemetostat)


title: CD4_mem_TCDD_JUN_CnR_Rep4


title: CD4_mem_TCDD_JUN_CnR_Rep3


title: BT-20 DMSO rep1, ATAC


title: CD4_mem_TCDD_IgG_CnR_Rep3


title: MDA-MB-468 TAZ rep2, ATAC


title: CD4_mem_TCDD_JUN_CnR_Rep2


title: EB differentiation D4, KH2-DGCR8, no Dox, Rep3

description:
EB_D4_KH2-DGCR8_noDox.Rep3
EB_DGCR8_overexpression.txt

value: EB differentiation D4


title: EB differentiation D1, KH2-DGCR8, no Dox, Rep3

description:
EB_D1_KH2-DGCR8_noDox.Rep3
EB_DGCR8_overexpression.txt

value: EB differentiation D1


title: CD4_mem_AHRinh_JUN_CnR_Rep4


title: MDA-MB-468 TAZ rep1, ATAC


title: CD4_mem_AHRinh_JUN_CnR_Rep2


title: MDA-MB-468 IPATA rep3, ATAC

value: AKTi (ipatasertib)


title: CD4_mem_AHRinh_JUN_CnR_Rep1

value: primary CD4+ memory T cells


title: EB differentiation D4, KH2-DGCR8, + Dox, Rep2

description:
EB_D4_KH2-DGCR8_Dox.Rep2
EB_DGCR8_overexpression.txt


title: CD4_mem_AHRinh_JUN_CnR_Rep3


title: EB differentiation D1, KH2-DGCR8, + Dox, Rep2

description:
EB_D1_KH2-DGCR8_Dox.Rep2
EB_DGCR8_overexpression.txt


title: CD4_mem_sgAHR_IgG_CnR_Rep2

value: sgAHR, AHR agonist (TCDD)


title: MDA-MB-468 IPATA rep2, ATAC

value: breast


title: EB differentiation D1, KH2-DGCR8, no Dox, Rep2

description:
EB_D1_KH2-DGCR8_noDox.Rep2
EB_DGCR8_overexpression.txt


title: CD4_mem_sgAHR_IgG_CnR_Rep1


title: MDA-MB-468 DMSO rep3, ATAC

value: DMSO


title: CD4_mem_sgNT_IgG_CnR_Rep1

value: Non-targeting guide, AHR agonist (TCDD)


title: MDA-MB-468 IPATA rep1, ATAC


title: EB differentiation D4, KH2-DGCR8, no Dox, Rep2

description:
EB_D4_KH2-DGCR8_noDox.Rep2
EB_DGCR8_overexpression.txt


title: CD4_mem_sgNT_IgG_CnR_Rep2


title: CD4_mem_sgAHR_AHR_CnR_Rep2


title: CD4_mem_sgAHR_AHR_CnR_Rep1


title: CD4_mem_sgNT_AHR_CnR_Rep2


title: CD4_mem_TCDD_JUN_CnR_Rep1

value: AHR agonist (TCDD)


title: EB differentiation D4, KH2-DGCR8, + Dox, Rep1

description:
EB_D4_KH2-DGCR8_Dox.Rep1
EB_DGCR8_overexpression.txt

value: mESCs


title: MDA-MB-468 DMSO rep2, ATAC


title: CD4_mem_sgNT_AHR_CnR_Rep1


title: D7 GEX

city: Melbourne VIC 3004, AU

first: Cameron

middle: Gerard

last: Williams

state: VIC

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data was processed using the “cellranger count” pipeline from Cell Ranger version 3.1.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Spleen

extract_protocol:
Spleens were harvested and homogenized through 100μm cell strainers to create single-cell suspensions. RBCs were lysed using Lysing Buffer Hybri-Max (Sigma-Aldrich). Samples were washed twice in PBS 2% BSA and resuspended in PBS 2% BSA containing propidium iodide at dilution of 1:500. Live cells were sorted using a BD FACS Aria III and loaded onto the 10X Genomics Chromium controller.
cDNA libraries were prepared using Single Cell 3’ Reagent Kits v4 (10x Genomics).

value: Spleen

value: splenocytes

tag: strain

value: P chabaudi infected

tag: age

value: 6-12 weeks


title: P0 GFP positive3 timeseries

city: Utrecht

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
The raw data was filtered and trimmed using trim_galore. Filtered data was subsequently subjected to gene expression and differential expression (Tophat2, DESeq2). For E14 lncRNA analysis, data was filtered by selecting for “lincRNA”, “antisense”, “sense intronic” and “sense overlapping” gene biotypes. For the lncRNA analysis of the timeseries data, “lncRNA” were selected (naming differs due to Ensembl update).
Circular RNA discovery for the E14 RNAseq (E14 Pitx3-GFP+ vs. Pitx3-GFP-) analysis, was performed by applying find_circ (Memczak et al., Nature. 2013) and CIRCexplorer Zhang et al., Genome Res. 2016) to detect BSJ reads. For the timeseries RNAseq (E14, E16 and P0 Pitx3-GFP+ neurons), CIRI2 (Gao et al., Brief Bioinform. 2018) and CIRCexplorer2 (Zhang et al., Genome Res. 2016) were applied.
CircRNA detection was run on individual samples and combined using a modified version of CircM. Differential expression of circRNAs was analysed with DESeq2 (Love et al., Genome Biol. 2014). To analyse differential exon usage, we employed the package DEXseq (Anders et al., Genome Res. 2012).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files contain read counts of different samples, list of differentially expressed genes.

source_name: ventral midbrain

extract_protocol:
RNA of sorted cells (E14 Pitx3-GFP+ vs GFP- and E14, E16, P0 Pitx3-GFP+) was extracted using the miRNeasy micro kit (Qiagen).
RNA was depleted for ribosomal RNA using riboZero (Illumina). Sequencing libraries were generated applying ScriptSeq v2 (Illumina).
Sequencing libraries were generated applying ScriptSeq v2 (Illumina).

value: ventral midbrain

value: dopamine neurons

value: purification by FACS

tag: time


title: EB differentiation D1, KH2-DGCR8, + Dox, Rep1

description:
EB_D1_KH2-DGCR8_Dox.Rep1
EB_DGCR8_overexpression.txt

value: EB differentiation D1,+Dox


title: D0 GEX

description: 10x Genomics

value: saline control


title: MDA-MB-468 DMSO rep1, ATAC


title: P0 GFP positive2 timeseries


title: EB differentiation D0, KH2-DGCR8, + Dox, Rep1

description:
EB_D0_KH2-DGCR8_Dox.Rep1
EB_DGCR8_overexpression.txt

value: EB differentiation D0,+Dox


title: MDA-MB-468 TAZ+IPATA (COMBO) rep3, ATAC

value: EZH2i (tazemetostat) and AKTi (ipatasertib)


title: P0 GFP positive1 timeseries


title: MDA-MB-468 TAZ+IPATA (COMBO) rep2, ATAC


title: E16 GFP positive3 timeseries


title: EB differentiation D8, KH2-DGCR8, no Dox, Rep1

description:
EB_D8_KH2-DGCR8_noDox.Rep1
EB_DGCR8_overexpression.txt
EB_MEK_inhibitor.txt

value: EB differentiation D8


title: E16 GFP positive2 timeseries


title: MDA-MB-468 TAZ+IPATA (COMBO) rep1, ATAC

value: breast


title: EB differentiation D8, KH2-DGCR8, + Dox, Rep1

description:
EB_D8_KH2-DGCR8_Dox.Rep1
EB_DGCR8_overexpression.txt

value: EB differentiation D8,+Dox


title: E16 GFP positive1 timeseries


title: E14 GFP positive3 timeseries


title: EB differentiation D4, KH2-DGCR8, no Dox, Rep1

description:
EB_D4_KH2-DGCR8_noDox.Rep1
EB_DGCR8_overexpression.txt
EB_MEK_inhibitor.txt

value: EB differentiation D4


title: EB differentiation D1, KH2-DGCR8, no Dox, Rep1

description:
EB_D1_KH2-DGCR8_noDox.Rep1
EB_DGCR8_overexpression.txt
EB_MEK_inhibitor.txt

value: EB differentiation D1


title: E14 GFP positive3


title: E14 GFP positive1 timeseries


title: 21_SS111

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: raw_counts.txt: raw reads for all miRNAs in all samples

source_name: Retina

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using the miRNeasy mini kit (Qiagen).
Small RNA sequencing libraries were constructed using the TruSeq Small RNA Library Prep Kit (Illumina) according to manufacturer protocol.

value: Retina

value: hTERT RPE1

value: epithelial cell

value: +chr 8; +chr 9; +chr18


title: 20_SS51

value: +chr 7; +chr 22


title: EB differentiation D0, KH2-DGCR8, no Dox, Rep1

description:
EB_D0_KH2-DGCR8_noDox.Rep1
EB_DGCR8_overexpression.txt
EB_MEK_inhibitor.txt

value: mESCs

value: EB differentiation D0


title: EB differentiation D4, Flii-/- mESCs, Rep3

description:
EB_D4_Flii-/- Rep3
EB_FLIIKO.txt

value: FLII knockout


title: E14 GFP positive1

value: ventral midbrain

value: dopamine neurons

value: purification by FACS


title: 19_SS119

value: +chr 8


title: 18_SS6

value: +chr 7


title: E14 GFP negative3


title: EB differentiation D1, Flii-/- mESCs, Rep3

description:
EB_D1_Flii-/- Rep3
EB_FLIIKO.txt


title: E14 GFP negative2


title: 17_SS77

value: WT; p53 mutated


title: E14 GFP positive2


title: irkoPC [R3966_SJIRKOPC_V1X_1_S46_L005]

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Individual FASTQ files were trimmed for adapter sequences and filtered for a minimum quality score of Q20 using AdapterRemoval v2.2.0
Preliminary alignment using HISAT2 v2.0.6 (48) was performed to a composite reference of rRNA, mtDNA, and PhiX bacteriophage sequences obtained from NCBI RefSeq (49). Reads aligning to these references were excluded in subsequent analyses. Primary alignment was performed against the mouse genome reference GRCm38p4 using HISAT2.
Gene expression values for genes described by the GENCODE (50, 51) Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v1.5.1 (52, 53) in unstranded mode.
Quality control was performed using a modification of the QuaCRS custom workflow (54). In brief, aligned read quality was verified using RNA-SeQC (55) and RSeQC (56). The exonic rate (the percentage of reads aligning to exons), intronic rate (the percentage of reads aligning to introns), and duplication rate (the percentage of reads that were identified as PCR duplicates) were evaluated.
Coverage depths across the aligned reference were calculated with a per-base resolution using the ‘genomecov’ utility tool of Bedtools v2.27.0 (57) in BedGraph format. These files were used as input into CLEAR: a gene-by-gene analysis workflow to identify robust genes in ultra-low input RNA-seq data for downstream analyses. Determination of analysis-ready CLEAR transcripts was done as outlined in (58).
Assembly: mm10
Supplementary files format and content: comma-separated values file include CLEAR count values for each sample
Supplementary files format and content: n/a

source_name: kidney

growth_protocol: Mice were maintained on standard rodent chow ad libitum with free access to water under controlled temperature and humidity with twelve-hour light and dark cycles.

extract_protocol:
The NucleoSpin RNA Plus XS Kit was used to extract RNA on enriched IC and PC fractions following the manufacturer’s instruction, with one modification: DNase digestion was performed in solution using DNase I. RNA integrity was measured using Agilent 2100 Bioanalyzer with RNA pico chip. Samples with RNA integrity scores > 7 were used for RNA sequencing.
1 ng of RNA was preamplified using the Takara Clontech SMARTer v4 kit and RNA sequencing libraries were generated with the Illumina Nextera XT DNA Library Prep Kit. Samples were sequenced to a depth of 15–20 million 2 × 150 bp clusters on the Illumina HiSeq 4000 platform.

value: kidney

value: principal cell

value: IRKO

value: baseline


title: E14 GFP negative1


title: irkoPC [R3965_SJIRKOPC_V1X_1_S45_L005]


title: EB differentiation D4, WT mESCs, Rep3

description:
EB_D4_WT_Rep3
EB_FLIIKO.txt

value: WT

value: EB differentiation D4


title: 16_SS31

value: Retina

value: hTERT RPE1

value: epithelial cell


title: EB differentiation D1, WT mESCs, Rep3

description:
EB_D1_WT_Rep3
EB_FLIIKO.txt

value: mESCs

value: EB differentiation D1


title: E14 GFP positive2 timeseries

value: ventral midbrain


title: irkoPC [R3962_SJIRKOPC_V1X_1_S42_L005]


title: 14_SS111

value: +chr 8; +chr 9; +chr18


title: irkoPC [R3964_SJIRKOPC_V1X_1_S44_L005]


title: irkoIC [R3957_SJIRKOIC_V1X_1_S37_L005]

value: intercalated cell


title: EB differentiation D1, Flii-/- mESCs, Rep2

description:
EB_D1_Flii-/- Rep2
EB_FLIIKO.txt

value: FLII knockout


title: irkoIC [R3960_SJIRKOIC_V1X_1_S40_L005]


title: EB differentiation D4, WT mESCs, Rep2

description:
EB_D4_WT_Rep2
EB_FLIIKO.txt


title: EB differentiation D4, Flii-/- mESCs, Rep2

description:
EB_D4_Flii-/- Rep2
EB_FLIIKO.txt


title: 15_SS48


title: 13_SS51

value: +chr 7; +chr 22


title: irkoIC [R3959_SJIRKOIC_V1X_1_S39_L005]


title: 12_SS119

value: +chr 8


title: wtPC [R3951_SJwtPC4_V1X_1_S31_L005]

value: kidney

value: IR flox (WT)


title: EB differentiation D1, WT mESCs, Rep2

description:
EB_D1_WT_Rep2
EB_FLIIKO.txt


title: wtPC [R3953_SJwtPC6_V1X_1_S33_L005]

value: principal cell


title: wtPC [R3949_SJwtPC2_V1X_1_S29_L005]

value: baseline


title: 11_SS6

value: +chr 7


title: 10_SS77

value: WT; p53 mutated


title: wtIC [R3947_SJwtIC6_V1X_1_S27_L005]


title: EB differentiation D4, Flii-/- mESCs, Rep1

description:
EB_D4_Flii-/- Rep1
EB_FLIIKO.txt

value: EB differentiation D4


title: wtIC [R3946_SJwtIC5_V1X_1_S25_L003]


title: irkoIC [R3956_SJIRKOIC_V1X_1_S36_L005]

value: IRKO


title: wtIC [R3948_SJwtIC7_V1X_1_S28_L005]


title: wtPC [R3954_SJWT8PC_V1X_1_S34_L005]


title: wtIC [R3944_SJwtIC2_V1X_1_S23_L003]


title: EB differentiation D8, WT mESCs, Rep1

description:
EB_D8_WT_Rep1
EB_FLIIKO.txt

value: WT

value: EB differentiation D8


title: Bmp4_explant_18h

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

description: 10x Genomics

data_processing:
Illumina sequencing reads were aligned to the zebrafish (GRCz11) or human mRNA reference genome (GRCh38) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCz11, GRCh38
Supplementary files format and content: tar archive includes filtered_gene_bc_matrices after running CellRanger pipeline

organism: Danio rerio

source_name: embryonic

growth_protocol: Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium (DMEM/F-12 with 10 mM HEPES, 1x MEM with non-essential amino acids, 7 mM CaCl2, 1 mM sodium pyruvate, 50 μg/ml gentamycin, 100 μM 2-mercaptoethanol, 1× antibiotic-antimycotic ,10% serum replacement) and kept at 28.5℃.BMP4 induced human embryoids were cultured in a 96-well U-shaped ultra-low plate with culture medium (TeSR-E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth). Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.

extract_protocol:
Single-cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.1(10x Genomics, PN-1000121) protocol.
Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cell recovery.

treatment_protocol: To generate bmp4 explants, bmp4 (8-10 pg) mRNA was injected into one animal pole blastomere at the 128-cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids, human embryonic stem cells (hESCs) of the H9 line were grown on Matrigel-coated 12-well plates for a period ranging from 48 to 72 hours, utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment, both wild-type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96-well U-bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells, using 50 μl of an aggregation medium based on TeSR-E6 and supplemented with the ROCK inhibitor 10μM Y27632. After a 24-hour incubation period, both types of cells formed embryoid bodies (EBs) in their respective wells. These H9 and ihBmp4 EBs were then co-cultured in the same well, with 80 μl of the TeSR-E6 based medium to encourage fusion. Between days 2 and 4 of the culture period, the EBs were subjected to an induction process to enhance Bmp4 expression, which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR-E6 medium that included 75 ng ml-1 Doxycycline and 50 ng ml-1 FGF2 to stimulate these processes. Starting from day 4, the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR-E6 based medium for continued growth and development.

value: embryonic

value: zebrafish embryonic stem cells

value: stem cell


title: 9_SS31

value: Retina

value: hTERT RPE1

value: epithelial cell


title: EB differentiation D4, WT mESCs, Rep1

description:
EB_D4_WT_Rep1
EB_FLIIKO.txt

value: mESCs


title: 8_SS48


title: 6_SS51

value: +chr 7; +chr 22


title: EB differentiation D1, WT mESCs, Rep1

description:
EB_D1_WT_Rep1
EB_FLIIKO.txt

value: EB differentiation D1


title: P2_CFM_Day8_A3

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

country: Germany

institute: University of Bielefeld

data_processing:
The single-end reads were mapped to the human transcriptome (RefSeq Transcripts GRCh38; downloaded from NCBI) and quantified using Kallisto v0.44.0.
Estimated counts were statistically analyzed usingedgeRv3.28. The fold-change gene expression values were calculated in pairwise comparisons between the undifferentiated cancer cells as the control and differentiated cancer cells as treated. Genes were considered differentially expressed if their p-value was <0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file

source_name: larynx carcinoma

extract_protocol:
Cells were cultured for eight days. Total RNA was isolated from cell culture (n=3) usinginnuPREPDNA/RNA Mini Kit (AnalytikJena, Jena, Germany) as recommended by the manufacturer's protocol. RNA quality was determined with aBioDropDuo+ spectral photometer (Biochrom, Holliston, USA).
PolyA-selected libraries were prepared from 200 ng of total RNA usingQuantSeq3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), according to the manufacturer's instructions. Size distribution and quality of the libraries were assessedby fragment analyzer (Agilent) and final libraries were sequenced in 75 bp single-end mode on a NextSeq2000 with P3 chemistry.

value: larynx carcinoma

value: epithelial cancer cells

value: differentiated


title: P2_CFM_Day8_A1


title: 7_SS111

value: +chr 8; +chr 9; +chr18


title: Bmp4_explant_12h

description: 10x Genomics


title: P2_CFM_Day8_A2


title: Bmp4_explant_10h

description: 10x Genomics


title: Bmp4_explant_6h

description: 10x Genomics


title: EB differentiation D0, WT mESCs, Rep1

description:
EB_D0_WT_Rep1
EB_FLIIKO.txt

value: EB differentiation D0


title: Bmp4_explant_8h

description: 10x Genomics


title: Bmp4_explant_24h

description: 10x Genomics


title: P2_PNEU_Day8_K3

value: undifferentiated


title: EB differentiation D1, Flii-/- mESCs, Rep1

description:
EB_D1_Flii-/- Rep1
EB_FLIIKO.txt

value: FLII knockout


title: 5_SS119

value: +chr 8


title: WT mESCs transfected with siDGCR8 and siFLII, Rep3

description:
WT_siDgcr8&siFlii_Rep3
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: WT

value: transfected with siDGCR8 and siFLII


title: Microglia, APOE-KO, replicate 5 RNA-seq]

city: London

first: Sarah

middle: J

last: Marzi

address: Maurice Wohl Clinical Neuroscience Institute

country: United Kingdom

institute: King's College London

data_processing:
General QC of each sample was assessed using fastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by adapter trimming using TrimGalore! (https://github.com/FelixKrueger/TrimGalore). Reads were aligned to the GRCh38 genome and transcriptome using STAR. Duplicate and multi-mapping reads were retained. Transcript quantification was performed using Salmon, using the gc bias flag. Two of the APOE knockout samples with high APOE expression were excluded from subsequent analyses.
Assembly: GRCh38 available at: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Supplementary files format and content: APOE_microglia_RNAseq_counts.csv: raw counts, row names are entrez gene ids and column names are sample ids

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
From snap frozen cell pellets of 200,000 cells per sample, RNA was extracted using the Monarch Total RNA Miniprep Kit (T2010) following the manufacturer’s instructions. RNA-seq was conducted using the rRNA depletion strategy rather than mRNA enrichment so that noncoding RNAs could be recovered. rRNA depletion was performed using NEBNext rRNA Depletion Kit v2 Human/Mouse/Rat with RNA Sample Purification Beads (E7405), followed by stranded (directional) library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765) following manufacturer’s protocols without adjustments. RNA quality was checked using the Agilent RNA 6000 Pico Kit (5067-1513) and final libraries were assessed using Agilent High Sensitivity DNA Kit (5067-2646) where all libraries were appropriate for sequencing apart from one replicate of the APOE3 microglia - therefore this isoform only has four biological replicates for RNA-seq.

value: Brain

value: Microglia

tag: mouse host_genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: P2_PNEU_Day8_K2


title: Microglia, APOE-KO, replicate 4 RNA-seq]


title: 3_SS77

value: Retina

value: hTERT RPE1

value: epithelial cell

value: WT; p53 mutated


title: P2_PNEU_Day8_K1

value: larynx carcinoma


title: 2_SS31


title: WT mESCs transfected with siNC, Rep3

description:
WT_siNC_Rep3
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: mESCs

value: transfected with siNC


title: WT mESCs transfected with siDROSHA Rep3

description:
WT_siDrosha_Rep3
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDROSHA


title: Microglia, APOE-KO, replicate 3 RNA-seq]


title: 1_SS48


title: Microglia, APOE-KO, replicate 1  RNA-seq]


title: P1_CFM_Day8_A2

value: epithelial cancer cells

value: differentiated


title: SINTH8 Hashtag Capture

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

institute: University of Cambridge

description: Hashtag Capture for multiplexed samples

library_source: other

data_processing:
Single-cell RNA-seq libraries were processed using the CellRanger pipeline (10x Genomics v.6.1.2) against the hg19 reference transcriptome.
Read counts were further analysed using the R Bioconductor package Seurat (v.4.3.0)
Hashtag demultiplexing was performed with HTODemux from Seurat and doublet identification was performed with DoubletFinder using the hashtag read counts. After selecting singlets, low quality cells were filtered out (mitochondrial content above 5%).
Assembly: hg19
Supplementary files format and content: Seurat output: count matrix, features list and barcodes list.

molecule: other

growth_protocol: IMR90 (ATCC) were cultured in DMEM supplemented with 10% FBS. Cells were maintained in physiological 5% O2.

extract_protocol:
Two replicate of IMR90 growing expressing vector control and RIS IMR90 cells expressing shA1 or vector control were individually labelled with 1ug of Biolegend TotalSeq™-B Cell Hashing antibodies diluted in Cell Staining Buffer (PBS with 3%FBS) for 30 minutes at 4˚C, then washed 3 times with Cell Staining buffer (centrifuge 2 minutes 350g at 4˚C).
Cells were resuspended to a concentration of 800 cells/uL for single-cell encapsulation using the Chromium Single Cell B Chip Kit (10x Genomics Cat # PN-1000073), followed by library prep using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10x Genomics Cat # PN-1000075) for the gene expression library and the Chromium Single Cell 3’ Feature Barcode Library Kit (10x Genomics Cat # PN-1000079) for the hashtag-oligo library. Both libraries were then pooled for paired-end sequencing on the NovaSeq 6000 platform (Illumina).

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells were treated for 6 days with 100nM 4OHT.

value: lung fibroblast


title: 4_SS6

value: +chr 7


title: P1_PNEU_Day8_K3

value: undifferentiated


title: P1_CFM_Day8_A1


title: HMGA1KO-RT-input-2

data_processing:
Reads were aligned using Bowtie2 (Langmead et al. 2012) against the hg19 genome build.
Duplicates were marked with samtools (Danecek et al. 2021) and blacklisted regions (hg19) were removed.
THOR (Thorvaldsdóttir et al. 2013) was used to normalise and to perform differential binding pairwise between conditions.
Assembly: hg19
Supplementary files format and content: BigWig: THOR-normalised ChIP-seq signal

growth_protocol: IMR90 and H1299 cells were cultured in DMEM (Gibco #12481-023) with 10% fetal calf serum (FCS) at 37°C in 5% (IMR90) or atmospheric (H1299) O2 and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min (RT) or at 4°C for 1 hour (4C).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645L) according to the manufacturer’s instructions except that size selection was performed after PCR amplification using AMPure XP beads (Beckman Coulter, A63881). Samples were sequenced paired-end using 50 bp reads on the Illumina platforms.

value: non-small cell lung carcinoma

value: HMGA1 KO_2

tag: antibody

value: Input

tag: i shhmga1

tag: dox

tag: fixation variations

value: RT


title: WT mESCs transfected with siDGCR8 and siFLII, Rep2

description:
WT_siDgcr8&siFlii_Rep2
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: WT

value: transfected with siDGCR8 and siFLII


title: P1_PNEU_Day8_K2


title: Microglia, APOE4, replicate 4 RNA-seq]

value: Brain

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: Microglia, APOE4, replicate 5 RNA-seq]


title: SITTE7 Gene Expression

description: Gene Expression (scRNA-seq)


title: WT mESCs transfected with siNC, Rep2

description:
WT_siNC_Rep2
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: mESCs


title: WT mESCs transfected with siDGCR8, Rep2

description:
WT_siDgcr8_Rep2
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDGCR8


title: WT mESCs transfected with siDGCR8, Rep3

description:
WT_siDgcr8_Rep3
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt


title: HMGA1KO-RT-input-1

value: HMGA1 KO_1


title: HMGA1KO-RT-HMGA1-2


title: WT mESCs transfected with siDROSHA Rep1

description:
WT_siDrosha_Rep1
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siDROSHA


title: Microglia, APOE4, replicate 3 RNA-seq]


title: Microglia, APOE4, replicate 2 RNA-seq]


title: P1_CFM_Day8_A3

value: larynx carcinoma

value: epithelial cancer cells

value: differentiated


title: WT mESCs transfected with siDGCR8 and siFLII, Rep1

description:
WT_siDgcr8&siFlii_Rep1
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt


title: Microglia, APOE-KO, replicate 2 RNA-seq]


title: WT mESCs transfected with siDROSHA Rep2

description:
WT_siDrosha_Rep2
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt


title: DKK1 treated hIPSC labeled with double pulse of EdU plate 4

first: Jeroen

last: van den Berg

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
scEdU-seq Libraries were sequenced 2x100 bp on Illumina NextSeq2000
See  van den Berg et al.,(scEdU-seq, 2024),
For scEdU-seq, van den Berg et al.,(scEdU-seq, Nature Methods, 2024)
Assembly: GRCh38 (Gencode)
Supplementary files format and content: deduplicated single cell count tables (tsv.gz)

growth_protocol: human induced pluripotent stem cells (hiPSCs) were cultured in were cultured in Essential E8 medium (Thermo 1282 Scientific) supplemented with Penicillin/Streptomycin. We added Revitacell Supplement (Thermo Scientific) for the first 24 h after plating. Media were changed every day, and cells were split every 3 to 4 days using Versene (Gibco). All the experiments were carried out with hiPSCs between passage 10 and 20

extract_protocol:
cells were sorted into 384 well plates and protK treated prior to library construction
See van den Berg et al.,(scEdU-seq, Nature Methods, 2024)
scEdU-seq library strategy was used. Briefly, cells were lysed with protein digestion. Subsequently, DNA was fragemented with NlaIII and  adapters were ligation followed by amplification with IVT and PCR

treatment_protocol: hiPSC cells were treated for inficiated times with DMSO Aphidicolin or DKK1

value: embryonic

value: hiPSC

value: human induced pluripotent stem cells


title: Microglia, APOE4, replicate 1 RNA-seq]


title: HMGA1KO-RT-HMGA1-1

value: non-small cell lung carcinoma


title: Microglia, APOE3, replicate 4 RNA-seq]


title: HMGA1KO-4C-HMGA1-2

value: HMGA1 KO_2


title: DKK1 treated hIPSC labeled with double pulse of EdU plate 3

value: WT


title: WT mESCs transfected with siDGCR8, Rep1

description:
WT_siDgcr8_Rep1
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt


title: WT mESCs transfected with siNC, Rep1

description:
WT_siNC_Rep1
Mouse_DGCR8_FLII_DROSHA_Knockdown.txt

value: transfected with siNC


title: DGCR8 FLII double knockouts mESC, FLII and DGCR8 (RBD deletion) rescue, Rep3

description:
DF-dKO_FLII_rescue_DGCR8_RBD_deletion_rescue_Rep3
Knockout_cellline.txt

value: DGCR8 FLII double knockouts

value: FLII and DGCR8 (RBD deletion)


title: P1_PNEU_Day8_K1

value: undifferentiated


title: DGCR8 FLII double knockouts mESC, FLII and DGCR8 (RBD deletion) rescue, Rep2

description:
DF-dKO__FLII_rescue_DGCR8_RBD_deletion_rescue_Rep2
Knockout_cellline.txt

value: mESCs


title: DKK1 treated hIPSC labeled with double pulse of EdU plate 2


title: HMGA1KO-4C-HMGA1-1


title: H1299-RT-input

value: Input

value: RT


title: Microglia, APOE3, replicate 3 RNA-seq]

value: Brain

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: Microglia, APOE3, replicate 1 RNA-seq]


title: 200nM Aphidicolin treated hIPSC labeled with double pulse of EdU plate 3

value: Aphidicolin


title: Microglia, APOE3, replicate 2 RNA-seq]


title: 200nM Aphidicolin treated hIPSC labeled with double pulse of EdU plate 4

value: embryonic


title: H1299-RT-HMGA1-2


title: DGCR8 FLII double knockouts mESC, FLII and DGCR8 (RBD deletion) rescue, Rep1

description:
DF-dKO_FLII_rescue_DGCR8_RBD_deletion_rescue_Rep1
Knockout_cellline.txt


title: H1299-4C-HMGA1-2


title: DGCR8 FLII double knockouts mESC, FLII rescue, Rep3

description:
DF-dKO_FLII_rescue_Rep3
Knockout_cellline.txt

value: FLII rescue


title: DGCR8 FLII double knockouts mESC, FLII  and DGCR8 rescue, Rep1

description:
DF-dKO_FLII_rescue_DGCR8_rescue_Rep1
Knockout_cellline.txt

value: FLII and DGCR8 rescue


title: 200nM Aphidicolin treated hIPSC labeled with double pulse of EdU plate 2

value: hiPSC

value: human induced pluripotent stem cells


title: Microglia, APOE2, replicate 4 RNA-seq]


title: 200nM Aphidicolin treated hIPSC labeled with double pulse of EdU plate 1

value: WT


title: H1299-RT-HMGA1-1

value: non-small cell lung carcinoma


title: H1299-4C-HMGA1-1


title: DKK1 treated hIPSC labeled with double pulse of EdU plate 1


title: IeR_shCEBPb_shp53_d6_5

data_processing:
Libraries were aligned using STAR (Dobin et al. 2013) against the hg19 genome and transcriptome (GENCODE19) reference.
Reads were counted over genes using the GENCODE19 annotation and the featureCounts functionality from the subread package (Liao et al. 2014).
Supplementary files format and content: TXT: Tab-separated raw read counts (per sample).

extract_protocol:
RNA was purified using the QIAGEN RNeasy plus kit according to the manufacturer’s instructions. The quality was checked using the Agilent High Sensitivity RNA Bioanalyser or ScreenTape System.
Libraries were prepared from six biological replicates of each condition using TruSeq stranded mRNA or Illumina Stranded mRNA Prep Kit (Illumina), according to the manufacturer’s instructions, and sequenced using using the HiSeq-4000 or the Novaseq-6000 platforms (Illumina).

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V

value: 4OHT (6 days)

tag: shcebpb

value: pSuper CEBPB

value: pMSCV miR p53


title: Microglia, APOE2, replicate 3 RNA-seq]


title: DMSO treated hIPSC labeled with double pulse of EdU plate 3

value: DMSO


title: DMSO treated hIPSC labeled with double pulse of EdU plate 4


title: DGCR8 FLII double knockouts mESC, FLII rescue, Rep2

description:
DF-dKO_FLII_rescue_Rep2
Knockout_cellline.txt

value: mESCs

value: DGCR8 FLII double knockouts


title: Microglia, APOE2, replicate 2 RNA-seq]

value: Brain

value: Microglia

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: Microglia, APOE2, replicate 5 RNA-seq]


title: Microglia, APOE2, replicate 1 RNA-seq]


title: IeR_shCEBPb_shp53_d6_4


title: DGCR8 FLII double knockouts mESC, Rep3

description:
DF-dKO_Rep3
Knockout_cellline.txt


title: DMSO treated hIPSC labeled with double pulse of EdU plate 2

value: embryonic


title: Microglia, APOE-KO, replicate 5 [ATAC-seq]

data_processing:
General QC of each sample was assessed using fastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by adapter trimming using TrimGalore! (https://github.com/FelixKrueger/TrimGalore). Reads were aligned to GRCh38 using bowtie2 with the following arguments: –local –very-sensitive –no-mixed –no-discordant -I 25 -X 1000. Post-alignment QC included removing: reads mapping to the mitochondrial genome, duplicate reads, multi-mapping reads, and reads with low mapping quality (q < 30). Read count generation was performed using featureCounts. Additionally, peaks were filtered using the filterByExpr() function in DESeq2 31, retaining only peaks with sufficiently high counts for statistical analysis. This left 228,041 peaks for downstream analyses. The 2 APOE-KO samples with high APOE expression in the ATAC-seq data were also excluded from the ATAC-seq dataset. Additionally, another APOE-KO and one APOE4 microglia sample were discarded due to having low QC metrics.
Assembly: GRCh38 available at: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Supplementary files format and content: APOE_microglia_ATACseq_counts.csv: raw counts, row names are peaks and column names are sample ids

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
ATAC-seq was conducted as previously described79. Following FACS collection of 100,000 cells per sample, cells were spun down at 500g for 5 min at 4oC, and the supernatant was removed. Cell pellets were gently resuspended in 50 µL of ice cold Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). 2.5 µL Tagment DNA Enzyme (Illumina; 20034197) was added directly and gently mixed by pipetting. The transposition reaction was incubated at 37oC for 30 minutes, then transferred to ice. DNA was purified immediately with the Zymo ChIP DNA Clean and Concentration Kit (D5205) following manufacturer’s instructions. The DNA column was spun dry prior to elution of transposed DNA, which was conducted with 11 µL Elution Buffer. Purified DNA was stored at -20oC until library preparation. 10 µL DNA per sample was transferred into a PCR tube and 34.25 µL PCR master mix was added per sample. 6.25 µL of 10 µM Nextera Primer 2 (with barcode) was added per sample, where a different barcode was used for each sample to enable multiplexing. PCR was conducted using the following settings: (1) 72oC for 5 min, (2) 98oC for 30s; (3) 98oC for 10s; (4) 63oC for 30s; (5) 72oC for 1 min; (6) repeat steps (3)-(5) for a total of 10 cycles; (7) hold at 4oC. Amplified library was purified using the Zymo ChIP DNA Clean and Concentration Kit (D5205). The purified library was eluted using 20 µL Elution Buffer. 5 µL of 5x TBE Loading Buffer (Invitrogen; LC6678) was added and loaded in a 12-well 10% TBE gel (Invitrogen; EC62752BOX). A ladder was prepared using 0.25-0.5µL ORangeRuler 50 bp DNA Ladder (ThermoFisher; SM0613) diluted in 5 µL 5x TBE loading buffer. The gel was run at 70 V until DNA enters the gel, then increased to 140 V for approximately one hour. The gel was stained using 10 mL 1x TBE with SYBR Gold Nucleic Acid Gel stain (Invitrogen; S11494) diluted at 1:10,000 (1 µL). The gel was cut between 175-225 bp markers into a 0.5 mL DNA LoBind tube perforated three times with a 22G needle. The gel was shredded by centrifugation at maximum speed for 2 min at room temperature into a 1.5 mL DNA LoBind tube. 150 µL Diffusion Buffer (0.5 M Ammonium Acetate, 0.1% SDS, 1 mM EDTA, 10 mM Magnesium Acetate, ddH2O) was added to the gel in the 1.5 mL tube and shaken at room temperature for 45 minutes. The sample was then transferred to filter columns using wide-bore tips and spun at max speed for 2 min. DNA was purified (~140 µL) using the Zymo ChIP DNA Clean and Concentration Kit and eluted with 10 µL Elution Buffer into 1.5 mL DNA LoBind tubes. Final libraries were quantified with the Qubit 1X dsDNA HS Assay Kit (ThermoFisher; Q33230) and stored at -20oC prior to sequencing (yield: ~0.25 ng/µL).


title: DGCR8 FLII double knockouts mESC, control of DGCR8/FLII_rescue

description:
DF-dKO_noFLII_noDGCR8
Knockout_cellline.txt


title: IeR_shCEBPb_shp53_d6_3


title: Microglia, APOE-KO, replicate 4 [ATAC-seq]


title: LNCaP cell, Ctrl

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: LNCaP-Ctrl

data_processing:
Base calling and de-multiplexing were performed using bcl-convert (v3.9.5) with default parameters as per Illumina recommendation.
The final base plus any bases with PHRED quality score <10 and potential adapter sequences (AGATCGGAAGAGCACACGTCTGAAC for Read 1 and AGATCGGAAGAGCGTCGTGTAGGGA for Read 2) were trimmed from the 3’ end of paired RNA-seq reads using CutAdapt (version 4.5).
Reads shorter than 21 bases after trimming were discarded. Trimmed reads were aligned to the hg38 human reference genome (GENCODE GRCh38 v39 primary assembly) using Spliced Transcripts Alignment to a Reference (STAR; version 2.7.11a) with the -peOverlapNbasesMin option set to 6.
Duplicate fragments were marked (though still retained) using Samtools markdup (Samtools version 2.16.0) with the optical distance (-d) option set to value 2500, as recommended for patterned flow cells, and the --no-multi-dup option applied.
The numbers of aligned fragments per gene were counted using featureCounts (Subread version 2.0.6) with the following options: -F GTF -t exon -g gene_id -p -C -d 21. The -p option specifies that fragments (which generally correspond to read pairs) should be counted rather than individual reads. The -C option specifies that read pairs whose ends map to different chromosomes or to different strands of the same chromosome should not be counted. The “-d 21” indicates that only fragments at least 21 bases long should be counted.
Assembly: FastQC (version 0.12.1)59 and QualiMap (version 2.2.2-dev)60 were used for quality control (QC), and various QC metrics for all samples were aggregated into a single report using MultiQC (version 1.17).
Supplementary files format and content: tab-delimited *.txt file containing raw count matrix

source_name: Prostate origin, lymph node mestatic

growth_protocol: LNCaP cell lines were cultured in RPMI-1640 media plus 5% FBS. Cells were collected for RNA sequencing.

extract_protocol:
Cells were washed with PBS 1x and detached by scraping in PBS/5mM EDTA/sodium vanadate, pelleted, and re-suspended in TRIzol for RNA extraction
Sample quality control wasperformed using the Agilent 2100 Bioanalyzer or the Agilent 4200 Tapestation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads.

treatment_protocol: cells were either not treated or treated with10µmol/L enzalutamide or ADA-308 for 72 hours

value: Prostate origin, lymph node mestatic

value: LNCaP

value: luminal epithelium

value: AR positive


title: IeR_shCEBPb_shp53_d6_2


title: DMSO treated hIPSC labeled with double pulse of EdU plate 1

value: hiPSC

value: human induced pluripotent stem cells

value: WT


title: DGCR8-sCLIP (+ S4U) performed in naïve mESCs, IP group, Rep2

data_processing:
For data analysis, we preprocessed reads as described previously (Krakau et al., 2017). Briefly, firstly, the adapters were trimmed by cutadapt, and then the barcode was appended to the read ID before mapping to the genome. The processed reads were mapped to mm10 genome with STAR, and only reads aligned to main chromosomes were included for further analyses. We remove PCR duplicates using UMI, and only the second read was used for peak calling using CLIPer. The peaks were normalized based on input sample using a Perl script (Peak_input_normalization_wrapper.pl). Significant threshold of peaks was defined as p<0.001 and fold enrichment >8. Finally, the peaks were annotated in Gencode (M23). ComputerMatrix were used to calculate the signal of the peaks from bigWig file normalized by CPM, and the results were visualized by plotHeatmap.
Assembly: mm10
Supplementary files format and content: The bigWig files normalized by CPM of each sample were provided to visualize in IGV or UCSC genome browser.

growth_protocol: The naive mESCs stated as “ECLIP/SCLIP...Naive" were cultured in Serum/Lif medium, while those stated as “ECLIP…Poised" were Day1 EBs derived from naïve mESCs.For sCLIP, the cells must be treated with 100 μM S4U for 30 minutes before UV-crosslinking.

extract_protocol:
FLAG-DGCR8/FLII expression was induced in 20-30 million KH2-DGCR8/FLII mESCs by 4 μg/ml Dox-treatment for 3 days and were crosslinked by UV (400 mJ/cm2) in a 10 cm dish. For sCLIP, the cells must be treated with 100 μM S4U for 30 minutes before UV-crosslinking. The cell lysate was extracted in ICLIP lysis buffer and subjected to sonication and DNase treatment. Next, RNase I was used to fragment RNA, and then the cell lysate was incubated with 5 μg FLAG antibody coupled with 50 μl Protein G beads at 4°C for 2 h. The protein-RNA complexes were washed with high salt solution, ligated to 3’ RNA linker, subjected to 4%-12% Bis-Tris gel and transferred to membranes. The DGCR8-binding RNA was isolated from the membrane based on protein size, and a size-matched input was also be generated. Especially for sCLIP, the isolated RNAs must undergo a 50 ul Thiol modification (5 μl 100 Mm Iodoacetamide, 5 ul 1M NaH2PO4, 25 ul DMSO, RNA: x ul, ddH20: (20-x) ul) and incubate at 50°C for 15 min. Next, 1 ul 1M DTT was added to quench the reaction and the RNA was purified using isopropanol precipitation.
Small RNA-seq libraries preparation using NEBNext® Small RNA Library Prep Set for Illumina kit。

value: EB differentiation D4, + Dox

tag: group

value: IP


title: IeR_shCEBPb_shp53_d6_1

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V

value: 4OHT (6 days)

value: pSuper CEBPB

value: pMSCV miR p53


title: Microglia, APOE-KO, replicate 3 [ATAC-seq]

value: Brain

value: Microglia


title: DGCR8 FLII double knockouts mESC, FLII rescue, Rep1

description:
DF-dKO_FLII_rescue_Rep1
Knockout_cellline.txt

data_processing:
For PolyA(+) RNA-seq,Adapteor was removed by trimmomatic-0.39, HISAT2 software was used to align sequencing reads to reference mRNA.,mouse Cdna database(UCSC, NCBI37)  was used for alignment. Reads per Million was calculated for the normalization
Assembly: mm10,hg38
Supplementary files format and content: the txt file provide the CPM of each gene in every sample

value: mESCs

value: DGCR8 FLII double knockouts

value: FLII rescue


title: DGCR8-sCLIP (+ S4U) performed in naïve mESCs, IP group, Rep1

value: EB differentiation D2, + Dox


title: LNCaP cell, ENZ, Rep1

description:
LNCaP-ENZ-rep1_depth20M
LNCaP_ENZ_countMatrix.txt

treatment_protocol: cells were treated with10µmol/L enzalutamide or ADA-308 for 72 hours

value: Prostate origin, lymph node mestatic

value: LNCaP

value: luminal epithelium

value: AR positive

value: AR inhibition by Enzalutamide


title: IeR_v_shp53_d6_5

value: pSuper v


title: Microglia, APOE-KO, replicate 2 [ATAC-seq]

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: Microglia, APOE-KO, replicate 1  [ATAC-seq]


title: IeR_v_shp53_d6_4

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V


title: LNCaP cell, ADA-308, Rep2

description:
LNCaP-ADA-rep2_depth20M
LNCaP_ADA-308_countMatrix.txt

value: AR inhibition by ADA-308


title: DGCR8-sCLIP (+ S4U) performed in naïve mESCs, Input group, Rep1

value: EB differentiation D2, no Dox

value: Input


title: IeR_v_shp53_d6_3

value: 4OHT (6 days)

value: pMSCV miR p53


title: LNCaP cell, ADA-308, Rep1

description:
LNCaP-ADA-rep1_depth20M
LNCaP_ADA-308_countMatrix.txt


title: DGCR8-sCLIP (no S4U) performed in naïve mESCs, IP group, Rep2

value: mESCs

value: EB differentiation D1, + Dox

value: IP


title: IeR_v_shp53_d6_2


title: DGCR8-sCLIP (+ S4U) performed in naïve mESCs, Input group, Rep2

value: EB differentiation D4, no Dox


title: Microglia, APOE4, replicate 4 [ATAC-seq]

value: Brain

value: Microglia


title: DGCR8-sCLIP (no S4U) performed in naïve mESCs, IP group, Rep1

value: EB differentiation D0, + Dox


title: DGCR8-sCLIP (no S4U) performed in naïve mESCs, Input group, Rep2

value: EB differentiation D1, no Dox


title: Microglia, APOE4, replicate 3 [ATAC-seq]


title: LNCaP cell, ENZ, Rep2

description:
LNCaP-ENZ-rep2_depth20M
LNCaP_ENZ_countMatrix.txt

value: Prostate origin, lymph node mestatic

value: LNCaP

value: luminal epithelium

value: AR positive

value: AR inhibition by Enzalutamide


title: IeR_v_shp53_d6_1

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V

value: pSuper v


title: IeR_shCEBPb_v_d6_5

value: 4OHT (6 days)

value: pSuper shCEBPB

value: pMSCV miR v


title: Microglia, APOE4, replicate 2 [ATAC-seq]

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: Microglia, APOE4, replicate 1 [ATAC-seq]


title: FLII-eCLIP performed in Poised mESCs, IP group, Rep2

value: mESCs

value: EB differentiation D4, + Dox

value: IP


title: Microglia, APOE3, replicate 5 [ATAC-seq]

value: Brain

value: Microglia


title: IeR_shCEBPb_v_d6_4


title: IeR_shCEBPb_v_d6_3


title: Microglia, APOE3, replicate 4 [ATAC-seq]


title: IeR_shCEBPb_v_d6_2


title: FLII-eCLIP performed in Poised mESCs, Input group, Rep2

value: EB differentiation D4, no Dox

value: Input


title: Microglia, APOE4, replicate 5 [ATAC-seq]


title: IeR_shCEBPb_v_d6_1


title: Microglia, APOE3, replicate 3 [ATAC-seq]


title: FLII-eCLIP performed in naïve mESCs, Input group, Rep2

value: EB differentiation D2, no Dox


title: FLII-eCLIP performed in naïve mESCs, IP group, Rep2

value: EB differentiation D2, + Dox


title: IeR_v_v_d6_5


title: IeR_v_v_d6_4


title: Microglia, APOE3, replicate 2 [ATAC-seq]


title: Microglia, APOE3, replicate 1 [ATAC-seq]


title: FLII-eCLIP performed in Poised mESCs, Input group, Rep1

value: EB differentiation D1, no Dox


title: DGCR8-sCLIP (no S4U) performed in naïve mESCs, Input group, Rep1

value: EB differentiation D0, no Dox


title: IeR_v_v_d6_3

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V


title: Microglia, APOE2, replicate 5 [ATAC-seq]


title: Microglia, APOE2, replicate 3 [ATAC-seq]


title: FLII-eCLIP performed in naïve mESCs, IP group, Rep1

value: EB differentiation D0, + Dox


title: Microglia, APOE2, replicate 4 [ATAC-seq]


title: EB differentiation D4, KH2-DGCR8, + Dox

data_processing:
For small RNA-seq, homemade PERL software was used to  remove adaptor sequences, and Bowtie sofeware was used to align sequencing reads to miRNA database
For small RNA-seq, 20-25nt small RNAs was aligned to known mature miRNA sequences(miRBase)
Reads per Million was calculated for the normalization
Assembly: mm10
Supplementary files format and content: the txt file provide the CPM of each miRNAs in every sample

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
Small RNA-seq libraries preparation using NEBNext® Small RNA Library Prep Set for Illumina kit。


title: IeR_v_v_d6_2

value: 4OHT (6 days)

value: pSuper v


title: Microglia, APOE2, replicate 2 [ATAC-seq]

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: IeR_v_v_d6_1

value: pMSCV miR v


title: FLII-eCLIP performed in naïve mESCs, Input group, Rep1

value: mESCs


title: EB differentiation D4, KH2-DGCR8, no Dox


title: EB differentiation D2, KH2-DGCR8, + Dox


title: HiC_RISshA1_2

description: RIS IMR90 with shHMGA1 rep2

data_processing:
Libraries were aligned using HiC-Pro (Servant 2016) against the hg19 genome.
Experimental artefacts and duplicates were removed prior to counting reads in matrices corresponding to different resolutions.
ICE-normalised and distance-corrected matrices were used for visualisation using HiCvizR, as described before (Olan 2020).
Assembly: hg19
Supplementary files format and content: BED: Bins at 200kb resolution, adjusted (with diffHiC) for the position of the HindIII cutting sites.
Supplementary files format and content: TXT: iced-normalised and distance-corrected files for condition (replicates were merged for visualisation only).

extract_protocol: Hi-C was carried out according to the in-nucleus ligation protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175).

value: normal human lung fibroblast

tag: replicate

tag: vector

value: pMSCV miR shHMGA1


title: Microglia, APOE2, replicate 1 [ATAC-seq]

tag: tissue

value: Brain

value: Microglia


title: IeR_v_v_d0_4

tag: cell line


title: EB differentiation D2, KH2-DGCR8, no Dox

tag: treatment


title: IeR_v_v_d0_3

tag: genotype


title: EB differentiation D1, KH2-DGCR8, no Dox

tag: cell type


title: FLII-eCLIP performed in Poised mESCs, IP group, Rep1

value: EB differentiation D1, + Dox

value: IP


title: IeR_v_v_d0_1


title: EB differentiation D1, KH2-DGCR8, + Dox


title: H3K27me3, no Dox, rep3

first: Qianxia

last: Zhang

address: 3 Blackfan Circle, RM 3117.16

institute: Boston Children's Hospital

data_processing:
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3). Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly) using bwa (v0.7.17). The resulting SAM files were converted to BAM files, sorted and indexed using Samtools (v1.6). Samples with drosophila spike-in chromatins were aligned to a customized reference genome consisting both hg38 and dm6, and the sorted and index BAM files were subsequently split into separate BAM files containing hg38- and dm6-mapped reads, respectively, using plit_bam.py module in the SPIKER tool. hg38- and dm6-mapped reads were deduplicated using the alignmentSieve function in deepTools (v3.5.1), and unique dm6-mapped reads were counted to calculate the scaling factors.
Peak calling was performed using MACS2 (v2.2.7.1) with the following parameters: macs2 callpeak -f BAMPE  -B -g 3.2e+9 --keep-dup 1 --SPMR --nomodel --extsize 250 -q 0.05 --cutoff-analysis. When calling peaks in WT and mutant AIRE ChIP-seq samples, corresponding input controls were included to remove the effect of background noise.
WT and mutant AIRE ChIP-seq BAM files and peaks were imported into DiffBind (v3.8.4), and a census of all AIRE peaks (n=13023, summits +/– 200 bp) were obtained after removing blacklisted and greylisted regions using dba.blacklist and dba.peakset functions. Trimmed Mean of M-values (TMM)-normalized counts-per-million (CPM) reads9 within each peak (summits +/– 200 bp) were obtained using the dba.count function in DiffBind with options.
Peaks called from H3K27ac ChIP-seq (–AIRE expression) were removed of blacklisted regions and subjected to Ranking Ordering of Super Enhancer (ROSE) analysis to obtain putative super-enhancer regions, using 12.5 Kb stitching distance and 2 Kb TSS exclusion parameters.
BAM files were converted to bigwig files using deepTools (v3.5.1). After verification of consistency between replicates, bigwig files were averaged using WiggleTools (v1.2.2) and bedGraphToBigWig (v366) and imported into IGV (v2.15.1) for visualization at specific loci or into deepTools (v3.5.1) for generation of heatmaps and average profiles using the computeMatrix, plotHeatmap and plotProfile functions.
Assembly: hg38, dm6
Supplementary files format and content: bigwig files contain ChIP signals for each sample

growth_protocol: 4D6 cells were maintained in RPMI supplemented with 10% FBS, 1% L-glutamine

extract_protocol:
For anti-FLAG (AIRE) and anti-p300 ChIP-seq, cells were washed 3 times with PBS and then crosslinked with 2mM Disuccinimidyl glutarate (DSG) in PBS for 45 minutes at room temperature. Cells were then washed again 3 times with PBS and then crosslinked with 1% formaldehyde (Sigma, Thermofisher, and Electron Microscopy Sciences) in PBS for 10 minutes at room temperature. For anti-histone mark ChIP-seq, cells were crosslinked with 1% formaldehyde in fresh media for 10 minutes at room temperature. After formaldehyde crosslinking, all cells were washed 1 time with PBS and quenched with 0.125 M glycine in PBS for 5 min at room temperature. Quenched cells were washed with ice cold PBS, then harvested in ice cold PBS supplemented with 0.5 mM PMSF. Cells were spun down at 500 g for 5 minutes and cell pellets were supplemented with 1 µl of 100mM PMSF and 1 µl 1X mammalian protease inhibitor cocktail (G-Biosciences), then flash frozen in liquid nitrogen and stored at -80°C until ready to use. For one ChIP pull-down, ~15x106 cells were used. Cells pellets were thawed on ice for 15 minutes and then resuspended in ice-cold One-Step Lysis Buffer (50 mM Tris H 7.5, 1% SDS, 0.25% Sodium Deoxycholate and 1 X mammalian protease inhibitor cocktail). Cells were incubated on ice for 10 min and then 700 µl ChIP Dilution Buffer (50 mM Tris pH 7.5, 0.01% SDS, 150 mM NaCl, 0.25% Triton-X, 1 X mammalian protease inhibitor cocktail) was added. Chromatin was sheared using with a Covaris M220 ultrasonicator (settings: 5% duty factor, 75W max power, 200 cycles per burst, 20 min) at 6°C. Lysates were spun down in a refrigerated centrifuge for 10 minutes at 18,000 g. Cleared lysate was 3-fold diluted with ChIP Dilution Buffer, spike-in chromatin (600ng per pull-down, Active Motif) was added when cells were treated with p300 inhibitors or DMSO, and 2-3% of the input was saved for later use. Lysates were nutated with antibodies [for each pull-down when indicated, 2.5 µg of anti-FLAG (M2, Sigma); 5 µg anti-H3K4me1, 5 µg anti-H3K27me3, 4 µg of anti-p300 (D2X6N, Cell Signaling Technologies); 4 µg of anti-H3K27Ac (Cell Signaling Technologies); 4 µg of anti-H3K4me0 (Active Motif); an additional 2 µg spike-in antibody (Active Motif) was included when cells had been treated with p300 inhibitors or DMSO] for 16 hrs at 4°C. Protein-DNA complexes were immunoprecipitated using Protein G magnetic beads (Active Motif) with 2 hrs nutation at 4°C. Protein G beads were washed with the following ice-cold buffers: RIPA buffer (0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X-100, 1 mM EDTA, 10 mM Tris pH 8, 150 mM NaCl); RIPA supplemented with 350 mM NaCl; LiCl Buffer (10 mM Tris pH 8, 250 mM LiCl, 0.5% Triton X-100, 0.5% Sodium Deoxycholate) and Tris Buffer (10 mM Tris pH 8.5). Protein-DNA complexes were eluted with Elution Buffer (10 mM Tris pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 5 mM DTT) with gentle agitation at 65°C for 1 hr. Reserved ChIP inputs were diluted two-fold with Elution Buffer. Dilute inputs and eluted protein-DNA were treated with RNAse (Machery-Nagel) at 37°C for 30 min, then Proteinase K (New England Biolabs) at 65°C for 16 hrs to ensure reverse crosslinking of DNA. Reverse cross-linked DNA was purified using SPRI Select beads (Beckman).
ChIP-seq DNA libraries were prepared using NEBNext Ultra II DNA library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s protocol.

treatment_protocol: 4D6 stable cells were seeded on 150mm plates with or without Dox and grown for 24 hrs. For drug-treated samples, equal volume of DMSO, 3 µm A-485 (Tocris Bioscience), or 0.25 µm dCBP-1 (MedChemExpress) was added to cells 4 hrs prior to harvest.

value: thymic epithelial cells

value: WT AIRE

value: no Dox


title: HiC_GrowshA1_2

description: Growing IMR90 with shHMGA1 rep2


title: EB differentiation D0, KH2-DGCR8, + Dox


title: HiC_GrowshA1_1

description: Growing IMR90 with shHMGA1 rep1


title: IeR_v_v_d0_5

value: lung fibroblast


title: HiC_RISshA1_1

description: RIS IMR90 with shHMGA1 rep1

value: pLNCX2 ER:HRAS G12V


title: IeR_v_v_d0_2


title: Nodule 1

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The integration of the replicates and the processing of the data was generated in Seurat.
Assembly: Glycine_max_v2.1.52 From: http://ftp.ensemblgenomes.org/pub/plants/release-52/gtf/; http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/glycine_max/

organism: Glycine max

source_name: Nodule

extract_protocol:
Roots and nodules were chopped and passed through a 30µm cell strainer. The filtered nuclei were purified by cell sorting using FACSAria II™ cell sorter (BD Biosciences). An average of 80-100,000 nuclei were collected for each sample, centrifuged, and re-suspended in phosphate buffered saline-bovine serum albumin 0.5%-RNA-inhibitor solution.
Libraries were performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Nodule cells

value: Nodule

tag: cultivar

value: Merr. Cultivar 'Williams 82'


title: H3K27me3, no Dox, rep2


title: Input_H1299_DoxshHMGA1_3

value: non-small cell lung carcinoma

value: Input

value: pCLIIPi iRFP shHMGA1

value: positive


title: Root 3

description: 10x Genomics

source_name: root

value: root cells

value: root

tag: age

value: 6 day-old


title: H3K27me3, no Dox, rep1


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both 2A-FLII and DGCR8 were rescued, Rep2

data_processing:
For the bioinformatics analysis, the adapters were cut by Trimmomatic. The data were aligned to mouse genome sequence (mm10) using Bowtie2 with options: –local–very-sensitive-local–no-unal–nomixed–no-discordant–phred33 -I 10 -X 700 . Samtools was used to remove duplication from bam files. The bigWig files were generated by bamCoverage using CPM as normalization method to show IGV examples . The differential peaks between samples were called using Macs2 with default parameters. ComputerMatrix was used to calculate the peak signals around poised-specific genes from bigWig file normalized by CPM, and the results were visualized by plotHeatmap. The read counts in each peak were extracted using bedtools .
Assembly: mm10
Supplementary files format and content: The bigWig files normalized by CPM of each sample were provided to visualize in IGV or UCSC genome browser.
Library strategy: Cut&Tag

growth_protocol: The mESCs stated as EpiLC 0h/2iLif were cultured in 2i/Lif medium, while those stated as EB D0/SL were cultured in Serum/Lif medium.ADFNK differentiation medium and N2B27 basal medium were used for EB differentiation and EpiLC differentiation, respectively.

extract_protocol:
Briefly, cells were harvested, counted, and centrifuged for 3 min at 1,000 rpm at room temperature. About 10,000 cells were washed using washing buffer followed by incubation with Concanavalin A beads at room temperature for 10 min. Next, 1 μl primary antibody was incubated with cells on a rotating platform at 4°C overnight. Secondary antibody incubation followed by pA/G-Tn5 incubation were performed on a rotating platform at room temperature each for 1 h. Between each of the above steps, the beads were washed using corresponding buffer. To activate the activity of Tn5, the beads were incubated in Tagmentation buffer at 37°C for 1 h followed by stop tagmentation using EDTA and extract DNA using DNA clean beads.
Cut&Tag libraries preparation using Hyperactive universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903)

value: mESCs

value: DGCR8 FLII double knockouts


title: Input_H1299_DoxshHMGA1_2


title: H3K4me1, no Dox, rep3

value: thymic epithelial cells


title: Input_H1299_DoxshHMGA1_1


title: Root 2

description: 10x Genomics


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which 2A-FLII was rescued, Rep2


title: Nodule 2

description: 10x Genomics


title: Root 1

description: 10x Genomics


title: H3K4me1, no Dox, rep2

value: WT AIRE


title: H3K4me1, no Dox, rep1

value: no Dox


title: HMGA1_H1299_DoxshHMGA1_3


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which 2D-FLII was rescued, Rep2


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both 2D-FLII and DGCR8 were rescued, Rep2


title: STR scRNA-seq

city: Charlestown

first: Ryuji

last: Morizane

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
The Cell Ranger v3 pipeline was utilized for sample demultiplexing, alignment based on the GRCh38 human genome assembly, filtering, unique molecular identifier (UMI) counting, single-cell 3’ end gene counting, and quality control according to the manufacturer's parameters. Seurat, aided by OmicsBox, was used to analyze and visualize the data.
Assembly: GRCh38 human genome
Supplementary files format and content: Matrix files

source_name: Human kidney organoids

extract_protocol:
Organoids were dissociated with Trypsin.
RNA from single cells was encapsulated, barcoded, and reverse-transcribed on a 10x Chromium Single Cell Platform (3’ ver3, 10x Genomics). The library was sequenced using the NovaSeq X Plus Series (PE150).

value: Human kidney organoids


title: HMGA1_H1299_DoxshHMGA1_1


title: Input_H1299_3

value: negative


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both WT-FLII and DGCR8 were rescued, Rep2


title: H3K27ac, no Dox, rep3


title: EB differentiation D0, KH2-DGCR8, no Dox

value: EB differentiation D0, no Dox


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 90 pmol eIF4A1, ADP+Pi

city: Wako

first: Shintaro

last: Iwasaki

address: 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software, 3' adapter trimming with FastX-toolkit, identical sequence aggregation with FastX-toolkit
Supplementary files format and content: csv files contain three columns: 1. 4 mer sequnece; 2. read counts ;3. the frequency of the 4 mer
Library strategy: RNA Bind-n-Seq

organism: synthetic construct

source_name: synthetic construct

extract_protocol: reverse transcription, PCR amplification

treatment_protocol: 3 μM DMDA-PatA

value: synthetic construct

value: 3 microM DMDA-PatA


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 90 pmol DDX3X (helicase core), ADP+Pi


title: H3K27ac, no Dox, rep1


title: Static scRNA-seq


title: Input_H1299_2

value: non-small cell lung carcinoma


title: RNA Bind-n-Seq, Input ADP


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium), Rep2


title: Input_H1299_1

value: Input


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 90 pmol eIF4A1, AMP-PNP


title: p300, no Dox, rep1


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 45 pmol eIF4A1, AMP-PNP


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which 2A-FLII was rescued, Rep1


title: HMGA1_H1299_2

value: pCLIIPi iRFP shHMGA1


title: H3K27ac, no Dox, rep2


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which WT-FLII was rescued, Rep2


title: HMGA1_H1299_DoxshHMGA1_2

value: positive


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which 2D-FLII was rescued, Rep1


title: AIRE WT, A485, rep3

value: Dox 24hr, A485 4hr


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both 2D-FLII and DGCR8 were rescued, Rep1


title: p300, no Dox, rep2


title: AIRE WT, A485, rep2


title: HMGA1_H1299_1


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 4.5 pmol eIF4A1, AMP-PNP


title: RNA Bind-n-Seq, 3 μM RocA, 90 pmol eIF4A1, AMP-PNP

treatment_protocol: 3 μM RocA

value: 3 microM RocA


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both WT-FLII and DGCR8 were rescued, Rep1


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which both 2A-FLII and DGCR8 were rescued, Rep1


title: AIRE WT, A485, rep1


title: RIS_Input_1

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V

value: 4OHT (6 days)


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium) in which WT-FLII was rescued, Rep1

value: mESCs

value: DGCR8 FLII double knockouts


title: RIS_Input_2


title: AIRE WT, dCBP1, rep2

value: thymic epithelial cells

value: WT AIRE

value: Dox 24hr, dCBP1 4hr


title: AIRE WT, dCBP1, rep1


title: RIS_HMGA1_2


title: HMGA1_H1299_3

value: negative


title: RNA Bind-n-Seq, 3 μM RocA, 45 pmol eIF4A1, AMP-PNP

value: synthetic construct


title: RNA Bind-n-Seq, 3 μM DMDA-PatA, 15 pmol eIF4A1, AMP-PNP

value: 3 microM DMDA-PatA


title: JUN Cut&Tag, DF-dKO mESCs (Serum/Lif medium), Rep1


title: Grow_Input_2


title: RNA Bind-n-Seq, 3 μM RocA, 15 pmol eIF4A1, AMP-PNP


title: AIRE WT, DMSO, rep3

value: Dox 24hr, DMSO 4hr


title: JUN Cut&Tag, Jun-/-Flii-/- mESCs (EpiLC-6h) in which JUN was rescued, Rep2

value: FLII and JUN double knockouts


title: RNA Bind-n-Seq, 0.1 % DMSO, 90 pmol eIF4A1, AMP-PNP

treatment_protocol: 0.1 % DMSO

value: 0.1 percent DMSO


title: RIS_HMGA1_1


title: AIRE WT, DMSO, rep2


title: JUN Cut&Tag, WT mESCs (EpiLC-6h), control of the JUN rescue assay, Rep2

value: WT


title: AIRE WT, DMSO, rep1


title: Grow_Input_1

value: Input


title: AIRE DPHD1, ChIP, rep2

value: Dox 24hr


title: JUN Cut&Tag, Jun-/-Flii-/- mESCs (EpiLC-6h) in which JUN was rescued, Rep1


title: RNA Bind-n-Seq, 0.1 % DMSO, 15 pmol eIF4A1, AMP-PNP


title: RNA Bind-n-Seq, 0.1 % DMSO, 45 pmol eIF4A1, AMP-PNP


title: Grow_HMGA1_2

value: lung fibroblast


title: AIRE DPHD1, ChIP, rep1


title: JUN Cut&Tag, WT mESCs (Serum/Lif medium)


title: Grow_HMGA1_1

value: pLNCX2 ER:HRAS G12V


title: RNA Bind-n-Seq, Input AMPPNP


title: JUN Cut&Tag, WT mESCs (EpiLC-6h), control of the JUN rescue assay, Rep1


title: RNA Bind-n-Seq, 0.1 % DMSO, 4.5 pmol eIF4A1, AMP-PNP


title: AIRE DPHD1, input ctrl


title: RNA Bind-n-Seq, 3 μM RocA, 4.5 pmol eIF4A1, AMP-PNP

value: 3 microM RocA


title: AIRE DCARD, ChIP, rep2


title: H1299_MSCVshHMGA1_R7

value: non-small cell lung carcinoma

value: pMSCV miR shHMGA1


title: RNA Bind-n-Seq, 3 μM iPr-DMDA-PatA, 90 pmol DDX3X (helicase core), ADP+Pi, rep2

data_processing:
Basecalling with Illumina Casava 1.8 software, error correction with FastX-toolkit, 3' adapter trimming with FastX-toolkit, identical sequence aggregation with FastX-toolkit
Supplementary files format and content: csv files contain three columns: 1. 4 mer sequnece; 2. read counts ;3. the frequency of the 4 mer
Library strategy: RNA Bind-n-Seq

treatment_protocol: 3 μM iPr-DMDA-PatA

value: 3 microM iPr-DMDA-PatA


title: JUN Cut&Tag, Jun-/-Flii-/- mESCs (EpiLC-0h) in which JUN was rescued

value: mESCs


title: H1299_MSCVshHMGA1_R6


title: AIRE DCARD, ChIP, rep1

value: thymic epithelial cells


title: JUN Cut&Tag, WT mESCs (EpiLC-0h), control of the JUN rescue assay.


title: H1299_MSCVshHMGA1_R5


title: H1299_MSCVshHMGA1_R4


title: RNA Bind-n-Seq, 3 μM iPr-DMDA-PatA, 90 pmol DDX3X (helicase core), ADP+Pi, rep1


title: AIRE DCARD, input ctrl


title: JUN Cut&Tag, KH2JUN (2iLif, + Dox 4h), Rep2


title: RNA Bind-n-Seq, 3 μM iPr-DMDA-PatA, 90 pmol eIF4A1, ADP+Pi, rep2


title: H1299_MSCVshHMGA1_R3


title: AIRE DCTT.R3, ChIP , rep2


title: JUN Cut&Tag, KH2JUN (2iLif, + Dox 12h), Rep2


title: RNA Bind-n-Seq, Input, rep2


title: AIRE DCTT.R3, ChIP , rep1


title: RNA Bind-n-Seq, 3 μM iPr-DMDA-PatA, 90 pmol eIF4A1, ADP+Pi, rep1


title: JUN Cut&Tag, KH2JUN (2iLif, + Dox 12h), Rep1


title: H1299_MSCVshHMGA1_R2


title: AIRE DCTT.R3, input ctrl


title: JUN Cut&Tag, KH2JUN (2iLif, + Dox 4h), Rep1


title: RNA Bind-n-Seq, Input, rep1


title: AIRE WT, ChIP, rep2

value: WT AIRE


title: AIRE WT, ChIP, rep1


title: H1299_MSCVvector_R7

value: pMSCV miR v


title: JUN Cut&Tag, KH2JUN (2iLif, no Dox), Rep1


title: Control brain, 9-month-old female biol rep #2

city: Lebanon

first: Arti

last: Gaur

state: NH

address: 1 Medical Center Dr

department: Neurology

institute: Dartmouth-Hitchcock Medical Center

data_processing:
Raw data were pre-processed by removing adapter sequences using Cutadapt (v3.4)
Raw data were aligned to the mm10 reference genome using HISAT2 (v2.1.0)
Read counts were quantified using the Featurecounts function (v2.0.1) from the subreads package to generate a gene expression matrix for downstream processing
Pseudogenes and genes without canonical names were filtered from the matrix
ComBat-seq (Zhang, 2020) was applied to adjust for sequencing batch effects
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for each sample

source_name: Bulk brain

extract_protocol:
Brain tissue was dissected from animals following perfusion with PBS and heparin. Samples were flash-frozen in liquid nitrogen and stored at -80°C. Samples were later placed in a deep-well 96-well plate with stainless steel RNase-free homogenization beads and QIAzol lysis buffer. Plates were inserted into the SPEX SamplePrep 1600 MiniG tissue homogenizer and run at maximum speed for 5 minutes. Following homogenization, the tissue solution was added to QIAzol lysis buffer and stored at -80°C. Lysed tissue solution was subsequently added to the QIAGEN miRNeasy Micro Kit for purification of total RNA.
RNA libraries for RNA-seq were prepared using the Kapa RNA HyperPrep kit (Roche) following the manufacturer’s instructions.

value: Bulk brain

tag: Sex

value: Female

tag: age (months)

tag: sequencing batch_#


title: H1299_MSCVvector_R4


title: H1299_MSCVvector_R5


title: AD brain, 18-month-old male biol rep #3

value: Male


title: AD brain, 6-month-old male biol rep #2


title: H1299_MSCVvector_R3


title: JUN Cut&Tag, KH2-FLII (EpiLC-6h, no Dox), Rep2

first: Xuehui

last: Lv

address: No.5 Yiheyuan Road, Haidian district, Beijing, 100871, China

institute: Peking University


title: WT AIRE 4D6, Dox, rep1

data_processing:
QC was performed on demultiplexed sequencing files using FASTQC (v0.11.3).
Sequencing reads were trimmed using Trimmomatic (v0.36) and aligned to reference genome (GRCh38 primary assembly, release v43) using STAR (v2.7.0a).
Read counting across genomic features was performed using featureCounts function within the Rsubread R package (v2.12.3).
Differential gene expression analysis was performed using the DEseq2 R package (v1.38.3) and visualized using the ggplot2 R package (v3.4.1).
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts
Supplementary files format and content: tab-delimited txt file includes normalized counts

extract_protocol:
Total RNA was immediately extracted by using Direct-zol RNA Miniprep Kit (Zymo Research, R2052) with DNase I digestion.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, E7775S) with ribosomal RNA depletion using the NEBNext rRNA Depletion Kit v2 (New England Biolabs, E7405L).

treatment_protocol: Dox-inducible AIRE-expressing 4D6 cells were cultured in the absence or presence of 1 µg/mL dox for 24 hrs.


title: AD brain, 18-month-old male biol rep #2


title: WT AIRE 4D6, Dox, rep2


title: JUN Cut&Tag, KH2-FLII (EpiLC-0h, no Dox), Rep2


title: JUN Cut&Tag, KH2JUN (2iLif, no Dox), Rep2


title: JUN Cut&Tag, KH2-FLII (EpiLC-6h, + Dox), Rep2


title: Control brain, 21-month-old female biol rep #3


title: H1299_MSCVvector_R2


title: JUN Cut&Tag, KH2-FLII (EpiLC-0h, + Dox), Rep2


title: H1299_MSCVvector_R6


title: H1299_MSCVvector_R1


title: WT AIRE 4D6, no Dox ctrl, rep2

value: no Dox ctrl


title: JUN Cut&Tag, KH2-FLII (EpiLC-6h, + Dox), Rep1


title: AD brain, 12-month-old male biol rep #3


title: WT AIRE 4D6, no Dox ctrl, rep1


title: AD brain, 9-month-old female biol rep #3


title: P26-T-II

first: Zemin

state: Beijing

address: Yiheyuan Road

department: BIOPIC

data_processing:
For 10X data, Cell Ranger 3.1.0 was used to quantify gene expression level and identify TCR sequences.
Assembly: GRCh38 for RNA expression
Supplementary files format and content: text files for expression matrices, cell metadata

source_name: Tumor

extract_protocol:
For tissue samples, collected tumor or adjacent normal biopsies was stored in the tissue storage solution immediately after resection and transferred on ice. Samples were washed twice and cut into approximately 1-2 mm3 pieces before being collected in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and projected to enzymatical digestion with gentleMACS Tumor Dissociation Kit (Miltenyi Biotec) for 60 min on a rotor at 37°C according to the manufacturer’s protocol. The dissociated cells then passed through a 100-mm SmartStrainer in the RPMI-1640 medium (Invitrogen) with 10% FBS and centrifuged at 400 g for 5 min. After the removal of the supernatant, the pelleted cells were suspended in 1 mL of red blood cell lysis buffer (TIANDZ) and incubated on ice for 1 min for red blood cell lysis and quickly terminate the reaction with RPMI-1640 medium (Invitrogen, with 10% FBS). After being centrifuged at 400 g for another 5 min, the cell pellets would be re-suspended in sorting buffer (PBS supplemented with 1% FBS).  Blood samples were collected in EDTA anticoagulant tubes and kept on ice for transferring. After restoring to room temperature and mixing thoroughly, peripheral blood mononuclear cells (PBMCs) were isolated using HISTOPAQUE-1077 (Sigma-Aldrich) solution. Briefly, peripheral blood was carefully layered onto equal volume HISTOPAQUE-1077 without breaking the plasma-HISTOPAQUE-1077 interface. After centrifugation at 400 g for 30 min, the lymphocyte layer was carefully transferred to a new tube and washed twice with 1x phosphate-buffered saline (PBS, Invitrogen). After red blood cells lysis following the aforementioned procedure, the collected lymphocytes were then re-suspended in sorting buffer (PBS supplemented with 1% FBS).
To obtain high-quality cell pools before subsequent library construction, single cell suspensions collected from blood or tissue samples were stained with antibodies against 7AAD (Thermo Fisher), CD235a (BioLegend) for FACS sorting (BD Aria III instrument). By gating 7AAD- CD235a- cells, living cells were enriched, and residuary red blood cells were excluded.  Gated cells were sorted into 1.5 mL LoBind tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/l. 10,000~18,000 cells were loaded for the 10x Chromium Single cell 5’ and VDJ library construction (10x Genomics), with subsequent steps performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq with 150-bp paired-end reads.
10x Chromium Single cell 5’ + VDJ Library

value: Tumor

tag: treatment stage

value: Post

tag: patientid

tag: cancer type

value: CRC


title: AIRE WT, input ctrl

value: Dox 24hr


title: JUN Cut&Tag, KH2-FLII (EpiLC-6h, no Dox), Rep1


title: JUN Cut&Tag, KH2-FLII (EpiLC-0h, + Dox), Rep1


title: RISshA1_7

value: lung fibroblast

value: pLNCX2 ER:HRAS G12V

value: 4OHT (6 days)

tag: shcebpb


title: Control brain, 21-month-old female biol rep #2


title: P26-N-II

source_name: Adjacent normal tissue

value: Adjacent normal tissue


title: RISshA1_6

value: pMSCV miR shHMGA1


title: RISshA1_5


title: P26-T-I

value: Pre


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep2

value: mESCs

value: FLII knockout


title: P26-N-I


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep2


title: AD brain, 9-month-old female biol rep #2


title: Control brain, 21-month-old female biol rep #1


title: P26-B-II

source_name: Peripheral blood

value: Peripheral blood


title: AD brain, 6-month-old male biol rep #1

value: Bulk brain


title: RISshA1_4


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-0h), Rep2


title: P25-T-II


title: P26-B-I


title: JUN Cut&Tag, WT mESCs (EpiLC-6h), Rep2

value: WT


title: AD brain, 12-month-old male biol rep #2

value: Male


title: AD brain, 9-month-old female biol rep #1

value: Female


title: RISshA1_8


title: RISshA1_1


title: Control brain, 21-month-old male biol rep #3


title: JUN Cut&Tag, KH2-FLII (EpiLC-0h, no Dox), Rep1


title: P25-N-II


title: JUN Cut&Tag, WT mESCs (EpiLC-0h), Rep2


title: AD brain, 12-month-old male biol rep #1


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-6h), Rep1


title: GrowshA1_7


title: GrowshA1_8


title: AD brain, 6-month-old male biol rep #6


title: P25-N-I


title: GrowshA1_6


title: P25-B-I


title: JUN Cut&Tag, Flii-/- mESCs (EpiLC-1h), Rep1


title: P25-T-I

value: Tumor


title: Control brain, 21-month-old male biol rep #2


title: RISshA1_2


title: RISshA1_3


title: JUN Cut&Tag, WT mESCs (EpiLC-1h), Rep2


title: P25-B-II

value: Post


title: JUN Cut&Tag, WT mESCs (EpiLC-6h), Rep1


title: AD brain, 12-month-old female biol rep #4